Science.gov

Sample records for genetically-encoded ratiometric indicator

  1. Optimal microscopic systems for long-term imaging of intracellular calcium using a ratiometric genetically-encoded calcium indicator.

    PubMed

    Miyamoto, Akitoshi; Bannai, Hiroko; Michikawa, Takayuki; Mikoshiba, Katsuhiko

    2013-05-03

    Monitoring the pattern of intracellular Ca(2+) signals that control many diverse cellular processes is essential for understanding regulatory mechanisms of cellular functions. Various genetically encoded Ca(2+) indicators (GECIs) are used for monitoring intracellular Ca(2+) changes under several types of microscope systems. However, it has not yet been explored which microscopic system is ideal for long-term imaging of the spatiotemporal patterns of Ca(2+) signals using GECIs. We here compared the Ca(2+) signals reported by a fluorescence resonance energy transfer (FRET)-based ratiometric GECI, yellow cameleon 3.60 (YC3.60), stably expressed in DT40 B lymphocytes, using three different imaging systems. These systems included a wide-field fluorescent microscope, a multipoint scanning confocal system, and a single-point scanning confocal system. The degree of photobleaching and the signal-to-noise ratio of YC3.60 in DT40 cells were highly dependent on the fluorescence excitation method, although the total illumination energy was maintained at a constant level within each of the imaging systems. More strikingly, the Ca(2+) responses evoked by B-cell antigen receptor stimulation in YC3.60-expressing DT40 cells were different among the imaging systems, and markedly affected by the illumination power used. Our results suggest that optimization of the imaging system, including illumination and acquisition conditions, is crucial for accurate visualization of intracellular Ca(2+) signals. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Auto-luminescent genetically-encoded ratiometric indicator for real-time Ca2+ imaging at the single cell level.

    PubMed

    Saito, Kenta; Hatsugai, Noriyuki; Horikawa, Kazuki; Kobayashi, Kentaro; Matsu-Ura, Toru; Mikoshiba, Katsuhiko; Nagai, Takeharu

    2010-04-01

    Efficient bioluminescence resonance energy transfer (BRET) from a bioluminescent protein to a fluorescent protein with high fluorescent quantum yield has been utilized to enhance luminescence intensity, allowing single-cell imaging in near real time without external light illumination. We applied BRET to develop an autoluminescent Ca(2+) indicator, BRAC, which is composed of Ca(2+)-binding protein, calmodulin, and its target peptide, M13, sandwiched between a yellow fluorescent protein variant, Venus, and an enhanced Renilla luciferase, RLuc8. Adjusting the relative dipole orientation of the luminescent protein's chromophores improved the dynamic range of BRET signal change in BRAC up to 60%, which is the largest dynamic range among BRET-based indicators reported so far. Using BRAC, we demonstrated successful visualization of Ca(2+) dynamics at the single-cell level with temporal resolution at 1 Hz. Moreover, BRAC signals were acquired by ratiometric imaging capable of canceling out Ca(2+)-independent signal drifts due to change in cell shape, focus shift, etc. The brightness and large dynamic range of BRAC should facilitate high-sensitive Ca(2+) imaging not only in single live cells but also in small living subjects.

  3. MagIC, a genetically encoded fluorescent indicator for monitoring cellular Mg2+ using a non-Förster resonance energy transfer ratiometric imaging approach

    NASA Astrophysics Data System (ADS)

    Koldenkova, Vadim Pérez; Matsuda, Tomoki; Nagai, Takeharu

    2015-10-01

    Intracellular Mg roles are commensurate with its abundance in the cell cytoplasm. However, little is known about Mg subcellular dynamics, primarily due to the lack of suitable Mg-selective tools to monitor this ion in intracellular compartments. To cope with this lack, we developed a Mg-sensitive indicator-MagIC (indicator for Magnesium Imaging in Cell) -composed of a functionalized yellow fluorescent protein (FP) variant fused to a red-emitting FP serving as a reference, thus allowing ratiometric imaging of Mg. MagIC expressed in mammalian cells is homogeneously distributed between the cytosol and nucleus but its fusion with appropriate targeting sequences redirects it to mitochondria or the endoplasmic reticulum. MagIC shows little interference by intracellular Ca [Kd(Mg2+)=5.1 mM Kd(Ca2+)=4.8 mM] and its kinetic properties (k=84 s-1) approach those of indicator dyes. With MagIC, as reported previously, we also observed a cytosolic Mg increase provoked by application of 50 mM MgCl2 in the medium. This effect is, however, mimicked by 75 mM KCl or 150 mM D-sorbitol addition, indicating that it is a response to the associated hyperosmotic shock and not to Mg itself. Our results confirm the functionality of MagIC as a useful tool for the long-awaited possibility of prolonged and organelle-specific monitoring of cellular Mg.

  4. MagIC, a genetically encoded fluorescent indicator for monitoring cellular Mg2+ using a non-Förster resonance energy transfer ratiometric imaging approach.

    PubMed

    Koldenkova, Vadim Pérez; Matsuda, Tomoki; Nagai, Takeharu

    2015-10-01

    Intracellular Mg(2+) roles are commensurate with its abundance in the cell cytoplasm. However, little is known about Mg(2+) subcellular dynamics, primarily due to the lack of suitable Mg(2+)-selective tools to monitor this ion in intracellular compartments. To cope with this lack, we developed a Mg(2+)-sensitive indicator--MagIC (indicator for Magnesium Imaging in Cell)--composed of a functionalized yellow fluorescent protein (FP) variant fused to a red-emitting FP serving as a reference, thus allowing ratiometric imaging of Mg(2+) MagIC expressed in mammalian cells is homogeneously distributed between the cytosol and nucleus but its fusion with appropriate targeting sequences redirects it to mitochondria or the endoplasmic reticulum. MagIC shows little interference by intracellular Ca(2+) [Kd (Mg(2+)) = 5.1 mM; Kd (Ca(2+)) = 4.8 mM] and its kinetic properties (k(off) = 84 s(-1)) approach those of indicator dyes. With MagIC, as reported previously, we also observed a cytosolic Mg(2+) increase provoked by application of 50 mM MgCl2 in the medium. This effect is, however, mimicked by 75 mM KCl or 150 mM D-sorbitol addition, indicating that it is a response to the associated hyperosmotic shock and not to Mg(2+) itself. Our results confirm the functionality of MagIC as a useful tool for the long-awaited possibility of prolonged and organelle-specific monitoring of cellular Mg(2+).

  5. Genetically Encoded Voltage Indicators: Opportunities and Challenges.

    PubMed

    Yang, Helen H; St-Pierre, François

    2016-09-28

    A longstanding goal in neuroscience is to understand how spatiotemporal patterns of neuronal electrical activity underlie brain function, from sensory representations to decision making. An emerging technology for monitoring electrical dynamics, voltage imaging using genetically encoded voltage indicators (GEVIs), couples the power of genetics with the advantages of light. Here, we review the properties that determine indicator performance and applicability, discussing both recent progress and technical limitations. We then consider GEVI applications, highlighting studies that have already deployed GEVIs for biological discovery. We also examine which classes of biological questions GEVIs are primed to address and which ones are beyond their current capabilities. As GEVIs are further developed, we anticipate that they will become more broadly used by the neuroscience community to eavesdrop on brain activity with unprecedented spatiotemporal resolution. Genetically encoded voltage indicators are engineered light-emitting protein sensors that typically report neuronal voltage dynamics as changes in brightness. In this review, we systematically discuss the current state of this emerging method, considering both its advantages and limitations for imaging neural activity. We also present recent applications of this technology and discuss what is feasible now and what we anticipate will become possible with future indicator development. This review will inform neuroscientists of recent progress in the field and help potential users critically evaluate the suitability of genetically encoded voltage indicator imaging to answer their specific biological questions. Copyright © 2016 the authors 0270-6474/16/369977-13$15.00/0.

  6. Genetically Encoded Voltage Indicators: Opportunities and Challenges

    PubMed Central

    Yang, Helen H.

    2016-01-01

    A longstanding goal in neuroscience is to understand how spatiotemporal patterns of neuronal electrical activity underlie brain function, from sensory representations to decision making. An emerging technology for monitoring electrical dynamics, voltage imaging using genetically encoded voltage indicators (GEVIs), couples the power of genetics with the advantages of light. Here, we review the properties that determine indicator performance and applicability, discussing both recent progress and technical limitations. We then consider GEVI applications, highlighting studies that have already deployed GEVIs for biological discovery. We also examine which classes of biological questions GEVIs are primed to address and which ones are beyond their current capabilities. As GEVIs are further developed, we anticipate that they will become more broadly used by the neuroscience community to eavesdrop on brain activity with unprecedented spatiotemporal resolution. SIGNIFICANCE STATEMENT Genetically encoded voltage indicators are engineered light-emitting protein sensors that typically report neuronal voltage dynamics as changes in brightness. In this review, we systematically discuss the current state of this emerging method, considering both its advantages and limitations for imaging neural activity. We also present recent applications of this technology and discuss what is feasible now and what we anticipate will become possible with future indicator development. This review will inform neuroscientists of recent progress in the field and help potential users critically evaluate the suitability of genetically encoded voltage indicator imaging to answer their specific biological questions. PMID:27683896

  7. Genetically encoded ratiometric fluorescent thermometer with wide range and rapid response

    PubMed Central

    Nakano, Masahiro; Arai, Yoshiyuki; Kotera, Ippei; Okabe, Kohki; Kamei, Yasuhiro; Nagai, Takeharu

    2017-01-01

    Temperature is a fundamental physical parameter that plays an important role in biological reactions and events. Although thermometers developed previously have been used to investigate several important phenomena, such as heterogeneous temperature distribution in a single living cell and heat generation in mitochondria, the development of a thermometer with a sensitivity over a wide temperature range and rapid response is still desired to quantify temperature change in not only homeotherms but also poikilotherms from the cellular level to in vivo. To overcome the weaknesses of the conventional thermometers, such as a limitation of applicable species and a low temporal resolution, owing to the narrow temperature range of sensitivity and the thermometry method, respectively, we developed a genetically encoded ratiometric fluorescent temperature indicator, gTEMP, by using two fluorescent proteins with different temperature sensitivities. Our thermometric method enabled a fast tracking of the temperature change with a time resolution of 50 ms. We used this method to observe the spatiotemporal temperature change between the cytoplasm and nucleus in cells, and quantified thermogenesis from the mitochondria matrix in a single living cell after stimulation with carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, which was an uncoupler of oxidative phosphorylation. Moreover, exploiting the wide temperature range of sensitivity from 5°C to 50°C of gTEMP, we monitored the temperature in a living medaka embryo for 15 hours and showed the feasibility of in vivo thermometry in various living species. PMID:28212432

  8. Genetically encoded ratiometric fluorescent thermometer with wide range and rapid response.

    PubMed

    Nakano, Masahiro; Arai, Yoshiyuki; Kotera, Ippei; Okabe, Kohki; Kamei, Yasuhiro; Nagai, Takeharu

    2017-01-01

    Temperature is a fundamental physical parameter that plays an important role in biological reactions and events. Although thermometers developed previously have been used to investigate several important phenomena, such as heterogeneous temperature distribution in a single living cell and heat generation in mitochondria, the development of a thermometer with a sensitivity over a wide temperature range and rapid response is still desired to quantify temperature change in not only homeotherms but also poikilotherms from the cellular level to in vivo. To overcome the weaknesses of the conventional thermometers, such as a limitation of applicable species and a low temporal resolution, owing to the narrow temperature range of sensitivity and the thermometry method, respectively, we developed a genetically encoded ratiometric fluorescent temperature indicator, gTEMP, by using two fluorescent proteins with different temperature sensitivities. Our thermometric method enabled a fast tracking of the temperature change with a time resolution of 50 ms. We used this method to observe the spatiotemporal temperature change between the cytoplasm and nucleus in cells, and quantified thermogenesis from the mitochondria matrix in a single living cell after stimulation with carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, which was an uncoupler of oxidative phosphorylation. Moreover, exploiting the wide temperature range of sensitivity from 5°C to 50°C of gTEMP, we monitored the temperature in a living medaka embryo for 15 hours and showed the feasibility of in vivo thermometry in various living species.

  9. Genetically Encoded Voltage Indicators in Circulation Research

    PubMed Central

    Kaestner, Lars; Tian, Qinghai; Kaiser, Elisabeth; Xian, Wenying; Müller, Andreas; Oberhofer, Martin; Ruppenthal, Sandra; Sinnecker, Daniel; Tsutsui, Hidekazu; Miyawaki, Atsushi; Moretti, Alessandra; Lipp, Peter

    2015-01-01

    Membrane potentials display the cellular status of non-excitable cells and mediate communication between excitable cells via action potentials. The use of genetically encoded biosensors employing fluorescent proteins allows a non-invasive biocompatible way to read out the membrane potential in cardiac myocytes and other cells of the circulation system. Although the approaches to design such biosensors date back to the time when the first fluorescent-protein based Förster Resonance Energy Transfer (FRET) sensors were constructed, it took 15 years before reliable sensors became readily available. Here, we review different developments of genetically encoded membrane potential sensors. Furthermore, it is shown how such sensors can be used in pharmacological screening applications as well as in circulation related basic biomedical research. Potentials and limitations will be discussed and perspectives of possible future developments will be provided. PMID:26370981

  10. Genetically encoded ratiometric biosensors to measure intracellular exchangeable zinc in Escherichia coli

    NASA Astrophysics Data System (ADS)

    Wang, Da; Hurst, Tamiika K.; Thompson, Richard B.; Fierke, Carol A.

    2011-08-01

    Zinc is an essential element for numerous cellular processes, therefore zinc homeostasis is regulated in living organisms. Fluorescent sensors have been developed as important tools to monitor the concentrations of readily exchangeable zinc in live cells. One type of biosensor uses carbonic anhydrase (CA) as the recognition element based on its tunable affinity, superior metal selectivity, and fluorescence signal from aryl sulfonamide ligands coupled to zinc binding. Here, we fuse carbonic anhydrase with a red fluorescent protein to create a series of genetically-encoded Förster resonance energy transfer-based excitation ratiometric zinc sensors that exhibit large signal increases in response to alterations in physiological-free zinc concentrations. These sensors were applied to the prokaryotic model organism Escherichia coli to quantify the readily exchangeable zinc concentration. In minimal media, E. coli BL21(DE3) cells expressing the CA sensor, exhibit a median intracellular readily exchangeable zinc concentration of 20 pM, much less than the total cellular zinc concentration of ~0.2 mM. Furthermore, the intracellular readily exchangeable zinc concentration varies with the concentration of environmental zinc.

  11. Genetically encoded ratiometric biosensors to measure intracellular exchangeable zinc in Escherichia coli

    PubMed Central

    Wang, Da; Hurst, Tamiika K.; Thompson, Richard B.; Fierke, Carol A.

    2011-01-01

    Zinc is an essential element for numerous cellular processes, therefore zinc homeostasis is regulated in living organisms. Fluorescent sensors have been developed as important tools to monitor the concentrations of readily exchangeable zinc in live cells. One type of biosensor uses carbonic anhydrase (CA) as the recognition element based on its tunable affinity, superior metal selectivity, and fluorescence signal from aryl sulfonamide ligands coupled to zinc binding. Here, we fuse carbonic anhydrase with a red fluorescent protein to create a series of genetically-encoded Förster resonance energy transfer-based excitation ratiometric zinc sensors that exhibit large signal increases in response to alterations in physiological-free zinc concentrations. These sensors were applied to the prokaryotic model organism Escherichia coli to quantify the readily exchangeable zinc concentration. In minimal media, E. coli BL21(DE3) cells expressing the CA sensor, exhibit a median intracellular readily exchangeable zinc concentration of 20 pM, much less than the total cellular zinc concentration of ∼0.2 mM. Furthermore, the intracellular readily exchangeable zinc concentration varies with the concentration of environmental zinc. PMID:21895338

  12. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator.

    PubMed

    Minderer, Matthias; Liu, Wenrui; Sumanovski, Lazar T; Kügler, Sebastian; Helmchen, Fritjof; Margolis, David J

    2012-01-01

    In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal precision, and furthermore, can be measured repeatedly in separate imaging sessions over multiple weeks. This method opens new possibilities for the longitudinal study of stability and plasticity of cortical sensory representations.

  13. Monitoring activity in neural circuits with genetically encoded indicators

    PubMed Central

    Broussard, Gerard J.; Liang, Ruqiang; Tian, Lin

    2014-01-01

    Recent developments in genetically encoded indicators of neural activity (GINAs) have greatly advanced the field of systems neuroscience. As they are encoded by DNA, GINAs can be targeted to genetically defined cellular populations. Combined with fluorescence microscopy, most notably multi-photon imaging, GINAs allow chronic simultaneous optical recordings from large populations of neurons or glial cells in awake, behaving mammals, particularly rodents. This large-scale recording of neural activity at multiple temporal and spatial scales has greatly advanced our understanding of the dynamics of neural circuitry underlying behavior—a critical first step toward understanding the complexities of brain function, such as sensorimotor integration and learning. Here, we summarize the recent development and applications of the major classes of GINAs. In particular, we take an in-depth look at the design of available GINA families with a particular focus on genetically encoded calcium indicators (GCaMPs), sensors probing synaptic activity, and genetically encoded voltage indicators. Using the family of the GCaMP as an example, we review established sensor optimization pipelines. We also discuss practical considerations for end users of GINAs about experimental methods including approaches for gene delivery, imaging system requirements, and data analysis techniques. With the growing toolbox of GINAs and with new microscopy techniques pushing beyond their current limits, the age of light can finally achieve the goal of broad and dense sampling of neuronal activity across time and brain structures to obtain a dynamic picture of brain function. PMID:25538558

  14. Genetically encoded optical indicators for the analysis of neuronal circuits.

    PubMed

    Knöpfel, Thomas

    2012-10-01

    In a departure from previous top-down or bottom-up strategies used to understand neuronal circuits, many forward-looking research programs now place the circuit itself at their centre. This has led to an emphasis on the dissection and elucidation of neuronal circuit elements and mechanisms, and on studies that ask how these circuits generate behavioural outputs. This movement towards circuit-centric strategies is progressing rapidly as a result of technological advances that combine genetic manipulation with light-based methods. The core tools of these new approaches are genetically encoded optical indicators and actuators that enable non-destructive interrogation and manipulation of neuronal circuits in behaving animals with cellular-level precision. This Review examines genetically encoded reporters of neuronal function and assesses their value for circuit-oriented neuroscientific investigations.

  15. A genetically encoded calcium indicator for chronic in vivo two-photon imaging.

    PubMed

    Mank, Marco; Santos, Alexandre Ferrão; Direnberger, Stephan; Mrsic-Flogel, Thomas D; Hofer, Sonja B; Stein, Valentin; Hendel, Thomas; Reiff, Dierk F; Levelt, Christiaan; Borst, Alexander; Bonhoeffer, Tobias; Hübener, Mark; Griesbeck, Oliver

    2008-09-01

    Neurons in the nervous system can change their functional properties over time. At present, there are no techniques that allow reliable monitoring of changes within identified neurons over repeated experimental sessions. We increased the signal strength of troponin C-based calcium biosensors in the low-calcium regime by mutagenesis and domain rearrangement within the troponin C calcium binding moiety to generate the indicator TN-XXL. Using in vivo two-photon ratiometric imaging, we show that TN-XXL exhibits enhanced fluorescence changes in neurons of flies and mice. TN-XXL could be used to obtain tuning curves of orientation-selective neurons in mouse visual cortex measured repeatedly over days and weeks. Thus, the genetically encoded calcium indicator TN-XXL allows repeated imaging of response properties from individual, identified neurons in vivo, which will be crucial for gaining new insights into cellular mechanisms of plasticity, regeneration and disease.

  16. Reporting neural activity with genetically encoded calcium indicators

    PubMed Central

    Hires, S. Andrew; Tian, Lin; Looger, Loren L.

    2009-01-01

    Genetically encoded calcium indicators (GECIs), based on recombinant fluorescent proteins, have been engineered to observe calcium transients in living cells and organisms. Through observation of calcium, these indicators also report neural activity. We review progress in GECI construction and application, particularly toward in vivo monitoring of sparse action potentials (APs). We summarize the extrinsic and intrinsic factors that influence GECI performance. A simple model of GECI response to AP firing demonstrates the relative significance of these factors. We recommend a standardized protocol for evaluating GECIs in a physiologically relevant context. A potential method of simultaneous optical control and recording of neuronal circuits is presented. PMID:18941901

  17. Genetically encoded bioluminescent voltage indicator for multi-purpose use in wide range of bioimaging

    PubMed Central

    Inagaki, Shigenori; Tsutsui, Hidekazu; Suzuki, Kazushi; Agetsuma, Masakazu; Arai, Yoshiyuki; Jinno, Yuka; Bai, Guirong; Daniels, Matthew J.; Okamura, Yasushi; Matsuda, Tomoki; Nagai, Takeharu

    2017-01-01

    We report development of the first genetically encoded bioluminescent indicator for membrane voltage called LOTUS-V. Since it is bioluminescent, imaging LOTUS-V does not require external light illumination. This allows bidirectional optogenetic control of cellular activity triggered by Channelrhodopsin2 and Halorhodopsin during voltage imaging. The other advantage of LOTUS-V is the robustness of a signal-to-background ratio (SBR) wherever it expressed, even in the specimens where autofluorescence from environment severely interferes fluorescence imaging. Through imaging of moving cardiomyocyte aggregates, we demonstrated the advantages of LOTUS-V in long-term imaging are attributable to the absence of phototoxicity, and photobleaching in bioluminescent imaging, combined with the ratiometric aspect of LOTUS-V design. Collectively LOTUS-V extends the scope of excitable cell control and simultaneous voltage phenotyping, which should enable applications in bioscience, medicine and pharmacology previously not possible. PMID:28205521

  18. Genetically Encoded Fluorescent Indicators for Organellar Calcium Imaging.

    PubMed

    Suzuki, Junji; Kanemaru, Kazunori; Iino, Masamitsu

    2016-09-20

    Optical Ca(2+) indicators are powerful tools for investigating intracellular Ca(2+) signals in living cells. Although a variety of Ca(2+) indicators have been developed, deciphering the physiological functions and spatiotemporal dynamics of Ca(2+) in intracellular organelles remains challenging. Genetically encoded Ca(2+) indicators (GECIs) using fluorescent proteins are promising tools for organellar Ca(2+) imaging, and much effort has been devoted to their development. In this review, we first discuss the key points of organellar Ca(2+) imaging and summarize the requirements for optimal organellar Ca(2+) indicators. Then, we highlight some of the recent advances in the engineering of fluorescent GECIs targeted to specific organelles. Finally, we discuss the limitations of currently available GECIs and the requirements for advancing the research on intraorganellar Ca(2+) signaling. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Genetically encoded Ca(2+) indicators: properties and evaluation.

    PubMed

    Pérez Koldenkova, Vadim; Nagai, Takeharu

    2013-07-01

    Genetically encoded calcium ion (Ca(2+)) indicators have become very useful and widely used tools for Ca(2+) imaging, not only in cellular models, but also in living organisms. However, the in vivo and in situ characterization of these indicators is tedious and time consuming, and it does not provide information regarding the suitability of an indicator for particular experimental environments. Thus, initial in vitro evaluation of these tools is typically performed to determine their properties. In this review, we examined the properties of dynamic range, affinity, selectivity, and kinetics for Ca(2+) indicators. Commonly used strategies for evaluating these properties are presented. This article is part of a Special Issue entitled: 12th European Symposium on Calcium.

  20. Calcium imaging with genetically encoded indicators in behaving primates.

    PubMed

    Seidemann, Eyal; Chen, Yuzhi; Bai, Yoon; Chen, Spencer C; Mehta, Preeti; Kajs, Bridget L; Geisler, Wilson S; Zemelman, Boris V

    2016-07-21

    Understanding the neural basis of behaviour requires studying brain activity in behaving subjects using complementary techniques that measure neural responses at multiple spatial scales, and developing computational tools for understanding the mapping between these measurements. Here we report the first results of widefield imaging of genetically encoded calcium indicator (GCaMP6f) signals from V1 of behaving macaques. This technique provides a robust readout of visual population responses at the columnar scale over multiple mm(2) and over several months. To determine the quantitative relation between the widefield GCaMP signals and the locally pooled spiking activity, we developed a computational model that sums the responses of V1 neurons characterized by prior single unit measurements. The measured tuning properties of the GCaMP signals to stimulus contrast, orientation and spatial position closely match the predictions of the model, suggesting that widefield GCaMP signals are linearly related to the summed local spiking activity.

  1. Photoactivatable Genetically-Encoded Calcium Indicators for targeted neuronal imaging

    PubMed Central

    Berlin, Shai; Carroll, Elizabeth C.; Newman, Zachary L.; Okada, Hitomi O.; Quinn, Carson M.; Kallman, Benjamin; Rockwell, Nathan C.; Martin, Shelley S.; Lagarias, J. Clark; Isacoff, Ehud Y.

    2015-01-01

    Circuit mapping requires knowledge of both structural and functional connectivity between cells. While optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactivatable Genetically Encoded Ca2+ Indicators (pa-GECIs) that combines attributes of high-contrast photo-labeling with high-sensitivity Ca2+ detection in a single-color, protein-sensor. We demonstrate the utility of pa-GECIs in cultured neurons and in vivo in Drosophila and zebrafish larvae. We show how single cells can be selected out of dense populations for Golgi-like visualization of morphology and high signal-to-noise measurements of activity, synaptic transmission and connectivity. Our design strategy is readily transferrable to other sensors based on circularly permutated GFP (cpGFP). PMID:26167640

  2. pHlash: A New Genetically Encoded and Ratiometric Luminescence Sensor of Intracellular pH

    PubMed Central

    Robertson, J. Brian; Johnson, Carl Hirschie

    2012-01-01

    We report the development of a genetically encodable and ratiometic pH probe named “pHlash” that utilizes Bioluminescence Resonance Energy Transfer (BRET) rather than fluorescence excitation. The pHlash sensor–composed of a donor luciferase that is genetically fused to a Venus fluorophore–exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H+ specific; neither Ca++, Mg++, Na+, nor K+ changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H+ ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate. PMID:22905204

  3. Generation of transgenic marmosets expressing genetically encoded calcium indicators

    PubMed Central

    Park, Jung Eun; Zhang, Xian Feng; Choi, Sang-Ho; Okahara, Junko; Sasaki, Erika; Silva, Afonso C.

    2016-01-01

    Chronic monitoring of neuronal activity in the living brain with optical imaging techniques became feasible owing to the continued development of genetically encoded calcium indicators (GECIs). Here we report for the first time the successful generation of transgenic marmosets (Callithrix jacchus), an important nonhuman primate model in neurophysiological research, which were engineered to express the green fluorescent protein (GFP)-based family of GECIs, GCaMP, under control of either the CMV or the hSyn promoter. High titer lentiviral vectors were produced, and injected into embryos collected from donor females. The infected embryos were then transferred to recipient females. Eight transgenic animals were born and shown to have stable and functional GCaMP expression in several different tissues. Germline transmission of the transgene was confirmed in embryos generated from two of the founder transgenic marmosets that reached sexual maturity. These embryos were implanted into six recipient females, three of which became pregnant and are in advanced stages of gestation. We believe these transgenic marmosets will be invaluable non-human primate models in neuroscience, allowing chronic in vivo monitoring of neural activity with functional confocal and multi-photon optical microscopy imaging of intracellular calcium dynamics. PMID:27725685

  4. Calcium imaging with genetically encoded indicators in behaving primates

    PubMed Central

    Seidemann, Eyal; Chen, Yuzhi; Bai, Yoon; Chen, Spencer C; Mehta, Preeti; Kajs, Bridget L; Geisler, Wilson S; Zemelman, Boris V

    2016-01-01

    Understanding the neural basis of behaviour requires studying brain activity in behaving subjects using complementary techniques that measure neural responses at multiple spatial scales, and developing computational tools for understanding the mapping between these measurements. Here we report the first results of widefield imaging of genetically encoded calcium indicator (GCaMP6f) signals from V1 of behaving macaques. This technique provides a robust readout of visual population responses at the columnar scale over multiple mm2 and over several months. To determine the quantitative relation between the widefield GCaMP signals and the locally pooled spiking activity, we developed a computational model that sums the responses of V1 neurons characterized by prior single unit measurements. The measured tuning properties of the GCaMP signals to stimulus contrast, orientation and spatial position closely match the predictions of the model, suggesting that widefield GCaMP signals are linearly related to the summed local spiking activity. DOI: http://dx.doi.org/10.7554/eLife.16178.001 PMID:27441501

  5. Live-Cell imaging and measurement of intracellular pH in filamentous fungi using a genetically encoded ratiometric probe.

    PubMed

    Bagar, Tanja; Altenbach, Kirsten; Read, Nick D; Bencina, Mojca

    2009-05-01

    A novel, genetically encoded, ratiometric pH probe (RaVC) was constructed to image and measure intracellular pH in living hyphae of Aspergillus niger. RaVC is a chimeric protein based on the pH-sensitive probe pHluorin, which was partially codon optimized for expression in Aspergillus. Intracellular pH imaging and measurement was performed by simultaneous, dual-excitation confocal ratio imaging. The mean cytoplasmic pH measured was 7.4 to 7.7 based on calibrating RaVC in situ within nigericin-treated hyphae. Pronounced, longitudinal cytoplasmic pH gradients were not observed in the apical 20 microm of actively growing hyphae at the periphery of 18-h-old colonies. The cytoplasmic pH remained unchanged after prolonged growth in buffered medium with pH values between 2.5 or 9.5. Sudden changes in external pH significantly changed cytoplasmic pH by <1.3 pH units, but it returned to its original value within 20 min following treatment. The weak acid and antifungal food preservative sorbic acid caused prolonged, concentration-dependent intracellular acidification. The inhibition of ATPases with N-ethylmaleimide, dicychlohexylcarbodimide, or sodium azide caused the cytoplasmic pH to decrease by <1 pH unit. Treatment with the protonophore carbonyl cyanide m-chlorophenylhydrazone or cyanide p-(trifluoromethoxy) phenylhydrazone reduced the cytoplasmic pH by <1 pH unit. In older hyphae from 32-h-old cultures, RaVC became sequestered within large vacuoles, which were shown to have pH values between 6.2 and 6.5. Overall, our study demonstrates that RaVC is an excellent probe for visualizing and quantifying intracellular pH in living fungal hyphae.

  6. Split-intein mediated re-assembly of genetically encoded Ca(2+) indicators.

    PubMed

    Wong, Stanley S C; Kotera, Ippei; Mills, Evan; Suzuki, Hiroshi; Truong, Kevin

    2012-01-01

    While genetically encoded Ca(2+) indicators (GECIs) allow Ca(2+) imaging in model organisms, the gene expression is often under the control of a single promoter that may drive expression beyond, the cell types of interest. To enable more cell-type specific targeting, GECIs can be brought under the, control of the intersecting expression from two promoters. Here, we present the splitting and, reassembly of two representative GECIs (TN-XL and GCaMP2) mediated by the split intein from Nostoc, punctiforme (NpuDnaE). While the split TN-XL biosensor offered ratiometric Ca(2+) imaging, it had a, diminished Ca(2+) response relative to the native TN-XL biosensor. In contrast, the split GCaMP2, biosensor retained similar Ca(2+) response to the native GCaMP2. The split GCaMP2 biosensor was, further targeted to the pharyngeal muscles of Caenorhabditis elegans where Ca(2+) signals from feeding C. elegans, were imaged. Thus, we envision that increased cell-type targetability of GECIs is feasible with two, complementary promoters.

  7. Redox Indicator Mice Stably Expressing Genetically Encoded Neuronal roGFP: Versatile Tools to Decipher Subcellular Redox Dynamics in Neuropathophysiology

    PubMed Central

    Wagener, Kerstin C.; Kolbrink, Benedikt; Dietrich, Katharina; Kizina, Kathrin M.; Terwitte, Lukas S.; Kempkes, Belinda; Bao, Guobin

    2016-01-01

    Abstract Aims: Reactive oxygen species (ROS) and downstream redox alterations not only mediate physiological signaling but also neuropathology. For long, ROS/redox imaging was hampered by a lack of reliable probes. Genetically encoded redox sensors overcame this gap and revolutionized (sub)cellular redox imaging. Yet, the successful delivery of sensor-coding DNA, which demands transfection/transduction of cultured preparations or stereotaxic microinjections of each subject, remains challenging. By generating transgenic mice, we aimed to overcome limiting cultured preparations, circumvent surgical interventions, and to extend effectively redox imaging to complex and adult preparations. Results: Our redox indicator mice widely express Thy1-driven roGFP1 (reduction–oxidation-sensitive green fluorescent protein 1) in neuronal cytosol or mitochondria. Negative phenotypic effects of roGFP1 were excluded and its proper targeting and functionality confirmed. Redox mapping by ratiometric wide-field imaging reveals most oxidizing conditions in CA3 neurons. Furthermore, mitochondria are more oxidized than cytosol. Cytosolic and mitochondrial roGFP1s reliably report cell endogenous redox dynamics upon metabolic challenge or stimulation. Fluorescence lifetime imaging yields stable, but marginal, response ranges. We therefore developed automated excitation ratiometric 2-photon imaging. It offers superior sensitivity, spatial resolution, and response dynamics. Innovation and Conclusion: Redox indicator mice enable quantitative analyses of subcellular redox dynamics in a multitude of preparations and at all postnatal stages. This will uncover cell- and compartment-specific cerebral redox signals and their defined alterations during development, maturation, and aging. Cross-breeding with other disease models will reveal molecular details on compartmental redox homeostasis in neuropathology. Combined with ratiometric 2-photon imaging, this will foster our mechanistic understanding

  8. Biocompatibility of a genetically encoded calcium indicator in a transgenic mouse model.

    PubMed

    Direnberger, Stephan; Mues, Marsilius; Micale, Vincenzo; Wotjak, Carsten T; Dietzel, Steffen; Schubert, Michael; Scharr, Andreas; Hassan, Sami; Wahl-Schott, Christian; Biel, Martin; Krishnamoorthy, Gurumoorthy; Griesbeck, Oliver

    2012-01-01

    Engineering efforts of genetically encoded calcium indicators predominantly focused on enhancing fluorescence changes, but how indicator expression affects the physiology of host organisms is often overlooked. Here, we demonstrate biocompatibility and widespread functional expression of the genetically encoded calcium indicator TN-XXL in a transgenic mouse model. To validate the model and characterize potential effects of indicator expression we assessed both indicator function and a variety of host parameters, such as anatomy, physiology, behaviour and gene expression profiles in these mice. We also demonstrate the usefulness of primary cells and organ explants prepared from these mice for imaging applications. Although we find mild signatures of indicator expression that may be further reduced in future sensor generations, the 'green' indicator mice generated provide a well-characterized resource of primary cells and tissues for in vitro and in vivo calcium imaging applications.

  9. Recent progress in the development of genetically encoded Ca2+ indicators.

    PubMed

    Horikawa, Kazuki

    2015-01-01

    Genetically encoded calcium indicators (GECIs) are powerful tools to monitor the dynamics of calcium ion (Ca(2+)) in living cells and organisms. With the help of GFP technology and DNA engineering, a dozen sets of GECIs have been developed so far. Their application has been widely extended into the analysis at the subcellular local, single and population of cell. In the past decades, GECIs have been dramatically improved in their performance and are becoming more and more useful for live imaging. In this review, the progress in the development of GECIs is discussed by introducing the history and emerging GECIs, which would help the selection of the appropriate GECI for a given application.

  10. Genetically encoded Ca2+ indicators: using genetics and molecular design to understand complex physiology

    PubMed Central

    Kotlikoff, Michael I

    2007-01-01

    This article reviews genetically encoded Ca2+ indicators (GECIs), with a focus on the use of these novel molecules in the context of understanding complex cell signalling in mammals, in vivo. The review focuses on the advantages and limitations of specific GECI design strategies and the results of experiments in which these molecules have been expressed in transgenic mice, concentrating particularly on recent experiments from our laboratory in which physiological signalling could be monitored in vivo. Finally, newer strategies for effective genetic specification of GECIs are briefly reviewed. PMID:17038427

  11. Genetically encoded Ca2+ indicators: using genetics and molecular design to understand complex physiology.

    PubMed

    Kotlikoff, Michael I

    2007-01-01

    This article reviews genetically encoded Ca2+ indicators (GECIs), with a focus on the use of these novel molecules in the context of understanding complex cell signalling in mammals, in vivo. The review focuses on the advantages and limitations of specific GECI design strategies and the results of experiments in which these molecules have been expressed in transgenic mice, concentrating particularly on recent experiments from our laboratory in which physiological signalling could be monitored in vivo. Finally, newer strategies for effective genetic specification of GECIs are briefly reviewed.

  12. Measuring calcium dynamics in living cells with genetically encodable calcium indicators.

    PubMed

    McCombs, Janet E; Palmer, Amy E

    2008-11-01

    Genetically encoded calcium indicators (GECIs) allow researchers to measure calcium dynamics in specific targeted locations within living cells. Such indicators enable dissection of the spatial and temporal control of calcium signaling processes. Here we review recent progress in the development of GECIs, highlighting which indicators are most appropriate for measuring calcium in specific organelles and localized domains in mammalian tissue culture cells. An overview of recent approaches that have been undertaken to ensure that the GECIs are minimally perturbed by the cellular environment is provided. Additionally, the procedures for introducing GECIs into mammalian cells, conducting calcium imaging experiments, and analyzing data are discussed. Because organelle-targeted indicators often pose an additional challenge, we underscore strategies for calibrating GECIs in these locations.

  13. Measuring calcium dynamics in living cells with Genetically Encodable Calcium Indicators

    PubMed Central

    McCombs, Janet E.

    2008-01-01

    Genetically encoded calcium indicators (GECIs) allow researchers to measure calcium dynamics in specific targeted locations within living cells. Such indicators enable dissection of the spatial and temporal control of calcium signaling processes. Here we review recent progress in the development of GECIs, highlighting which indicators are most appropriate for measuring calcium in specific organelles and localized domains in mammalian tissue culture cells. An overview of recent approaches that have been undertaken to ensure that the GECIs are minimally perturbed by the cellular environment is provided. Additionally, the procedures for introducing GECIs into mammalian cells, conducting calcium imaging experiments, and analyzing data are discussed. Because organelle-targeted indicators often pose an additional challenge, we underscore strategies for calibrating GECIs in these locations. PMID:18848629

  14. In vivo performance of genetically encoded indicators of neural activity in flies.

    PubMed

    Reiff, Dierk F; Ihring, Alexandra; Guerrero, Giovanna; Isacoff, Ehud Y; Joesch, Maximilian; Nakai, Junichi; Borst, Alexander

    2005-05-11

    Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals.

  15. In Vivo Performance of Genetically Encoded Indicators of Neural Activity in Flies

    PubMed Central

    Reiff, Dierk F.; Ihring, Alexandra; Guerrero, Giovanna; Isacoff, Ehud Y.; Joesch, Maximilian; Nakai, Junichi; Borst, Alexander

    2006-01-01

    Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals. PMID:15888652

  16. Imaging spinal neuron ensembles active during locomotion with genetically encoded calcium indicators.

    PubMed

    Hinckley, Christopher A; Pfaff, Samuel L

    2013-03-01

    Advances in molecular-genetic tools for labeling neuronal subtypes, and the emerging development of robust genetic probes for neural activity, are likely to revolutionize our understanding of the functional organization of neural circuits. In principle, these tools should be able to detect activity at cellular resolution for large ensembles of identified neuron types as they participate in specific behaviors. This report describes the use of genetically encoded calcium indicators (GECIs), combined with two-photon microscopy, to characterize V1 interneurons, known to be critical for setting the duration of the step cycle. All V1 interneurons arise from a common precursor population and express engrailed-1 (En1). Our data show that although neighboring interneurons that arise from the same developmental lineage and share many features, such as projection patterns and neurotransmitter profiles, they are not irrevocably committed to having the same pattern of activity.

  17. Imaging spinal neuron ensembles active during locomotion with genetically-encoded calcium indicators

    PubMed Central

    Hinckley, Christopher A.; Pfaff, Samuel L.

    2013-01-01

    Advances in molecular-genetic tools for labeling neuronal subtypes, and the emerging development of robust genetic probes for neural activity, are likely to revolutionize our understanding of the functional organization of neural circuits. In principle, these tools should be able to detect activity at cellular resolution for large ensembles of identified neuron types as they participate in specific behaviors. This review describes the use of genetically encoded calcium indicators (GECI's), combined with two-photon microscopy, to characterize V1 interneurons, known to be critical for setting the duration of the step cycle. All V1 interneurons arise from a common precursor population and express Engrailed-1 (En1). Our data show that although neighboring interneurons arising from the same developmental lineages often share features, such as projection patterns and neurotransmitter profiles, they are not irrevocably committed to have the same pattern of activity. PMID:23531004

  18. pHTomato: A genetically-encoded indicator that enables multiplex interrogation of synaptic activity

    PubMed Central

    Li, Yulong; Tsien, Richard W.

    2013-01-01

    The usefulness of genetically-encoded probes for optical monitoring of neuronal activity and brain circuits would be greatly advanced by the generation of multiple indicators with non-overlapping color spectra. Most existing indicators are derived from or spectrally convergent on GFP. We generated a bright, red, pH-sensitive fluorescent protein, pHTomato, that can be used in parallel with green probes to monitor neuronal activity. SypHTomato, made by fusing pHTomato to the vesicular membrane protein synaptophysin, reports activity-dependent exocytosis as efficiently as green reporters. When coexpressed with the GFP-based indicator GCaMP3 in the same neuron, SypHTomato enabled concomitant imaging of transmitter release and presynaptic Ca2+ transients at single nerve terminals. Expressing SypHTomato and GCaMP3 in separate cells enabled the simultaneous determination of presynaptic vesicular turnover and postsynaptic sub- and supra-threshold responses from a connected pair of neurons. With these new tools, we observed a close size matching between pre- and postsynaptic compartments as well as interesting target-cell dependent regulation of presynaptic vesicle pools. Lastly, by coupling expression of pHTomato- and GFP-based probes with distinct variants of channelrhodopsin, we provided proof-of-principle for an all-optical approach to multiplex control and tracking of distinct circuit pathways. PMID:22634730

  19. Imaging the response of the retina to electrical stimulation with genetically encoded calcium indicators.

    PubMed

    Weitz, Andrew C; Behrend, Matthew R; Lee, Nan Sook; Klein, Ronald L; Chiodo, Vince A; Hauswirth, William W; Humayun, Mark S; Weiland, James D; Chow, Robert H

    2013-04-01

    Epiretinal implants for the blind are designed to stimulate surviving retinal neurons, thus bypassing the diseased photoreceptor layer. Single-unit or multielectrode recordings from isolated animal retina are commonly used to inform the design of these implants. However, such electrical recordings provide limited information about the spatial patterns of retinal activation. Calcium imaging overcomes this limitation, as imaging enables high spatial resolution mapping of retinal ganglion cell (RGC) activity as well as simultaneous recording from hundreds of RGCs. Prior experiments in amphibian retina have demonstrated proof of principle, yet experiments in mammalian retina have been hindered by the inability to load calcium indicators into mature mammalian RGCs. Here, we report a method for labeling the majority of ganglion cells in adult rat retina with genetically encoded calcium indicators, specifically GCaMP3 and GCaMP5G. Intravitreal injection of an adeno-associated viral vector targets ∼85% of ganglion cells with high specificity. Because of the large fluorescence signals provided by the GCaMP sensors, we can now for the first time visualize the response of the retina to electrical stimulation in real-time. Imaging transduced retinas mounted on multielectrode arrays reveals how stimulus pulse shape can dramatically affect the spatial extent of RGC activation, which has clear implications in prosthetic applications. Our method can be easily adapted to work with other fluorescent indicator proteins in both wild-type and transgenic mammals.

  20. A neuron-based screening platform for optimizing genetically-encoded calcium indicators.

    PubMed

    Wardill, Trevor J; Chen, Tsai-Wen; Schreiter, Eric R; Hasseman, Jeremy P; Tsegaye, Getahun; Fosque, Benjamin F; Behnam, Reza; Shields, Brenda C; Ramirez, Melissa; Kimmel, Bruce E; Kerr, Rex A; Jayaraman, Vivek; Looger, Loren L; Svoboda, Karel; Kim, Douglas S

    2013-01-01

    Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude.

  1. A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

    PubMed Central

    Schreiter, Eric R.; Hasseman, Jeremy P.; Tsegaye, Getahun; Fosque, Benjamin F.; Behnam, Reza; Shields, Brenda C.; Ramirez, Melissa; Kimmel, Bruce E.; Kerr, Rex A.; Jayaraman, Vivek; Looger, Loren L.; Svoboda, Karel; Kim, Douglas S.

    2013-01-01

    Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude. PMID:24155972

  2. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain.

    PubMed

    Mishina, Yukiko; Mutoh, Hiroki; Song, Chenchen; Knöpfel, Thomas

    2014-01-01

    Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviors. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs) has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP) prototypical design or on the voltage-dependent state transitions of microbial opsins. We recently introduced a new VSFP design in which the voltage-sensing domain (VSD) is sandwiched between a fluorescence resonance energy transfer pair of fluorescent proteins (termed VSFP-Butterflies) and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.

  3. Imaging the Awake Visual Cortex with a Genetically Encoded Voltage Indicator

    PubMed Central

    Rossi, L. Federico; Sato, Tatsuo K.; Benucci, Andrea; Knöpfel, Thomas

    2015-01-01

    Genetically encoded voltage indicators (GEVIs) promise to reveal the membrane potential of genetically targeted neuronal populations through noninvasive, chronic imaging of large portions of cortical space. Here we test a promising GEVI in mouse cortex during wakefulness, a challenging condition due to large hemodynamic activity, and we introduce a straightforward projection method to separate a signal dominated by membrane voltage from a signal dominated by hemodynamic activity. We expressed VSFP-Butterfly 1.2 plasmid in layer 2/3 pyramidal cells of visual cortex through electroporation in utero. We then used wide-field imaging with two cameras to measure both fluorophores of the indicator in response to visual stimuli. By taking weighted sums and differences of the two measurements, we obtained clear separation of hemodynamic and voltage signals. The hemodynamic signal showed strong heartbeat oscillations, superimposed on slow dynamics similar to blood oxygen level-dependent (BOLD) or “intrinsic” signals. The voltage signal had fast dynamics similar to neural responses measured electrically, and showed an orderly retinotopic mapping. We compared this voltage signal with calcium signals imaged in transgenic mice that express a calcium indicator (GCaMP3) throughout cortex. The voltage signal from VSFP had similar signal-to-noise ratios as the calcium signal, it was more immune to vascular artifacts, and it integrated over larger regions of visual space, which was consistent with its reporting mostly subthreshold activity rather than the spiking activity revealed by calcium signals. These results demonstrate that GEVIs provide a powerful tool to study the dynamics of neural populations at mesoscopic spatial scales in the awake cortex. PMID:25568102

  4. Imaging the awake visual cortex with a genetically encoded voltage indicator.

    PubMed

    Carandini, Matteo; Shimaoka, Daisuke; Rossi, L Federico; Sato, Tatsuo K; Benucci, Andrea; Knöpfel, Thomas

    2015-01-07

    Genetically encoded voltage indicators (GEVIs) promise to reveal the membrane potential of genetically targeted neuronal populations through noninvasive, chronic imaging of large portions of cortical space. Here we test a promising GEVI in mouse cortex during wakefulness, a challenging condition due to large hemodynamic activity, and we introduce a straightforward projection method to separate a signal dominated by membrane voltage from a signal dominated by hemodynamic activity. We expressed VSFP-Butterfly 1.2 plasmid in layer 2/3 pyramidal cells of visual cortex through electroporation in utero. We then used wide-field imaging with two cameras to measure both fluorophores of the indicator in response to visual stimuli. By taking weighted sums and differences of the two measurements, we obtained clear separation of hemodynamic and voltage signals. The hemodynamic signal showed strong heartbeat oscillations, superimposed on slow dynamics similar to blood oxygen level-dependent (BOLD) or "intrinsic" signals. The voltage signal had fast dynamics similar to neural responses measured electrically, and showed an orderly retinotopic mapping. We compared this voltage signal with calcium signals imaged in transgenic mice that express a calcium indicator (GCaMP3) throughout cortex. The voltage signal from VSFP had similar signal-to-noise ratios as the calcium signal, it was more immune to vascular artifacts, and it integrated over larger regions of visual space, which was consistent with its reporting mostly subthreshold activity rather than the spiking activity revealed by calcium signals. These results demonstrate that GEVIs provide a powerful tool to study the dynamics of neural populations at mesoscopic spatial scales in the awake cortex. Copyright © 2015 Carandini et al.

  5. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

    PubMed Central

    Akerboom, Jasper; Carreras Calderón, Nicole; Tian, Lin; Wabnig, Sebastian; Prigge, Matthias; Tolö, Johan; Gordus, Andrew; Orger, Michael B.; Severi, Kristen E.; Macklin, John J.; Patel, Ronak; Pulver, Stefan R.; Wardill, Trevor J.; Fischer, Elisabeth; Schüler, Christina; Chen, Tsai-Wen; Sarkisyan, Karen S.; Marvin, Jonathan S.; Bargmann, Cornelia I.; Kim, Douglas S.; Kügler, Sebastian; Lagnado, Leon; Hegemann, Peter; Gottschalk, Alexander; Schreiter, Eric R.; Looger, Loren L.

    2013-01-01

    Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics. PMID:23459413

  6. Genetically encoded green fluorescent Ca2+ indicators with improved detectability for neuronal Ca2+ signals.

    PubMed

    Ohkura, Masamichi; Sasaki, Takuya; Sadakari, Junko; Gengyo-Ando, Keiko; Kagawa-Nagamura, Yuko; Kobayashi, Chiaki; Ikegaya, Yuji; Nakai, Junichi

    2012-01-01

    Imaging the activities of individual neurons with genetically encoded Ca(2+) indicators (GECIs) is a promising method for understanding neuronal network functions. Here, we report GECIs with improved neuronal Ca(2+) signal detectability, termed G-CaMP6 and G-CaMP8. Compared to a series of existing G-CaMPs, G-CaMP6 showed fairly high sensitivity and rapid kinetics, both of which are suitable properties for detecting subtle and fast neuronal activities. G-CaMP8 showed a greater signal (F(max)/F(min) = 38) than G-CaMP6 and demonstrated kinetics similar to those of G-CaMP6. Both GECIs could detect individual spikes from pyramidal neurons of cultured hippocampal slices or acute cortical slices with 100% detection rates, demonstrating their superior performance to existing GECIs. Because G-CaMP6 showed a higher sensitivity and brighter baseline fluorescence than G-CaMP8 in a cellular environment, we applied G-CaMP6 for Ca(2+) imaging of dendritic spines, the putative postsynaptic sites. By expressing a G-CaMP6-actin fusion protein for the spines in hippocampal CA3 pyramidal neurons and electrically stimulating the granule cells of the dentate gyrus, which innervate CA3 pyramidal neurons, we found that sub-threshold stimulation triggered small Ca(2+) responses in a limited number of spines with a low response rate in active spines, whereas supra-threshold stimulation triggered large fluorescence responses in virtually all of the spines with a 100% activity rate.

  7. Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals

    PubMed Central

    Sadakari, Junko; Gengyo-Ando, Keiko; Kagawa-Nagamura, Yuko; Kobayashi, Chiaki; Ikegaya, Yuji; Nakai, Junichi

    2012-01-01

    Imaging the activities of individual neurons with genetically encoded Ca2+ indicators (GECIs) is a promising method for understanding neuronal network functions. Here, we report GECIs with improved neuronal Ca2+ signal detectability, termed G-CaMP6 and G-CaMP8. Compared to a series of existing G-CaMPs, G-CaMP6 showed fairly high sensitivity and rapid kinetics, both of which are suitable properties for detecting subtle and fast neuronal activities. G-CaMP8 showed a greater signal (Fmax/Fmin = 38) than G-CaMP6 and demonstrated kinetics similar to those of G-CaMP6. Both GECIs could detect individual spikes from pyramidal neurons of cultured hippocampal slices or acute cortical slices with 100% detection rates, demonstrating their superior performance to existing GECIs. Because G-CaMP6 showed a higher sensitivity and brighter baseline fluorescence than G-CaMP8 in a cellular environment, we applied G-CaMP6 for Ca2+ imaging of dendritic spines, the putative postsynaptic sites. By expressing a G-CaMP6-actin fusion protein for the spines in hippocampal CA3 pyramidal neurons and electrically stimulating the granule cells of the dentate gyrus, which innervate CA3 pyramidal neurons, we found that sub-threshold stimulation triggered small Ca2+ responses in a limited number of spines with a low response rate in active spines, whereas supra-threshold stimulation triggered large fluorescence responses in virtually all of the spines with a 100% activity rate. PMID:23240011

  8. Imaging activity in astrocytes and neurons with genetically encoded calcium indicators following in utero electroporation

    PubMed Central

    Gee, J. Michael; Gibbons, Meredith B.; Taheri, Marsa; Palumbos, Sierra; Morris, S. Craig; Smeal, Roy M.; Flynn, Katherine F.; Economo, Michael N.; Cizek, Christian G.; Capecchi, Mario R.; Tvrdik, Petr; Wilcox, Karen S.; White, John A.

    2015-01-01

    Complex interactions between networks of astrocytes and neurons are beginning to be appreciated, but remain poorly understood. Transgenic mice expressing fluorescent protein reporters of cellular activity, such as the GCaMP family of genetically encoded calcium indicators (GECIs), have been used to explore network behavior. However, in some cases, it may be desirable to use long-established rat models that closely mimic particular aspects of human conditions such as Parkinson's disease and the development of epilepsy following status epilepticus. Methods for expressing reporter proteins in the rat brain are relatively limited. Transgenic rat technologies exist but are fairly immature. Viral-mediated expression is robust but unstable, requires invasive injections, and only works well for fairly small genes (<5 kb). In utero electroporation (IUE) offers a valuable alternative. IUE is a proven method for transfecting populations of astrocytes and neurons in the rat brain without the strict limitations on transgene size. We built a toolset of IUE plasmids carrying GCaMP variants 3, 6s, or 6f driven by CAG and targeted to the cytosol or the plasma membrane. Because low baseline fluorescence of GCaMP can hinder identification of transfected cells, we included the option of co-expressing a cytosolic tdTomato protein. A binary system consisting of a plasmid carrying a piggyBac inverted terminal repeat (ITR)-flanked CAG-GCaMP-IRES-tdTomato cassette and a separate plasmid encoding for expression of piggyBac transposase was employed to stably express GCaMP and tdTomato. The plasmids were co-electroporated on embryonic days 13.5–14.5 and astrocytic and neuronal activity was subsequently imaged in acute or cultured brain slices prepared from the cortex or hippocampus. Large spontaneous transients were detected in slices obtained from rats of varying ages up to 127 days. In this report, we demonstrate the utility of this toolset for interrogating astrocytic and neuronal

  9. Fluorescent ratiometric pH indicator SypHer2: Applications in neuroscience and regenerative biology.

    PubMed

    Matlashov, Mikhail E; Bogdanova, Yulia A; Ermakova, Galina V; Mishina, Natalia M; Ermakova, Yulia G; Nikitin, Evgeny S; Balaban, Pavel M; Okabe, Shigeo; Lukyanov, Sergey; Enikolopov, Grigori; Zaraisky, Andrey G; Belousov, Vsevolod V

    2015-11-01

    SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, the relatively low brightness of the indicator limits its use. Here we designed a new version of pH-sensor called SypHer-2, which has up to three times brighter fluorescence in cultured mammalian cells compared to the SypHer. Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent transient neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop that occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate. SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo. The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Fluorescent ratiometric pH indicator SypHer2: applications in neuroscience and regenerative biology

    PubMed Central

    Matlashov, Mikhail E.; Bogdanova, Yulia A.; Ermakova, Galina V.; Mishina, Natalia M.; Ermakova, Yulia G.; Nikitin, Evgeny S.; Balaban, Pavel M.; Okabe, Shigeo; Lukyanov, Sergey; Enikolopov, Grigori; Zaraisky, Andrey G.; Belousov, Vsevolod V.

    2015-01-01

    Background SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, a relatively low brightness of the indicator limits its use. Methods Here we designed a new version of pH-sensor - SypHer-2, that has up to three times brighter fluorescence signal in cultured mammalian cells compared to the SypHer. Results Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent temporal neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop which occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate. Conclusions SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo. General significance The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies. PMID:26259819

  11. Optical Quantification of Intracellular pH in Drosophila melanogaster Malpighian Tubule Epithelia with a Fluorescent Genetically-encoded pH Indicator.

    PubMed

    Rossano, Adam J; Romero, Michael F

    2017-08-11

    Epithelial ion transport is vital to systemic ion homeostasis as well as maintenance of essential cellular electrochemical gradients. Intracellular pH (pHi) is influenced by many ion transporters and thus monitoring pHi is a useful tool for assessing transporter activity. Modern Genetically Encoded pH-Indicators (GEpHIs) provide optical quantification of pHi in intact cells on a cellular and subcellular scale. This protocol describes real-time quantification of cellular pHi regulation in Malpighian Tubules (MTs) of Drosophila melanogaster through ex vivo live-imaging of pHerry, a pseudo-ratiometric GEpHI with a pKa well-suited to track pH changes in the cytosol. Extracted adult fly MTs are composed of morphologically and functionally distinct sections of single-cell layer epithelia, and can serve as an accessible and genetically tractable model for investigation of epithelial transport. GEpHIs offer several advantages over conventional pH-sensitive fluorescent dyes and ion-selective electrodes. GEpHIs can label distinct cell populations provided appropriate promoter elements are available. This labeling is particularly useful in ex vivo, in vivo, and in situ preparations, which are inherently heterogeneous. GEpHIs also permit quantification of pHi in intact tissues over time without need for repeated dye treatment or tissue externalization. The primary drawback of current GEpHIs is the tendency to aggregate in cytosolic inclusions in response to tissue damage and construct over-expression. These shortcomings, their solutions, and the inherent advantages of GEpHIs are demonstrated in this protocol through assessment of basolateral proton (H(+)) transport in functionally distinct principal and stellate cells of extracted fly MTs. The techniques and analysis described are readily adaptable to a wide variety of vertebrate and invertebrate preparations, and the sophistication of the assay can be scaled from teaching labs to intricate determination of ion flux via

  12. Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

    SciTech Connect

    Rodríguez Guilbe, María M.; Alfaro Malavé, Elisa C.; Akerboom, Jasper; Marvin, Jonathan S.; Looger, Loren L.; Schreiter, Eric R.

    2008-07-01

    The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, this protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.

  13. An easy ratiometric compensation for the extracellular Ca2+ indicator-caused fluorescence artifact.

    PubMed

    Kukkonen, Jyrki P

    2009-07-15

    Measurement of intracellular Ca(2+) dynamics is one of the most central real-time assays for cellular signaling. Ratiometric methods reduce the need for internal calibration and also effectively compensate for most artifacts when used in imaging. However, ratiometric calculation cannot compensate for extracellularly leaked (and fluorescent) Ca(2+) indicator and will instead indicate erroneous Ca(2+) concentration. This frequently occurs in systems where extracellular indicator is accumulated such as fluorescence spectrophotometers and plate readers. Here I present a method that, for the first time, fully compensates for this phenomenon. The method uses a single-step internal calibration together with a predefined ratiometric calibration protocol.

  14. A genetically encoded indicator for assaying bioactive chemicals that induce nuclear transport of glucocorticoid receptor.

    PubMed

    Kim, Sung Bae; Ozawa, Takeaki; Umezawa, Yoshio

    2005-12-15

    Glucocorticoids, the adrenal steroid hormones secreted during stress, are essential to homeostasis and metabolism in the human body. An impaired glucocorticoid signaling due to dysfunction of the glucocorticoid receptor (GR) by synthetic chemicals can cause diseases and disruptions of the homeostasis and metabolism. Here we demonstrate the development of a method for screening endocrine-disrupting chemicals and potent risk factors of human diseases based on the nuclear trafficking of the GR. We constructed a new assay using a pair of genetic indicators with the full length of the GR, split Renilla luciferase (RLuc), and split DnaE (a protein splicing element). The GR-containing fusion protein with C-terminal halves of DnaE and RLuc is localized in cytosol due to the cytosolic character of the GR, whereas the fusion protein with N-terminal halves of DnaE and RLuc stays in the nucleus due to the cofused nucleus localization signal. On being stimulated with a ligand, the GR is translocated into the cellular nucleus. Thus, a protein splicing occurs in the nucleus by an interaction between the splicing junctions of each DnaE fragment. The enzymatic activities from the reconstituted RLuc allow the ligand-dependent luminescence intensities. The feasibility of the method was evaluated by quantifying the hormonal activities of 20 different kinds of steroids and synthetic chemicals using the NIH 3T3 cells carrying the pair of indicators. The hormonal activities of tested ligands are discussed based on the chemical structure-activity relationship. We found that androgens, testosterone, and 19-nortestosterone weakly induce the nuclear transport of the GR. The current assay allows high-throughput screening of risk chemicals and drug candidates influential to a signal transduction pathway of the GR.

  15. Use of genetically-encoded calcium indicators for live cell calcium imaging and localization in virus-infected cells.

    PubMed

    Perry, Jacob L; Ramachandran, Nina K; Utama, Budi; Hyser, Joseph M

    2015-11-15

    Calcium signaling is a ubiquitous and versatile process involved in nearly every cellular process, and exploitation of host calcium signals is a common strategy used by viruses to facilitate replication and cause disease. Small molecule fluorescent calcium dyes have been used by many to examine changes in host cell calcium signaling and calcium channel activation during virus infections, but disadvantages of these dyes, including poor loading and poor long-term retention, complicate analysis of calcium imaging in virus-infected cells due to changes in cell physiology and membrane integrity. The recent expansion of genetically-encoded calcium indicators (GECIs), including blue and red-shifted color variants and variants with calcium affinities appropriate for calcium storage organelles like the endoplasmic reticulum (ER), make the use of GECIs an attractive alternative for calcium imaging in the context of virus infections. Here we describe the development and testing of cell lines stably expressing both green cytoplasmic (GCaMP5G and GCaMP6s) and red ER-targeted (RCEPIAer) GECIs. Using three viruses (rotavirus, poliovirus and respiratory syncytial virus) previously shown to disrupt host calcium homeostasis, we show the GECI cell lines can be used to detect simultaneous cytoplasmic and ER calcium signals. Further, we demonstrate the GECI expression has sufficient stability to enable long-term confocal imaging of both cytoplasmic and ER calcium during the course of virus infections.

  16. Imaging Intracellular Ca2+ Signals in Striatal Astrocytes from Adult Mice Using Genetically-encoded Calcium Indicators

    PubMed Central

    Jiang, Ruotian; Haustein, Martin D.; Sofroniew, Michael V.; Khakh, Baljit S.

    2014-01-01

    Astrocytes display spontaneous intracellular Ca2+ concentration fluctuations ([Ca2+]i) and in several settings respond to neuronal excitation with enhanced [Ca2+]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca2+]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca2+]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca2+]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca2+]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca2+]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca2+]i signals in the striatal microcircuitry. PMID:25490346

  17. Use of Genetically-encoded Calcium Indicators for Live Cell Calcium Imaging and Localization in Virus-infected Cells

    PubMed Central

    Perry, Jacob L.; Ramachandran, Nina K.; Utama, Budi; Hyser, Joseph M.

    2015-01-01

    Calcium signaling is a ubiquitous and versatile process involved in nearly every cellular process, and exploitation of host calcium signals is a common strategy used by viruses to facilitate replication and cause disease. Small molecule fluorescent calcium dyes have been used by many to examine changes in host cell calcium signaling and calcium channel activation during virus infections, but disadvantages of these dyes, including poor loading and poor long-term retention, complicate analysis of calcium imaging in virus-infected cells due to changes in cell physiology and membrane integrity. The recent expansion of genetically-encoded calcium indicators (GECIs), including blue and red-shifted color variants and variants with calcium affinities appropriate for calcium storage organelles like the endoplasmic reticulum (ER), make the use of GECIs an attractive alternative for calcium imaging in the context of virus infections. Here we describe the development and testing of cell lines stably expressing both green cytoplasmic (GCaMP5G and GCaMP6s) and red ER-targeted (RCEPIAer) GECIs. Using three viruses (rotavirus, poliovirus and respiratory syncytial virus) previously shown to disrupt host calcium homeostasis, we show the GECI cell lines can be used to detect simultaneous cytoplasmic and ER calcium signals. Further, we demonstrate the GECI expression has sufficient stability to enable long-term confocal imaging of both cytoplasmic and ER calcium during the course of virus infections. PMID:26344758

  18. Imaging intracellular Ca²⁺ signals in striatal astrocytes from adult mice using genetically-encoded calcium indicators.

    PubMed

    Jiang, Ruotian; Haustein, Martin D; Sofroniew, Michael V; Khakh, Baljit S

    2014-11-19

    Astrocytes display spontaneous intracellular Ca(2+) concentration fluctuations ([Ca(2+)]i) and in several settings respond to neuronal excitation with enhanced [Ca(2+)]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca(2+)]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca(2+)]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca(2+)]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca(2+)]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca(2+)]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca(2+)]i signals in the striatal microcircuitry.

  19. Ethanol Inhibition of Up-States in Prefrontal Cortical Neurons Expressing the Genetically Encoded Calcium Indicator GCaMP3

    PubMed Central

    Woodward, John J; Pava, Matthew

    2011-01-01

    Background The prefrontal cortex (PFC) is critically involved in working memory, cognition and decision-making; processes significantly affected by ethanol. During quiet restfulness or sleep, prefrontal cortical neurons show synaptically-evoked oscillations in membrane potential between hyperpolarized down-states and depolarized up-states. Previous studies from this laboratory used whole-cell electrophysiology and demonstrated that in individual neurons, ethanol inhibited PFC up-states at concentrations associated with behavioral impairment. While those studies monitored activity in one or two neurons at a time, it is likely that in vivo, larger networks of neurons participate in the complex functions of the prefrontal cortex. In the present study, we used imaging and a genetically encoded calcium sensor to examine the effects of ethanol on the activity of multiple neurons simultaneously during up-states. Methods Slice cultures of mouse prefrontal cortex were infected with an AAV virus encoding the calcium indicator GCaMP3 whose expression was driven by the neuron-specific synapsin promoter. After 2–3 weeks in culture, a fast CCD-camera imaging system was used to capture changes in GCaMP3 fluorescence before, during and after exposure to ethanol. Results PFC neurons displayed robust and reproducible changes in GCaMP3 fluorescence during evoked and spontaneous up-states. Simultaneous whole-cell patch-clamp recording and GCaMP3 imaging verified that neurons transitioned into and out of up-states together. Acute application of ethanol reliably depressed up-state calcium signals with lower doses having a greater effect on up-state duration than amplitude. These effects of ethanol on up-state parameters were reversed during washout. Conclusions The results of the present study indicate that ethanol has profound effects on upstate activity in prefrontal neurons and suggest that this action may underlie some of the cognitive impairment associated with acute alcohol

  20. Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo

    PubMed Central

    Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T

    2013-01-01

    All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pHcyto) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pHcyto shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2′,7′-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pHcyto. Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤4 s) trains of action potentials but did buffer slow (∼60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca2+ increase upon stimulation, and partial inhibition of the plasma membrane Ca2+-ATPase, a Ca2+/H+ exchanger, attenuated pHcyto shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (∼0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pHcyto shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pHcyto shifts cannot be dismissed as artifacts of ex vivo preparations. PMID:23401611

  1. Expression and testing in plants of ArcLight, a genetically-encoded voltage indicator used in neuroscience research.

    PubMed

    Matzke, Antonius J M; Matzke, Marjori

    2015-10-12

    It is increasingly appreciated that electrical controls acting at the cellular and supra-cellular levels influence development and initiate rapid responses to environmental cues. An emerging method for non-invasive optical imaging of electrical activity at cell membranes uses genetically-encoded voltage indicators (GEVIs). Developed by neuroscientists to chart neuronal circuits in animals, GEVIs comprise a fluorescent protein that is fused to a voltage-sensing domain. One well-known GEVI, ArcLight, undergoes strong shifts in fluorescence intensity in response to voltage changes in mammalian cells. ArcLight consists of super-ecliptic (SE) pHluorin (pH-sensitive fluorescent protein) with an A227D substitution, which confers voltage sensitivity in neurons, fused to the voltage-sensing domain of the voltage-sensing phosphatase of C iona i ntestinalis (Ci-VSD). In an ongoing effort to adapt tools of optical electrophysiology for plants, we describe here the expression and testing of ArcLight and various derivatives in different membranes of root cells in Arabidopsis thaliana. Transgenic constructs were designed to express ArcLight and various derivatives targeted to the plasma membrane and nuclear membranes of Arabidopsis root cells. In transgenic seedlings, changes in fluorescence intensity of these reporter proteins following extracellular ATP (eATP) application were monitored using a fluorescence microscope equipped with a high speed camera. Coordinate reductions in fluorescence intensity of ArcLight and Ci-VSD-containing derivatives were observed at both the plasma membrane and nuclear membranes following eATP treatments. However, similar responses were observed for derivatives lacking the Ci-VSD. The dispensability of the Ci-VSD suggests that in plants, where H(+) ions contribute substantially to electrical activities, the voltage-sensing ability of ArcLight is subordinate to the pH sensitivity of its SEpHluorin base. The transient reduction of Arc

  2. Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight

    PubMed Central

    2017-01-01

    Genetically encoded calcium indicators (GECIs) produce unprecedentedly large signals that have enabled routine optical recording of single neuron activity in vivo in rodent brain. Genetically encoded voltage indicators (GEVIs) offer a more direct measure of neuronal electrical status, however the signal-to-noise characteristics and signal polarity of the probes developed to date have precluded routine use in vivo. We applied directed evolution to target modulable areas of the fluorescent protein in GEVI ArcLight to create the first GFP-based GEVI (Marina) that exhibits a ΔF/ΔV with a positive slope relationship. We found that only three rounds of site-directed mutagenesis produced a family of “brightening” GEVIs with voltage sensitivities comparable to that seen in the parent probe ArcLight. This shift in signal polarity is an essential first step to producing voltage indicators with signal-to-noise characteristics comparable to GECIs to support widespread use in vivo. PMID:28045247

  3. Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight.

    PubMed

    Platisa, Jelena; Vasan, Ganesh; Yang, Amy; Pieribone, Vincent A

    2017-02-02

    Genetically encoded calcium indicators (GECIs) produce unprecedentedly large signals that have enabled routine optical recording of single neuron activity in vivo in rodent brain. Genetically encoded voltage indicators (GEVIs) offer a more direct measure of neuronal electrical status, however the signal-to-noise characteristics and signal polarity of the probes developed to date have precluded routine use in vivo. We applied directed evolution to target modulable areas of the fluorescent protein in GEVI ArcLight to create the first GFP-based GEVI (Marina) that exhibits a ΔF/ΔV with a positive slope relationship. We found that only three rounds of site-directed mutagenesis produced a family of "brightening" GEVIs with voltage sensitivities comparable to that seen in the parent probe ArcLight. This shift in signal polarity is an essential first step to producing voltage indicators with signal-to-noise characteristics comparable to GECIs to support widespread use in vivo.

  4. Genetically-encoded Reporters

    NASA Astrophysics Data System (ADS)

    Isacoff, Ehud

    2002-03-01

    One of the principle goals of neuroscience has been to understand the cellular basis of information processing and the plasticity that underlies learning and memory. Efforts in this area have mainly relied on electrical recording and optical imaging with chemical dyes. Over the last few years we and others have begun to develop genetically-encoded optical reporter "dyes" which should provide several important advantages over the classical methods for monitoring signal transmission in the nervous system. The advantages are that genetically-encoded reporters can be molecularly targeted a) to specific cell types via cell-specific promoters, and b) to specific subcellular compartments by peptides that are recognized by the protein sorting machinery of the cell. This makes it possible, in principle, to exclude signals from non-neuronal cells and to visualize selectively, in a brain region that contains many cell types with numerous kinds of synaptic connections, the activity of specific types of neurons (e.g. GABAergic interneurons) and specific synaptic elements (e.g. nerve terminals or dendrites), something that has hitherto not been possible. An additional advantage is that protein reporters may be rationally and irrationally "tuned" with mutations in functional domains known to control their dynamic range of operation. The general idea behind genetically-encoded reporters of cell signaling is to encode a protein that is either intrinsically fluorescent, or that can be labeled orthogonally with a fluorescent probe, and where the physiological signal changes fluorescence emission. I will describe recent progress employing both kinds of approaches.

  5. Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators

    PubMed Central

    Imamura, Hiromi; Huynh Nhat, Kim P.; Togawa, Hiroko; Saito, Kenta; Iino, Ryota; Kato-Yamada, Yasuyuki; Nagai, Takeharu; Noji, Hiroyuki

    2009-01-01

    Adenosine 5′-triphosphate (ATP) is the major energy currency of cells and is involved in many cellular processes. However, there is no method for real-time monitoring of ATP levels inside individual living cells. To visualize ATP levels, we generated a series of fluorescence resonance energy transfer (FRET)-based indicators for ATP that were composed of the ε subunit of the bacterial FoF1-ATP synthase sandwiched by the cyan- and yellow-fluorescent proteins. The indicators, named ATeams, had apparent dissociation constants for ATP ranging from 7.4 μM to 3.3 mM. By targeting ATeams to different subcellular compartments, we unexpectedly found that ATP levels in the mitochondrial matrix of HeLa cells are significantly lower than those of cytoplasm and nucleus. We also succeeded in measuring changes in the ATP level inside single HeLa cells after treatment with inhibitors of glycolysis and/or oxidative phosphorylation, revealing that glycolysis is the major ATP-generating pathway of the cells grown in glucose-rich medium. This was also confirmed by an experiment using oligomycin A, an inhibitor of FoF1-ATP synthase. In addition, it was demonstrated that HeLa cells change ATP-generating pathway in response to changes of nutrition in the environment. PMID:19720993

  6. Validation of optical voltage reporting by the genetically encoded voltage indicator VSFP-Butterfly from cortical layer 2/3 pyramidal neurons in mouse brain slices.

    PubMed

    Empson, Ruth M; Goulton, Chelsea; Scholtz, David; Gallero-Salas, Yasir; Zeng, Hongkui; Knöpfel, Thomas

    2015-07-29

    Understanding how behavior emerges from brain electrical activity is one of the ultimate goals of neuroscience. To achieve this goal we require methods for large-scale recording of the electrical activity of specific neuronal circuits. A very promising approach is to use optical reporting of membrane voltage transients, particularly if the voltage reporter is genetically targeted to specific neuronal populations. Targeting in this way allows population signals to be recorded and interpreted without blindness to neuronal diversity. Here, we evaluated the voltage-sensitive fluorescent protein, VSFP Butterfly 2.1, a genetically encoded voltage indicator (GEVI), for monitoring electrical activity of layer 2/3 cortical pyramidal neurons in mouse brain slices. Standard widefield fluorescence and two-photon imaging revealed robust, high signal-to-noise ratio read-outs of membrane voltage transients that are predominantly synaptic in nature and can be resolved as discrete areas of synaptically connected layer 2/3 neurons. We find that targeted expression of this GEVI in the cortex provides a flexible and promising tool for the analysis of L2/3 cortical network function. © 2015 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

  7. Dual optical recordings for action potentials and calcium handling in induced pluripotent stem cell models of cardiac arrhythmias using genetically encoded fluorescent indicators.

    PubMed

    Song, LouJin; Awari, Daniel W; Han, Elizabeth Y; Uche-Anya, Eugenia; Park, Seon-Hye E; Yabe, Yoko A; Chung, Wendy K; Yazawa, Masayuki

    2015-05-01

    Reprogramming of human somatic cells to pluripotency has been used to investigate disease mechanisms and to identify potential therapeutics. However, the methods used for reprogramming, in vitro differentiation, and phenotyping are still complicated, expensive, and time-consuming. To address the limitations, we first optimized a protocol for reprogramming of human fibroblasts and keratinocytes into pluripotency using single lipofection and the episomal vectors in a 24-well plate format. This method allowed us to generate multiple lines of integration-free and feeder-free induced pluripotent stem cells (iPSCs) from seven patients with cardiac diseases and three controls. Second, we differentiated human iPSCs derived from patients with Timothy syndrome into cardiomyocytes using a monolayer differentiation method. We found that Timothy syndrome cardiomyocytes showed slower, irregular contractions and abnormal calcium handling compared with the controls. The results are consistent with previous reports using a retroviral method for reprogramming and an embryoid body-based method for cardiac differentiation. Third, we developed an efficient approach for recording the action potentials and calcium transients simultaneously in control and patient cardiomyocytes using genetically encoded fluorescent indicators, ArcLight and R-GECO1. The dual optical recordings enabled us to observe prolonged action potentials and abnormal calcium handling in Timothy syndrome cardiomyocytes. We confirmed that roscovitine rescued the phenotypes in Timothy syndrome cardiomyocytes and that these findings were consistent with previous studies using conventional electrophysiological recordings and calcium imaging with dyes. The approaches using our optimized methods and dual optical recordings will improve iPSC applicability for disease modeling to investigate mechanisms underlying cardiac arrhythmias and to test potential therapeutics.

  8. Colorimetric sensing of anions in water using ratiometric indicator-displacement assay.

    PubMed

    Feng, Liang; Li, Hui; Li, Xiao; Chen, Liang; Shen, Zheng; Guan, Yafeng

    2012-09-19

    The analysis of anions in water presents a difficult challenge due to their low charge-to-radius ratio, and the ability to discriminate among similar anions often remains problematic. The use of a 3×6 ratiometric indicator-displacement assay (RIDA) array for the colorimetric detection and identification of ten anions in water is reported. The sensor array consists of different combinations of colorimetric indicators and metal cations. The colorimetric indicators chelate with metal cations, forming the color changes. Upon the addition of anions, anions compete with the indicator ligands according to solubility product constants (K(sp)). The indicator-metal chelate compound changes color back dramatically when the competition of anions wins. The color changes of the RIDA array were used as a digital representation of the array response and analyzed with standard statistical methods, including principal component analysis and hierarchical clustering analysis. No confusion or errors in classification by hierarchical clustering analysis were observed in 44 trials. The limit of detection was calculated approximately, and most limits of detections of anions are well below μM level using our RIDA array. The pH effect, temperature influence, interfering anions were also investigated, and the RIDA array shows the feasibility of real sample testing.

  9. Recent developments of genetically encoded optical sensors for cell biology.

    PubMed

    Bolbat, Andrey; Schultz, Carsten

    2017-01-01

    Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future. © 2016 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  10. Development of a novel GFP-based ratiometric excitation and emission pH indicator for intracellular studies.

    PubMed

    Bizzarri, Ranieri; Arcangeli, Caterina; Arosio, Daniele; Ricci, Fernanda; Faraci, Paolo; Cardarelli, Francesco; Beltram, Fabio

    2006-05-01

    We report on the development of the F64L/S65T/T203Y/L231H GFP mutant (E2GFP) as an effective ratiometric pH indicator for intracellular studies. E2GFP shows two distinct spectral forms that are convertible upon pH changes both in excitation and in emission with pK close to 7.0. The excitation of the protein at 488 and 458 nm represents the best choice in terms of signal dynamic range and ratiometric deviation from the thermodynamic pK. This makes E2GFP ideally suited for imaging setups equipped with the most widespread light sources and filter settings. We used E2GFP to determine the average intracellular pH (pH(i)) and spatial pH(i) maps in two different cell lines, CHO and U-2 OS, under physiological conditions. In CHO, we monitored the evolution of the pH(i) during mitosis. We also showed the possibility to target specific subcellular compartments such as nucleoli (by fusing E2GFP with the transactivator protein of HIV, (Tat) and nuclear promyelocytic leukemia bodies (by coexpression of promyelocytic leukemia protein).

  11. Illumination of the Spatial Order of Intracellular pH by Genetically Encoded pH-Sensitive Sensors

    PubMed Central

    Benčina, Mojca

    2013-01-01

    Fluorescent proteins have been extensively used for engineering genetically encoded sensors that can monitor levels of ions, enzyme activities, redox potential, and metabolites. Certain fluorescent proteins possess specific pH-dependent spectroscopic features, and thus can be used as indicators of intracellular pH. Moreover, concatenated pH-sensitive proteins with target proteins pin the pH sensors to a definite location within the cell, compartment, or tissue. This study provides an overview of the continually expanding family of pH-sensitive fluorescent proteins that have become essential tools for studies of pH homeostasis and cell physiology. We describe and discuss the design of intensity-based and ratiometric pH sensors, their spectral properties and pH-dependency, as well as their performance. Finally, we illustrate some examples of the applications of pH sensors targeted at different subcellular compartments. PMID:24316570

  12. Engineering Genetically Encoded FRET Sensors

    PubMed Central

    Lindenburg, Laurens; Merkx, Maarten

    2014-01-01

    Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening. PMID:24991940

  13. Intracellular pH imaging in cancer cells in vitro and tumors in vivo using the new genetically encoded sensor SypHer2.

    PubMed

    Shirmanova, Marina V; Druzhkova, Irina N; Lukina, Maria M; Matlashov, Mikhail E; Belousov, Vsevolod V; Snopova, Ludmila B; Prodanetz, Natalia N; Dudenkova, Varvara V; Lukyanov, Sergey A; Zagaynova, Elena V

    2015-09-01

    Measuring intracellular pH (pHi) in tumors is essential for the monitoring of cancer progression and the response of cancer cells to various treatments. The purpose of the study was to develop a method for pHi mapping in living cancer cells in vitro and in tumors in vivo, using the novel genetically encoded indicator, SypHer2. A HeLa Kyoto cell line stably expressing SypHer2 in the cytoplasm was used, to perform ratiometric (dual excitation) imaging of the probe in cell culture, in 3D tumor spheroids and in tumor xenografts in living mice. Using SypHer2, pHi was demonstrated to be 7.34±0.11 in monolayer HeLa cells in vitro under standard cultivation conditions. An increasing pHi gradient from the center to the periphery of the spheroids was displayed. We obtained fluorescence ratio maps for HeLa tumors in vivo and ex vivo. Comparison of the map with the pathomorphology and with hypoxia staining of the tumors revealed a correspondence of the zones with higher pHi to the necrotic and hypoxic areas. Our results demonstrate that pHi imaging with the genetically encoded pHi indicator, SypHer2, can be a valuable tool for evaluating tumor progression in xenograft models. We have demonstrated, for the first time, the possibility of using the genetically encoded sensor SypHer2 for ratiometric pH imaging in cancer cells in vitro and in tumors in vivo. SypHer2 shows great promise as an instrument for pHi monitoring able to provide high accuracy and spatiotemporal resolution. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Ionic selectivity of low-affinity ratiometric calcium indicators: mag-Fura-2, Fura-2FF and BTC.

    PubMed

    Hyrc, K L; Bownik, J M; Goldberg, M P

    2000-02-01

    Accurate measurement of elevated intracellular calcium levels requires indicators with low calcium affinity and high selectivity. We examined fluorescence spectral properties and ionic specificity of three low-affinity, ratiometric indicators structurally related to Fura-2: mag-Fura-2 (furaptra), Fura-2FF, and BTC. The indicators differed in respect to their excitation wavelengths, affinity for Ca2+ (Kd approximately 20 microM, 6 microM and 12 microM respectively) and selectivity over Mg2+ (Kd approximately 2 mM for mag-Fura-2, > 10 mM for Fura-2FF and BTC). Among the tested indicators, BTC was limited by a modest dynamic range upon Ca2+ binding, susceptibility to photodamage, and sensitivity to alterations in pH. All three indicators bound other metal ions including Zn2+, Cd2+ and Gd3+. Interestingly, only in the case of BTC were spectral differences apparent between Ca2+ and other metal ions. For example, the presence of Zn2+ increased BTC fluorescence 6-fold at the Ca2+ isosbestic point, suggesting that this dye may be used as a fluorescent Zn2+ indicator. Fura-2FF has high specificity, wide dynamic range, and low pH sensitivity, and is an optimal low-affinity Ca2+ indicator for most imaging applications. BTC may be useful if experimental conditions require visible wavelength excitation or sensitivity to other metal ions including Zn2+.

  15. Genetically Encoded Sensors for Metabolites

    PubMed Central

    Deuschle, Karen; Fehr, Marcus; Hilpert, Melanie; Lager, Ida; Lalonde, Sylvie; Looger, Loren L.; Okumoto, Sakiko; Persson, Jörgen; Schmidt, Anja; Frommer, Wolf B.

    2009-01-01

    Background Metabolomics, i.e., the multiparallel analysis of metabolite changes occurring in a cell or an organism, has become feasible with the development of highly efficient mass spectroscopic technologies. Functional genomics as a standard tool helped to identify the function of many of the genes that encode important transporters and metabolic enzymes over the past few years. Advanced expression systems and analysis technologies made it possible to study the biochemical properties of the corresponding proteins in great detail. We begin to understand the biological functions of the gene products by systematic analysis of mutants using systematic PTGS/RNAi, knockout and TILLING approaches. However, one crucial set of data especially relevant in the case of multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of metabolite levels at cellular and subcellular levels. Methods We therefore developed genetically encoded nanosensors for several metabolites to provide a basic set of tools for the determination of cytosolic and subcellular metabolite levels in real time by using fluorescence microscopy. Results Prototypes of these sensors were successfully used in vitro and also in vivo, i.e., to measure sugar levels in fungal and animal cells. Conclusions One of the future goals will be to expand the set of sensors to a wider spectrum of substrates by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets in conjunction with mutagenesis. This toolbox can then be applied for four-dimensional imaging of cells and tissues to elucidate the spatial and temporal distribution of metabolites as a discovery tool in functional genomics, as a tool for high-throughput, high-content screening for drugs, to test metabolic models, and to analyze the interplay of cells in a tissue or organ. PMID:15688353

  16. A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging

    PubMed Central

    Wu, Jiahui; Abdelfattah, Ahmed S.; Miraucourt, Loïs S.; Kutsarova, Elena; Ruangkittisakul, Araya; Zhou, Hang; Ballanyi, Klaus; Wicks, Geoffrey; Drobizhev, Mikhail; Rebane, Aleksander; Ruthazer, Edward S.; Campbell, Robert E.

    2016-01-01

    The introduction of calcium ion (Ca2+) indicators based on red fluorescent proteins (RFPs) has created new opportunities for multicolour visualization of intracellular Ca2+ dynamics. However, one drawback of these indicators is that they have optimal two-photon excitation outside the near-infrared window (650–1,000 nm) where tissue is most transparent to light. To address this shortcoming, we developed a long Stokes shift RFP-based Ca2+ indicator, REX-GECO1, with optimal two-photon excitation at <1,000 nm. REX-GECO1 fluoresces at 585 nm when excited at 480 nm or 910 nm by a one- or two-photon process, respectively. We demonstrate that REX-GECO1 can be used as either a ratiometric or intensiometric Ca2+ indicator in organotypic hippocampal slice cultures (one- and two-photon) and the visual system of albino tadpoles (two-photon). Furthermore, we demonstrate single excitation wavelength two-colour Ca2+ and glutamate imaging in organotypic cultures. PMID:25358432

  17. A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging.

    PubMed

    Wu, Jiahui; Abdelfattah, Ahmed S; Miraucourt, Loïs S; Kutsarova, Elena; Ruangkittisakul, Araya; Zhou, Hang; Ballanyi, Klaus; Wicks, Geoffrey; Drobizhev, Mikhail; Rebane, Aleksander; Ruthazer, Edward S; Campbell, Robert E

    2014-10-31

    The introduction of calcium ion (Ca(2+)) indicators based on red fluorescent proteins (RFPs) has created new opportunities for multicolour visualization of intracellular Ca(2+) dynamics. However, one drawback of these indicators is that they have optimal two-photon excitation outside the near-infrared window (650-1,000 nm) where tissue is most transparent to light. To address this shortcoming, we developed a long Stokes shift RFP-based Ca(2+) indicator, REX-GECO1, with optimal two-photon excitation at <1,000 nm. REX-GECO1 fluoresces at 585 nm when excited at 480 nm or 910 nm by a one- or two-photon process, respectively. We demonstrate that REX-GECO1 can be used as either a ratiometric or intensiometric Ca(2+) indicator in organotypic hippocampal slice cultures (one- and two-photon) and the visual system of albino tadpoles (two-photon). Furthermore, we demonstrate single excitation wavelength two-colour Ca(2+) and glutamate imaging in organotypic cultures.

  18. Ratiometric bioluminescence indicators for monitoring cyclic adenosine 3',5'-monophosphate in live cells based on luciferase-fragment complementation.

    PubMed

    Takeuchi, Masaki; Nagaoka, Yasutaka; Yamada, Toshimichi; Takakura, Hideo; Ozawa, Takeaki

    2010-11-15

    Bioluminescent indicators for cyclic 3',5'-monophosphate AMP (cAMP) are powerful tools for noninvasive detection with high sensitivity. However, the absolute photon counts are affected substantially by adenosine 5'-triphosphate (ATP) and d-luciferin concentrations, limiting temporal analysis in live cells. This report describes a genetically encoded bioluminescent indicator for detecting intracellular cAMP based on complementation of split fragments of two-color luciferase mutants originated from click beetles. A cAMP binding domain of protein kinase A was connected with an engineered carboxy-terminal fragment of luciferase, of which ends were connected with amino-terminal fragments of green luciferase and red luciferase. We demonstrated that the ratio of green to red bioluminescence intensities was less influenced by the changes of ATP and d-luciferin concentrations. We also showed an applicability of the bioluminescent indicator for time-course and quantitative assessments of intracellular cAMP in living cells and mice. The bioluminescent indicator will enable quantitative analysis and imaging of spatiotemporal dynamics of cAMP in opaque and autofluorescent living subjects.

  19. Imaging Cellular Inorganic Phosphate in Caenorhabditis elegans Using a Genetically Encoded FRET-Based Biosensor

    PubMed Central

    Banerjee, Swayoma; Versaw, Wayne K.; Garcia, L. Rene

    2015-01-01

    Inorganic phosphate (Pi) has central roles in metabolism, cell signaling and energy conversion. The distribution of Pi to each cell and cellular compartment of an animal must be tightly coordinated with its dietary supply and with the varied metabolic demands of individual cells. An analytical method for monitoring Pi dynamics with spatial and temporal resolution is therefore needed to gain a comprehensive understanding of mechanisms governing the transport and recycling of this essential nutrient. Here we demonstrate the utility of a genetically encoded FRET-based Pi sensor to assess cellular Pi levels in the nematode Caenorhabditis elegans. The sensor was expressed in different cells and tissues of the animal, including head neurons, tail neurons, pharyngeal muscle, and the intestine. Cytosolic Pi concentrations were monitored using ratiometric imaging. Injection of phosphate buffer into intestinal cells confirmed that the sensor was responsive to changes in Pi concentration in vivo. Live Pi imaging revealed cell-specific and developmental stage-specific differences in cytosolic Pi concentrations. In addition, cellular Pi levels were perturbed by food deprivation and by exposure to the respiratory inhibitor cyanide. These results suggest that Pi concentration is a sensitive indicator of metabolic status. Moreover, we propose that live Pi imaging in C. elegans is a powerful approach to discern mechanisms that govern Pi distribution in individual cells and throughout an animal. PMID:26484766

  20. Use of Genetically Encoded Calcium Indicators (GECIs) Combined with Advanced Motion Tracking Techniques to Examine the Behavior of Neurons and Glia in the Enteric Nervous System of the Intact Murine Colon

    PubMed Central

    Hennig, Grant W.; Gould, Thomas W.; Koh, Sang Don; Corrigan, Robert D.; Heredia, Dante J.; Shonnard, Matthew C.; Smith, Terence K.

    2015-01-01

    Genetically encoded Ca2+ indicators (GECIs) have been used extensively in many body systems to detect Ca2+ transients associated with neuronal activity. Their adoption in enteric neurobiology has been slower, although they offer many advantages in terms of selectivity, signal-to-noise and non-invasiveness. Our aims were to utilize a number of cell-specific promoters to express the Ca2+ indicator GCaMP3 in different classes of neurons and glia to determine their effectiveness in measuring activity in enteric neural networks during colonic motor behaviors. We bred several GCaMP3 mice: (1) Wnt1-GCaMP3, all enteric neurons and glia; (2) GFAP-GCaMP3, enteric glia; (3) nNOS-GaMP3, enteric nitrergic neurons; and (4) ChAT-GCaMP3, enteric cholinergic neurons. These mice allowed us to study the behavior of the enteric neurons in the intact colon maintained at a physiological temperature, especially during the colonic migrating motor complex (CMMC), using low power Ca2+ imaging. In this preliminary study, we observed neuronal and glial cell Ca2+ transients in specific cells in both the myenteric and submucous plexus in all of the transgenic mice variants. The number of cells that could be simultaneously imaged at low power (100–1000 active cells) through the undissected gut required advanced motion tracking and analysis routines. The pattern of Ca2+ transients in myenteric neurons showed significant differences in response to spontaneous, oral or anal stimulation. Brief anal elongation or mucosal stimulation, which evokes a CMMC, were the most effective stimuli and elicited a powerful synchronized and prolonged burst of Ca2+ transients in many myenteric neurons, especially when compared with the same neurons during a spontaneous CMMC. In contrast, oral elongation, which normally inhibits CMMCs, appeared to suppress Ca2+ transients in some of the neurons active during a spontaneous or an anally evoked CMMC. The activity in glial networks appeared to follow neural activity

  1. Calibration and functional analysis of three genetically encoded Cl(-)/pH sensors.

    PubMed

    Mukhtarov, M; Liguori, L; Waseem, T; Rocca, F; Buldakova, S; Arosio, D; Bregestovski, P

    2013-01-01

    Monitoring of the intracellular concentrations of Cl(-) and H(+) requires sensitive probes that allow reliable quantitative measurements without perturbation of cell functioning. For these purposes the most promising are genetically encoded fluorescent biosensors, which have become powerful tools for non-invasive intracellular monitoring of ions, molecules, and enzymatic activity. A ratiometric CFP/YFP-based construct with a relatively good sensitivity to Cl(-) has been developed (Markova et al., 2008; Waseem et al., 2010). Recently, a combined Cl(-)/pH sensor (ClopHensor) opened the way for simultaneous ratiometric measurement of these two ions (Arosio et al., 2010). ClopHensor was obtained by fusion of a red-fluorescent protein (DsRed-monomer) to the E(2)GFP variant that contains a specific Cl(-)-binding site. This construct possesses pK a = 6.8 for H(+) and K d in the 40-50 mM range for Cl(-) at physiological pH (~7.3). As in the majority of cell types the intracellular Cl(-) concentration ([Cl(-)] i ) is about 10 mM, the development of sensors with higher sensitivity is highly desirable. Here, we report the intracellular calibration and functional characterization of ClopHensor and its two derivatives: the membrane targeting PalmPalm-ClopHensor and the H148G/V224L mutant with improved Cl(-) affinity, reduced pH dependence, and pK a shifted to more alkaline values. For functional analysis, constructs were expressed in CHO cells and [Cl(-)] i was changed by using pipettes with different Cl(-) concentrations during whole-cell recordings. K d values for Cl(-) measured at 33°C and pH ~7.3 were, respectively, 39, 47, and 21 mM for ClopHensor, PalmPalm-ClopHensor, and the H148G/V224L mutant. PalmPalm-ClopHensor resolved responses to activation of Cl(-)-selective glycine receptor (GlyR) channels better than did ClopHensor. Our observations indicate that these different ClopHensor constructs are promising tools for non-invasive measurement of [Cl(-)] i in various

  2. Tuning the Spectroscopic Properties of Ratiometric Fluorescent Metal Indicators: Experimental and Computational Studies on Mag-fura-2 and Analogues.

    PubMed

    Zhang, Guangqian; Jacquemin, Denis; Buccella, Daniela

    2017-02-02

    In this joint theoretical and experimental work, we investigate the properties of Mag-fura-2 and seven structurally related fluorescent sensors designed for the ratiometric detection of Mg(2+) cations. The synthesis of three new compounds is described, and the absorption and emission spectra of all of the sensors in both their free and metal-bound forms are reported. A time-dependent density functional theory approach accounting for hydration effects using a hybrid implicit/explicit model is employed to calculate the absorption and fluorescence emission wavelengths, study the origins of the hypsochromic shift caused by metal binding for all of the sensors in this family, and investigate the auxochromic effects of various modifications of the "fura" core. The metal-free forms of the sensors are shown to undergo a strong intramolecular charge transfer upon light absorption, which is largely suppressed by metal complexation, resulting in predominantly locally excited states upon excitation of the metal complexes. Our computational protocol might aid in the design of new generations of fluorescent sensors with low-energy excitation and enhanced properties for ratiometric imaging of metal cations in biological samples.

  3. Mouse redox histology using genetically encoded probes.

    PubMed

    Fujikawa, Yuuta; Roma, Leticia P; Sobotta, Mirko C; Rose, Adam J; Diaz, Mauricio Berriel; Locatelli, Giuseppe; Breckwoldt, Michael O; Misgeld, Thomas; Kerschensteiner, Martin; Herzig, Stephan; Müller-Decker, Karin; Dick, Tobias P

    2016-03-15

    Mapping the in vivo distribution of endogenous oxidants in animal tissues is of substantial biomedical interest. Numerous health-related factors, including diet, physical activity, infection, aging, toxins, or pharmacological intervention, may cause redox changes. Tools are needed to pinpoint redox state changes to particular organs, tissues, cell types, and subcellular organelles. We describe a procedure that preserves the in vivo redox state of genetically encoded redox biosensors within histological tissue sections, thus providing "redox maps" for any tissue and comparison of interest. We demonstrate the utility of the technique by visualizing endogenous redox differences and changes in the context of tumor growth, inflammation, embryonic development, and nutrient starvation.

  4. Enhanced dynamic range in a genetically encoded Ca2+ sensor.

    PubMed

    Liu, Shun; He, Jun; Jin, Honglin; Yang, Fei; Lu, Jinling; Yang, Jie

    2011-08-19

    Genetically encoded fluorescence resonance energy transfer (FRET) indicators are powerful tools for real-time detection of second messenger molecules and activation of signal proteins. However, these fluorescent protein-based sensors typically display marginal FRET efficiency. To improve their FRET efficiency for optical imaging and screening, we developed a number of fluorescent protein mutants based on cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). To improve FRET ratios, which were initially within a narrow dynamic range, we used DNA shuffling to develop a new FRET pair called 3xCFP/Venus. The optimized 3xCFP/Venus pair exhibited higher FRET ratios than CyPet/YPet, which has one of the greatest dynamic ranges of protein-based FRET pairs. We converted this FRET pair to a Ca(2+) FRET indicators using circular permutation Venus (cpVenus) linked with 3xCFP to form 3xCFP/cpVenus, which displayed an ∼11-fold change in dynamic range in response to Ca(2+) binding. The enhanced dynamic range for Ca(2+) concentration detection using 3xCFP/cpVenus was confirmed in PC12 cells using previously established indicators (TN-XXL, ECFP/cpCitrine). To our knowledge, this FRET pair displays the largest dynamic range so far among genetically-encoded sensors, and can be used for sensitive FRET detection. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Genetically encoded sensors for calcium and zinc

    NASA Astrophysics Data System (ADS)

    Palmer, Amy E.; Dittmer, Philip; McCombs, Janet E.

    2008-02-01

    Our lab focuses on developing fluorescent biosensors based on fluorescence resonance energy transfer (FRET) so that we can monitor signaling ions in living cells. These sensors are comprised of two fluorescent proteins and a sensing domain that undergoes a conformational change upon binding the target ligand. These sensors can be genetically encoded and hence incorporated into cells by transgenic technologies. Here we discuss the latest developments in our efforts to reengineer calcium sensors as well as develop new sensors for zinc. In these efforts we employ a combination of naturally occurring calcium and zinc binding domains, combined with protein engineering. We are also developing new methodologies to screen and sort sensor libraries using optically-integrated microfluidic devices. Thus far, we have targeted sensors to the ER, mitochondria, Golgi, nucleus, and plasma membrane in order to examine the spatial heterogeneity and localization of signaling processes.

  6. Genetically Encoded Libraries of Nonstandard Peptides

    PubMed Central

    Kawakami, Takashi; Murakami, Hiroshi

    2012-01-01

    The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides. PMID:23097693

  7. Genetically Encoded Protein Sensors of Membrane Potential.

    PubMed

    Storace, Douglas; Rad, Masoud Sepehri; Han, Zhou; Jin, Lei; Cohen, Lawrence B; Hughes, Thom; Baker, Bradley J; Sung, Uhna

    2015-01-01

    Organic voltage-sensitive dyes offer very high spatial and temporal resolution for imaging neuronal function. However these dyes suffer from the drawbacks of non-specificity of cell staining and low accessibility of the dye to some cell types. Further progress in imaging activity is expected from the development of genetically encoded fluorescent sensors of membrane potential. Cell type specificity of expression of these fluorescent protein (FP) voltage sensors can be obtained via several different mechanisms. One is cell type specificity of infection by individual virus subtypes. A second mechanism is specificity of promoter expression in individual cell types. A third, depends on the offspring of transgenic animals with cell type specific expression of cre recombinase mated with an animal that has the DNA for the FP voltage sensor in all of its cells but its expression is dependent on the recombinase activity. Challenges remain. First, the response time constants of many of the new FP voltage sensors are slower (2-10 ms) than those of organic dyes. This results in a relatively small fractional fluorescence change, ΔF/F, for action potentials. Second, the largest signal presently available is only ~40% for a 100 mV depolarization and many of the new probes have signals that are substantially smaller. Large signals are especially important when attempting to detect fast events because the shorter measurement interval results in a relatively small number of detected photons and therefore a relatively large shot noise (see Chap. 1). Another kind of challenge has occurred when attempts were made to transition from one species to another or from one cell type to another or from cell culture to in vivo measurements.Several laboratories have recently described a number of novel FP voltage sensors. Here we attempt to critically review the current status of these developments in terms of signal size, time course, and in vivo function.

  8. A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics

    PubMed Central

    Wend, Sabrina; Bosco, Cristina Dal; Kämpf, Michael M.; Ren, Fugang; Palme, Klaus; Weber, Wilfried; Dovzhenko, Alexander; Zurbriggen, Matias D.

    2013-01-01

    Time-resolved quantitative analysis of auxin-mediated processes in plant cells is as of yet limited. By applying a synergistic mammalian and plant synthetic biology approach, we have developed a novel ratiometric luminescent biosensor with wide applicability in the study of auxin metabolism, transport, and signalling. The sensitivity and kinetic properties of our genetically encoded biosensor open new perspectives for the analysis of highly complex auxin dynamics in plant growth and development. PMID:23787479

  9. A genetically encoded, high-signal-to-noise maltose sensor

    SciTech Connect

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L.

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  10. GAP, an aequorin-based fluorescent indicator for imaging Ca2+ in organelles.

    PubMed

    Rodriguez-Garcia, Arancha; Rojo-Ruiz, Jonathan; Navas-Navarro, Paloma; Aulestia, Francisco Javier; Gallego-Sandin, Sonia; Garcia-Sancho, Javier; Alonso, Maria Teresa

    2014-02-18

    Genetically encoded calcium indicators allow monitoring subcellular Ca(2+) signals inside organelles. Most genetically encoded calcium indicators are fusions of endogenous calcium-binding proteins whose functionality in vivo may be perturbed by competition with cellular partners. We describe here a novel family of fluorescent Ca(2+) sensors based on the fusion of two Aequorea victoria proteins, GFP and apo-aequorin (GAP). GAP exhibited a unique combination of features: dual-excitation ratiometric imaging, high dynamic range, good signal-to-noise ratio, insensitivity to pH and Mg(2+), tunable Ca(2+) affinity, uncomplicated calibration, and targetability to five distinct organelles. Moreover, transgenic mice for endoplasmic reticulum-targeted GAP exhibited a robust long-term expression that correlated well with its reproducible performance in various neural tissues. This biosensor fills a gap in the actual repertoire of Ca(2+) indicators for organelles and becomes a valuable tool for in vivo Ca(2+) imaging applications.

  11. GAP, an aequorin-based fluorescent indicator for imaging Ca2+ in organelles

    PubMed Central

    Rodriguez-Garcia, Arancha; Rojo-Ruiz, Jonathan; Navas-Navarro, Paloma; Aulestia, Francisco Javier; Gallego-Sandin, Sonia; Garcia-Sancho, Javier; Alonso, Maria Teresa

    2014-01-01

    Genetically encoded calcium indicators allow monitoring subcellular Ca2+ signals inside organelles. Most genetically encoded calcium indicators are fusions of endogenous calcium-binding proteins whose functionality in vivo may be perturbed by competition with cellular partners. We describe here a novel family of fluorescent Ca2+ sensors based on the fusion of two Aequorea victoria proteins, GFP and apo-aequorin (GAP). GAP exhibited a unique combination of features: dual-excitation ratiometric imaging, high dynamic range, good signal-to-noise ratio, insensitivity to pH and Mg2+, tunable Ca2+ affinity, uncomplicated calibration, and targetability to five distinct organelles. Moreover, transgenic mice for endoplasmic reticulum-targeted GAP exhibited a robust long-term expression that correlated well with its reproducible performance in various neural tissues. This biosensor fills a gap in the actual repertoire of Ca2+ indicators for organelles and becomes a valuable tool for in vivo Ca2+ imaging applications. PMID:24501126

  12. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Shapiro, Mikhail G.; Ramirez, R. Matthew; Sperling, Lindsay J.; Sun, George; Sun, Jinny; Pines, Alexander; Schaffer, David V.; Bajaj, Vikram S.

    2014-07-01

    Magnetic resonance imaging (MRI) enables high-resolution non-invasive observation of the anatomy and function of intact organisms. However, previous MRI reporters of key biological processes tied to gene expression have been limited by the inherently low molecular sensitivity of conventional 1H MRI. This limitation could be overcome through the use of hyperpolarized nuclei, such as in the noble gas xenon, but previous reporters acting on such nuclei have been synthetic. Here, we introduce the first genetically encoded reporters for hyperpolarized 129Xe MRI. These expressible reporters are based on gas vesicles (GVs), gas-binding protein nanostructures expressed by certain buoyant microorganisms. We show that GVs are capable of chemical exchange saturation transfer interactions with xenon, which enables chemically amplified GV detection at picomolar concentrations (a 100- to 10,000-fold improvement over comparable constructs for 1H MRI). We demonstrate the use of GVs as heterologously expressed indicators of gene expression and chemically targeted exogenous labels in MRI experiments performed on living cells.

  13. Bacterially produced Pt-GFP as ratiometric dual-excitation sensor for in planta mapping of leaf apoplastic pH in intact Avena sativa and Vicia faba.

    PubMed

    Geilfus, Christoph-Martin; Mühling, Karl H; Kaiser, Hartmut; Plieth, Christoph

    2014-01-01

    Ratiometric analysis with H(+)-sensitive fluorescent sensors is a suitable approach for monitoring apoplastic pH dynamics. For the acidic range, the acidotropic dual-excitation dye Oregon Green 488 is an excellent pH sensor. Long lasting (hours) recordings of apoplastic pH in the near neutral range, however, are more problematic because suitable pH indicators that combine a good pH responsiveness at a near neutral pH with a high photostability are lacking. The fluorescent pH reporter protein from Ptilosarcus gurneyi (Pt-GFP) comprises both properties. But, as a genetically encoded indicator and expressed by the plant itself, it can be used almost exclusively in readily transformed plants. In this study we present a novel approach and use purified recombinant indicators for measuring ion concentrations in the apoplast of crop plants such as Vicia faba L. and Avena sativa L. Pt-GFP was purified using a bacterial expression system and subsequently loaded through stomata into the leaf apoplast of intact plants. Imaging verified the apoplastic localization of Pt-GFP and excluded its presence in the symplast. The pH-dependent emission signal stood out clearly from the background. PtGFP is highly photostable, allowing ratiometric measurements over hours. By using this approach, a chloride-induced alkalinizations of the apoplast was demonstrated for the first in oat. Pt-GFP appears to be an excellent sensor for the quantification of leaf apoplastic pH in the neutral range. The presented approach encourages to also use other genetically encoded biosensors for spatiotemporal mapping of apoplastic ion dynamics.

  14. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing.

    PubMed

    Polizzi, Karen M; Kontoravdi, Cleo

    2015-02-01

    With the current wealth of transcriptomic data, it is possible to design genetically-encoded biosensors for the detection of stress responses and apply these to high-throughput bioprocess development and monitoring of cellular health. Such biosensors can sense extrinsic factors such as nutrient or oxygen deprivation and shear stress, as well as intrinsic stress factors like oxidative damage and unfolded protein accumulation. Alongside, there have been developments in biosensing hardware and software applicable to the field of genetically-encoded biosensors in the near future. This review discusses the current state-of-the-art in biosensors for monitoring cultures during biological manufacturing and the future challenges for the field. Connecting the individual achievements into a coherent whole will enable the application of genetically-encoded biosensors in industry. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis

    PubMed Central

    Steffen, Victoria; Otten, Julia; Engelmann, Susann; Radek, Andreas; Limberg, Michael; Koenig, Bernd W.; Noack, Stephan; Wiechert, Wolfgang; Pohl, Martina

    2016-01-01

    Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET)-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP) flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP), Citrine). Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum) strain DM1933 in a BioLector® microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization. PMID:27690044

  16. A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis.

    PubMed

    Steffen, Victoria; Otten, Julia; Engelmann, Susann; Radek, Andreas; Limberg, Michael; Koenig, Bernd W; Noack, Stephan; Wiechert, Wolfgang; Pohl, Martina

    2016-09-28

    Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET)-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP) flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP), Citrine). Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum) strain DM1933 in a BioLector(®) microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization.

  17. Live cell monitoring of glycine betaine by FRET-based genetically encoded nanosensor.

    PubMed

    Ahmad, Mohammad; Ameen, Seema; Siddiqi, Tariq Omar; Khan, Parvez; Ahmad, Altaf

    2016-12-15

    Glycine betaine (GB) is one of the key compatible solutes that accumulate in the cell at exceedingly high level under the conditions of high salinity. It plays a crucial role in the maintenance of osmolarity of the cell without affecting the physiological processes. Analysis of stress-induced physiological conditions in living cells, therefore, requires real-time monitoring of cellular GB level. Glycine Betaine Optical Sensor (GBOS), a genetically-encoded FRET-based nanosensor developed in this study, allows the real-time monitoring of GB levels inside living cells. This nanosensor has been developed by sandwiching GB binding protein (ProX) between the Förster resonance energy transfer (FRET) pair, the cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Conformational change in ProX, which was used as sensory domain, reported the change in the level of this compatible solute in in vitro and in vivo conditions. Binding of the GB to the sensory domain fetches close to both the fluorescent moieties that result in the form of increased FRET ratio. So, any change in the concentration of GB is correlated with change in FRET ratio. This sensor also reported the GB cellular dynamics in real-time in Escherichia coli cells after the addition of its precursor, choline. The GBOS was also expressed in yeast and mammalian cells to monitor the intracellular GB. Therefore, the GBOS represents a unique FRET-based nanosensor which allows the non-invasive ratiometric analysis of the GB in living cells.

  18. Rational design, synthesis, and spectroscopic and photophysical properties of a visible-light-excitable, ratiometric, fluorescent near-neutral pH indicator based on BODIPY.

    PubMed

    Boens, Noël; Qin, Wenwu; Baruah, Mukulesh; De Borggraeve, Wim M; Filarowski, Aleksander; Smisdom, Nick; Ameloot, Marcel; Crovetto, Luis; Talavera, Eva M; Alvarez-Pez, Jose M

    2011-09-19

    A visible-light-excitable, ratiometric, brightly fluorescent pH indicator for measurements in the pH range 5-7 has been designed and synthesized by conjugatively linking the BODIPY fluorophore at the 3-position to the pH-sensitive ligand imidazole through an ethenyl bridge. The probe is available as cell membrane permeable methyl ester 8-(4-carbomethoxyphenyl)-4,4-difluoro-3-[2-(1H-imidazol-4-yl)ethenyl]-1,5,7-trimethyl-3a,4a-diaza-4-bora-s-indacene (I) and corresponding water-soluble sodium carboxylate, sodium 8-(4-carboxylatophenyl)-4,4-difluoro-3-[2-(1H-imidazol-4-yl)ethenyl]-1,5,7-trimethyl-3a,4a-diaza-4-bora-s-indacene (II). The fluorescence quantum yield Φ(f) of ester I is very high (0.8-1.0) in the organic solvents tested. The fluorescence lifetime (ca. 4 ns) of I in organic solvents with varying polarity/polarizability (from cyclohexane to acetonitrile) is independent of the solvent with a fluorescence rate constant k(f) of 2.4×10(8) s(-1). Probe I is readily loaded in the cytosol of live cells, where its high fluorescence intensity remains nearly constant over an extended time period. Water-soluble indicator II exhibits two acid-base equilibria in aqueous solution, characterized by pK(a) values of 6.0 and 12.6. The Φ(f) value of II in aqueous solution is high: 0.6 for the cationic and anionic forms of the imidazole ligand, and 0.8 for neutral imidazole. On protonation-deprotonation in the near-neutral pH range, UV/Vis absorption and fluorescence spectral shifts along with isosbestic and pseudo-isoemissive points are observed. This dual-excitation and dual-emission pH indicator emits intense green-yellow fluorescence at lower pH and intense orange fluorescence at higher pH. The influence of ionic strength and buffer concentration on the absorbance and steady-state fluorescence of II has also been investigated. The apparent pK(a) of the near-neutral acid-base equilibrium determined by spectrophotometric and fluorometric titration is nearly independent of

  19. A Unique Genetically Encoded FRET Pair in Mammalian Cells.

    PubMed

    Mitchell, Amanda L; Addy, Partha Sarathi; Chin, Melissa A; Chatterjee, Abhishek

    2017-03-16

    Förster resonance energy transfer (FRET) between two suitable fluorophores is a powerful tool to monitor dynamic changes in protein structure in vitro and in vivo. The ability to genetically encode a FRET pair represents a convenient "labeling-free" strategy to incorporate them into target protein(s). Currently, the only genetically encoded FRET pairs available for use in mammalian cells use fluorescent proteins. However, their large size can lead to unfavorable perturbations, particularly when two are used at the same time. Additionally, fluorescent proteins are largely restricted to a terminal attachment to the target, which might not be optimal. Here, we report the development of an alternative genetically encoded FRET pair in mammalian cells that circumvents these challenges by taking advantage of a small genetically encoded fluorescent unnatural amino acid as the donor and enhanced green fluorescent protein (EGFP) as the acceptor. The small size of Anap relative to fluorescent proteins, and the ability to co-translationally incorporate it into internal sites on the target protein, endows this novel FRET pair with improved versatility over its counterparts that rely upon two fluorescent proteins. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. A new approach for ratiometric in vivo calcium imaging of microglia.

    PubMed

    Brawek, Bianca; Liang, Yajie; Savitska, Daria; Li, Kaizhen; Fomin-Thunemann, Natalie; Kovalchuk, Yury; Zirdum, Elizabeta; Jakobsson, Johan; Garaschuk, Olga

    2017-07-20

    Microglia, resident immune cells of the brain, react to the presence of pathogens/danger signals with a large repertoire of functional responses including morphological changes, proliferation, chemotaxis, production/release of cytokines, and phagocytosis. In vitro studies suggest that many of these effector functions are Ca(2+)-dependent, but our knowledge about in vivo Ca(2+) signalling in microglia is rudimentary. This is mostly due to technical reasons, as microglia largely resisted all attempts of in vivo labelling with Ca(2+) indicators. Here, we introduce a novel approach, utilizing a microglia-specific microRNA-9-regulated viral vector, enabling the expression of a genetically-encoded ratiometric Ca(2+) sensor Twitch-2B in microglia. The Twitch-2B-assisted in vivo imaging enables recording of spontaneous and evoked microglial Ca(2+) signals and allows for the first time to monitor the steady state intracellular Ca(2+) levels in microglia. Intact in vivo microglia show very homogenous and low steady state intracellular Ca(2+) levels. However, the levels increase significantly after acute slice preparation and cell culturing along with an increase in the expression of activation markers CD68 and IL-1β. These data identify the steady state intracellular Ca(2+) level as a versatile microglial activation marker, which is highly sensitive to the cell's environment.

  1. Cell-Specific Targeting of Genetically Encoded Tools for Neuroscience

    PubMed Central

    Sjulson, Lucas; Cassataro, Daniela; DasGupta, Shamik; Miesenböck, Gero

    2017-01-01

    Genetically encoded tools for visualizing and manipulating neurons in vivo have led to significant advances in neuroscience, in large part because of the ability to target expression to specific cell populations of interest. Current methods enable targeting based on marker gene expression, development, anatomical projection pattern, synaptic connectivity, and recent activity as well as combinations of these factors. Here, we review these methods, focusing on issues of practical implementation as well as areas for future improvement. PMID:27732792

  2. Genetically-encoded probes for measurement of intracellular calcium

    PubMed Central

    Whitaker, Michael

    2012-01-01

    Small, fluorescent, calcium-sensing molecules have been enormously useful in mapping intracellular calcium signals in time and space, as chapters in this volume attest. Despite their widespread adoption and utility, they suffer some disadvantages. Genetically-encoded calcium sensors that can by expressed inside cells by transfection or transgenesis are desirable. The last ten years have been marked by a rapid evolution in the laboratory of genetically encoded calcium sensors two families both figuratively and literally, resulting in11distinct configurations of fluorescent proteins and their attendant calcium sensor modules. Here, I described the design logic and performance of this abundant collection of sensors and describe their use and performance in intro and in vivo. Genetically-encoded calcium sensors have proved valuable in the measurement of calcium concentration in cellular organelles, for the most part in single cells in vitro. Their success as quantitative calcium sensors in tissues in vitro and in vivo is qualified, but they have proved valuable in imaging the pattern of calcium signals within tissues in whole animals. Some branches of the calcium sensor evolutionary tree continue to evolve rapidly and the steady progress in optimising sensor parameters leads to the certain hope that these drawbacks will eventually be overcome by further genetic engineering. PMID:21035686

  3. Photoacoustic imaging using genetically encoded reporters: a review

    NASA Astrophysics Data System (ADS)

    Brunker, Joanna; Yao, Junjie; Laufer, Jan; Bohndiek, Sarah E.

    2017-07-01

    Genetically encoded contrast in photoacoustic imaging (PAI) is complementary to the intrinsic contrast provided by endogenous absorbing chromophores such as hemoglobin. The use of reporter genes expressing absorbing proteins opens the possibility of visualizing dynamic cellular and molecular processes. This is an enticing prospect but brings with it challenges and limitations associated with generating and detecting different types of reporters. The purpose of this review is to compare existing PAI reporters and signal detection strategies, thereby offering a practical guide, particularly for the nonbiologist, to choosing the most appropriate reporter for maximum sensitivity in the biological and technological system of interest.

  4. Genetically encoded sensors and fluorescence microscopy for anticancer research

    NASA Astrophysics Data System (ADS)

    Zagaynova, Elena V.; Shirmanova, Marina V.; Sergeeva, Tatiana F.; Klementieva, Natalia V.; Mishin, Alexander S.; Gavrina, Alena I.; Zlobovskay, Olga A.; Furman, Olga E.; Dudenkova, Varvara V.; Perelman, Gregory S.; Lukina, Maria M.; Lukyanov, Konstantin A.

    2017-02-01

    Early response of cancer cells to chemical compounds and chemotherapeutic drugs were studied using novel fluorescence tools and microscopy techniques. We applied confocal microscopy, two-photon fluorescence lifetime imaging microscopy and super-resolution localization-based microscopy to assess structural and functional changes in cancer cells in vitro. The dynamics of energy metabolism, intracellular pH, caspase-3 activation during staurosporine-induced apoptosis as well as actin cytoskeleton rearrangements under chemotherapy were evaluated. We have showed that new genetically encoded sensors and advanced fluorescence microscopy methods provide an efficient way for multiparameter analysis of cell activities

  5. Recent Advances in Development of Genetically Encoded Fluorescent Sensors.

    PubMed

    Sanford, Lynn; Palmer, Amy

    2017-01-01

    Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications. © 2017 Elsevier Inc. All rights reserved.

  6. The genetic encoded toolbox for electron microscopy and connectomics.

    PubMed

    Shigemoto, Ryuichi; Joesch, Maximilian

    2017-08-11

    Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure-function studies of synaptic connections in the brain. We review the current state-of-the-art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs. For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  7. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    NASA Astrophysics Data System (ADS)

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves, H. James, II

    2015-03-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or ``chemistry space.'' Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

  8. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

    PubMed Central

    Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

    2015-01-01

    Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

  9. Visualizing Presynaptic Calcium Dynamics and Vesicle Fusion with a Single Genetically Encoded Reporter at Individual Synapses.

    PubMed

    Jackson, Rachel E; Burrone, Juan

    2016-01-01

    Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs) that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses.

  10. Visualizing Presynaptic Calcium Dynamics and Vesicle Fusion with a Single Genetically Encoded Reporter at Individual Synapses

    PubMed Central

    Jackson, Rachel E.; Burrone, Juan

    2016-01-01

    Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs) that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses. PMID:27507942

  11. Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution.

    PubMed

    Liu, Xueliang; Lopez, Paola A; Giessen, Tobias W; Giles, Michael; Way, Jeffrey C; Silver, Pamela A

    2016-11-29

    Genetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ferritin protein, we discovered key mutations that lead to significantly enhanced cellular magnetism, resulting in increased physical attraction of ferritin-expressing cells to magnets and increased contrast for cellular magnetic resonance imaging (MRI). The magnetic mutants further demonstrate increased iron biomineralization measured by a novel fluorescent genetic sensor for intracellular free iron. In addition, we engineered Escherichia coli cells with multiple genomic knockouts to increase cellular accumulation of various metals. Lastly to explore further protein candidates for biomagnetism, we characterized members of the DUF892 family using the iron sensor and magnetic columns, confirming their intracellular iron sequestration that results in increased cellular magnetization.

  12. Genetically encoding lysine modifications on histone H4.

    PubMed

    Wilkins, Bryan J; Hahn, Liljan E; Heitmüller, Svenja; Frauendorf, Holm; Valerius, Oliver; Braus, Gerhard H; Neumann, Heinz

    2015-04-17

    Post-translational modifications of proteins are important modulators of protein function. In order to identify the specific consequences of individual modifications, general methods are required for homogeneous production of modified proteins. The direct installation of modified amino acids by genetic code expansion facilitates the production of such proteins independent of the knowledge and availability of the enzymes naturally responsible for the modification. The production of recombinant histone H4 with genetically encoded modifications has proven notoriously difficult in the past. Here, we present a general strategy to produce histone H4 with acetylation, propionylation, butyrylation, and crotonylation on lysine residues. We produce homogeneous histone H4 containing up to four simultaneous acetylations to analyze the impact of the modifications on chromatin array compaction. Furthermore, we explore the ability of antibodies to discriminate between alternative lysine acylations by incorporating these modifications in recombinant histone H4.

  13. Monitoring thioredoxin redox with a genetically encoded red fluorescent biosensor.

    PubMed

    Fan, Yichong; Makar, Merna; Wang, Michael X; Ai, Hui-Wang

    2017-09-01

    Thioredoxin (Trx) is one of the two major thiol antioxidants, playing essential roles in redox homeostasis and signaling. Despite its importance, there is a lack of methods for monitoring Trx redox dynamics in live cells, hindering a better understanding of physiological and pathological roles of the Trx redox system. In this work, we developed the first genetically encoded fluorescent biosensor for Trx redox by engineering a redox relay between the active-site cysteines of human Trx1 and rxRFP1, a redox-sensitive red fluorescent protein. We used the resultant biosensor-TrxRFP1-to selectively monitor perturbations of Trx redox in various mammalian cell lines. We subcellularly localized TrxRFP1 to image compartmentalized Trx redox changes. We further combined TrxRFP1 with a green fluorescent Grx1-roGFP2 biosensor to simultaneously monitor Trx and glutathione redox dynamics in live cells in response to chemical and physiologically relevant stimuli.

  14. Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution

    PubMed Central

    Liu, Xueliang; Lopez, Paola A.; Giessen, Tobias W.; Giles, Michael; Way, Jeffrey C.; Silver, Pamela A.

    2016-01-01

    Genetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ferritin protein, we discovered key mutations that lead to significantly enhanced cellular magnetism, resulting in increased physical attraction of ferritin-expressing cells to magnets and increased contrast for cellular magnetic resonance imaging (MRI). The magnetic mutants further demonstrate increased iron biomineralization measured by a novel fluorescent genetic sensor for intracellular free iron. In addition, we engineered Escherichia coli cells with multiple genomic knockouts to increase cellular accumulation of various metals. Lastly to explore further protein candidates for biomagnetism, we characterized members of the DUF892 family using the iron sensor and magnetic columns, confirming their intracellular iron sequestration that results in increased cellular magnetization. PMID:27897245

  15. Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor

    PubMed Central

    2012-01-01

    Background Molecular oxygen (O2) is one of the key metabolites of all obligate and facultative aerobic pro- and eukaryotes. It plays a fundamental role in energy homeostasis whereas oxygen deprivation, in turn, broadly affects various physiological and pathophysiological processes. Therefore, real-time monitoring of cellular oxygen levels is basically a prerequisite for the analysis of hypoxia-induced processes in living cells and tissues. Results We developed a genetically encoded Förster resonance energy transfer (FRET)-based biosensor allowing the observation of changing molecular oxygen concentrations inside living cells. This biosensor named FluBO (fluorescent protein-based biosensor for oxygen) consists of the yellow fluorescent protein (YFP) that is sensitive towards oxygen depletion and the hypoxia-tolerant flavin-binding fluorescent protein (FbFP). Since O2 is essential for the formation of the YFP chromophore, efficient FRET from the FbFP donor domain to the YFP acceptor domain only occurs in the presence but not in the absence of oxygen. The oxygen biosensor was used for continuous real-time monitoring of temporal changes of O2 levels in the cytoplasm of Escherichia coli cells during batch cultivation. Conclusions FluBO represents a unique FRET-based oxygen biosensor which allows the non-invasive ratiometric readout of cellular oxygen. Thus, FluBO can serve as a novel and powerful probe for investigating the occurrence of hypoxia and its effects on a variety of (patho)physiological processes in living cells. PMID:22439625

  16. A genetically encoded biosensor for visualising hypoxia responses in vivo

    PubMed Central

    Misra, Tvisha; Baccino-Calace, Martin; Meyenhofer, Felix; Rodriguez-Crespo, David; Akarsu, Hatice; Armenta-Calderón, Ricardo; Gorr, Thomas A.; Frei, Christian; Cantera, Rafael; Egger, Boris

    2017-01-01

    ABSTRACT Cells experience different oxygen concentrations depending on location, organismal developmental stage, and physiological or pathological conditions. Responses to reduced oxygen levels (hypoxia) rely on the conserved hypoxia-inducible factor 1 (HIF-1). Understanding the developmental and tissue-specific responses to changing oxygen levels has been limited by the lack of adequate tools for monitoring HIF-1 in vivo. To visualise and analyse HIF-1 dynamics in Drosophila, we used a hypoxia biosensor consisting of GFP fused to the oxygen-dependent degradation domain (ODD) of the HIF-1 homologue Sima. GFP-ODD responds to changing oxygen levels and to genetic manipulations of the hypoxia pathway, reflecting oxygen-dependent regulation of HIF-1 at the single-cell level. Ratiometric imaging of GFP-ODD and a red-fluorescent reference protein reveals tissue-specific differences in the cellular hypoxic status at ambient normoxia. Strikingly, cells in the larval brain show distinct hypoxic states that correlate with the distribution and relative densities of respiratory tubes. We present a set of genetic and image analysis tools that enable new approaches to map hypoxic microenvironments, to probe effects of perturbations on hypoxic signalling, and to identify new regulators of the hypoxia response. PMID:28011628

  17. A genetically encoded biosensor for visualising hypoxia responses in vivo.

    PubMed

    Misra, Tvisha; Baccino-Calace, Martin; Meyenhofer, Felix; Rodriguez-Crespo, David; Akarsu, Hatice; Armenta-Calderón, Ricardo; Gorr, Thomas A; Frei, Christian; Cantera, Rafael; Egger, Boris; Luschnig, Stefan

    2017-02-15

    Cells experience different oxygen concentrations depending on location, organismal developmental stage, and physiological or pathological conditions. Responses to reduced oxygen levels (hypoxia) rely on the conserved hypoxia-inducible factor 1 (HIF-1). Understanding the developmental and tissue-specific responses to changing oxygen levels has been limited by the lack of adequate tools for monitoring HIF-1 in vivo. To visualise and analyse HIF-1 dynamics in Drosophila, we used a hypoxia biosensor consisting of GFP fused to the oxygen-dependent degradation domain (ODD) of the HIF-1 homologue Sima. GFP-ODD responds to changing oxygen levels and to genetic manipulations of the hypoxia pathway, reflecting oxygen-dependent regulation of HIF-1 at the single-cell level. Ratiometric imaging of GFP-ODD and a red-fluorescent reference protein reveals tissue-specific differences in the cellular hypoxic status at ambient normoxia. Strikingly, cells in the larval brain show distinct hypoxic states that correlate with the distribution and relative densities of respiratory tubes. We present a set of genetic and image analysis tools that enable new approaches to map hypoxic microenvironments, to probe effects of perturbations on hypoxic signalling, and to identify new regulators of the hypoxia response.

  18. In Vivo Measurement of Intramolecular Distances Using Genetically Encoded Reporters

    PubMed Central

    Sandtner, Walter; Bezanilla, Francisco; Correa, Ana M.

    2007-01-01

    The function of membrane proteins occurs in the context of the cell membrane in living cells acting in concert with various cell components such as other proteins, cofactors, etc. The understanding of the function at the molecular level requires structural techniques, but high resolution structural studies are normally obtained in vitro and in artificial membranes or detergent. Ideally the correlation of structure and function should be carried out in the native environment but most of the techniques applicable in vivo lack the high resolution necessary to track conformational changes on a molecular level. Here we report on the successful application of an improved variant of lanthanide-based resonance energy transfer a fluorescent based technique, to Shaker potassium channels expressed in live Xenopus oocytes. Lanthanide-based resonance energy transfer is particularly suitable to measure intramolecular distances with high resolution. The improvements reported in this work are mainly based on the use of two different small genetically encoded tags (the Lanthanide Binding Tag and the hexa-histidine tag), which due to their small size can be encoded at will in many positions of interest without distorting the protein's function. The technique reported here has the additional improvement that the two tags can be placed independently in contrast to previously described techniques that rely on chemical labeling procedures of thiols. PMID:17766346

  19. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    PubMed Central

    Hochreiter, Bernhard; Pardo Garcia, Alan; Schmid, Johannes A.

    2015-01-01

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them. PMID:26501285

  20. Genetically Encoded Fluorescent Probe for Detecting Sirtuins in Living Cells.

    PubMed

    Xuan, Weimin; Yao, Anzhi; Schultz, Peter G

    2017-09-13

    Sirtuins are NAD(+) dependent protein deacetylases, which are involved in many biological processes. We now report a novel genetically encoded fluorescent probe (EGFP-K85AcK) that responds to sirtuins in living cells. The probe design exploits a lysyl residue in EGFP that is essential for chromophore maturation, and is also an efficient deacetylation substrate for sirtuins. Analysis of activity in Escherichia coli ΔcobB revealed that the probe can respond to various human sirtuins, including SIRT1, SIRT2, SIRT3 and SIRT5. We also directly monitored SIRT1 and SIRT2 activity in HEK293T cells with an mCherry fusion of EGFP-K85AcK, and showed that this approach can be extended to other fluorescent proteins. Finally, we demonstrate that this approach can be used to examine the activity of sirtuins toward additional lysyl posttranslational modifications, and show that sirtuins can act as erasers of HibK modified proteins.

  1. Fluorescent proteins as genetically encoded FRET biosensors in life sciences.

    PubMed

    Hochreiter, Bernhard; Garcia, Alan Pardo; Schmid, Johannes A

    2015-10-16

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  2. Transgenic mouse lines for non-invasive ratiometric monitoring of intracellular chloride

    PubMed Central

    Batti, Laura; Mukhtarov, Marat; Audero, Enrica; Ivanov, Anton; Paolicelli, Rosa Chiara; Zurborg, Sandra; Gross, Cornelius; Bregestovski, Piotr; Heppenstall, Paul A.

    2013-01-01

    Chloride is the most abundant physiological anion and participates in a variety of cellular processes including trans-epithelial transport, cell volume regulation, and regulation of electrical excitability. The development of tools to monitor intracellular chloride concentration ([Cli]) is therefore important for the evaluation of cellular function in normal and pathological conditions. Recently, several Cl-sensitive genetically encoded probes have been described which allow for non-invasive monitoring of [Cli]. Here we describe two mouse lines expressing a CFP-YFP-based Cl probe called Cl-Sensor. First, we generated transgenic mice expressing Cl-Sensor under the control of the mouse Thy1 mini promoter. Cl-Sensor exhibited good expression from postnatal day two (P2) in neurons of the hippocampus and cortex, and its level increased strongly during development. Using simultaneous whole-cell monitoring of ionic currents and Cl-dependent fluorescence, we determined that the apparent EC50 for Cli was 46 mM, indicating that this line is appropriate for measuring neuronal [Cli] in postnatal mice. We also describe a transgenic mouse reporter line for Cre-dependent conditional expression of Cl-Sensor, which was targeted to the Rosa26 locus and by incorporating a strong exogenous promoter induced robust expression upon Cre-mediated recombination. We demonstrate high levels of tissue-specific expression in two different Cre-driver lines targeting cells of the myeloid lineage and peripheral sensory neurons. Using these mice the apparent EC50 for Cli was estimated to be 61 and 54 mM in macrophages and DRG, respectively. Our data suggest that these mouse lines will be useful models for ratiometric monitoring of Cli in specific cell types in vivo. PMID:23734096

  3. RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins.

    PubMed

    Cetin, Mehmet; Evenson, William E; Gross, Garrett G; Jalali-Yazdi, Farzad; Krieger, Daniel; Arnold, Don; Takahashi, Terry T; Roberts, Richard W

    2017-02-17

    K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside the cells and when fused with a fluorescent protein label, the constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2.1μM to H-Ras(G12V) (GTP), excellent state selectivity, and remarkable specificity for K- and H-Ras. RasIn1 recognizes residues in the Switch I region of Ras, similar to Raf-RBD, and competes with Raf-RBD for binding. An affinity maturation selection based on RasIn1 resulted in RasIn2, which binds with a KD of 120nM and also retains excellent state selectivity. Both of these intrabodies colocalize with H-Ras, K-Ras, and G12V mutants inside the cells, providing new potential tools to monitor and modulate Ras-mediated signaling. Finally, RasIn1 and Rasin2 both display selectivity for the G12V mutants as compared with wild-type Ras providing a potential route for mutant selective recognition of Ras. Copyright © 2016. Published by Elsevier Ltd.

  4. Genetically encoded sensors of protein hydrodynamics and molecular proximity

    PubMed Central

    Hoepker, Alexander C.; Wang, Ariel; Le Marois, Alix; Suhling, Klaus; Yan, Yuling; Marriott, Gerard

    2015-01-01

    The specialized light organ of the ponyfish supports the growth of the bioluminescent symbiont Photobacterium leiognathi. The bioluminescence of P. leiognathi is generated within a heteromeric protein complex composed of the bacterial luciferase and a 20-kDa lumazine binding protein (LUMP), which serves as a Förster resonance energy transfer (FRET) acceptor protein, emitting a cyan-colored fluorescence with an unusually long excited state lifetime of 13.6 ns. The long fluorescence lifetime and small mass of LUMP are exploited for the design of highly optimized encoded sensors for quantitative fluorescence anisotropy (FA) measurements of protein hydrodynamics. In particular, large differences in the FA values of the free and target-bound states of LUMP fusions appended with capture sequences of up to 20 kDa are used in quantitative FA imaging and analysis of target proteins. For example, a fusion protein composed of LUMP and a 5-kDa G protein binding domain is used as an FA sensor to quantify the binding of the GTP-bound cell division control protein 42 homolog (Cdc42) (21 kDa) in solution and within Escherichia coli. Additionally, the long fluorescence lifetime and the surface-bound fluorescent cofactor 6,7-dimethyl-8- (1′-dimethyl-ribityl) lumazine in LUMP are utilized in the design of highly optimized FRET probes that use Venus as an acceptor probe. The efficiency of FRET in a zero-length LUMP-Venus fusion is 62% compared to ∼31% in a related CFP-Venus fusion. The improved FRET efficiency obtained by using LUMP as a donor probe is used in the design of a FRET-optimized genetically encoded LUMP-Venus substrate for thrombin. PMID:25931526

  5. Genetically encoded sensors of protein hydrodynamics and molecular proximity.

    PubMed

    Hoepker, Alexander C; Wang, Ariel; Le Marois, Alix; Suhling, Klaus; Yan, Yuling; Marriott, Gerard

    2015-05-19

    The specialized light organ of the ponyfish supports the growth of the bioluminescent symbiont Photobacterium leiognathi. The bioluminescence of P. leiognathi is generated within a heteromeric protein complex composed of the bacterial luciferase and a 20-kDa lumazine binding protein (LUMP), which serves as a Förster resonance energy transfer (FRET) acceptor protein, emitting a cyan-colored fluorescence with an unusually long excited state lifetime of 13.6 ns. The long fluorescence lifetime and small mass of LUMP are exploited for the design of highly optimized encoded sensors for quantitative fluorescence anisotropy (FA) measurements of protein hydrodynamics. In particular, large differences in the FA values of the free and target-bound states of LUMP fusions appended with capture sequences of up to 20 kDa are used in quantitative FA imaging and analysis of target proteins. For example, a fusion protein composed of LUMP and a 5-kDa G protein binding domain is used as an FA sensor to quantify the binding of the GTP-bound cell division control protein 42 homolog (Cdc42) (21 kDa) in solution and within Escherichia coli. Additionally, the long fluorescence lifetime and the surface-bound fluorescent cofactor 6,7-dimethyl-8- (1'-dimethyl-ribityl) lumazine in LUMP are utilized in the design of highly optimized FRET probes that use Venus as an acceptor probe. The efficiency of FRET in a zero-length LUMP-Venus fusion is 62% compared to ∼ 31% in a related CFP-Venus fusion. The improved FRET efficiency obtained by using LUMP as a donor probe is used in the design of a FRET-optimized genetically encoded LUMP-Venus substrate for thrombin.

  6. KillerRed and miniSOG as genetically encoded photosensitizers for photodynamic therapy of cancer

    NASA Astrophysics Data System (ADS)

    Shirmanova, Marina V.; Serebrovskaya, Ekaterina O.; Snopova, Ludmila B.; Kuznetsova, Maria M.; Ryumina, Alina P.; Turchin, Ilya V.; Sergeeva, Ekaterina A.; Ignatova, Nadezhda I.; Klementieva, Natalia V.; Lukyanov, Konstantin A.; Lukyanov, Sergey A.; Zagaynova, Elena V.

    2013-06-01

    Despite of the success of photodynamic therapy (PDT) in cancer treatment, the problems of low selective accumulation of a photosensitizer in a tumor and skin phototoxicity have not resolved yet. The idea of encoding of a photosensitizer in genome of cancer cells is attractive, particularly because it can provide highly selective light induced cell killing. This work is aimed at the development of new approach to PDT of cancer, namely to using genetically encoded photosensitizers. A phototoxicity of red fluorescent GFP-like protein KillerRed and FMN-binding protein miniSOG was investigated on HeLa tumor xenografts in nude mice. The tumors were generated by subcutaneous injection of HeLa cells stably expressing the phototoxic proteins. The tumors were irradiated with 594 nm or 473 nm laser at 150 mW/cm2 for 20 or 30 min, repeatedly. Fluorescence intensity of the tumors was measured in vivo before and after each treatment procedure. Detailed pathomorphological analysis was performed 24 h after the therapy. On the epi-fluorescence images in vivo photobleaching of both proteins was observed indicating photodynamic reaction. Substantial pathomorphological abnormalities were found in the treated KillerRed-expressing tumor tissue, such as vacuolization of cytoplasm, cellular and nuclear membrane destruction, activation of apoptosis. In contrast, miniSOG-expressing tumors displayed no reaction to PDT, presumably due to the lack of FMN cofactor needed for fluorescence recovery of the flavoprotein. The results are of interest for photodynamic therapy as a proof of possibility to induce photodamages in cancer cells in vivo using genetically encoded photosensitizers.

  7. A naked-eye and ratiometric near-infrared probe for palladium via modulation of a π-conjugated system of cyanines.

    PubMed

    Wang, Xiaohang; Guo, Zhiqian; Zhu, Shiqin; Tian, He; Zhu, Weihong

    2014-11-14

    A ratiometric and colorimetric cyanine-based palladium sensor with an excellent selectivity and sensitivity has been designed. Notably, the modulation of π-conjugated electrons in cyanine dyes can result in a ratiometric fluorescence change with a large Stokes shift (270 nm), especially for realizing palladium detection in aqueous samples using indicator paper and in living cells by ratiometric mode. The limit of detection is as low as 0.3 ppb.

  8. Quantification of labile heme in live malaria parasites using a genetically encoded biosensor

    PubMed Central

    Abshire, James R.; Rowlands, Christopher J.; Ganesan, Suresh M.; So, Peter T. C.; Niles, Jacquin C.

    2017-01-01

    Heme is ubiquitous, yet relatively little is known about the maintenance of labile pools of this cofactor, which likely ensures its timely bioavailability for proper cellular function. Quantitative analysis of labile heme is of fundamental importance to understanding how nature preserves access to the diverse chemistry heme enables, while minimizing cellular damage caused by its redox activity. Here, we have developed and characterized a protein-based sensor that undergoes fluorescence quenching upon heme binding. By genetically encoding this sensor in the human malarial parasite, Plasmodium falciparum, we have quantified cytosolic labile heme levels in intact, blood-stage parasites. Our findings indicate that a labile heme pool (∼1.6 µM) is stably maintained throughout parasite development within red blood cells, even during a period coincident with extensive hemoglobin degradation by the parasite. We also find that the heme-binding antimalarial drug chloroquine specifically increases labile cytosolic heme, indicative of dysregulation of this homeostatic pool that may be a relevant component of the antimalarial activity of this compound class. We propose that use of this technology under various environmental perturbations in P. falciparum can yield quantitative insights into fundamental heme biology. PMID:28242687

  9. Imaging Membrane Potential with Two Types of Genetically Encoded Fluorescent Voltage Sensors.

    PubMed

    Lee, Sungmoo; Piao, Hong Hua; Sepheri-Rad, Masoud; Jung, Arong; Sung, Uhna; Song, Yoon-Kyu; Baker, Bradley J

    2016-02-04

    Genetically encoded voltage indicators (GEVIs) have improved to the point where they are beginning to be useful for in vivo recordings. While the ultimate goal is to image neuronal activity in vivo, one must be able to image activity of a single cell to ensure successful in vivo preparations. This procedure will describe how to image membrane potential in a single cell to provide a foundation to eventually image in vivo. Here we describe methods for imaging GEVIs consisting of a voltage-sensing domain fused to either a single fluorescent protein (FP) or two fluorescent proteins capable of Förster resonance energy transfer (FRET) in vitro. Using an image splitter enables the projection of images created by two different wavelengths onto the same charge-coupled device (CCD) camera simultaneously. The image splitter positions a second filter cube in the light path. This second filter cube consists of a dichroic and two emission filters to separate the donor and acceptor fluorescent wavelengths depending on the FPs of the GEVI. This setup enables the simultaneous recording of both the acceptor and donor fluorescent partners while the membrane potential is manipulated via whole cell patch clamp configuration. When using a GEVI consisting of a single FP, the second filter cube can be removed allowing the mirrors in the image splitter to project a single image onto the CCD camera.

  10. Site-directed spin labeling of a genetically encoded unnatural amino acid

    PubMed Central

    Fleissner, Mark R.; Brustad, Eric M.; Kálai, Tamás; Altenbach, Christian; Cascio, Duilio; Peters, Francis B.; Hideg, Kálmán; Peuker, Sebastian; Schultz, Peter G.; Hubbell, Wayne L.

    2009-01-01

    The traditional site-directed spin labeling (SDSL) method, which utilizes cysteine residues and sulfhydryl-reactive nitroxide reagents, can be challenging for proteins that contain functionally important native cysteine residues or disulfide bonds. To make SDSL amenable to any protein, we introduce an orthogonal labeling strategy, i.e., one that does not rely on any of the functional groups found in the common 20 amino acids. In this method, the genetically encoded unnatural amino acid p-acetyl-L-phenylalanine (p-AcPhe) is reacted with a hydroxylamine reagent to generate a nitroxide side chain (K1). The utility of this scheme was demonstrated with seven mutants of T4 lysozyme, each containing a single p-AcPhe at a solvent-exposed helix site; the mutants were expressed in amounts qualitatively similar to the wild-type protein. In general, the EPR spectra of the resulting K1 mutants reflect higher nitroxide mobilities than the spectra of analogous mutants containing the more constrained disulfide-linked side chain (R1) commonly used in SDSL. Despite this increased flexibility, site dependence of the EPR spectra suggests that K1 will be a useful sensor of local structure and of conformational changes in solution. Distance measurements between pairs of K1 residues using double electron electron resonance (DEER) spectroscopy indicate that K1 will also be useful for distance mapping. PMID:19995976

  11. Exploring dynamics of molybdate in living animal cells by a genetically encoded FRET nanosensor.

    PubMed

    Nakanishi, Yoichi; Iida, Syuntaro; Ueoka-Nakanishi, Hanayo; Niimi, Tomoaki; Tomioka, Rie; Maeshima, Masayoshi

    2013-01-01

    Molybdenum (Mo) is an essential trace element for almost all living organisms including animals. Mo is used as a catalytic center of molybdo-enzymes for oxidation/reduction reactions of carbon, nitrogen, and sulfur metabolism. Whilst living cells are known to import inorganic molybdate oxyanion from the surrounding environment, the in vivo dynamics of cytosolic molybdate remain poorly understood as no appropriate indicator is available for this trace anion. We here describe a genetically encoded Förester-resonance-energy-transfer (FRET)-based nanosensor composed of CFP, YFP and the bacterial molybdate-sensor protein ModE. The nanosensor MolyProbe containing an optimized peptide-linker responded to nanomolar-range molybdate selectively, and increased YFP:CFP fluorescence intensity ratio by up to 109%. By introduction of the nanosensor, we have been able to successfully demonstrate the real-time dynamics of molybdate in living animal cells. Furthermore, time course analyses of the dynamics suggest that novel oxalate-sensitive- and sulfate-resistant- transporter(s) uptake molybdate in a model culture cell.

  12. Exploring Dynamics of Molybdate in Living Animal Cells by a Genetically Encoded FRET Nanosensor

    PubMed Central

    Nakanishi, Yoichi; Iida, Syuntaro; Ueoka-Nakanishi, Hanayo; Niimi, Tomoaki; Tomioka, Rie; Maeshima, Masayoshi

    2013-01-01

    Molybdenum (Mo) is an essential trace element for almost all living organisms including animals. Mo is used as a catalytic center of molybdo-enzymes for oxidation/reduction reactions of carbon, nitrogen, and sulfur metabolism. Whilst living cells are known to import inorganic molybdate oxyanion from the surrounding environment, the in vivo dynamics of cytosolic molybdate remain poorly understood as no appropriate indicator is available for this trace anion. We here describe a genetically encoded Förester-resonance-energy-transfer (FRET)-based nanosensor composed of CFP, YFP and the bacterial molybdate-sensor protein ModE. The nanosensor MolyProbe containing an optimized peptide-linker responded to nanomolar-range molybdate selectively, and increased YFP:CFP fluorescence intensity ratio by up to 109%. By introduction of the nanosensor, we have been able to successfully demonstrate the real-time dynamics of molybdate in living animal cells. Furthermore, time course analyses of the dynamics suggest that novel oxalate-sensitive- and sulfate-resistant- transporter(s) uptake molybdate in a model culture cell. PMID:23472155

  13. Detection of Liposome Membrane Viscosity Perturbations with Ratiometric Molecular Rotors

    PubMed Central

    Nipper, Matthew E.; Dakanali, Marianna; Theodorakis, Emmanuel

    2011-01-01

    Molecular rotors are a form of fluorescent intramolecular charge-transfer complexes that can undergo intramolecular twisting motion upon photoexcitation. Twisted-state formation leads to non-radiative relaxation that competes with fluorescence emission. In bulk solutions, these molecules exhibit a viscosity-dependent quantum yield. On the molecular scale, the fluorescence emission is a function of the local free volume, which in turn is related to the local microviscosity. Membrane viscosity, and the inverse; fluidity, are characteristic terms used to describe the ease of movement withing the membrane. Often, changes in membrane viscosity govern intracellular processes and are indicative of a disease state. Molecular rotors have been used to investigate viscosity changes in liposomes and cells, but accuracy is affected by local concentration gradients and sample optical properties. We have developed self-calibrating ratiometric molecular rotors to overcome this challenge and integrated the new molecules into a DLPC liposome model exposed to the membrane-fluidizing agent propanol. We show that the ratiometric emission intensity linearly decreases with the pentanol exposure and that the ratiometric intensity is widely independent of the total liposome concentration. Conversely, dye concentration inside liposomes influences the sensitivity of the system. We suggest that the new self-calibrating dyes can be used for real-time viscosity sensing in liposome systems with the advantages of lifetime measurements, but with low-cost steady-state instrumentation. PMID:21354253

  14. Detection of liposome membrane viscosity perturbations with ratiometric molecular rotors.

    PubMed

    Nipper, Matthew E; Dakanali, Marianna; Theodorakis, Emmanuel; Haidekker, Mark A

    2011-06-01

    Molecular rotors are a form of fluorescent intramolecular charge-transfer complexes that can undergo intramolecular twisting motion upon photoexcitation. Twisted-state formation leads to non-radiative relaxation that competes with fluorescence emission. In bulk solutions, these molecules exhibit a viscosity-dependent quantum yield. On the molecular scale, the fluorescence emission is a function of the local free volume, which in turn is related to the local micro-viscosity. Membrane viscosity, and the inverse; fluidity, are characteristic terms used to describe the ease of movement withing the membrane. Often, changes in membrane viscosity govern intracellular processes and are indicative of a disease state. Molecular rotors have been used to investigate viscosity changes in liposomes and cells, but accuracy is affected by local concentration gradients and sample optical properties. We have developed self-calibrating ratiometric molecular rotors to overcome this challenge and integrated the new molecules into a DLPC liposome model exposed to the membrane-fluidizing agent propanol. We show that the ratiometric emission intensity linearly decreases with the propanol exposure and that the ratiometric intensity is widely independent of the total liposome concentration. Conversely, dye concentration inside liposomes influences the sensitivity of the system. We suggest that the new self-calibrating dyes can be used for real-time viscosity sensing in liposome systems with the advantages of lifetime measurements, but with low-cost steady-state instrumentation.

  15. Internally ratiometric fluorescent sensors for evaluation of intracellular GTP levels and distribution.

    PubMed

    Bianchi-Smiraglia, Anna; Rana, Mitra S; Foley, Colleen E; Paul, Leslie M; Lipchick, Brittany C; Moparthy, Sudha; Moparthy, Kalyana; Fink, Emily E; Bagati, Archis; Hurley, Edward; Affronti, Hayley C; Bakin, Andrei V; Kandel, Eugene S; Smiraglia, Dominic J; Feltri, Maria Laura; Sousa, Rui; Nikiforov, Mikhail A

    2017-10-01

    GTP is a major regulator of multiple cellular processes, but tools for quantitative evaluation of GTP levels in live cells have not been available. We report the development and characterization of genetically encoded GTP sensors, which we constructed by inserting a circularly permuted yellow fluorescent protein (cpYFP) into a region of the bacterial G protein FeoB that undergoes a GTP-driven conformational change. GTP binding to these sensors results in a ratiometric change in their fluorescence, thereby providing an internally normalized response to changes in GTP levels while minimally perturbing those levels. Mutations introduced into FeoB to alter its affinity for GTP created a series of sensors with a wide dynamic range. Critically, in mammalian cells the sensors showed consistent changes in ratiometric signal upon depletion or restoration of GTP pools. We show that these GTP evaluators (GEVALs) are suitable for detection of spatiotemporal changes in GTP levels in living cells and for high-throughput screening of molecules that modulate GTP levels.

  16. Genetically encoded tools: bridging the gap between neuronal identity and function.

    PubMed

    Cho, Yong Ku

    2015-01-21

    Genetically encoded tools are positioned to serve a unique and critical role in bridging the gap between the genetic identity of neurons and their functional properties. However, the use of these tools is limited by our current understanding of cell-type identity. As we make technological advances that focus on capturing functional aspects of neurons such as connectivity, activity, and metabolic states, our understanding of neuronal identity will deepen and may enable the use of genetically encoded tools for modulating disease-specific circuits for therapeutic purposes.

  17. Advances in Imaging Techniques and Genetically Encoded Probes for Photoacoustic Imaging

    PubMed Central

    Liu, Chengbo; Gong, Xiaojing; Lin, Riqiang; Liu, Feng; Chen, Jingqin; Wang, Zhiyong; Song, Liang; Chu, Jun

    2016-01-01

    Photoacoustic (PA) imaging is a rapidly emerging biomedical imaging modality that is capable of visualizing cellular and molecular functions with high detection sensitivity and spatial resolution in deep tissue. Great efforts and progress have been made on the development of various PA imaging technologies with improved resolution and sensitivity over the past two decades. Various PA probes with high contrast have also been extensively developed, with many important biomedical applications. In comparison with chemical dyes and nanoparticles, genetically encoded probes offer easier labeling of defined cells within tissues or proteins of interest within a cell, have higher stability in vivo, and eliminate the need for delivery of exogenous substances. Genetically encoded probes have thus attracted increasing attention from researchers in engineering and biomedicine. In this review, we aim to provide an overview of the existing PA imaging technologies and genetically encoded PA probes, and describe further improvements in PA imaging techniques and the near-infrared photochromic protein BphP1, the most sensitive genetically encoded probe thus far, as well as the potential biomedical applications of BphP1-based PA imaging in vivo. PMID:27877244

  18. Genetically encoded sensors enable real-time observation of metabolite production

    DOE PAGES

    Rogers, Jameson K.; Church, George M.

    2016-02-08

    Here, engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allowsmore » us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of 14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of 51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.« less

  19. Genetically encoded sensors enable real-time observation of metabolite production

    PubMed Central

    Rogers, Jameson K.; Church, George M.

    2016-01-01

    Engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allows us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of $14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of $51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules. PMID:26858408

  20. Dual-emitting nanocomposites derived from rare-earth compound nanotubes for ratiometric fluorescence sensing applications.

    PubMed

    Sun, Tian-Ying; Zhang, Da-Quan; Yu, Xue-Feng; Xiang, Yang; Luo, Min; Wang, Jia-Hong; Tan, Guo-Long; Wang, Qu-Quan; Chu, Paul K

    2013-02-21

    A new class of ratiometric fluorescence sensors composed of rare-earth (RE) compound nanotubes is described. Polyethylenimine-coated yttrium hydroxide fluoride nanotubes (YHF NTs) that were synthesized hydrothermally exhibit highly efficient fluorescence when doped with RE ions. The polyethylenimine on the NTs facilitates the incorporation of phosphors such as quantum dots or organic dyes onto the NT surface to produce dual-emitting nanocomposites which are excellent ratiometric fluorescence sensors. The phosphor layer and underlying tubes in the nanocomposites act as the indicator and reference probes, respectively. This ratiometric fluorescence method which can be applied to the detection of heavy metals in solutions, temperature sensing, and pH sensing boasts high sensitivity and selectivity as well as better accuracy than traditional intensity-based fluorescence methods.

  1. Dual-emitting nanocomposites derived from rare-earth compound nanotubes for ratiometric fluorescence sensing applications

    NASA Astrophysics Data System (ADS)

    Sun, Tian-Ying; Zhang, Da-Quan; Yu, Xue-Feng; Xiang, Yang; Luo, Min; Wang, Jia-Hong; Tan, Guo-Long; Wang, Qu-Quan; Chu, Paul K.

    2013-01-01

    A new class of ratiometric fluorescence sensors composed of rare-earth (RE) compound nanotubes is described. Polyethylenimine-coated yttrium hydroxide fluoride nanotubes (YHF NTs) that were synthesized hydrothermally exhibit highly efficient fluorescence when doped with RE ions. The polyethylenimine on the NTs facilitates the incorporation of phosphors such as quantum dots or organic dyes onto the NT surface to produce dual-emitting nanocomposites which are excellent ratiometric fluorescence sensors. The phosphor layer and underlying tubes in the nanocomposites act as the indicator and reference probes, respectively. This ratiometric fluorescence method which can be applied to the detection of heavy metals in solutions, temperature sensing, and pH sensing boasts high sensitivity and selectivity as well as better accuracy than traditional intensity-based fluorescence methods.A new class of ratiometric fluorescence sensors composed of rare-earth (RE) compound nanotubes is described. Polyethylenimine-coated yttrium hydroxide fluoride nanotubes (YHF NTs) that were synthesized hydrothermally exhibit highly efficient fluorescence when doped with RE ions. The polyethylenimine on the NTs facilitates the incorporation of phosphors such as quantum dots or organic dyes onto the NT surface to produce dual-emitting nanocomposites which are excellent ratiometric fluorescence sensors. The phosphor layer and underlying tubes in the nanocomposites act as the indicator and reference probes, respectively. This ratiometric fluorescence method which can be applied to the detection of heavy metals in solutions, temperature sensing, and pH sensing boasts high sensitivity and selectivity as well as better accuracy than traditional intensity-based fluorescence methods. Electronic supplementary information (ESI) available: EA and TGA profiles, emission spectra of YHF:Eu NTs. See DOI: 10.1039/c2nr33217e

  2. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

    PubMed Central

    Yang, Yi; Song, Haiping; He, Dan; Zhang, Shuai; Dai, Shizhong; Lin, Shixian; Meng, Rong; Wang, Chu; Chen, Peng R.

    2016-01-01

    Coupling photocrosslinking reagents with mass spectrometry has become a powerful tool for studying protein–protein interactions in living systems, but it still suffers from high rates of false-positive identifications as well as the lack of information on interaction interface due to the challenges in deciphering crosslinking peptides. Here we develop a genetically encoded photo-affinity unnatural amino acid that introduces a mass spectrometry-identifiable label (MS-label) to the captured prey proteins after photocrosslinking and prey–bait separation. This strategy, termed IMAPP (In-situ cleavage and MS-label transfer After Protein Photocrosslinking), enables direct identification of photo-captured substrate peptides that are difficult to uncover by conventional genetically encoded photocrosslinkers. Taking advantage of the MS-label, the IMAPP strategy significantly enhances the confidence for identifying protein–protein interactions and enables simultaneous mapping of the binding interface under living conditions. PMID:27460181

  3. Remote regulation of glucose homeostasis in mice using genetically encoded nanoparticles.

    PubMed

    Stanley, Sarah A; Sauer, Jeremy; Kane, Ravi S; Dordick, Jonathan S; Friedman, Jeffrey M

    2015-01-01

    Means for temporally regulating gene expression and cellular activity are invaluable for elucidating underlying physiological processes and would have therapeutic implications. Here we report the development of a genetically encoded system for remote regulation of gene expression by low-frequency radio waves (RFs) or a magnetic field. Iron oxide nanoparticles are synthesized intracellularly as a GFP-tagged ferritin heavy and light chain fusion. The ferritin nanoparticles associate with a camelid anti-GFP-transient receptor potential vanilloid 1 fusion protein, αGFP-TRPV1, and can transduce noninvasive RF or magnetic fields into channel activation, also showing that TRPV1 can transduce a mechanical stimulus. This, in turn, initiates calcium-dependent transgene expression. In mice with stem cell or viral expression of these genetically encoded components, remote stimulation of insulin transgene expression with RF or a magnet lowers blood glucose. This robust, repeatable method for remote regulation in vivo may ultimately have applications in basic science, technology and therapeutics.

  4. Genetically-encoded FRET-based sensors for monitoring Zn(2+) in living cells.

    PubMed

    Hessels, Anne M; Merkx, Maarten

    2015-02-01

    Genetically-encoded fluorescent sensor proteins are attractive tools for studying intracellular Zn(2+) homeostasis and signaling. Here we provide an overview of recently developed sensors based on Förster Resonance Energy Transfer (FRET). The pros and cons of the various sensors are discussed with respect to Zn(2+) affinity, dynamic range, intracellular targeting and multicolor imaging. Recent applications of these sensors are described, as well as some of the challenges that remain to be addressed in future research.

  5. DeActs: genetically encoded tools for perturbing the actin cytoskeleton in single cells.

    PubMed

    Harterink, Martin; da Silva, Marta Esteves; Will, Lena; Turan, Julia; Ibrahim, Adiljan; Lang, Alexander E; van Battum, Eljo Y; Pasterkamp, R Jeroen; Kapitein, Lukas C; Kudryashov, Dmitri; Barres, Ben A; Hoogenraad, Casper C; Zuchero, J Bradley

    2017-05-01

    The actin cytoskeleton is essential for many fundamental biological processes, but tools for directly manipulating actin dynamics are limited to cell-permeable drugs that preclude single-cell perturbations. Here we describe DeActs, genetically encoded actin-modifying polypeptides, which effectively induce actin disassembly in eukaryotic cells. We demonstrate that DeActs are universal tools for studying the actin cytoskeleton in single cells in culture, tissues, and multicellular organisms including various neurodevelopmental model systems.

  6. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems

    PubMed Central

    Sample, Vedangi; Mehta, Sohum; Zhang, Jin

    2014-01-01

    ABSTRACT In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction. PMID:24634506

  7. Facile synthesis of a ratiometric oxygen nanosensor for cellular imaging.

    PubMed

    Lu, Sisi; Xu, Wei; Zhang, Jinliang; Chen, Yiying; Xie, Lei; Yao, Qiuhong; Jiang, Yaqi; Wang, Yiru; Chen, Xi

    2016-12-15

    A new type of cell-penetrating ratiometric fluorescence oxygen sensing nanoparticle was prepared through a facile co-precipitation method. Amphiphilic polymer poly (styrene-co-maleic anhydride) (PSMA) was firstly cooperated with polystyrene (PS) to envelop the highly photostable phosphorescent oxygen indicator, platinum(II)-tetrakis(pentafluorophenyl)porphyrin (PtTFPP, emission at 648nm), and the reference fluorophore, poly(9, 9-dioctylfluorene) (PFO, emission at 440nm ), via hydrophobic interaction in aqueous solution. To improve the sensor biocompatibility, the biomacromolecule poly-l-lysine (PLL) was selected to act as a shell via electrostatic forces. The as-prepared PtTFPP doped core-shell nanoparticles (called PPMA/PLL NPs) exhibited an excellent ratiometric luminescence response to O2 content with high quenching efficiency and full reversibility in the oxygen sensing. More importantly, these oxygen nanosensors passed across the cell membrane after co-incubation without external force. Labeled cells exhibited high brightness in the matching blue and red channels of a digital camera. And most nanosensors were found locating in cytoplasm rather than being trapped in endosomes.

  8. Unconventional ratiometric-enhanced optical sensing of oxygen by mixed-phase TiO2

    NASA Astrophysics Data System (ADS)

    Lettieri, S.; Pallotti, D. K.; Gesuele, F.; Maddalena, P.

    2016-07-01

    We show that mixed-phase titanium dioxide (TiO2) can be effectively employed as an unconventional, inorganic, dual-emitting, and ratiometric optical sensor of O2. Simultaneous availability of rutile and anatase TiO2 photoluminescence (PL) and their peculiar "anti-correlated" PL responses to O2 allow using their ratio as a measurement parameter associated with the O2 concentration, leading to an experimental responsivity being by construction larger than the one obtainable for single-phase PL detection. A proof of this concept is given, showing a two-fold enhancement of the optical responsivity provided by the ratiometric approach. Besides the peculiar ratiometric-enhanced responsivity, other characteristics of mixed phase TiO2 can be envisaged as favorable for O2 optical probing, namely (a) low production costs, (b) absence of heterogeneous components, and (c) self-supporting properties. These characteristics encourage experimenting with its use for applications requiring high indicator quantities at a competitive price, possibly also tackling the need to develop supporting matrixes that carry the luminescent probes and avoiding issues related to the use of different components for ratiometric sensing.

  9. StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity

    PubMed Central

    Samodelov, Sophia L.; Beyer, Hannes M.; Guo, Xiujie; Augustin, Maximilian; Jia, Kun-Peng; Baz, Lina; Ebenhöh, Oliver; Beyer, Peter; Weber, Wilfried; Al-Babili, Salim; Zurbriggen, Matias D.

    2016-01-01

    Strigolactones are key regulators of plant development and interaction with symbiotic fungi; however, quantitative tools for strigolactone signaling analysis are lacking. We introduce a genetically encoded hormone biosensor used to analyze strigolactone-mediated processes, including the study of the components involved in the hormone perception/signaling complex and the structural specificity and sensitivity of natural and synthetic strigolactones in Arabidopsis, providing quantitative insights into the stereoselectivity of strigolactone perception. Given the high specificity, sensitivity, dynamic range of activity, modular construction, ease of implementation, and wide applicability, the biosensor StrigoQuant will be useful in unraveling multiple levels of strigolactone metabolic and signaling networks. PMID:27847871

  10. KillerOrange, a Genetically Encoded Photosensitizer Activated by Blue and Green Light

    PubMed Central

    Bozhanova, Nina G.; Sharonov, George V.; Staroverov, Dmitriy B.; Egorov, Evgeny S.; Ryabova, Anastasia V.; Solntsev, Kyril M.; Mishin, Alexander S.; Lukyanov, Konstantin A.

    2015-01-01

    Genetically encoded photosensitizers, proteins that produce reactive oxygen species when illuminated with visible light, are increasingly used as optogenetic tools. Their applications range from ablation of specific cell populations to precise optical inactivation of cellular proteins. Here, we report an orange mutant of red fluorescent protein KillerRed that becomes toxic when illuminated with blue or green light. This new protein, KillerOrange, carries a tryptophan-based chromophore that is novel for photosensitizers. We show that KillerOrange can be used simultaneously and independently from KillerRed in both bacterial and mammalian cells offering chromatic orthogonality for light-activated toxicity. PMID:26679300

  11. Genetically Encoded Photoactuators and Photosensors for Characterization and Manipulation of Pluripotent Stem Cells

    PubMed Central

    Pomeroy, Jordan E.; Nguyen, Hung X.; Hoffman, Brenton D.; Bursac, Nenad

    2017-01-01

    Our knowledge of pluripotent stem cell biology has advanced considerably in the past four decades, but it has yet to deliver on the great promise of regenerative medicine. The slow progress can be mainly attributed to our incomplete understanding of the complex biologic processes regulating the dynamic developmental pathways from pluripotency to fully-differentiated states of functional somatic cells. Much of the difficulty arises from our lack of specific tools to query, or manipulate, the molecular scale circuitry on both single-cell and organismal levels. Fortunately, the last two decades of progress in the field of optogenetics have produced a variety of genetically encoded, light-mediated tools that enable visualization and control of the spatiotemporal regulation of cellular function. The merging of optogenetics and pluripotent stem cell biology could thus be an important step toward realization of the clinical potential of pluripotent stem cells. In this review, we have surveyed available genetically encoded photoactuators and photosensors, a rapidly expanding toolbox, with particular attention to those with utility for studying pluripotent stem cells. PMID:28912894

  12. FRET-based genetically-encoded sensors for quantitative monitoring of metabolites.

    PubMed

    Mohsin, Mohd; Ahmad, Altaf; Iqbal, Muhammad

    2015-10-01

    Neighboring cells in the same tissue can exist in different states of dynamic activities. After genomics, proteomics and metabolomics, fluxomics is now equally important for generating accurate quantitative information on the cellular and sub-cellular dynamics of ions and metabolite, which is critical for functional understanding of organisms. Various spectrometry techniques are used for monitoring ions and metabolites, although their temporal and spatial resolutions are limited. Discovery of the fluorescent proteins and their variants has revolutionized cell biology. Therefore, novel tools and methods targeting sub-cellular compartments need to be deployed in specific cells and targeted to sub-cellular compartments in order to quantify the target-molecule dynamics directly. We require tools that can measure cellular activities and protein dynamics with sub-cellular resolution. Biosensors based on fluorescence resonance energy transfer (FRET) are genetically encoded and hence can specifically target sub-cellular organelles by fusion to proteins or targetted sequences. Since last decade, FRET-based genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of cellular physiology. This review, describing the design and principles of sensors, presents a database of sensors for different analytes/processes, and illustrate examples of application in quantitative live cell imaging.

  13. Genetically encoded FRET-based nanosensor for in vivo measurement of leucine.

    PubMed

    Mohsin, Mohd; Abdin, M Z; Nischal, Lata; Kardam, Hemant; Ahmad, Altaf

    2013-12-15

    Besides fundamental role in protein synthesis, leucine has metabolic roles as energy substrates, precursors for synthesis of other amino acids and as a modulator of muscle protein synthesis via the insulin-signaling pathway. Leucine concentration in cell and tissue is temporally dynamic as the metabolism of leucine is regulated through multiple enzymes and transporters. Assessment of cell-type specific activities of transporters and enzymes by physical fractionation is extremely challenging. Therefore, a method of reporting leucine dynamics at the cellular level is highly desirable. Given this, we developed a series of genetically encoded nanosensors for real-time in vivo measurement of leucine at cellular level. A leucine binding periplasmic binding protein (LivK) of Escherichia coli K12 was flanked with CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein) at N-terminus and C-terminus, respectively. The constructed nanosensors allowed in vitro determination of fluorescence resonance energy transfer (FRET) changes in a concentration-dependent manner. These sensors were found to be specific to leucine, and stable to pH-changes within a physiological range. Genetically encoded sensors can be targeted to a specific cell type, and allow dynamic measurement of leucine concentration in bacterial and yeast cells.

  14. A genetically encoded toolkit for tracking live-cell histidine dynamics in space and time

    PubMed Central

    Hu, Hanyang; Gu, Yanfang; Xu, Lei; Zou, Yejun; Wang, Aoxue; Tao, Rongkun; Chen, Xianjun; Zhao, Yuzheng; Yang, Yi

    2017-01-01

    High-resolution spatiotemporal imaging of histidine in single living mammalian cells faces technical challenges. Here, we developed a series of ratiometric, highly responsive, and single fluorescent protein-based histidine sensors of wide dynamic range. We used these sensors to quantify subcellular free-histidine concentrations in glucose-deprived cells and glucose-fed cells. Results showed that cytosolic free-histidine concentration was higher and more sensitive to the environment than free histidine in the mitochondria. Moreover, histidine was readily transported across the plasma membrane and mitochondrial inner membrane, which had almost similar transport rates and transport constants, and histidine transport was not influenced by cellular metabolic state. These sensors are potential tools for tracking histidine dynamics inside subcellular organelles, and they will open an avenue to explore complex histidine signaling. PMID:28252043

  15. Shining light on signaling and metabolic networks by genetically encoded biosensors

    PubMed Central

    Lalonde, Sylvie; Ehrhardt, David W; Frommer, Wolf B

    2009-01-01

    Fluorescent labels have revolutionized cell biology. Signaling intermediates and metabolites can be measured in real time with subcellular spatial resolution. Most of these sensors are based on fluorescent proteins, and many report fluorescence resonance energy transfer. Because the biosensors are genetically encoded, a toolbox for addressing cell biological questions at the systems level is now available. Fluorescent biosensors are able to determine the localization of proteins and their dynamics, to reveal the cellular and subcellular localization of the respective interactions and activities, and to provide complementary data on the steady state levels of ions, metabolites, and signaling intermediates with high temporal and spatial resolution. They represent the basis for cell-based high-throughput assays that are necessary for a systems perspective on plant cell function. PMID:16188489

  16. Genetically Encoded Spin Labels for In Vitro and In-Cell EPR Studies of Native Proteins.

    PubMed

    Schmidt, M J; Fedoseev, A; Summerer, D; Drescher, M

    2015-01-01

    Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful approach to study the structure, dynamics, and interactions of proteins. The genetic encoding of the noncanonical amino acid spin-labeled lysine 1 (SLK-1) eliminates the need for any chemical labeling steps in SDSL-EPR studies and enables the investigation of native, endogenous proteins with minimal structural perturbation, and without the need to create unique reactive sites for chemical labeling. We report detailed experimental procedures for the efficient synthesis of SLK-1, the expression and purification of SLK-1-containing proteins under conditions that ensure maximal integrity of the nitroxide radical moiety, and procedures for intramolecular EPR distance measurements in proteins by double electron-electron resonance.

  17. The study of hydrogen peroxide level under cisplatin action using genetically encoded sensor hyper

    NASA Astrophysics Data System (ADS)

    Belova, A. S.; Orlova, A. G.; Maslennikova, A. V.; Brilkina, A. A.; Balalaeva, I. V.; Antonova, N. O.; Mishina, N. M.; Shakhova, N. M.; Belousov, V. V.

    2014-03-01

    The aim of the work was to study the participation of hydrogen peroxide in reaction of cervical cancer cell line HeLa Kyoto on cisplatin action. Determination of hydrogen peroxide level was performed using genetically encoded fluorescent sensor HyPer2. The dependence of cell viability on cisplatin concentration was determined using MTT assay. Mechanisms of cell death as well as HyPer2 reaction was revealed by flow cytometry after 6-hours of incubation with cisplatin in different concentrations. Cisplatin used in low concentrations had no effect on hydrogen peroxide level in HeLa Kyoto cells. Increase of HyPer2 fluorescence was detected only after exposure with cisplatin in high concentration. The reaction was not the consequence of cell death.

  18. Efficient genetic encoding of phosphoserine and its non-hydrolyzable analog

    PubMed Central

    Rogerson, Daniel T.; Sachdeva, Amit; Wang, Kaihang; Haq, Tamanna; Kazlauskaite, Agne; Hancock, Susan M.; Huguenin-Dezot, Nicolas; Muqit, Miratul M. K.; Fry, Andrew M.; Bayliss, Richard; Chin, Jason W.

    2015-01-01

    Serine phosphorylation is a key post-translational modification that regulates diverse biological processes. Powerful analytical methods have identified thousands of phosphorylation sites, but many of their functions remain to be deciphered. A key to understanding the function of protein phosphorylation is access to phosphorylated proteins, but this is often challenging or impossible. Here we evolve an orthogonal aminoacyl-tRNA synthetase/tRNACUA pair that directs the efficient incorporation of phosphoserine into recombinant proteins in E. coli. Moreover, combining the orthogonal pair with a metabolically engineered E. coli enables the site-specific incorporation of a non-hydrolyzable analog of phosphoserine. Our approach enables quantitative decoding of the amber stop codon as phosphoserine and we purify several milligrams-per-liter of proteins bearing biologically relevant phosphorylations that were previously challenging or impossible to access: including phosphorylated ubiquitin and a kinase (Nek7) that is synthetically activated by a genetically encoded phosphorylation in its activation loop. PMID:26030730

  19. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains.

    PubMed

    Xuan, Weimin; Shao, Sida; Schultz, Peter G

    2017-04-03

    The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification. FPheK reacted with adjacent Lys, Cys, and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab.

  20. Development and properties of genetically encoded pH sensors in plants.

    PubMed

    Martinière, Alexandre; Desbrosses, Guilhem; Sentenac, Hervé; Paris, Nadine

    2013-01-01

    Fluorescent proteins (FPs) have given access to a large choice of live imaging techniques and have thereby profoundly modified our view of plant cells. Together with technological improvement of imaging, they have opened the possibility to monitor physico-chemical changes within cells. For this purpose, a new generation of FPs has been engineered. For instance, pHluorin, a point mutated version of green fluorescent protein, allows to get local pH estimates. In this paper, we will describe how genetically encoded sensors can be used to measure pH in the microenvironment of living tissues and subsequently discuss the role of pH in (i) exocytosis, (ii) ion uptake by plant roots, (iii) cell growth, and (iv) protein trafficking.

  1. Reporting from the Field: Genetically Encoded Fluorescent Reporters Uncover Signaling Dynamics in Living Biological Systems

    PubMed Central

    Mehta, Sohum; Zhang, Jin

    2015-01-01

    Real-time visualization of a wide range of biochemical processes in living systems is being made possible through the development and application of genetically encoded fluorescent reporters. These versatile biosensors have proven themselves tailor-made to the study of signal transduction, and in this review, we discuss some of the unique insights that they continue to provide regarding the spatial organization and dynamic regulation of intracellular signaling networks. In addition, we explore the more recent push to expand the scope of biological phenomena that can be monitored using these reporters, while also considering the potential to integrate this highly adaptable technology with a number of emerging techniques that may significantly broaden our view of how networks of biochemical processes shape larger biological phenomena. PMID:21495849

  2. Real time Measurement of Metabolic States in Living Cells using Genetically-encoded NADH Sensors

    PubMed Central

    Zhao, Yuzheng; Yang, Yi; Loscalzo, Joseph

    2014-01-01

    Redox metabolism plays critical roles in multiple biological processes and diseases. Until recently, knowledge of specific, key redox processes in living systems was limited by the lack of adequate methodology. Reduced nicotinamide adenine dinucleotide (NADH) and its oxidized form (NAD+) is the most important small molecule in the redox metabolism of mammalian cells. We previously reported a series of genetically encoded fluorescent sensors for intracellular NADH detection. Here, we present an accounting of experimental components and considerations, such as protein expression and purification, fluorescence titration, transfections, and confocal imaging, necessary to perform a standardized NADH assay experiment with these probes. In addition, we outline initial experiments used to derive basic principles of NADH/NAD+ redox biology in vitro. Finally, we describe a protocol for a steady-state kinetics experiment, and the processing of experimental data to measure intracellular NADH levels. PMID:24862275

  3. Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics.

    PubMed

    Sharma, Vangmayee; Wang, Yane-Shih; Liu, Wenshe R

    2016-12-16

    Histidine is a unique amino acid with an imidazole side chain in which both of the nitrogen atoms are capable of serving as a proton donor and proton acceptor in hydrogen bonding interactions. In order to probe the functional role of histidine involved in hydrogen bonding networks, fine-tuning the hydrogen bonding potential of the imidazole side chain is required but not feasible through traditional mutagenesis methods. Here, we show that two close mimetics of histidine, 3-methyl-histidine and thiazole alanine, can be genetically encoded using engineered pyrrolysine incorporation machinery. Replacement of the three histidine residues predicted to be involved in an extended charge-relay system in alanine racemase with 3-methyl-histidine or thiazole alanine shows a dramatic loss in the enzyme's catalytic efficiency, implying the role of this extended charge-relay system in activating the active site residue Y265, a general acid/base catalyst in the enzyme.

  4. Statistical sulcal shape comparisons: application to the detection of genetic encoding of the central sulcus shape.

    PubMed

    Le Goualher, G; Argenti, A M; Duyme, M; Baaré, W F; Hulshoff Pol, H E; Boomsma, D I; Zouaoui, A; Barillot, C; Evans, A C

    2000-05-01

    Principal Component Analysis allows a quantitative description of shape variability with a restricted number of parameters (or modes) which can be used to quantify the difference between two shapes through the computation of a modal distance. A statistical test can then be applied to this set of measurements in order to detect a statistically significant difference between two groups. We have applied this methodology to highlight evidence of genetic encoding of the shape of neuroanatomical structures. To investigate genetic constraint, we studied if shapes were more similar within 10 pairs of monozygotic twins than within interpairs and compared the results with those obtained from 10 pairs of dizygotic twins. The statistical analysis was performed using a Mantel permutation test. We show, using simulations, that this statistical test applied on modal distances can detect a possible genetic encoding. When applied to real data, this study highlighted genetic constraints on the shape of the central sulcus. We found from 10 pairs of monozygotic twins that the intrapair modal distance of the central sulcus was significantly smaller than the interpair modal distance, for both the left central sulcus (Z = -2.66; P < 0.005) and the right central sulcus (Z = -2.26; P < 0.05). Genetic constraints on the definition of the central sulcus shape were confirmed by applying the same experiment to 10 pairs of normal young individuals (Z = -1.39; Z = -0.63, i.e., values not significant at the P < 0.05 level) and 10 pairs of dizygotic twins (Z = 0.47; Z = 0.03, i.e., values not significant at the P < 0.05 level).

  5. Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome

    NASA Astrophysics Data System (ADS)

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.

    2016-03-01

    Optical imaging of genetically encoded probes has revolutionized biomedical studies by providing valuable information about targeted biological processes. Here, we report a novel imaging technique, termed reversibly switchable photoacoustic tomography (RS-PAT), which exhibits large penetration depth, high detection sensitivity, and super-resolution. RS-PAT combines advanced photoacoustic imaging techniques with, for the first time, a nonfluorescent photoswitchable bacterial phytochrome. This bacterial phytochrome is the most near-infrared shifted genetically encoded probe reported so far. Moreover, this bacterial phytochrome is reversibly photoconvertible between its far-red and near-infrared light absorption states. Taking maximum advantage of the powerful imaging capability of PAT and the unique photochemical properties of the phytochrome, RS-PAT has broken through both the optical diffusion limit for deep-tissue imaging and the optical diffraction limit for super-resolution photoacoustic microscopy. Specifically, with RS-PAT we have achieved an unprecedented detection sensitivity of ~2 μM, or as few as ~20 tumor cells, at a centimeter depth. Such high sensitivity is fully demonstrated in our study by monitoring tumor growth and metastasis at whole-body level with ~100 μm resolution. Moreover, our microscopic implementation of RS-PAT is capable of imaging mammalian cells with a sub-diffraction lateral resolution of ~140 nm and axial resolution of ~400 nm, which are respectively ~2-fold and ~75-fold finer than those of our conventional photoacoustic microscopy. Overall, RS-PAT is a new and promising imaging technology for studying biological processes at different length scales.

  6. A mitochondria-targeted ratiometric two-photon fluorescent probe for biological zinc ions detection

    PubMed Central

    Ning, Peng; Jiang, Jiacheng; Li, Longchun; Wang, Shuxin; Yu, Haizhu; Feng, Yan; Zhu, Manzhou; Zhang, Buchang; Yin, Hang; Guo, Qingxiang; Meng, Xiangming

    2015-01-01

    A mitochondria-targeted ratiometric two-photon fluorescent probe (Mito-MPVQ) for biological zinc ions detection was developed based on quinolone platform. Mito-MPVQ showed large red shifts (68nm) and selective ratiometric signal upon Zn2+ binding. The ratio of emission intensity (I488 nm/I420 nm) increases dramatically from 0.45 to 3.79 (ca. 8-fold). NMR titration and theoretical calculation confirmed the binding of Mito-MPVQ and Zn2+. Mito-MPVQ also exhibited large two-photon absorption cross sections (150GM) at nearly 720 nm and insensitivity to pH within the biologically relevant pH range. Cell imaging indicated that Mito-MPVQ could efficiently located in mitochondria and monitor mitochondrial Zn2+ under two-photon excitation with low cytotoxicity. PMID:26528806

  7. A cell-surface-anchored ratiometric fluorescent probe for extracellular pH sensing.

    PubMed

    Ke, Guoliang; Zhu, Zhi; Wang, Wei; Zou, Yuan; Guan, Zhichao; Jia, Shasha; Zhang, Huimin; Wu, Xuemeng; Yang, Chaoyong James

    2014-09-10

    Accurate sensing of the extracellular pH is a very important yet challenging task in biological and clinical applications. This paper describes the development of an amphiphilic lipid-DNA molecule as a simple yet useful cell-surface-anchored ratiometric fluorescent probe for extracellular pH sensing. The lipid-DNA probe, which consists of a hydrophobic diacyllipid tail and a hydrophilic DNA strand, is modified with two fluorescent dyes; one is pH-sensitive as pH indicator and the other is pH-insensitive as an internal reference. The lipid-DNA probe showed sensitive and reversible response to pH change in the range of 6.0-8.0, which is suitable for most extracellular studies. In addition, based on simple hydrophobic interactions with the cell membrane, the lipid-DNA probe can be easily anchored on the cell surface with negligible cytotoxicity, excellent stability, and unique ratiometric readout, thus ensuring its accurate sensing of extracellular pH. Finally, this lipid-DNA-based ratiometric pH indicator was successfully used for extracellular pH sensing of cells in 3D culture environment, demonstrating the potential applications of the sensor in biological and medical studies.

  8. Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding.

    PubMed

    Yan, Xiu-Fang; Chen, Zeng-Ping; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin

    2016-05-19

    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFMGRP) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFMGRP has been tested on the quantitative determination of free Ca(2+) in both simulated and real turbid media using a Ca(2+) sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFMGRP could realize precise and accurate quantification of free Ca(2+) in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca(2+) bound Rhod-2. The average relative predictive error value of QFMGRP for the test simulated turbid samples was 5.9%, about 2-4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca(2+) bound Rhod-2 and eosin B. The recovery rates of QFMGRP for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry.

  9. Studies of Hematopoietic Cell Differentiation with a Ratiometric and Reversible Sensor of Mitochondrial Reactive Oxygen Species

    PubMed Central

    Kaur, Amandeep; Jankowska, Karolina; Pilgrim, Chelsea; Fraser, Stuart T.

    2016-01-01

    Abstract Aims: Chronic elevations in cellular redox state are known to result in the onset of various pathological conditions, but transient increases in reactive oxygen species (ROS)/reactive nitrogen species (RNS) are necessary for signal transduction and various physiological functions. There is a distinct lack of reversible fluorescent tools that can aid in studying and unraveling the roles of ROS/RNS in physiology and pathology by monitoring the variations in cellular ROS levels over time. In this work, we report the development of ratiometric fluorescent sensors that reversibly respond to changes in mitochondrial redox state. Results: Photophysical studies of the developed flavin–rhodamine redox sensors, flavin–rhodamine redox sensor 1 (FRR1) and flavin–rhodamine redox sensor 2 (FRR2), confirmed the reversible response of the probes upon reduction and re-oxidation over more than five cycles. The ratiometric output of FRR1 and FRR2 remained unaltered in the presence of other possible cellular interferants (metals and pH). Microscopy studies indicated clear mitochondrial localization of both probes, and FRR2 was shown to report the time-dependent increase of mitochondrial ROS levels after lipopolysaccharide stimulation in macrophages. Moreover, it was used to study the variations in mitochondrial redox state in mouse hematopoietic cells at different stages of embryonic development and maturation. Innovation: This study provides the first ratiometric and reversible probes for ROS, targeted to the mitochondria, which reveal variations in mitochondrial ROS levels at different stages of embryonic and adult blood cell production. Conclusions: Our results suggest that with their ratiometric and reversible outputs, FRR1 and FRR2 are valuable tools for the future study of oxidative stress and its implications in physiology and pathology. Antioxid. Redox Signal. 24, 667–679. PMID:26865422

  10. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways.

    PubMed

    Michener, Joshua K; Thodey, Kate; Liang, Joe C; Smolke, Christina D

    2012-05-01

    Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability.

  11. Genetic encoding of caged cysteine and caged homocysteine in bacterial and mammalian cells.

    PubMed

    Uprety, Rajendra; Luo, Ji; Liu, Jihe; Naro, Yuta; Samanta, Subhas; Deiters, Alexander

    2014-08-18

    We report the genetic incorporation of caged cysteine and caged homocysteine into proteins in bacterial and mammalian cells. The genetic code of these cells was expanded with an engineered pyrrolysine tRNA/tRNA synthetase pair that accepts both light-activatable amino acids as substrates. Incorporation was validated by reporter assays, western blots, and mass spectrometry, and differences in incorporation efficiency were explained by molecular modeling of synthetase-amino acid interactions. As a proof-of-principle application, the genetic replacement of an active-site cysteine residue with a caged cysteine residue in Renilla luciferase led to a complete loss of enzyme activity; however, upon brief exposure to UV light, a >150-fold increase in enzymatic activity was observed, thus showcasing the applicability of the caged cysteine in live human cells. A simultaneously conducted genetic replacement with homocysteine yielded an enzyme with greatly reduced activity, thereby demonstrating the precise probing of a protein active site. These discoveries provide a new tool for the optochemical control of protein function in mammalian cells and expand the set of genetically encoded unnatural amino acids.

  12. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria

    PubMed Central

    Elbaz, Johann; Yin, Peng; Voigt, Christopher A.

    2016-01-01

    The field of DNA nanotechnology has harnessed the programmability of DNA base pairing to direct single-stranded DNAs (ssDNAs) to assemble into desired 3D structures. Here, we show the ability to express ssDNAs in Escherichia coli (32–205 nt), which can form structures in vivo or be purified for in vitro assembly. Each ssDNA is encoded by a gene that is transcribed into non-coding RNA containing a 3′-hairpin (HTBS). HTBS recruits HIV reverse transcriptase, which nucleates DNA synthesis and is aided in elongation by murine leukemia reverse transcriptase. Purified ssDNA that is produced in vivo is used to assemble large 1D wires (300 nm) and 2D sheets (5.8 μm2) in vitro. Intracellular assembly is demonstrated using a four-ssDNA crossover nanostructure that recruits split YFP when properly assembled. Genetically encoding DNA nanostructures provides a route for their production as well as applications in living cells. PMID:27091073

  13. Genetically encoding a light switch in an ionotropic glutamate receptor reveals subunit-specific interfaces

    PubMed Central

    Zhu, Shujia; Riou, Morgane; Yao, C. Andrea; Carvalho, Stéphanie; Rodriguez, Pamela C.; Bensaude, Olivier; Paoletti, Pierre; Ye, Shixin

    2014-01-01

    Reprogramming receptors to artificially respond to light has strong potential for molecular studies and interrogation of biological functions. Here, we design a light-controlled ionotropic glutamate receptor by genetically encoding a photoreactive unnatural amino acid (UAA). The photo–cross-linker p-azido-l-phenylalanine (AzF) was encoded in NMDA receptors (NMDARs), a class of glutamate-gated ion channels that play key roles in neuronal development and plasticity. AzF incorporation in the obligatory GluN1 subunit at the GluN1/GluN2B N-terminal domain (NTD) upper lobe dimer interface leads to an irreversible allosteric inhibition of channel activity upon UV illumination. In contrast, when pairing the UAA-containing GluN1 subunit with the GluN2A subunit, light-dependent inactivation is completely absent. By combining electrophysiological and biochemical analyses, we identify subunit-specific structural determinants at the GluN1/GluN2 NTD dimer interfaces that critically dictate UV-controlled inactivation. Our work reveals that the two major NMDAR subtypes differ in their ectodomain-subunit interactions, in particular their electrostatic contacts, resulting in GluN1 NTD coupling more tightly to the GluN2B NTD than to the GluN2A NTD. It also paves the way for engineering light-sensitive ligand-gated ion channels with subtype specificity through the genetic code expansion. PMID:24715733

  14. Genetically Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins

    DOE PAGES

    Ng, Simon; Lin, Edith; Kitov, Pavel I.; ...

    2015-04-10

    Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 108 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3 outmore » of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.« less

  15. Genetically Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins

    SciTech Connect

    Ng, Simon; Lin, Edith; Kitov, Pavel I.; Tjhung, Katrina F.; Gerlits, Oksana O.; Deng, Lu; Kasper, Brian; Sood, Amika; Paschal, Beth M.; Zhang, Ping; Ling, Chang-Chun; Klassen, John S.; Noren, Christopher J.; Mahal, Lara K.; Woods, Robert J.; Coates, Leighton; Derda, Ratmir

    2015-04-10

    Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 108 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.

  16. A fluorescent, genetically-encoded voltage probe capable of resolving action potentials.

    PubMed

    Barnett, Lauren; Platisa, Jelena; Popovic, Marko; Pieribone, Vincent A; Hughes, Thomas

    2012-01-01

    There is a pressing need in neuroscience for genetically-encoded, fluorescent voltage probes that can be targeted to specific neurons and circuits to allow study of neural activity using fluorescent imaging. We created 90 constructs in which the voltage sensing portion (S1-S4) of Ciona intestinalis voltage sensitive phosphatase (CiVSP) was fused to circularly permuted eGFP. This led to ElectricPk, a probe that is an order of magnitude faster (taus ~1-2 ms) than any currently published fluorescent protein-based voltage probe. ElectricPk can follow the rise and fall of neuronal action potentials with a modest decrease in fluorescence intensity (~0.7% ΔF/F). The probe has a nearly linear fluorescence/membrane potential response to both hyperpolarizing and depolarizing steps. This is the first probe based on CiVSP that captures the rapid movements of the voltage sensor, suggesting that voltage probes designed with circularly permuted fluorescent proteins may have some advantages.

  17. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.

    PubMed

    Shu, Xiaokun; Lev-Ram, Varda; Deerinck, Thomas J; Qi, Yingchuan; Ramko, Ericka B; Davidson, Michael W; Jin, Yishi; Ellisman, Mark H; Tsien, Roger Y

    2011-04-01

    Electron microscopy (EM) achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce "miniSOG" (for mini Singlet Oxygen Generator), a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy.

  18. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria.

    PubMed

    Elbaz, Johann; Yin, Peng; Voigt, Christopher A

    2016-04-19

    The field of DNA nanotechnology has harnessed the programmability of DNA base pairing to direct single-stranded DNAs (ssDNAs) to assemble into desired 3D structures. Here, we show the ability to express ssDNAs in Escherichia coli (32-205 nt), which can form structures in vivo or be purified for in vitro assembly. Each ssDNA is encoded by a gene that is transcribed into non-coding RNA containing a 3'-hairpin (HTBS). HTBS recruits HIV reverse transcriptase, which nucleates DNA synthesis and is aided in elongation by murine leukemia reverse transcriptase. Purified ssDNA that is produced in vivo is used to assemble large 1D wires (300 nm) and 2D sheets (5.8 μm(2)) in vitro. Intracellular assembly is demonstrated using a four-ssDNA crossover nanostructure that recruits split YFP when properly assembled. Genetically encoding DNA nanostructures provides a route for their production as well as applications in living cells.

  19. A genetically encoded biosensor for in vitro and in vivo detection of NADP(.).

    PubMed

    Zhao, Feng-Lan; Zhang, Chang; Zhang, Chen; Tang, Yun; Ye, Bang-Ce

    2016-03-15

    NADP(+), the oxidized form of nicotinamide adenine dinucleotide phosphate, plays an essential role as a coenzyme in cellular electron transfer reactions. The concentration of NADP(+) in cytoplasm or organelles is dynamic due to its conversion to many important derivatives. To track the NADP(+) concentration in single living cells, we developed a genetically encoded NADP(+) biosensor by inserting a reporter element, ketopantoate reductase (KPR), between the Förster resonance energy transfer (FRET) pair, cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). This recombinant sensor showed a NADP(+) concentration-dependent decrease in the fluorescence ratio in vitro assay. In order to optimize this biosensor, we performed peptide-length optimization and site-directed mutagenesis in the binding pocket of KPR guided by predictions from computational protein redesign. This modified biosensor showed a 70% Δratio increase compared to the wild type and was found to be highly specific to NADP(+), with a detection limit of 1 μM. The sensor also reported NADP(+) real-time cellular dynamics in Escherichia coli (E. coli) after the addition of its precursor, nicotinic acid (NA). Altogether, these results demonstrate the feasibility of the biosensor for visualizing NADP(+) both in vitro and in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Organoids and the genetically encoded self-assembly of embryonic stem cells.

    PubMed

    Turner, David A; Baillie-Johnson, Peter; Martinez Arias, Alfonso

    2016-02-01

    Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to self-organization, as often suggested, but rather to a process of genetically encoded self-assembly where genetic programs encode and control the emergence of biological structures. © 2015 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  1. Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae.

    PubMed

    Teo, Wei Suong; Chang, Matthew Wook

    2015-02-01

    Lignocellulosic biomass is a sustainable and abundant starting material for biofuel production. However, lignocellulosic hydrolysates contain not only glucose, but also other sugars including xylose which cannot be metabolized by the industrial workhorse Saccharomyces cerevisiae. Hence, engineering of xylose assimilating S. cerevisiae has been much studied, including strain optimization strategies. In this work, we constructed genetically encoded xylose biosensors that can control protein expression upon detection of xylose sugars. These were constructed with the constitutive expression of heterologous XylR repressors, which function as protein sensors, and cloning of synthetic promoters with XylR operator sites. Three XylR variants and the corresponding synthetic promoters were used: XylR from Tetragenococcus halophile, Clostridium difficile, and Lactobacillus pentosus. To optimize the biosensor, two promoters with different strengths were used to express the XylR proteins. The ability of XylR to repress yEGFP expression from the synthetic promoters was demonstrated. Furthermore, xylose sugars added exogenously to the cells were shown to regulate gene expression. We envision that the xylose biosensors can be used as a tool to engineer and optimize yeast that efficiently utilizes xylose as carbon source for growth and biofuel production. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.

    PubMed

    Martell, Jeffrey D; Deerinck, Thomas J; Sancak, Yasemin; Poulos, Thomas L; Mootha, Vamsi K; Sosinsky, Gina E; Ellisman, Mark H; Ting, Alice Y

    2012-11-01

    Electron microscopy (EM) is the standard method for imaging cellular structures with nanometer resolution, but existing genetic tags are inactive in most cellular compartments or require light and can be difficult to use. Here we report the development of 'APEX', a genetically encodable EM tag that is active in all cellular compartments and does not require light. APEX is a monomeric 28-kDa peroxidase that withstands strong EM fixation to give excellent ultrastructural preservation. We demonstrate the utility of APEX for high-resolution EM imaging of a variety of mammalian organelles and specific proteins using a simple and robust labeling procedure. We also fused APEX to the N or C terminus of the mitochondrial calcium uniporter (MCU), a recently identified channel whose topology is disputed. These fusions give EM contrast exclusively in the mitochondrial matrix, suggesting that both the N and C termini of MCU face the matrix. Because APEX staining is not dependent on light activation, APEX should make EM imaging of any cellular protein straightforward, regardless of the size or thickness of the specimen.

  3. Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid.

    PubMed

    Hao, Bing; Zhao, Gang; Kang, Patrick T; Soares, Jitesh A; Ferguson, Tsuneo K; Gallucci, Judith; Krzycki, Joseph A; Chan, Michael K

    2004-09-01

    L-pyrrolysine, the 22(nd) genetically encoded amino acid, was previously deduced to be (4R, 5R)-4-substituted-pyrroline-5-carboxylate attached to the epsilon-nitrogen of lysine based on the crystal structure of the M. barkeri monomethylamine methyltransferase (MtmB). To confirm L-pyrrolysine's identity, structures of MtmB have been determined following treatment with hydroxylamine, N-methylhydroxylamine, or dithionite. Analysis of these structures has provided additional support for the presence of the pyrroline ring and, together with previous mass spectroscopy data, has led us to assign the C(4)-substituent to a methyl group. Based on this assignment, synthetic L-pyrrolysine was prepared by chemical methods. Detailed study of this chemically synthesized L-pyrrolysine has allowed us to characterize its physical properties, to study its chemical stability, and to elucidate the role of its C(4) substituent. Future applications of this synthetic L-pyrrolysine include its in vivo incorporation into recombinant proteins.

  4. Mechanism of a Genetically Encoded Dark-to-Bright Reporter for Caspase Activity*

    PubMed Central

    Nicholls, Samantha B.; Chu, Jun; Abbruzzese, Genevieve; Tremblay, Kimberly D.; Hardy, Jeanne A.

    2011-01-01

    Fluorescent proteins have revolutionized modern biology with their ability to report the presence of tagged proteins in living systems. Although several fluorescent proteins have been described in which the excitation and emission properties can be modulated by external triggers, no fluorescent proteins have been described that can be activated from a silent dark state to a bright fluorescent state directly by the activity of an enzyme. We have developed a version of GFP in which fluorescence is completely quenched by appendage of a hydrophobic quenching peptide that tetramerizes GFP and prevents maturation of the chromophore. The fluorescence can be fully restored by catalytic removal of the quenching peptide, making it a robust reporter of proteolysis. We have demonstrated the utility of this uniquely dark state of GFP as a genetically encoded apoptosis reporter that monitors the function of caspases, which catalyze the fate-determining step in programmed cell death. Caspase Activatable-GFP (CA-GFP) can be activated both in vitro and in vivo, resulting in up to a 45-fold increase in fluorescent signal in bacteria and a 3-fold increase in mammalian cells. We used CA-GFP successfully to monitor real-time apoptosis in mammalian cells. This dark state of GFP may ultimately serve as a useful platform for probes of other enzymatic processes. PMID:21558267

  5. Organoids and the genetically encoded self‐assembly of embryonic stem cells

    PubMed Central

    Baillie‐Johnson, Peter

    2015-01-01

    Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to “self‐organization,” as often suggested, but rather to a process of genetically encoded self‐assembly where genetic programs encode and control the emergence of biological structures. PMID:26666846

  6. Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations.

    PubMed

    Ewald, Jennifer C; Reich, Sabrina; Baumann, Stephan; Frommer, Wolf B; Zamboni, Nicola

    2011-01-01

    Citrate is an intermediate in catabolic as well as biosynthetic pathways and is an important regulatory molecule in the control of glycolysis and lipid metabolism. Mass spectrometric and NMR based metabolomics allow measuring citrate concentrations, but only with limited spatial and temporal resolution. Methods are so far lacking to monitor citrate levels in real-time in-vivo. Here, we present a series of genetically encoded citrate sensors based on Förster resonance energy transfer (FRET). We screened databases for citrate-binding proteins and tested three candidates in vitro. The citrate binding domain of the Klebsiella pneumoniae histidine sensor kinase CitA, inserted between the FRET pair Venus/CFP, yielded a sensor highly specific for citrate. We optimized the peptide linkers to achieve maximal FRET change upon citrate binding. By modifying residues in the citrate binding pocket, we were able to construct seven sensors with different affinities spanning a concentration range of three orders of magnitude without losing specificity. In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation.

  7. Singlet oxygen generation by the genetically encoded tag miniSOG.

    PubMed

    Ruiz-González, Rubén; Cortajarena, Aitziber L; Mejias, Sara H; Agut, Montserrat; Nonell, Santi; Flors, Cristina

    2013-07-03

    The genetically encodable fluorescent tag miniSOG is expected to revolutionize correlative light- and electron microscopy due to its ability to produce singlet oxygen upon light irradiation. The quantum yield of this process was reported as ΦΔ = 0.47 ± 0.05, as derived from miniSOG's ability to photooxidize the fluorescent probe anthracene dipropionic acid (ADPA). In this report, a significantly smaller value of ΦΔ = 0.03 ± 0.01 is obtained by two methods: direct measurement of its phosphorescence at 1275 nm and chemical trapping using uric acid as an alternative probe. We present insight into the photochemistry of miniSOG and ascertain the reasons for the discrepancy in ΦΔ values. We find that miniSOG oxidizes ADPA by both singlet oxygen-dependent and -independent processes. We also find that cumulative irradiation of miniSOG increases its ΦΔ value ~10-fold due to a photoinduced transformation of the protein. This may be the reason why miniSOG outperforms other fluorescent proteins reported to date as singlet oxygen generators.

  8. Probing Protein-Protein Interactions with Genetically Encoded Photoactivatable Cross-Linkers.

    PubMed

    Cooley, Richard B; Sondermann, Holger

    2017-01-01

    Fundamental to all living organisms is the ability of proteins to interact with other biological molecules at the right time and location, with the proper affinity, and to do so reversibly. One well-established technique to study protein interactions is chemical cross-linking, a process in which proteins in close spatial proximity are covalently tethered together. An emerging technology that overcomes many limitations of traditional cross-linking methods is one in which photoactivatable cross-linking noncanonical amino acids are genetically encoded into a protein of interest using the cell's native translational machinery. These proteins can then be used to trap interacting biomolecules upon UV illumination. Here, we describe a method for the site-specific incorporation of photoactivatable cross-linking amino acids into fluorescently tagged proteins of interest in E. coli. Photo-cross-linking and analysis by SDS-PAGE using in-gel fluorescence detection, which provides rapid, highly sensitive, and specific detection of cross-linked adducts even in impure systems, are also described. An example expression and cross-linking experiment involving transmembrane signaling of a bacterial second messenger receptor system that controls biofilm formation is shown. All reagents needed to carry out these experiments are commercially available, and do not require special or unique technology to perform, making this method tractable to a broad community studying protein structure and function.

  9. Visualization of Nicotine Adenine Dinucleotide Redox Homeostasis with Genetically Encoded Fluorescent Sensors.

    PubMed

    Zhao, Yuzheng; Zhang, Zhuo; Zou, Yejun; Yang, Yi

    2017-08-09

    Beyond their roles as redox currency in living organisms, pyridine dinucleotides (NAD(+)/NADH and NADP(+)/NADPH) are also precursors or cosubstrates of great significance in various physiologic and pathologic processes. Recent Advances: For many years, it was challenging to develop methodologies for monitoring pyridine dinucleotides in situ or in vivo. Recent advances in fluorescent protein-based sensors provide a rapid, sensitive, specific, and real-time readout of pyridine dinucleotide dynamics in single cells or in vivo, thereby opening a new era of pyridine dinucleotide bioimaging. In this article, we summarize the developments in genetically encoded fluorescent sensors for NAD(+)/NADH and NADP(+)/NADPH redox states, as well as their applications in life sciences and drug discovery. The strengths and weaknesses of individual sensors are also discussed. These sensors have the advantages of being specific and organelle targetable, enabling real-time monitoring and subcellular-level quantification of targeted molecules in living cells and in vivo. NAD(+)/NADH and NADP(+)/NADPH have distinct functions in metabolic and redox regulation, and thus, a comprehensive evaluation of metabolic and redox states must be multiplexed with a combination of various metabolite sensors in a single cell. Antioxid. Redox Signal. 00, 000-000.

  10. A highly sensitive ratiometric fluorescent probe for the detection of cytoplasmic and nuclear hydrogen peroxide.

    PubMed

    Wen, Ying; Liu, Keyin; Yang, Huiran; Li, Yi; Lan, Haichuang; Liu, Yi; Zhang, Xinyu; Yi, Tao

    2014-10-07

    As a marker for oxidative stress and a second messenger in signal transduction, hydrogen peroxide (H2O2) plays an important role in living systems. It is thus critical to monitor the changes in H2O2 in cells and tissues. Here, we developed a highly sensitive and versatile ratiometric H2O2 fluorescent probe (NP1) based on 1,8-naphthalimide and boric acid ester. In response to H2O2, the ratio of its fluorescent intensities at 555 and 403 nm changed 1020-fold within 200 min. The detecting limit of NP1 toward H2O2 is estimated as 0.17 μM. It was capable of imaging endogenous H2O2 generated in live RAW 264.7 macrophages as a cellular inflammation response, and especially, it was able to detect H2O2 produced as a signaling molecule in A431 human epidermoid carcinoma cells through stimulation by epidermal growth factor. This probe contains an azide group and thus has the potential to be linked to various molecules via the click reaction. After binding to a Nuclear Localization Signal peptide, the peptide-based combination probe (pep-NP1) was successfully targeted to nuclei and was capable of ratiometrically detecting nuclear H2O2 in living cells. These results indicated that NP1 was a highly sensitive ratiometric H2O2 dye with promising biological applications.

  11. Targeted silver nanoparticles for ratiometric cell phenotyping

    NASA Astrophysics Data System (ADS)

    Willmore, Anne-Mari A.; Simón-Gracia, Lorena; Toome, Kadri; Paiste, Päärn; Kotamraju, Venkata Ramana; Mölder, Tarmo; Sugahara, Kazuki N.; Ruoslahti, Erkki; Braun, Gary B.; Teesalu, Tambet

    2016-04-01

    Affinity targeting is used to deliver nanoparticles to cells and tissues. For efficient targeting, it is critical to consider the expression and accessibility of the relevant receptors in the target cells. Here, we describe isotopically barcoded silver nanoparticles (AgNPs) as a tool for auditing affinity ligand receptors in cells. Tumor penetrating peptide RPARPAR (receptor: NRP-1) and tumor homing peptide GKRK (receptor: p32) were used as affinity ligands on the AgNPs. The binding and uptake of the peptide-functionalized AgNPs by cultured PPC-1 prostate cancer and M21 melanoma cells was dependent on the cell surface expression of the cognate peptide receptors. Barcoded peptide-functionalized AgNPs were synthesized from silver and palladium isotopes. The cells were incubated with a cocktail of the barcoded nanoparticles [RPARPAR (R), GKRK (K), and control], and cellular binding and internalization of each type of nanoparticle was assessed by inductively coupled plasma mass spectrometry. The results of isotopic analysis were in agreement with data obtained using optical methods. Using ratiometric measurements, we were able to classify the PPC-1 cell line as mainly NRP-1-positive, with 75 +/- 5% R-AgNP uptake, and the M21 cell line as only p32-positive, with 89 +/- 9% K-AgNP uptake. The isotopically barcoded multiplexed AgNPs are useful as an in vitro ratiometric phenotyping tool and have potential uses in functional evaluation of the expression of accessible homing peptide receptors in vivo.Affinity targeting is used to deliver nanoparticles to cells and tissues. For efficient targeting, it is critical to consider the expression and accessibility of the relevant receptors in the target cells. Here, we describe isotopically barcoded silver nanoparticles (AgNPs) as a tool for auditing affinity ligand receptors in cells. Tumor penetrating peptide RPARPAR (receptor: NRP-1) and tumor homing peptide GKRK (receptor: p32) were used as affinity ligands on the AgNPs. The

  12. Genetically-encoded tools for cAMP probing and modulation in living systems

    PubMed Central

    Paramonov, Valeriy M.; Mamaeva, Veronika; Sahlgren, Cecilia; Rivero-Müller, Adolfo

    2015-01-01

    Intracellular 3′-5′-cyclic adenosine monophosphate (cAMP) is one of the principal second messengers downstream of a manifold of signal transduction pathways, including the ones triggered by G protein-coupled receptors. Not surprisingly, biochemical assays for cAMP have been instrumental for basic research and drug discovery for decades, providing insights into cellular physiology and guiding pharmaceutical industry. However, despite impressive track record, the majority of conventional biochemical tools for cAMP probing share the same fundamental shortcoming—all the measurements require sample disruption for cAMP liberation. This common bottleneck, together with inherently low spatial resolution of measurements (as cAMP is typically analyzed in lysates of thousands of cells), underpin the ensuing limitations of the conventional cAMP assays: (1) genuine kinetic measurements of cAMP levels over time in a single given sample are unfeasible; (2) inability to obtain precise information on cAMP spatial distribution and transfer at subcellular levels, let alone the attempts to pinpoint dynamic interactions of cAMP and its effectors. At the same time, tremendous progress in synthetic biology over the recent years culminated in drastic refinement of our toolbox, allowing us not only to bypass the limitations of conventional assays, but to put intracellular cAMP life-span under tight control—something, that seemed scarcely attainable before. In this review article we discuss the main classes of modern genetically-encoded tools tailored for cAMP probing and modulation in living systems. We examine the capabilities and weaknesses of these different tools in the context of their operational characteristics and applicability to various experimental set-ups involving living cells, providing the guidance for rational selection of the best tools for particular needs. PMID:26441653

  13. Visualization of glutamine transporter activities in living cells using genetically encoded glutamine sensors.

    PubMed

    Gruenwald, Katrin; Holland, John Todd; Stromberg, Verlyn; Ahmad, Altaf; Watcharakichkorn, Daisy; Okumoto, Sakiko

    2012-01-01

    Glutamine plays a central role in the metabolism of critical biological molecules such as amino acids, proteins, neurotransmitters, and glutathione. Since glutamine metabolism is regulated through multiple enzymes and transporters, the cellular glutamine concentration is expected to be temporally dynamic. Moreover, differentiation in glutamine metabolism between cell types in the same tissue (e.g. neuronal and glial cells) is often crucial for the proper function of the tissue as a whole, yet assessing cell-type specific activities of transporters and enzymes in such heterogenic tissue by physical fractionation is extremely challenging. Therefore, a method of reporting glutamine dynamics at the cellular level is highly desirable. Genetically encoded sensors can be targeted to a specific cell type, hence addressing this knowledge gap. Here we report the development of Föster Resonance Energy Transfer (FRET) glutamine sensors based on improved cyan and yellow fluorescent proteins, monomeric Teal Fluorescent Protein (mTFP)1 and venus. These sensors were found to be specific to glutamine, and stable to pH-changes within a physiological range. Using cos7 cells expressing the human glutamine transporter ASCT2 as a model, we demonstrate that the properties of the glutamine transporter can easily be analyzed with these sensors. The range of glutamine concentration change in a given cell can also be estimated using sensors with different affinities. Moreover, the mTFP1-venus FRET pair can be duplexed with another FRET pair, mAmetrine and tdTomato, opening up the possibility for real-time imaging of another molecule. These novel glutamine sensors will be useful tools to analyze specificities of glutamine metabolism at the single-cell level.

  14. Mechanistic studies of the genetically encoded fluorescent protein voltage probe ArcLight.

    PubMed

    Han, Zhou; Jin, Lei; Chen, Fuyi; Loturco, Joseph J; Cohen, Lawrence B; Bondar, Alexey; Lazar, Josef; Pieribone, Vincent A

    2014-01-01

    ArcLight, a genetically encoded fluorescent protein voltage probe with a large ΔF/ΔV, is a fusion between the voltage sensing domain of the Ciona instestinalis voltage sensitive phosphatase and super ecliptic pHluorin carrying a single mutation (A227D in the fluorescent protein). Without this mutation the probe produces only a very small change in fluorescence in response to voltage deflections (∼ 1%). The large signal afforded by this mutation allows optical detection of action potentials and sub-threshold electrical events in single-trials in vitro and in vivo. However, it is unclear how this single mutation produces a probe with such a large modulation of its fluorescence output with changes in membrane potential. In this study, we identified which residues in super ecliptic pHluorin (vs eGFP) are critical for the ArcLight response, as a similarly constructed probe based on eGFP also exhibits large response amplitude if it carries these critical residues. We found that D147 is responsible for determining the pH sensitivity of the fluorescent protein used in these probes but by itself does not result in a voltage probe with a large signal. We also provide evidence that the voltage dependent signal of ArcLight is not simply sensing environmental pH changes. A two-photon polarization microscopy study showed that ArcLight's response to changes in membrane potential includes a reorientation of the super ecliptic pHluorin. We also explored different changes including modification of linker length, deletion of non-essential amino acids in the super ecliptic pHluorin, adding a farnesylation site, using tandem fluorescent proteins and other pH sensitive fluorescent proteins.

  15. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library.

    PubMed

    Jafari, Mohammad R; Deng, Lu; Kitov, Pavel I; Ng, Simon; Matochko, Wadim L; Tjhung, Katrina F; Zeberoff, Anthony; Elias, Anastasia; Klassen, John S; Derda, Ratmir

    2014-02-21

    Light-responsive ligands are useful tools in biochemistry and cell biology because the function of these ligands can be spatially and temporally controlled. Conventional design of such ligands relies on previously available data about the structure of both the ligand and the receptor. In this paper, we describe de novo discovery of light-responsive ligands through screening of a genetically encoded light-responsive library. We ligated a photoresponsive azobenzene core to a random CX7C peptide library displayed on the coat protein of M13 phage. A one-pot alkylation/reduction of the cysteines yielded a photoresponsive library of random heptapeptide macrocycles with over 2 × 10(8) members. We characterized the reaction on-phage and optimized the yield of the modifications in phage libraries. Screening of the library against streptavidin yielded three macrocycles that bind to streptavidin in the dark and cease binding upon irradiation with 370 nm light. All ligands restored their binding properties upon thermal relaxation and could be turned ON and OFF for several cycles. We measured dissociation constants, Kd, by electrospray ionization mass spectrometry (ESI-MS) binding assay. For ligand ACGFERERTCG, the Kd of cis and trans isomers differed by 22-fold; an incomplete isomerization (85%), however, resulted in the apparent difference of 4.5-fold between the dark and the irradiated state. We anticipate that the selection strategy described in this report can be used to find light-responsive ligands for many targets that do not have known natural ligands.

  16. Visualization of Glutamine Transporter Activities in Living Cells Using Genetically Encoded Glutamine Sensors

    PubMed Central

    Gruenwald, Katrin; Holland, John Todd; Stromberg, Verlyn; Ahmad, Altaf; Watcharakichkorn, Daisy; Okumoto, Sakiko

    2012-01-01

    Glutamine plays a central role in the metabolism of critical biological molecules such as amino acids, proteins, neurotransmitters, and glutathione. Since glutamine metabolism is regulated through multiple enzymes and transporters, the cellular glutamine concentration is expected to be temporally dynamic. Moreover, differentiation in glutamine metabolism between cell types in the same tissue (e.g. neuronal and glial cells) is often crucial for the proper function of the tissue as a whole, yet assessing cell-type specific activities of transporters and enzymes in such heterogenic tissue by physical fractionation is extremely challenging. Therefore, a method of reporting glutamine dynamics at the cellular level is highly desirable. Genetically encoded sensors can be targeted to a specific cell type, hence addressing this knowledge gap. Here we report the development of Föster Resonance Energy Transfer (FRET) glutamine sensors based on improved cyan and yellow fluorescent proteins, monomeric Teal Fluorescent Protein (mTFP)1 and venus. These sensors were found to be specific to glutamine, and stable to pH-changes within a physiological range. Using cos7 cells expressing the human glutamine transporter ASCT2 as a model, we demonstrate that the properties of the glutamine transporter can easily be analyzed with these sensors. The range of glutamine concentration change in a given cell can also be estimated using sensors with different affinities. Moreover, the mTFP1-venus FRET pair can be duplexed with another FRET pair, mAmetrine and tdTomato, opening up the possibility for real-time imaging of another molecule. These novel glutamine sensors will be useful tools to analyze specificities of glutamine metabolism at the single-cell level. PMID:22723868

  17. Genetically encoded molecular biosensors to image histone methylation in living animals.

    PubMed

    Sekar, Thillai V; Foygel, Kira; Gelovani, Juri G; Paulmurugan, Ramasamy

    2015-01-20

    Post-translational addition of methyl groups to the amino terminal tails of histone proteins regulates cellular gene expression at various stages of development and the pathogenesis of cellular diseases, including cancer. Several enzymes that modulate these post-translational modifications of histones are promising targets for development of small molecule drugs. However, there is no promising real-time histone methylation detection tool currently available to screen and validate potential small molecule histone methylation modulators in small animal models. With this in mind, we developed genetically encoded molecular biosensors based on the split-enzyme complementation approach for in vitro and in vivo imaging of lysine 9 (H3-K9 sensor) and lysine 27 (H3-K27 sensor) methylation marks of histone 3. These methylation sensors were validated in vitro in HEK293T, HepG2, and HeLa cells. The efficiency of the histone methylation sensor was assessed by employing methyltransferase inhibitors (Bix01294 and UNC0638), demethylase inhibitor (JIB-04), and siRNA silencing at the endogenous histone K9-methyltransferase enzyme level. Furthermore, noninvasive bioluminescence imaging of histone methylation sensors confirmed the potential of these sensors in monitoring histone methylation status in response to histone methyltransferase inhibitors in living animals. Experimental results confirmed that the developed H3-K9 and H3-K27 sensors are specific and sensitive to image the drug-induced histone methylation changes in living animals. These novel histone methylation sensors can facilitate the in vitro screening and in vivo characterization of new histone methyltransferase inhibitors and accelerate the pace of introduction of epigenetic therapies into the clinic.

  18. In Situ Ratiometric Quantitative Tracing of Intracellular Leucine Aminopeptidase Activity via an Activatable Near-Infrared Fluorescent Probe.

    PubMed

    Gu, Kaizhi; Liu, Yajing; Guo, Zhiqian; Lian, Cheng; Yan, Chenxu; Shi, Ping; Tian, He; Zhu, Wei-Hong

    2016-10-03

    Leucine aminopeptidase (LAP), one of the important proteolytic enzymes, is intertwined with the progress of many pathological disorders as a well-defined biomarker. To explore fluorescent aminopeptidase probe for quantitative detection of LAP distribution and dynamic changes, herein we report a LAP-targeting near-infrared (NIR) fluorescent probe (DCM-Leu) for ratiometric quantitative trapping of LAP activity in different kinds of living cells. DCM-Leu is composed of a NIR-emitting fluorophore (DCM) as a reporter and l-leucine as a triggered moiety, which are linked together by an amide bond specific for LAP cleavage. High contrast on the ratiometric NIR fluorescence signal can be achieved in response to LAP activity, thus enabling quantification of endogenous LAP with "build-in calibration" as well as minimal background interference. Its ratiometric NIR signal can be blocked in a dose-dependent manner by bestatin, an LAP inhibitor, indicating that the alteration of endogenous LAP activity results in these obviously fluorescent signal responses. It is worth noting that DCM-Leu features striking characteristics such as a large Stokes shift (∼205 nm), superior selectivity, and strong photostability responding to LAP. Impressively, not only did we successfully exemplify DCM-Leu in situ ratiometric trapping and quantification of endogenous LAP activity in various types of living cells, but also, with the aid of three-dimensional confocal imaging, the intracellular LAP distribution is clearly observed from different perspectives for the first time, owing to the high signal-to-noise of ratiometric NIR fluorescent response. Collectively, these results demonstrate preclinical potential value of DCM-Leu serving as a useful NIR fluorescent probe for early detection of LAP-associated disease and screening inhibitor.

  19. Development of an automated fluorescence microscopy system for photomanipulation of genetically encoded photoactivatable proteins (optogenetics) in live cells.

    PubMed

    Araki, Nobukazu; Ikeda, Yuka; Kato, Takuma; Kawai, Katsuhisa; Egami, Youhei; Miyake, Katsuya; Tsurumaki, Nobuhide; Yamaguchi, Mitsunari

    2014-06-01

    Photomanipulation of genetically encoded light-sensitive protein activity, also known as optogenetics, is one of the most innovative recent microscopy techniques in the fields of cell biology and neurobiology. Although photomanipulation is usually performed by diverting the photobleaching mode of a confocal laser microscope, photobleaching by the laser scanning unit is not always suitable for photoactivation. We have developed a simple automated wide-field fluorescence microscopy system for the photomanipulation of genetically encoded photoactivatable proteins in live cells. An electrically automated fluorescence microscope can be controlled through MetaMorph imaging software, making it possible to acquire time-lapse, multiwavelength images of live cells. Using the journal (macro recording) function of MetaMorph, we wrote a macro program to change the excitation filter for photoactivation and illumination area during the intervals of image acquisition. When this program was run on the wide-field fluorescence microscope, cells expressing genetically encoded photoactivatable Rac1, which is activated under blue light, showed morphological changes such as lamellipodial extension and cell surface ruffling in the illuminated region. Using software-based development, we successfully constructed a fully automated photoactivation microscopy system for a mercury lamp-based fluorescence microscope. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. A novel reaction-based colorimetric and ratiometric fluorescent sensor for cyanide anion with a large emission shift and high selectivity.

    PubMed

    Wang, Shaodan; Fei, Xiaoliang; Guo, Jing; Yang, Qingbiao; Li, Yaoxian; Song, Yan

    2016-01-01

    A hybrid carbazole-hemicyanine dye (Cac) has been developed as a novel colorimetric and ratiometric fluorescent sensor for cyanide detection. Upon treatment with cyanide, Cac displayed a remarkable fluorescence ratiometric response, with the emission wavelength displaying a very large emission shift (214 nm). The detection of cyanide was performed via the nucleophilic addition of cyanide anion to the indolium group of the sensor, which resulted in the blocking of the intramolecular charge transfer (ICT) process in the sensor, inducing a ratiometric fluorescence change and simultaneously an obvious color change. Furthermore, competitive anions did not showed any significant changes both in color and emission intensity ratio (I381/I595), indicating the high selectivity of the sensor to CN(-).

  1. Ratiometric Fluorescent Polymeric Thermometer for Thermogenesis Investigation in Living Cells.

    PubMed

    Qiao, Juan; Hwang, Yoon-Ho; Chen, Chuan-Fang; Qi, Li; Dong, Ping; Mu, Xiao-Yu; Kim, Dong-Pyo

    2015-10-20

    Intracellular temperature has a fundamental effect on cellular events. Herein, a novel fluorescent polymer ratiometric nanothermometer has been developed based on transferrin protein-stabilized gold nanoclusters as the targeting and fluorescent ratiometric unit and the thermosensitve polymer as the temperature sensing unit. The resultant nanothermometer could feature a high and spontaneous uptake into the HeLa cells and the ratiometric temperature sensing over the physiological temperature range. Moreover, the precise temperature sensing for intracellular heat generation in HeLa cells following calcium ions stress has been achieved. This practical intracellular thermometry could eliminate the interference of the intracellular surrounding environment in cancer cells without a microinjection procedure, which is user-friendly. The prepared new nanothermometer can provide tools for unveiling the intrinsic relationship between the intracellular temperature and ion channel function.

  2. A pyrene-based fluorescent sensor for ratiometric detection of heparin and its complex with heparin for reversed ratiometric detection of protamine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Gong, Weiwei; Wang, Shihuai; Wei, Yuting; Ding, Liping; Fang, Yu

    2017-01-01

    An imidazolium-modified pyrene derivative, IPy, was used for ratiometric detection of heparin, and its complex with heparin was used for reversed ratiometric detection of protamine in both aqueous solution and serum samples. The cationic fluorescent probe could interact with anionic heparin via electrostatic interaction to bring about blue-to-green fluorescence changes as monomer emission significantly decreases and excimer increases. The binary combination of IPy and heparin could be further used for green-to-blue detection of protamine since heparin prefers to bind to protamine instead of the probe due to its stronger affinity with protamine. The cationic probe shows high sensitivity to heparin with a low detection limit of 8.5 nM (153 ng/mL) and its combination with heparin displays high sensitivity to protamine with a detection limit as low as 15.4 nM (107.8 ng/mL) according to the 3σ IUPAC criteria. Moreover, both sensing processes are fast and can be performed in serum solutions, indicating possibility for practical applications.

  3. A single-wavelength-emitting ratiometric probe based on phototriggered fluorescence switching of graphene quantum dots.

    PubMed

    Qu, Zhi-bei; Zhang, Min; Zhou, Tianshu; Shi, Guoyue

    2014-10-13

    Ratiometric fluorescent probes are of great importance in research, because a built-in correction for environmental effects can be provided to reduce background interference. However, the traditional ratiometric fluorescent probes require two luminescent materials with different emission bands. Herein a novel ratiometric probe based on a single-wavelength-emitting material is reported. The probe works by regulating the luminescent property of graphene quantum dots with UV illumination as activator. The ratiometric sensor shows high sensitivity and specificity for iron ions. Moreover, the ratiometric sensor was successfully employed to monitor ferritin levels in Sprague Dawley rats with chemical-induced acute liver damage. The proposed single-wavelength ratiometric fluorescent probe may greatly broaden the applicability of ratiometric sensors in diagnostic devices, medical applications, and analytical chemistry.

  4. Fluorescent Strips of Electrospun Fibers for Ratiometric Sensing of Serum Heparin and Urine Trypsin.

    PubMed

    Zhao, Long; Wang, Tao; Wu, Qiang; Liu, Yuan; Chen, Zhoujiang; Li, Xiaohong

    2017-02-01

    "Turn-on" or "turn-off" probes remain challenges in the establishment of sensitive, easily operated, and reliable methods for in situ monitoring bioactive substances. In the current study, electrospun fibrous strips are designed to provide straightforward observations of ratiometric color changes with the naked eye in the presence of serum heparin or urine trypsin. A tetraphenylethene (TPE) derivative is constructed and along with phloxine B is grafted on fibers, followed by protamine adsorption to induce static quenching of phloxine B and aggregation-induced emission of the TPE derivative. The presence of heparin or trypsin removes protamine to restore the fluorescence of phloxine B at 574 nm (I574) and relieve the emission of the TPE derivative at 472 nm (I472). The grafting densities of phloxine B and the TPE derivative are essential to achieve the optimal fluorescence-intensity ratio of I574/I472 for the ratiometric detection of heparin and trypsin. Under illumination by an ultraviolet lamp, the fibrous mats turn from cyan to green in the presence of heparin at 0.4 U/mL and to a bright yellow at 0.8 U/mL, which is feasible in sensing serum heparin levels during postoperative and long-term care of patients after cardiovascular surgery. The protamine digestion results in similar color transitions with increasing trypsin levels up to 8 μg/mL, indicating the potential for monitoring urine trypsin levels of pancreas transplant patients. The color strips based on the ratiometric fluorescent response indicate advantages in lowering the detection limit and improving the accuracy and reproducibility, bearing great potential for a real-time and naked-eye detection of bioactive substances as self-test devices.

  5. Enantiospecific Synthesis of a Genetically Encodable Fluorescent Unnatural Amino Acid L-3-(6-Acetylnaphthalen-2-ylamino)-2-aminopropanoic Acid

    PubMed Central

    Xiang, Zheng; Wang, Lei

    2011-01-01

    Fluorescent unnatural amino acids (Uaas), when genetically incorporated into proteins, can provide unique advantages for imaging biological processes in vivo. Synthesis of optically pure L-enantiomer of fluorescent Uaas is crucial for their effective application in live cells. An efficient six-step synthesis of L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (L-Anap), a genetically encodable and polarity-sensitive fluorescent Uaa, has been developed. The synthesis takes advantage of a high-yield and enantiospecific Fukuyama-Mitsunobu reaction as the key transformation. PMID:21732687

  6. Development of ratiometric optical fiber sensor for ammonia gas detection

    NASA Astrophysics Data System (ADS)

    Chu, Cheng-Shane; Chen, Yen-Fu

    2017-04-01

    A simple, low cost technique to fabricate a ratiometric optical fiber ammonia (NH3) sensor has been presented. The ratiometric optical fiber ammonia sensor was based on the ammonia induced absorbance change of sensing material Oxazine 170 perchlorate (O170) in ethyl cellulose (EC) with the luminescence intensity of 7-amino-4-trifluoromethyl coumarin (AFC). The observed luminescence intensity from AFC at 487 nm decreased with increasing the ammonia concentration. The sensitivity of optical ammonia sensor is quantified in terms of the ratio I0/I100, where I0 and I100 represent the detected luminescence intensities in nitrogen and 1000 ppm ammonia concentration, respectively. The experimental result shows that the sensitivity of the ratiometric optical fiber ammonia sensor is estimated to be 1.44. The sensitive optical ammonia sensor based on fluorescence intensity changes of AFC due to the absorption change of Oxazine 170 perchlorate in EC layer with ammonia is achieved. The ratiometric sensing approach presented in this study has the advantage of suppressing spurious fluctuations in the intensity of the excitation source and optical transmission properties of the optical sensor.

  7. Analyzing cell physiology in C. elegans with fluorescent ratiometric reporters

    PubMed Central

    Wang, Hongning; Karadge, Uma; Humphries, William H.; Fisher, Alfred L.

    2014-01-01

    Ratiometric fluorescent reporters have recently emerged a new technique to non-invasively measure aspects of cell physiology such as redox status, calcium levels, energy production, and NADH levels. These reporters consist of either a single or pair of fluorophores along with specific modifications, such as the addition of a protein domain which binds to a metabolite of interest, thereby producing gradual alterations in fluorescence in response to changes in the measured parameter. Measurement of the changes in fluorescence produces a quantitative read-out of the cellular environment. While these reporters were initially developed to easily visualize and track changes in cultured cells, several groups have adapted these reporters to use in Caenorhabditis elegans which opens a new avenue through which to explore cell physiology during development or aging, in response to changes in external environment, or in response to genetic manipulation. These reporters have the advantage of being easily targeted to any part of the worm, and because C. elegans is transparent both the reporters and changes in their fluorescence can be clearly observed in vivo. Here we discuss the application of ratiometric reporters to C. elegans, and outline a method to quantitatively measure changes in intracellular peroxide levels using the HyPer ratiometric reporter. However, these principles can be applied to alternate ratiometric reporters which are designed to measure either other chemical species or other cellular parameters. PMID:24915644

  8. Super-Resolution Microscopy and Single-Protein Tracking in Live Bacteria Using a Genetically Encoded, Photostable Fluoromodule.

    PubMed

    Saurabh, Saumya; Perez, Adam M; Comerci, Colin J; Shapiro, Lucy; Moerner, W E

    2017-06-19

    Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types. However, their use in bacteria has been limited due to challenges imposed by a complex bacterial cell wall. Here, we describe the use of a genetically encoded photostable fluoromodule that can be targeted to cytosolic and membrane proteins in the Gram negative bacterium Caulobacter crescentus. Additionally, we summarize methods to use this fluoromodule for single protein imaging and super-resolution microscopy using stimulated emission depletion. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  9. Ratiometric fluorescent response of electrospun fibrous strips for real-time sensing of alkaline phosphatase in serum.

    PubMed

    Zhao, Long; Xie, Songzhi; Song, Xiaojie; Wei, Jiaojun; Zhang, Zhao; Li, Xiaohong

    2017-05-15

    The development of rapid, convenient and reliable assays for monitoring alkaline phosphatase (ALP) levels is valuable for clinical diagnoses and biomedical research. In the current study, a ratiometric assay of ALP activity has been realized by covalent immobilization of fluorescein onto polyethylene terephthalate (PET) fibers, followed by electrostatic adsorption of bisquaternary ammonium salt of tetraphenylethene (TPE-2N(+)). In the absence of ALP, the complex formation between phosphorylated fluorescein and TPE-2N(+) results in the aggregation-induced emission (AIE) of TPE at 471nm. While in the presence of ALP, the hydrolysis of phosphoesters leads to a gradual removal of TPE-2N(+) and the restoration of fluorescein emission at 514nm. Fibers with surface amine densities of 30 nmol/mg show the most significant and almost linear increases in I514/I471 ratios from 0.73 to 3.05 with increasing ALP concentrations from 0 to 100 mU/mL. The ratiometric fluorescence responses result in color changes of fibrous strips from blue (TPE-2N(+)) to green (fluorescein) under an ultraviolet lamp in a matter of minutes. The color changes are more suitable for an eyeball detection of ALP levels ranging from 0 to 80 mU/mL, which is included in the concentration range of ALP in human serum considering the dilution factor if necessary. The ALP detection indicates no apparent interference by serum components and good agreement with enzyme-linked immunosorbent assay (ELISA). Thus, this is the first study on ratiometric fluorescent assay of serum ALP levels by fibrous strips, which offers a capacity to exploit electrospun fibrous mats and ratiometric responses for real-time assays of bioactive substances as self-test devices.

  10. Rational design of a solvatochromic fluorescent uracil analogue with a dual-band ratiometric response based on 3-hydroxychromone.

    PubMed

    Dziuba, Dmytro; Karpenko, Iuliia A; Barthes, Nicolas P F; Michel, Benoît Y; Klymchenko, Andrey S; Benhida, Rachid; Demchenko, Alexander P; Mély, Yves; Burger, Alain

    2014-02-10

    Fluorescent nucleoside analogues with strong and informative responses to their local environment are in urgent need for DNA research. In this work, the design, synthesis and investigation of a new solvatochromic ratiometric fluorophore compiled from 3-hydroxychromones (3HCs) and uracil fragments are reported. 3HC dyes are a class of multi-parametric, environment-sensitive fluorophores providing a ratiometric response due to the presence of two well-resolved bands in their emission spectra. The synthesized conjugate demonstrates not only the preservation but also the improvement of these properties. The absorption and fluorescence spectra are shifted to longer wavelengths together with an increase of brightness. Moreover, the two fluorescence bands are better resolved and provide ratiometric responses across a broader range of solvent polarities. To understand the photophysical properties of this new fluorophore, a series of model compounds were synthesized and comparatively investigated. The obtained data indicate that uracil and 3HC fragments of this derivative are coupled into an electronic conjugated system, which on excitation attains strong charge-transfer character. The developed fluorophore is a prospective label for nucleic acids. Abstract in Ukrainian: . Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Ratiometric luminescent detection of bacterial spores with terbium chelated semiconducting polymer dots.

    PubMed

    Li, Qiong; Sun, Kai; Chang, Kaiwen; Yu, Jiangbo; Chiu, Daniel T; Wu, Changfeng; Qin, Weiping

    2013-10-01

    We report a ratiometric fluorescent sensor based on semiconducting polymer dots chelated with terbium ions to detect bacterial spores in aqueous solution. Fluorescent polyfluorene (PFO) dots serve as a scaffold to coordinate with lanthanide ions that can be sensitized by calcium dipicolinate (CaDPA), an important biomarker of bacterial spores. The absorption band of PFO dots extends to deep UV region, allowing both the reference and the sensitizer can be excited with a single wavelength (~275 nm). The fluorescence of PFO remains constant as a reference, while the Tb(3+) ions exhibit enhanced luminescence upon binding with DPA. The sharp fluorescence peaks of β-phase PFO dots and the narrow-band emissions of Tb(3+) ions enable ratiometric and sensitive CaDPA detection with a linear response over nanomolar concentration and a detection limit of ~0.2 nM. The Pdots based sensor also show excellent selectivity to CaDPA over other aromatic ligands. Our results indicate that the Tb(3+) chelated Pdots sensor is promising for sensitive and rapid detection of bacterial spores.

  12. Ratiometric analysis of in vivo retinal layer thicknesses in multiple sclerosis

    NASA Astrophysics Data System (ADS)

    Bhaduri, Basanta; Nolan, Ryan M.; Shelton, Ryan L.; Pilutti, Lara A.; Motl, Robert W.; Boppart, Stephen A.

    2016-09-01

    We performed ratiometric analysis of retinal optical coherence tomography images for the first time in multiple sclerosis (MS) patients. The ratiometric analysis identified differences in several retinal layer thickness ratios in the cohort of MS subjects without a history of optic neuritis (ON) compared to healthy control (HC) subjects, and there was no difference in standard retinal nerve fiber layer thickness (RNFLT). The difference in such ratios between HC subjects and those with mild MS-disability, without a difference in RNFLT, further suggests the possibility of using layer ratiometric analysis for detecting early retinal changes in MS. Ratiometric analysis may be useful and potentially more sensitive for detecting disease changes in MS.

  13. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Amino-Thiol Unnatural Amino Acids

    PubMed Central

    Frost, John R.; Jacob, Nicholas T.; Papa, Louis J.; Owens, Andrew E.

    2015-01-01

    A versatile method for orchestrating the formation of side-chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side-chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro, or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low micromolar streptavidin binder (KD = 1.1 µM) from a library of cyclic peptides produced in E. coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles. PMID:25933125

  14. [Genetically encoded FRET-pair on the basis of terbium-binding peptide and red fluorescent protein].

    PubMed

    Arslanbaeva, L R; Zherdeva, V V; Ivashina, T V; Vinokurov, L M; Rusanov, A L; Savitskiĭ, A P

    2010-01-01

    The genetically encoded FRET-pair was developed on the basis of terbium-binding peptide and red fluorescent protein DsRed2. To study fluorescence resonance energy transfer within FRET-pair, the gene-engineered construction was obtained, where sequences of terbium-binding peptide and red fluorescent protein DsRed2 were fused in single reading frame. The expression of this construction in strain E. coli BL21 (DE3) was studied and conditions of synthesis, isolation and purification of recombinant protein were optimized. The hydrodynamic radius of hybrid protein was determined by the method of dynamic light scattering. Energy transfer between sensitized terbium and red fluorescent protein was confirmed by the methods of phosporescent spectroscopy. The obtained FRET-pair can be used both for studies in vitro and as a reporter in living cells.

  15. Two Rapid Catalyst-Free Click Reactions for In Vivo Protein Labeling of Genetically Encoded Strained Alkene/Alkyne Functionalities

    PubMed Central

    2015-01-01

    Detailed kinetic analyses of inverse electron-demand Diels–Alder cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition reactions were conducted and the reactions were applied for rapid protein bioconjugation. When reacted with a tetrazine or a diaryl nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics. To apply these “click” reactions for site-specific protein labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNACUAPyl pair. Proteins bearing these noncanonical amino acids were successively labeled with a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro and in living cells. PMID:25158039

  16. Two rapid catalyst-free click reactions for in vivo protein labeling of genetically encoded strained alkene/alkyne functionalities.

    PubMed

    Kurra, Yadagiri; Odoi, Keturah A; Lee, Yan-Jiun; Yang, Yanyan; Lu, Tongxiang; Wheeler, Steven E; Torres-Kolbus, Jessica; Deiters, Alexander; Liu, Wenshe R

    2014-09-17

    Detailed kinetic analyses of inverse electron-demand Diels–Alder cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition reactions were conducted and the reactions were applied for rapid protein bioconjugation. When reacted with a tetrazine or a diaryl nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics. To apply these “click” reactions for site-specific protein labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pair. Proteins bearing these noncanonical amino acids were successively labeled with a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro and in living cells.

  17. Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain.

    PubMed

    Edwardraja, Selvakumar; Eichinger, Andreas; Theobald, Ina; Sommer, Carina Andrea; Reichert, Andreas J; Skerra, Arne

    2017-09-22

    The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins towards sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded L-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the binding site of the Anticalin, as confirmed by X-ray crystallography. Com-pared with the metal-ion and/or avidity-dependent oligovalent lectins that prevail in nature, our approach offers a novel and promising route to generate tight sugar-binding reagents both as research reagents and for biomedical applications.

  18. Using Genetically Encodable Self-Assembling Gd(III) Spin Labels To Make In-Cell Nanometric Distance Measurements.

    PubMed

    Mascali, Florencia C; Ching, H Y Vincent; Rasia, Rodolfo M; Un, Sun; Tabares, Leandro C

    2016-09-05

    Double electron-electron resonance (DEER) can be used to study the structure of a protein in its native cellular environment. Until now, this has required isolation, in vitro labeling, and reintroduction of the protein back into the cells. We describe a completely biosynthetic approach that avoids these steps. It exploits genetically encodable lanthanide-binding tags (LBT) to form self-assembling Gd(III) metal-based spin labels and enables direct in-cell measurements. This approach is demonstrated using a pair of LBTs encoded one at each end of a 3-helix bundle expressed in E. coli grown on Gd(III) -supplemented medium. DEER measurements directly on these cells produced readily detectable time traces from which the distance between the Gd(III) labels could be determined. This work is the first to use biosynthetically produced self-assembling metal-containing spin labels for non-disruptive in-cell structural measurements.

  19. A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells.

    PubMed

    San Martín, Alejandro; Ceballo, Sebastián; Ruminot, Iván; Lerchundi, Rodrigo; Frommer, Wolf B; Barros, Luis Felipe

    2013-01-01

    Lactate is shuttled between and inside cells, playing metabolic and signaling roles in healthy tissues. Lactate is also a harbinger of altered metabolism and participates in the pathogenesis of inflammation, hypoxia/ischemia, neurodegeneration and cancer. Many tumor cells show high rates of lactate production in the presence of oxygen, a phenomenon known as the Warburg effect, which has diagnostic and possibly therapeutic implications. In this article we introduce Laconic, a genetically-encoded Forster Resonance Energy Transfer (FRET)-based lactate sensor designed on the bacterial transcription factor LldR. Laconic quantified lactate from 1 µM to 10 mM and was not affected by glucose, pyruvate, acetate, betahydroxybutyrate, glutamate, citrate, α-ketoglutarate, succinate, malate or oxalacetate at concentrations found in mammalian cytosol. Expressed in astrocytes, HEK cells and T98G glioma cells, the sensor allowed dynamic estimation of lactate levels in single cells. Used in combination with a blocker of the monocarboxylate transporter MCT, the sensor was capable of discriminating whether a cell is a net lactate producer or a net lactate consumer. Application of the MCT-block protocol showed that the basal rate of lactate production is 3-5 fold higher in T98G glioma cells than in normal astrocytes. In contrast, the rate of lactate accumulation in response to mitochondrial inhibition with sodium azide was 10 times lower in glioma than in astrocytes, consistent with defective tumor metabolism. A ratio between the rate of lactate production and the rate of azide-induced lactate accumulation, which can be estimated reversibly and in single cells, was identified as a highly sensitive parameter of the Warburg effect, with values of 4.1 ± 0.5 for T98G glioma cells and 0.07 ± 0.007 for astrocytes. In summary, this article describes a genetically-encoded sensor for lactate and its use to measure lactate concentration, lactate flux, and the Warburg effect in single

  20. Integration of a Genetically Encoded Calcium Molecular Sensor into Photopolymerizable Hydrogels for Micro-Optrode-Based Sensing.

    PubMed

    Kahyaoglu, Leyla Nesrin; Madangopal, Rajtarun; Park, Joon Hyeong; Rickus, Jenna L

    2017-09-20

    Genetically encoded molecular-protein sensors (GEMS) are engineered to sense and quantify a wide range of biological substances and events in cells, in vitro and even in vivo with high spatial and temporal resolution. Here, we aim to stably incorporate these proteins into a photopatternable matrix, while preserving their functionality, to extend the application of these proteins as spatially addressable optical biosensors. For this reason, we examined the fabrication of 3D hydrogel microtips doped with a genetically encoded fluorescent biosensor, GCaMP3, at the end of an optical fiber. Stable incorporation parameters of GCaMP3 into a photo-cross-linkable monomer matrix were investigated through a series of characterization and optimization experiments. Different precursor-solution formulations and irradiation parameters of in situ photopolymerization were tested to determine the factors affecting protein stability and sensor reproducibility during photoencapsulation. The microstructure and performance of hydrogel microtips were controlled by varying UV irradiation intensity as well as the molecular weight and concentration of the photocurable monomer, PEGDA (polyethylene glycol diacrylate), in precursor solution. Protein-doped hydrogel micro-optrodes (microtip sensors) were fabricated successfully and reproducibly at the distal end of optical fiber. Under optimized conditions, the bioactivity of GCaMP3 within a hydrogel matrix of micro-optrodes remained similar to that of the protein-free matrix in buffer. The limit of detection of protein optrodes for free calcium was also determined to be 4.3 nM. The hydrogel formulation and fabrication process demonstrated here using microtip optrodes can be easily adapted to other conformation-dependent protein biosensors and can be used in sensing applications.

  1. ESIPT-Based Photoactivatable Fluorescent Probe for Ratiometric Spatiotemporal Bioimaging

    PubMed Central

    Zhou, Xiaohong; Jiang, Yuren; Zhao, Xiongjie; Guo, Dong

    2016-01-01

    Photoactivatable fluorophores have become an important technique for the high spatiotemporal resolution of biological imaging. Here, we developed a novel photoactivatable probe (PHBT), which is based on 2-(2-hydroxyphenyl)benzothiazole (HBT), a small organic fluorophore known for its classic luminescence mechanism through excited-state intramolecular proton transfer (ESIPT) with the keto form and the enol form. After photocleavage, PHBT released a ratiometric fluorophore HBT, which showed dual emission bands with more than 73-fold fluorescence enhancement at 512 nm in buffer and more than 69-fold enhancement at 452 nm in bovine serum. The probe displayed a high ratiometric imaging resolution and is believed to have a wide application in biological imaging. PMID:27754338

  2. Label-Free Ratiometric Imaging of Serotonin in Live Cells.

    PubMed

    Das, Anand Kant; Maity, Barun Kumar; Surendran, Dayana; Tripathy, Umakanta; Maiti, Sudipta

    2017-08-24

    Ratiometric imaging can quantitatively measure changes in cellular analyte concentrations using specially designed fluorescent labels. We describe a label-free ratiometric imaging technique for direct detection of changes in intravesicular serotonin concentration in live cells. At higher concentrations, serotonin forms transient oligomers whose ultraviolet emission is shifted to longer wavelengths. We access the ultraviolet/blue emission using relatively benign three-photon excitation and split it into two imaging channels, whose ratio reports the concentration. The technique is sensitive at a physiologically relevant concentration range (10-150 mM serotonin). As a proof of principle, we measure the increase of intravesicular serotonin concentration with the addition of external serotonin. In general, since emission spectra of molecules are often sensitive to concentration, our method may be applicable to other natively fluorescent intracellular molecules which are present at high concentrations.

  3. Synthesis and evaluation of self-calibrating ratiometric viscosity sensors.

    PubMed

    Yoon, Hyung-Jo; Dakanali, Marianna; Lichlyter, Darcy; Chang, Willy M; Nguyen, Karen A; Nipper, Matthew E; Haidekker, Mark A; Theodorakis, Emmanuel A

    2011-05-07

    We describe the design, synthesis and fluorescent profile of a family of self-calibrating dyes that provide ratiometric measurements of fluid viscosity. The design is based on covalently linking a primary fluorophore (reference) that displays a viscosity-independent fluorescence emission with a secondary fluorophore (sensor) that exhibits a viscosity-sensitive fluorescence emission. Characterization of fluorescent properties was made with separate excitation of the units and through Resonance Energy Transfer from the reference to the sensor dye. The chemical structures of both fluorophores and the linker length have been evaluated in order to optimize the overall brightness and sensitivity of the viscosity measurements. We also present an application of such ratiometric dyes for the detection of membrane viscosity changes in a liposome model.

  4. Chemoselective ratiometric imaging of protein S-sulfenylation.

    PubMed

    Tom, Christopher T M B; Crellin, John E; Motiwala, Hashim F; Stone, Matthew B; Davda, Dahvid; Walker, William; Kuo, Yu-Hsuan; Hernandez, Jeannie L; Labby, Kristin J; Gomez-Rodriguez, Lyanne; Jenkins, Paul M; Veatch, Sarah L; Martin, Brent R

    2017-06-29

    Here we report a ratiometric fluorescent probe for chemoselective conjugation to sulfenic acids in living cells. Our approach couples an α-fluoro-substituted dimedone to an aminonaphthalene fluorophore (F-DiNap), which upon sulfenic acid conjugation is locked as the 1,3-diketone, changing the fluorophore excitation. F-DiNap reacts with S-sulfenylated proteins at equivalent rates to current probes, but the α-fluorine substitution blocks side-reactions with biological aldehydes.

  5. Ion-Switchable Quantum Dot Förster Resonance Energy Transfer Rates in Ratiometric Potassium Sensors.

    PubMed

    Ruckh, Timothy T; Skipwith, Christopher G; Chang, Wendi; Senko, Alexander W; Bulovic, Vladimir; Anikeeva, Polina O; Clark, Heather A

    2016-04-26

    The tools for optically imaging cellular potassium concentrations in real-time are currently limited to a small set of molecular indicator dyes. Quantum dot-based nanosensors are more photostable and tunable than organic indicators, but previous designs have fallen short in size, sensitivity, and selectivity. Here, we introduce a small, sensitive, and selective nanosensor for potassium measurements. A dynamic quencher modulates the fluorescence emitted by two different quantum dot species to produce a ratiometric signal. We characterized the potassium-modulated sensor properties and investigated the photonic interactions within the sensors. The quencher's protonation changes in response to potassium, which modulates its Förster radiative energy transfer rate and the corresponding interaction radii with each quantum dot species. The nanosensors respond to changes in potassium concentrations typical of the cellular environment and thus provide a promising tool for imaging potassium fluxes during biological events.

  6. Reassessing cellular glutathione homoeostasis: novel insights revealed by genetically encoded redox probes.

    PubMed

    Morgan, Bruce

    2014-08-01

    Glutathione is the most abundant small molecule thiol in nearly all eukaryotes. Whole-cell levels of oxidized (GSSG) and reduced (GSH) glutathione are variable and responsive to genetic and chemical manipulations, which has led to their relative levels being widely used as a marker of the 'cellular redox state' and to indicate the level of 'oxidative stress' experienced by cells, tissues and organisms. However, the applicability of glutathione as a marker for a generalized 'cellular redox state' is questionable, especially in the light of recent observations in yeast cells. In yeast, whole-cell GSSG changes are almost completely dependent upon the activity of an ABC-C (ATP-binding cassette-C) transporter, Ycf1 (yeast cadmium factor 1), which mediates sequestration of GSSG to the vacuole. In the absence of Ycf1 whole-cell GSSG content is strongly decreased and extremely robust to perturbation. These observations are consistent with highly specific redox-sensitive GFP probe-based measurements of the cytosolic glutathione pool and indicate that cytosolic GSSG reductive systems are easily able to reduce nearly all GSSG formed, even following treatment with large concentrations of oxidant. In the present paper, I discuss the consequences of these new findings for our understanding of glutathione homoeostasis in the eukaryotic cell.

  7. Tight Coupling of Astrocyte pH Dynamics to Epileptiform Activity Revealed by Genetically Encoded pH Sensors.

    PubMed

    Raimondo, Joseph V; Tomes, Hayley; Irkle, Agnese; Kay, Louise; Kellaway, Lauriston; Markram, Henry; Millar, Robert P; Akerman, Colin J

    2016-06-29

    Astrocytes can both sense and shape the evolution of neuronal network activity and are known to possess unique ion regulatory mechanisms. Here we explore the relationship between astrocytic intracellular pH dynamics and the synchronous network activity that occurs during seizure-like activity. By combining confocal and two-photon imaging of genetically encoded pH reporters with simultaneous electrophysiological recordings, we perform pH measurements in defined cell populations and relate these to ongoing network activity. This approach reveals marked differences in the intracellular pH dynamics between hippocampal astrocytes and neighboring pyramidal neurons in rodent in vitro models of epilepsy. With three different genetically encoded pH reporters, astrocytes are observed to alkalinize during epileptiform activity, whereas neurons are observed to acidify. In addition to the direction of pH change, the kinetics of epileptiform-associated intracellular pH transients are found to differ between the two cell types, with astrocytes displaying significantly more rapid changes in pH. The astrocytic alkalinization is shown to be highly correlated with astrocytic membrane potential changes during seizure-like events and mediated by an electrogenic Na(+)/HCO3 (-) cotransporter. Finally, comparisons across different cell-pair combinations reveal that astrocytic pH dynamics are more closely related to network activity than are neuronal pH dynamics. This work demonstrates that astrocytes exhibit distinct pH dynamics during periods of epileptiform activity, which has relevance to multiple processes including neurometabolic coupling and the control of network excitability. Dynamic changes in intracellular ion concentrations are central to the initiation and progression of epileptic seizures. However, it is not known how changes in intracellular H(+) concentration (ie, pH) differ between different cell types during seizures. Using recently developed pH-sensitive proteins, we

  8. A Genetically Encoded Alkyne Directs Palladium-Mediated Protein Labeling on Live Mammalian Cell Surface

    PubMed Central

    2015-01-01

    The merging of site-specific incorporation of small bioorthogonal functional groups into proteins via amber codon suppression with bioorthogonal chemistry has created exciting opportunities to extend the power of organic reactions to living systems. Here we show that a new alkyne amino acid can be site-selectively incorporated into mammalian proteins via a known orthogonal pyrrolysyl-tRNA synthetase/tRNACUA pair and directs an unprecedented, palladium-mediated cross-coupling reaction-driven protein labeling on live mammalian cell surface. A comparison study with the alkyne-encoded proteins in vitro indicated that this terminal alkyne is better suited for the palladium-mediated cross-coupling reaction than the copper-catalyzed click chemistry. PMID:25347611

  9. Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo.

    PubMed

    Bedbrook, Claire N; Kato, Mihoko; Ravindra Kumar, Sripriya; Lakshmanan, Anupama; Nath, Ravi D; Sun, Fei; Sternberg, Paul W; Arnold, Frances H; Gradinaru, Viviana

    2015-08-20

    Membrane proteins are the main gatekeepers of cellular state, especially in neurons, serving either to maintain homeostasis or instruct response to synaptic input or other external signals. Visualization of membrane protein localization and trafficking in live cells facilitates understanding the molecular basis of cellular dynamics. We describe here a method for specifically labeling the plasma membrane-localized fraction of heterologous membrane protein expression using channelrhodopsins as a case study. We show that the genetically encoded, covalent binding SpyTag and SpyCatcher pair from the Streptococcus pyogenes fibronectin-binding protein FbaB can selectively label membrane-localized proteins in living cells in culture and in vivo in Caenorhabditis elegans. The SpyTag/SpyCatcher covalent labeling method is highly specific, modular, and stable in living cells. We have used the binding pair to develop a channelrhodopsin membrane localization assay that is amenable to high-throughput screening for opsin discovery and engineering. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Redesign of genetically encoded biosensors for monitoring mitochondrial redox status in a broad range of model eukaryotes.

    PubMed

    Albrecht, Simone C; Sobotta, Mirko C; Bausewein, Daniela; Aller, Isabel; Hell, Rüdiger; Dick, Tobias P; Meyer, Andreas J

    2014-03-01

    The development of genetically encoded redox biosensors has paved the way toward chemically specific, quantitative, dynamic, and compartment-specific redox measurements in cells and organisms. In particular, redox-sensitive green fluorescent proteins (roGFPs) have attracted major interest as tools to monitor biological redox changes in real time and in vivo. Most recently, the engineering of a redox relay that combines glutaredoxin (Grx) with roGFP2 as a translational fusion (Grx1-roGFP2) led to a biosensor for the glutathione redox potential (EGSH ). The expression of this probe in mitochondria is of particular interest as mitochondria are the major source of oxidants, and their redox status is closely connected to cell fate decisions. While Grx1-roGFP2 can be expressed in mammalian mitochondria, it fails to enter mitochondria in various nonmammalian model organisms. Here we report that inversion of domain order from Grx1-roGFP2 to roGFP2-Grx1 yields a biosensor with perfect mitochondrial targeting while fully maintaining its biosensor capabilities. The redesigned probe thus allows extending in vivo observations of mitochondrial redox homeostasis to important nonmammalian model organisms, particularly plants and insects.

  11. Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR.

    PubMed

    Tian, He; Sakmar, Thomas P; Huber, Thomas

    2015-06-15

    Genetically encoded p-azido-phenylalanine (azF) residues in G protein-coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne-modified (DIBO-modified) fluorescent probes by means of strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent-solubilized receptors exhibit up to 1000-fold rate enhancement relative to azF residues on water-exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle-enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.

  12. Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway.

    PubMed

    Leung, Daisy W; Otomo, Chinatsu; Chory, Joanne; Rosen, Michael K

    2008-09-02

    General methods to engineer genetically encoded, reversible, light-mediated control over protein function would be useful in many areas of biomedical research and technology. We describe a system that yields such photo-control over actin assembly. We fused the Rho family GTPase Cdc42 in its GDP-bound form to the photosensory domain of phytochrome B (PhyB) and fused the Cdc42 effector, the Wiskott-Aldrich Syndrome Protein (WASP), to the light-dependent PhyB-binding domain of phytochrome interacting factor 3 (Pif3). Upon red light illumination, the fusion proteins bind each other, activating WASP, and consequently stimulating actin assembly by the WASP target, the Arp2/3 complex. Binding and WASP activation are reversed by far-red illumination. Our approach, in which the biochemical specificity of the nucleotide switch in Cdc42 is overridden by the light-dependent PhyB-Pif3 interaction, should be generally applicable to other GTPase-effector pairs.

  13. Molecular protein adaptor with genetically encoded interaction sites guiding the hierarchical assembly of plasmonically active nanoparticle architectures

    NASA Astrophysics Data System (ADS)

    Schreiber, Andreas; Huber, Matthias C.; Cölfen, Helmut; Schiller, Stefan M.

    2015-03-01

    The control over the defined assembly of nano-objects with nm-precision is important to create systems and materials with enhanced properties, for example, metamaterials. In nature, the precise assembly of inorganic nano-objects with unique features, for example, magnetosomes, is accomplished by efficient and reliable recognition schemes involving protein effectors. Here we present a molecular approach using protein-based ‘adaptors/connectors’ with genetically encoded interaction sites to guide the assembly and functionality of different plasmonically active gold nanoparticle architectures (AuNP). The interaction of the defined geometricaly shaped protein adaptors with the AuNP induces the self-assembly of nanoarchitectures ranging from AuNP encapsulation to one-dimensional chain-like structures, complex networks and stars. Synthetic biology and bionanotechnology are applied to co-translationally encode unnatural amino acids as additional site-specific modification sites to generate functionalized biohybrid nanoarchitectures. This protein adaptor-based nano-object assembly approach might be expanded to other inorganic nano-objects creating biohybrid materials with unique electronic, photonic, plasmonic and magnetic properties.

  14. Site-specific labeling of genetically encoded azido groups for multicolor, single-molecule fluorescence imaging of GPCRs.

    PubMed

    Tian, He; Sakmar, Thomas P; Huber, Thomas

    2013-01-01

    Heptahelical G protein-coupled receptors (GPCRs) mediate transmembrane signal transduction to facilitate intercellular communication. GPCRs assemble in the membrane bilayer with a variety of cytoplasmic adapter and scaffold proteins to form molecular machines, or "signalosomes," which undergo complex dynamic assembly and disassembly reactions. Despite significant recent advances in structural studies of GPCRs and their associated cytoplasmic components, understanding transmembrane signaling in four dimensions with chemical precision requires new approaches. One promising approach to study allosteric effects involved in signalosome reaction pathways is to use multicolor single-molecule detection (SMD) fluorescence experiments in biochemically defined systems. We describe here the methodological foundation for automated, multicolor, single-molecule fluorescence studies of the structural and compositional dynamics of macromolecular complexes involved in signal transduction. We present a general, simple, and robust method for stoichiometric, site-specific fluorescence labeling of expressed GPCRs. The method is based on bioorthogonal conjugation of a fluorescent reporter group to a genetically encoded azido group introduced into expressed GPCRs using amber codon suppression. We then present a strategy to reconstitute labeled GPCRs in native-like membranes and to tether-oriented samples onto surfaces amenable for interrogation by total internal reflectance fluorescence (TIRF) spectroscopy. We describe how to assemble an automated four-color epifluorescence microscope with SMD-TIRF optics. Finally, we discuss how to adapt engineered samples for high-throughput imaging with the aim of understanding the kinetic relationships between ligand binding and the dynamic regulation of the GPCR signalosome.

  15. Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity.

    PubMed

    Goryashchenko, Alexander S; Khrenova, Maria G; Bochkova, Anna A; Ivashina, Tatiana V; Vinokurov, Leonid M; Savitsky, Alexander P

    2015-07-22

    This article describes the genetically encoded caspase-3 FRET-sensor based on the terbium-binding peptide, cleavable linker with caspase-3 recognition site, and red fluorescent protein TagRFP. The engineered construction performs two induction-resonance energy transfer processes: from tryptophan of the terbium-binding peptide to Tb(3+) and from sensitized Tb(3+) to acceptor--the chromophore of TagRFP. Long-lived terbium-sensitized emission (microseconds), pulse excitation source, and time-resolved detection were utilized to eliminate directly excited TagRFP fluorescence and background cellular autofluorescence, which lasts a fraction of nanosecond, and thus to improve sensitivity of analyses. Furthermore the technique facilitates selective detection of fluorescence, induced by uncleaved acceptor emission. For the first time it was shown that fluorescence resonance energy transfer between sensitized terbium and TagRFP in the engineered construction can be studied via detection of microsecond TagRFP fluorescence intensities. The lifetime and distance distribution between donor and acceptor were calculated using molecular dynamics simulation. Using this data, quantum yield of terbium ions with binding peptide was estimated.

  16. In vivo imaging of neuronal activity by targeted expression of a genetically encoded probe in the mouse.

    PubMed

    Bozza, Thomas; McGann, John P; Mombaerts, Peter; Wachowiak, Matt

    2004-04-08

    Genetically encoded probes show great promise in permitting functional imaging of specified neuronal populations in the intact nervous system, yet their in vivo application has been limited. Here, we have targeted expression of synapto-pHluorin, a pH-sensitive protein that reports synaptic vesicle fusion, to olfactory sensory neurons in mouse. Synapto-pHluorin selectively labeled presynaptic terminals of sensory neurons in glomeruli of the olfactory bulb. Odorant stimulation evoked large-amplitude fluorescence increases that were localized to individual glomeruli in vivo, correlated with presynaptic calcium influx, graded with stimulus intensity, and stable over a period of days. Spatial patterns of odorant-activated glomeruli were distributed and did not change systematically with increasing carbon chain length, in contrast to the finely organized chemotopy that has been reported using other imaging methods. Targeted expression of synapto-pHluorin in mouse will permit the analysis of previously inaccessible neuronal populations and chronic imaging from genetically identified neurons in vivo.

  17. Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway

    PubMed Central

    Leung, Daisy W.; Otomo, Chinatsu; Chory, Joanne; Rosen, Michael K.

    2008-01-01

    General methods to engineer genetically encoded, reversible, light-mediated control over protein function would be useful in many areas of biomedical research and technology. We describe a system that yields such photo-control over actin assembly. We fused the Rho family GTPase Cdc42 in its GDP-bound form to the photosensory domain of phytochrome B (PhyB) and fused the Cdc42 effector, the Wiskott-Aldrich Syndrome Protein (WASP), to the light-dependent PhyB-binding domain of phytochrome interacting factor 3 (Pif3). Upon red light illumination, the fusion proteins bind each other, activating WASP, and consequently stimulating actin assembly by the WASP target, the Arp2/3 complex. Binding and WASP activation are reversed by far-red illumination. Our approach, in which the biochemical specificity of the nucleotide switch in Cdc42 is overridden by the light-dependent PhyB-Pif3 interaction, should be generally applicable to other GTPase-effector pairs. PMID:18728185

  18. Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity

    PubMed Central

    Goryashchenko, Alexander S.; Khrenova, Maria G.; Bochkova, Anna A.; Ivashina, Tatiana V.; Vinokurov, Leonid M.; Savitsky, Alexander P.

    2015-01-01

    This article describes the genetically encoded caspase-3 FRET-sensor based on the terbium-binding peptide, cleavable linker with caspase-3 recognition site, and red fluorescent protein TagRFP. The engineered construction performs two induction-resonance energy transfer processes: from tryptophan of the terbium-binding peptide to Tb3+ and from sensitized Tb3+ to acceptor—the chromophore of TagRFP. Long-lived terbium-sensitized emission (microseconds), pulse excitation source, and time-resolved detection were utilized to eliminate directly excited TagRFP fluorescence and background cellular autofluorescence, which lasts a fraction of nanosecond, and thus to improve sensitivity of analyses. Furthermore the technique facilitates selective detection of fluorescence, induced by uncleaved acceptor emission. For the first time it was shown that fluorescence resonance energy transfer between sensitized terbium and TagRFP in the engineered construction can be studied via detection of microsecond TagRFP fluorescence intensities. The lifetime and distance distribution between donor and acceptor were calculated using molecular dynamics simulation. Using this data, quantum yield of terbium ions with binding peptide was estimated. PMID:26204836

  19. Genetically encoded fluorescent voltage sensors using the voltage-sensing domain of Nematostella and Danio phosphatases exhibit fast kinetics.

    PubMed

    Baker, Bradley J; Jin, Lei; Han, Zhou; Cohen, Lawrence B; Popovic, Marko; Platisa, Jelena; Pieribone, Vincent

    2012-07-15

    A substantial increase in the speed of the optical response of genetically encoded fluorescent protein voltage sensors (FP voltage sensors) was achieved by using the voltage-sensing phosphatase genes of Nematostella vectensis and Danio rerio. A potential N. vectensis voltage-sensing phosphatase was identified in silico. The voltage-sensing domain (S1-S4) of the N. vectensis homolog was used to create an FP voltage sensor called Nema. By replacing the phosphatase with a cerulean/citrine FRET pair, a new FP voltage sensor was synthesized with fast off kinetics (Tau(off)<5ms). However, the signal was small (ΔF/F=0.4%/200mV). FP voltage sensors using the D. rerio voltage-sensing phosphatase homolog, designated Zahra and Zahra 2, exhibited fast on and off kinetics within 2ms of the time constants observed with the organic voltage-sensitive dye, di4-ANEPPS. Mutagenesis of the S4 region of the Danio FP voltage sensor shifted the voltage dependence to more negative potentials but did not noticeably affect the kinetics of the optical signal.

  20. A New Genetically Encoded Single-Chain Biosensor for Cdc42 Based on FRET, Useful for Live-Cell Imaging

    PubMed Central

    Cox, Dianne; Hodgson, Louis

    2014-01-01

    Cdc42 is critical in a myriad of cellular morphogenic processes, requiring precisely regulated activation dynamics to affect specific cellular events. To facilitate direct observations of Cdc42 activation in live cells, we developed and validated a new biosensor of Cdc42 activation. The biosensor is genetically encoded, of single-chain design and capable of correctly localizing to membrane compartments as well as interacting with its upstream regulators including the guanine nucleotide dissociation inhibitor. We characterized this new biosensor in motile mouse embryonic fibroblasts and observed robust activation dynamics at leading edge protrusions, similar to those previously observed for endogenous Cdc42 using the organic dye-based biosensor system. We then extended our validations and observations of Cdc42 activity to macrophages, and show that this new biosensor is able to detect differential activation patterns during phagocytosis and cytokine stimulation. Furthermore, we observe for the first time, a highly transient and localized activation of Cdc42 during podosome formation in macrophages, which was previously hypothesized but never directly visualized. PMID:24798463

  1. Real Time Monitoring of Intracellular Bile Acid Dynamics Using a Genetically Encoded FRET-based Bile Acid Sensor.

    PubMed

    Van de Wiel, Sandra; Merkx, Maarten; Van de Graaf, Stan

    2016-01-04

    Förster Resonance Energy Transfer (FRET) has become a powerful tool for monitoring protein folding, interaction and localization in single cells. Biosensors relying on the principle of FRET have enabled real-time visualization of subcellular signaling events in live cells with high temporal and spatial resolution. Here, we describe the application of a genetically encoded Bile Acid Sensor (BAS) that consists of two fluorophores fused to the farnesoid X receptor ligand binding domain (FXR-LBD), thereby forming a bile acid sensor that can be activated by a large number of bile acids species and other (synthetic) FXR ligands. This sensor can be targeted to different cellular compartments including the nucleus (NucleoBAS) and cytosol (CytoBAS) to measure bile acid concentrations locally. It allows rapid and simple quantitation of cellular bile acid influx, efflux and subcellular distribution of endogenous bile acids without the need for labeling with fluorescent tags or radionuclei. Furthermore, the BAS FRET sensors can be useful for monitoring FXR ligand binding. Finally, we show that this FRET biosensor can be combined with imaging of other spectrally distinct fluorophores. This allows for combined analysis of intracellular bile acid dynamics and i) localization and/or abundance of proteins of interest, or ii) intracellular signaling in a single cell.

  2. A molecular rotor based ratiometric sensor for basic amino acids.

    PubMed

    Pettiwala, Aafrin M; Singh, Prabhat K

    2018-01-05

    The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Genetically encoding new bioreactivity.

    PubMed

    Wang, Lei

    2017-09-25

    The genetic code can be expanded to include unnatural amino acids (Uaas) by engineering orthogonal components involved in protein translation. To be compatible with live cells, side chains of Uaas have been limited to either chemically inert or bio-orthogonal (i.e., nonreactive toward biomolecules) functionalities. To introduce bioreactivity into live systems, the genetic code has recently been engineered to encode a new class of Uaas, the bioreactive Uaas. These Uaas, after being incorporated into proteins, specifically react with target natural amino acid residues via proximity-enabled bioreactivity, enabling the selective formation of new covalent linkages within and between proteins both in vitro and in live systems. The new covalent bonding ability has been harnessed within proteins to enhance photostability, increase thermostability, staple proteins recombinantly, and build optical nano-switches, and between proteins to pinpoint ligand-receptor interaction, target native receptors irreversibly, and generate covalent macromolecular inhibitors. These diverse bioreactivities, inaccessible to natural proteins, thus open doors to novel protein engineering and provide new avenues for biological studies, biotherapeutics and synthetic biology. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Ratiometric high-resolution imaging of JC-1 fluorescence reveals the subcellular heterogeneity of astrocytic mitochondria.

    PubMed

    Keil, Vera C; Funke, Frank; Zeug, Andre; Schild, Detlev; Müller, Michael

    2011-11-01

    Using the mitochondrial potential (ΔΨ(m)) marker JC-1 (5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine iodide) and high-resolution imaging, we functionally analyzed mitochondria in cultured rat hippocampal astrocytes. Ratiometric detection of JC-1 fluorescence identified mitochondria with high and low ΔΨ(m). Mitochondrial density was highest in the perinuclear region, whereas ΔΨ(m) tended to be higher in peripheral mitochondria. Spontaneous ΔΨ(m) fluctuations, representing episodes of increased energization, appeared in individual mitochondria or synchronized in mitochondrial clusters. They continued upon withdrawal of extracellular Ca(2+), but were antagonized by dantrolene or 2-aminoethoxydiphenylborate (2-APB). Fluo-3 imaging revealed local cytosolic Ca(2+) transients with similar kinetics that also were depressed by dantrolene and 2-APB. Massive cellular Ca(2+) load or metabolic impairment abolished ΔΨ(m) fluctuations, occasionally evoking heterogeneous mitochondrial depolarizations. The detected diversity and ΔΨ(m) heterogeneity of mitochondria confirms that even in less structurally polarized cells, such as astrocytes, specialized mitochondrial subpopulations coexist. We conclude that ΔΨ(m) fluctuations are an indication of mitochondrial viability and are triggered by local Ca(2+) release from the endoplasmic reticulum. This spatially confined organelle crosstalk contributes to the functional heterogeneity of mitochondria and may serve to adapt the metabolism of glial cells to the activity and metabolic demand of complex neuronal networks. The established ratiometric JC-1 imaging-especially combined with two-photon microscopy-enables quantitative functional analyses of individual mitochondria as well as the comparison of mitochondrial heterogeneity in different preparations and/or treatment conditions.

  5. eZinCh-2: A Versatile, Genetically Encoded FRET Sensor for Cytosolic and Intraorganelle Zn2+ Imaging

    PubMed Central

    2015-01-01

    Zn2+ plays essential and diverse roles in numerous cellular processes. To get a better understanding of intracellular Zn2+ homeostasis and the putative signaling role of Zn2+, various fluorescent sensors have been developed that allow monitoring of Zn2+ concentrations in single living cells in real time. Thus far, two families of genetically encoded FRET-based Zn2+ sensors have been most widely applied, the eCALWY sensors developed by our group and the ZapCY sensors developed by Palmer and co-workers. Both have been successfully used to measure cytosolic free Zn2+, but distinctly different concentrations have been reported when using these sensors to measure Zn2+ concentrations in the ER and mitochondria. Here, we report the development of a versatile alternative FRET sensor containing a de novo Cys2His2 binding pocket that was created on the surface of the donor and acceptor fluorescent domains. This eZinCh-2 sensor binds Zn2+ with a high affinity that is similar to that of eCALWY-4 (Kd = 1 nM at pH 7.1), while displaying a substantially larger change in emission ratio. eZinCh-2 not only provides an attractive alternative for measuring Zn2+ in the cytosol but was also successfully used for measuring Zn2+ in the ER, mitochondria, and secretory vesicles. Moreover, organelle-targeted eZinCh-2 can also be used in combination with the previously reported redCALWY sensors to allow multicolor imaging of intracellular Zn2+ simultaneously in the cytosol and the ER or mitochondria. PMID:26151333

  6. A luminescence lifetime assisted ratiometric fluorimeter for biological applications

    NASA Astrophysics Data System (ADS)

    Lam, Hung; Kostov, Yordan; Rao, Govind; Tolosa, Leah

    2009-12-01

    In general, the most difficult task in developing devices for fluorescence ratiometric sensing is the isolation of signals from overlapping emission wavelengths. Wavelength discrimination can be achieved by using monochromators or bandpass filters, which often lead to decreased signal intensities. The result is a device that is both complex and expensive. Here we present an alternative system—a low-cost standalone optical fluorimeter based on luminescence lifetime assisted ratiometric sensing (LARS). This paper describes the principle of this technique and the overall design of the sensor device. The most significant innovation of LARS is the ability to discriminate between two overlapping luminescence signals based on differences in their luminescence decay rates. Thus, minimal filtering is required and the two signals can be isolated despite significant overlap of luminescence spectra. The result is a device that is both simple and inexpensive. The electronic circuit employs the lock-in amplification technique for the signal processing and the system is controlled by an onboard microcontroller. In addition, the system is designed to communicate with external devices via Bluetooth.

  7. Ratiometric Photoacoustic Molecular Imaging for Methylmercury Detection in Living Subjects.

    PubMed

    Liu, Yi; Wang, Sheng; Ma, Ying; Lin, Jing; Wang, Hai-Yan; Gu, Yueqing; Chen, Xiaoyuan; Huang, Peng

    2017-02-22

    Photoacoustic molecular imaging is an emerging and promising diagnostic tool for heavy metal ions detection. Methylmercury (MeHg(+) ) is one of the most potent neurotoxins, which damages the brain and nervous system of human beings through fish consumption. The development of a selective and sensitive method for MeHg(+) detection is highly desirable. In this Communication, we develope a chemoselective photoacoustic sensor (LP-hCy7) composed of the liposome (LP) and MeHg(+) -responsive near-infrared (NIR) cyanine dye (hCy7) for MeHg(+) detection within living subjects, such as zebrafish and mouse. The as-prepared LP-hCy7 nanoprobe displays unique dual-shift NIR absorbance peaks and produces a normalized turn-on response after the reaction of MeHg(+) and hCy7 through a mercury-promoted cyclization reaction. The absorbance intensities of LP-hCy7 nanoprobe at 690 and 860 nm are decreased and increased, respectively. The ratiometric photoacoustic signal (PA860/PA690) is noticeably increased in the presence of MeHg(+) . These findings not only provide a ratiometric photoacoustic molecular imaging probe for the detection of metal ions in vivo, but also provides a tool for spectroscopic photoacoustic molecular imaging.

  8. A luminescence lifetime assisted ratiometric fluorimeter for biological applications.

    PubMed

    Lam, Hung; Kostov, Yordan; Rao, Govind; Tolosa, Leah

    2009-12-01

    In general, the most difficult task in developing devices for fluorescence ratiometric sensing is the isolation of signals from overlapping emission wavelengths. Wavelength discrimination can be achieved by using monochromators or bandpass filters, which often lead to decreased signal intensities. The result is a device that is both complex and expensive. Here we present an alternative system--a low-cost standalone optical fluorimeter based on luminescence lifetime assisted ratiometric sensing (LARS). This paper describes the principle of this technique and the overall design of the sensor device. The most significant innovation of LARS is the ability to discriminate between two overlapping luminescence signals based on differences in their luminescence decay rates. Thus, minimal filtering is required and the two signals can be isolated despite significant overlap of luminescence spectra. The result is a device that is both simple and inexpensive. The electronic circuit employs the lock-in amplification technique for the signal processing and the system is controlled by an onboard microcontroller. In addition, the system is designed to communicate with external devices via Bluetooth.

  9. Highly sensitive ratiometric fluorescent chemosensor for silver ion and silver nanoparticles in aqueous solution.

    PubMed

    Jang, Sujung; Thirupathi, Ponnaboina; Neupane, Lok Nath; Seong, Junho; Lee, Hyunsook; Lee, Wan In; Lee, Keun-Hyeung

    2012-09-21

    A pyrene derivative chemosensor (Pyr-WH) based on a dipeptide shows a highly sensitive ratiometric response to Ag(I) as well as silver nanoparticles in aqueous solution at physiological pH. Pyr-WH penetrated live HeLa cells and exhibits a ratiometric response to intracellular Ag(I). The binding mode of Pyr-WH with Ag(I) was characterized based on fluorescence changes in different pH, NMR, and ESI mass spectrometer experiments.

  10. Highly sensitive ratiometric detection of heparin and its oversulfated chondroitin sulfate contaminant by fluorescent peptidyl probe.

    PubMed

    Mehta, Pramod Kumar; Lee, Hyeri; Lee, Keun-Hyeung

    2017-05-15

    The selective and sensitive detection of heparin, an anticoagulant in clinics as well as its contaminant oversulfated chondroitin sulfate (OSCS) is of great importance. We first reported a ratiometric sensing method for heparin as well as OSCS contaminants in heparin using a fluorescent peptidyl probe (Pep1, pyrene-GSRKR) and heparin-digestive enzyme. Pep1 exhibited a highly sensitive ratiometric response to nanomolar concentration of heparin in aqueous solution over a wide pH range (2~11) and showed highly selective ratiometric response to heparin among biological competitors such as hyaluronic acid and chondroitin sulfate. Pep1 showed a linear ratiometric response to nanomolar concentrations of heparin in aqueous solutions and in human serum samples. The detection limit for heparin was calculated to be 2.46nM (R(2)=0.99) in aqueous solutions, 2.98nM (R(2)=0.98) in 1% serum samples, and 3.43nM (R(2)=0.99) in 5% serum samples. Pep1 was applied to detect the contaminated OSCS in heparin with heparinase I, II, and III, respectively. The ratiometric sensing method using Pep1 and heparinase II was highly sensitive, fast, and efficient for the detection of OSCS contaminant in heparin. Pep1 with heparinase II could detect as low as 0.0001% (w/w) of OSCS in heparin by a ratiometric response.

  11. Ratiometric fluorescent probe for alkaline phosphatase based on betaine-modified polyethylenimine via excimer/monomer conversion.

    PubMed

    Zheng, Fangyuan; Guo, Sihua; Zeng, Fang; Li, Jun; Wu, Shuizhu

    2014-10-07

    Alkaline phosphatase (ALP) is an important diagnostic indicator for a number of human diseases since abnormal level of ALP is closely related to a variety of pathological processes; hence, the development of convenient and reliable assay methods for monitoring ALP is of great significance for medical sciences as well as biological diagnostics. Herein, we report the first ratiometric fluorescent sensing system for ALP. This sensing system consists of two components: the betaine-modified and positively charged polyethylenimine (PEI) and the negatively charged pyrene derivative containing one ALP-responsive phosphate group (Py-P, an aliphatic phosphate ester). In the absence of ALP, the two-component sensing system shows the excimer's emission of Py-P, since Py-P molecules complex with the positively charged polyelectrolyte via electrostatic interactions, leading to the formation of pyrene excimers. While in the presence of ALP, the phosphate moieties are cleaved from Py-P molecules due to the enzymatic reaction, thereby destroying the electrostatic interactions; as a result, the system displays the monomer emission of Py-P. This assay system is operable in aqueous media with a very low detection limit of 0.1 U/mL. The system is capable of detecting ALP in such biological fluid as serum, and this strategy may provide a new and effective approach for designing ratiometric sensing systems for detecting other biomolecules.

  12. FRET ratiometric probes reveal the chiral-sensitive cysteine-dependent H2S production and regulation in living cells

    NASA Astrophysics Data System (ADS)

    Wei, Lv; Yi, Long; Song, Fanbo; Wei, Chao; Wang, Bai-Fan; Xi, Zhen

    2014-04-01

    Hydrogen sulfide (H2S) is an endogenously produced gaseous signalling molecule with multiple biological functions. In order to visualize and quantify the endogenous in situ production of H2S in living cells, here we developed two new sulphide ratiometric probes (SR400 and SR550) based on fluorescence resonance energy transfer (FRET) strategy for live capture of H2S. The FRET-based probes show excellent selectivity toward H2S in a high thiol background under physiological buffer. The probe can be used to in situ visualize cysteine-dependent H2S production in a chiral-sensitive manner in living cells. The ratiometric imaging studies indicated that D-Cys induces more H2S production than that of L-Cys in mitochondria of human embryonic kidney 293 cells (HEK293). The cysteine mimics propargylglycine (PPG) has also been found to inhibit the cysteine-dependent endogenous H2S production in a chiral-sensitive manner in living cells. D-PPG inhibited D-Cys-dependent H2S production more efficiently than L-PPG, while, L-PPG inhibited L-Cys-dependent H2S production more efficiently than D-PPG. Our bioimaging studies support Kimura's discovery of H2S production from D-cysteine in mammalian cells and further highlight the potential of D-cysteine and its derivatives as an alternative strategy for classical H2S-releasing drugs.

  13. A Simple and Effective Ratiometric Fluorescent Probe for the Selective Detection of Cysteine and Homocysteine in Aqueous Media.

    PubMed

    Na, Risong; Zhu, Meiqing; Fan, Shisuo; Wang, Zhen; Wu, Xiangwei; Tang, Jun; Liu, Jia; Wang, Yi; Hua, Rimao

    2016-08-05

    Biothiols such as cysteine (Cys) and homocysteine (Hcy) are essential biomolecules participating in molecular and physiological processes in an organism. However, their selective detection remains challenging. In this study, ethyl 2-(3-formyl-4-hydroxyphenyl)-4-methylthiazole-5-carboxylate (NL) was synthesized as a ratiometric fluorescent probe for the rapid and selective detection of Cys and Hcy over glutathione (GSH) and other amino acids. The fluorescence intensity of the probe in the presence of Cys/Hcy increased about 3-fold at a concentration of 20 equiv. of the probe, compared with that in the absence of these chemicals in aqueous media. The limits of detection of the fluorescent assay were 0.911 μM and 0.828 μM of Cys and Hcy, respectively. ¹H-NMR and MS analyses indicated that an excited-state intramolecular proton transfer is the mechanism of fluorescence sensing. This ratiometric probe is structurally simple and highly selective. The results suggest that it has useful applications in analytical chemistry and diagnostics.

  14. Efficient ratiometric fluorescence probe based on dual-emission quantum dots hybrid for on-site determination of copper ions.

    PubMed

    Yao, Jianlei; Zhang, Kui; Zhu, Houjuan; Ma, Fang; Sun, Mingtai; Yu, Huan; Sun, Jian; Wang, Suhua

    2013-07-02

    Of various chemosensory protocols, the color change observed by the naked eye is considered to be a conceivable and on-site way to indicate the presence of an analyte. We herein designed a ratiometric fluorescence probe by hybridizing dual-emission quantum dots (QDs) and demonstrated its efficiency for on-site visual determination of copper ions. The hybrid probe comprises two sizes of cadmium telluride QDs emitting red and green fluorescence, respectively, in which the red-emitting ones are embedded in silica nanoparticles and the green-emitting ones are covalently linked onto the surface. The fluorescence of the embedded QDs is insensitive to the analyte, whereas the green emissive QDs are functionalized to be selectively quenched by the analyte. Upon exposure to different amounts of copper ions, the variations of the dual emission intensity ratios display continuous color changes from green to red, which can be clearly observed by the naked eye. The limit of detection for copper is estimated to be 1.1 nM, much lower than the allowable level of copper (~20 μM) in drinking water set by U.S. Environmental Protection Agency. The probe is demonstrated for the determination of copper ions in lake water and mineral water samples, especially for visually monitoring copper residues on herb leaves. This prototype ratiometric probe is simple, fully self-contained, and thus potentially attractive for visual identification without the need for elaborate equipment.

  15. Microscopic imaging of intracellular calcium in live cells using lifetime-based ratiometric measurements of Oregon Green BAPTA-1.

    PubMed

    Lattarulo, Carli; Thyssen, Diana; Kuchibholta, Kishore V; Hyman, Bradley T; Bacskaiq, Brian J

    2011-01-01

    Calcium is a ubiquitous intracellular messenger that has important functions in normal neuronal function. The pathology of Alzheimer's disease has been shown to alter calcium homeostasis in neurons and astrocytes. Several calcium dye indicators are available to measure intracellular calcium within cells, including Oregon Green BAPTA-1 (OGB-1). Using fluorescence lifetime imaging microscopy, we adapted this single wavelength calcium dye into a ratiometric dye to allow quantitative imaging of cellular calcium. We used this approach for in vitro calibrations, single-cell microscopy, high-throughput imaging in automated plate readers, and in single cells in the intact living brain. While OGB is a commonly used fluorescent dye for imaging calcium qualitatively, there are distinct advantages to using a ratiometric approach, which allows quantitative determinations of calcium that are independent of dye concentration. Taking advantage of the distinct lifetime contrast of the calcium-free and calcium-bound forms of OGB, we used time-domain lifetime measurements to generate calibration curves for OGB lifetime ratios as a function of calcium concentration. In summary, we demonstrate approaches using commercially available tools to measure calcium concentrations in live cells at multiple scales using lifetime contrast. These approaches are broadly applicable to other fluorescent readouts that exhibit lifetime contrast and serve as powerful alternatives to spectral or intensity readouts in multiplexing experiments.

  16. A sensitive colorimetric and ratiometric chemosensor for trivalent metal cations.

    PubMed

    Zhao, Xu; Yin, Guohui; Jin, Di; Yan, Xilong; Li, Yang; Chen, Ligong

    2015-03-01

    A novel hydroxyethyl piperazine functionalized cyanine derivative was designed and synthesized. It presents selective colorimetric as well as ratiometric absorption responses to trivalent metal cations (Cr(3+), Fe(3+) and Al(3+)) over a variety of divalent and monovalent metal cations in 3:7 ethanol-water solution. Detection limits of this method for Cr(3+), Fe(3+) and Al(3+) were 3.99 μM, 4.30 μM and 1.85 μM, respectively. The recognition mechanism was attributed to the protonation of the organic probe, which blocked the photoinduced electron transfer (PET) process. In addition, the sensor was also successfully applied to the determination of Cr(3+) in prepared samples.

  17. Ratiometric Imaging of Extracellular pH in Dental Biofilms.

    PubMed

    Schlafer, Sebastian; Dige, Irene

    2016-03-09

    The pH in bacterial biofilms on teeth is of central importance for dental caries, a disease with a high worldwide prevalence. Nutrients and metabolites are not distributed evenly in dental biofilms. A complex interplay of sorption to and reaction with organic matter in the biofilm reduces the diffusion paths of solutes and creates steep gradients of reactive molecules, including organic acids, across the biofilm. Quantitative fluorescent microscopic methods, such as fluorescence life time imaging or pH ratiometry, can be employed to visualize pH in different microenvironments of dental biofilms. pH ratiometry exploits a pH-dependent shift in the fluorescent emission of pH-sensitive dyes. Calculation of the emission ratio at two different wavelengths allows determining local pH in microscopic images, irrespective of the concentration of the dye. Contrary to microelectrodes the technique allows monitoring both vertical and horizontal pH gradients in real-time without mechanically disturbing the biofilm. However, care must be taken to differentiate accurately between extra- and intracellular compartments of the biofilm. Here, the ratiometric dye, seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) is employed to monitor extracellular pH in in vivo grown dental biofilms of unknown species composition. Upon exposure to glucose the dye is up-concentrated inside all bacterial cells in the biofilms; it is thus used both as a universal bacterial stain and as a marker of extracellular pH. After confocal microscopic image acquisition, the bacterial biomass is removed from all pictures using digital image analysis software, which permits to exclusively calculate extracellular pH. pH ratiometry with the ratiometric dye is well-suited to study extracellular pH in thin biofilms of up to 75 µm thickness, but is limited to the pH range between 4.5 and 7.0.

  18. Quantitative description of radiofrequency (RF) power-based ratiometric chemical exchange saturation transfer (CEST) pH imaging.

    PubMed

    Wu, Renhua; Longo, Dario Livio; Aime, Silvio; Sun, Phillip Zhe

    2015-05-01

    Chemical exchange saturation transfer (CEST) MRI holds great promise for the imaging of pH. However, routine CEST measurement varies not only with the pH-dependent chemical exchange rate, but also with CEST agent concentration, providing pH-weighted information. Conventional ratiometric CEST imaging normalizes the confounding concentration factor by analyzing the relative CEST effect from different exchangeable groups, requiring CEST agents with multiple chemically distinguishable labile proton sites. Recently, a radiofrequency (RF) power-based ratiometric CEST MRI approach has been developed for concentration-independent pH MRI using CEST agents with a single exchangeable group. To facilitate quantification and optimization of the new ratiometric analysis, we quantified the RF power-based ratiometric CEST ratio (rCESTR) and derived its signal-to-noise and contrast-to-noise ratios. Using creatine as a representative CEST agent containing a single exchangeable site, our study demonstrated that optimized RF power-based ratiometric analysis provides good pH sensitivity. We showed that rCESTR follows a base-catalyzed exchange relationship with pH independent of creatine concentration. The pH accuracy of RF power-based ratiometric MRI was within 0.15-0.20 pH units. Furthermore, the absolute exchange rate can be obtained from the proposed ratiometric analysis. To summarize, RF power-based ratiometric CEST analysis provides concentration-independent pH-sensitive imaging and complements conventional multiple labile proton group-based ratiometric CEST analysis.

  19. Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiometric flow cytometry.

    PubMed

    Valkonen, Mari; Mojzita, Dominik; Penttilä, Merja; Bencina, Mojca

    2013-12-01

    The ability of cells to maintain pH homeostasis in response to environmental changes has elicited interest in basic and applied research and has prompted the development of methods for intracellular pH measurements. Many traditional methods provide information at population level and thus the average values of the studied cell physiological phenomena, excluding the fact that cell cultures are very heterogeneous. Single-cell analysis, on the other hand, offers more detailed insight into population variability, thereby facilitating a considerably deeper understanding of cell physiology. Although microscopy methods can address this issue, they suffer from limitations in terms of the small number of individual cells that can be studied and complicated image processing. We developed a noninvasive high-throughput method that employs flow cytometry to analyze large populations of cells that express pHluorin, a genetically encoded ratiometric fluorescent probe that is sensitive to pH. The method described here enables measurement of the intracellular pH of single cells with high sensitivity and speed, which is a clear improvement compared to previously published methods that either require pretreatment of the cells, measure cell populations, or require complex data analysis. The ratios of fluorescence intensities, which correlate to the intracellular pH, are independent of the expression levels of the pH probe, making the use of transiently or extrachromosomally expressed probes possible. We conducted an experiment on the kinetics of the pH homeostasis of Saccharomyces cerevisiae cultures grown to a stationary phase after ethanol or glucose addition and after exposure to weak acid stress and glucose pulse. Minor populations with pH homeostasis behaving differently upon treatments were identified.

  20. Chemical calcium indicators.

    PubMed

    Paredes, R Madelaine; Etzler, Julie C; Watts, Lora Talley; Zheng, Wei; Lechleiter, James D

    2008-11-01

    Our understanding of the underlying mechanisms of Ca2+ signaling as well as our appreciation for its ubiquitous role in cellular processes has been rapidly advanced, in large part, due to the development of fluorescent Ca2+ indicators. In this chapter, we discuss some of the most common chemical Ca2+ indicators that are widely used for the investigation of intracellular Ca2+ signaling. Advantages, limitations and relevant procedures will be presented for each dye including their spectral qualities, dissociation constants, chemical forms, loading methods and equipment for optimal imaging. Chemical indicators now available allow for intracellular Ca2+ detection over a very large range (<50 nM to >50 microM). High affinity indicators can be used to quantify Ca2+ levels in the cytosol while lower affinity indicators can be optimized for measuring Ca2+ in subcellular compartments with higher concentrations. Indicators can be classified into either single wavelength or ratiometric dyes. Both classes require specific lasers, filters, and/or detection methods that are dependent upon their spectral properties and both classes have advantages and limitations. Single wavelength indicators are generally very bright and optimal for Ca2+ detection when more than one fluorophore is being imaged. Ratiometric indicators can be calibrated very precisely and they minimize the most common problems associated with chemical Ca2+ indicators including uneven dye loading, leakage, photobleaching, and changes in cell volume. Recent technical advances that permit in vivo Ca2+ measurements will also be discussed.

  1. Chemical Calcium Indicators

    PubMed Central

    Paredes, R. Madelaine; Etzler, Julie C.; Watts, Lora Talley; Lechleiter, James D.

    2008-01-01

    Our understanding of the underlying mechanisms of Ca2+ signaling as well as our appreciation for its ubiquitous role in cellular processes and has been rapidly advanced, in large part, due to the development of fluorescent Ca2+ indicators. In this chapter, we discuss some of the most common chemical Ca2+ indicators that are widely used for the investigation of intracellular Ca2+ signaling. Advantages, limitations and relevant procedures will be presented for each dye including their spectral qualities, dissociation constants, chemical forms, loading methods and equipment for optimal imaging. Chemical indicators that are now available allow for intracellular Ca2+ detection over a very large range (<50 nM to >50 μM). Higher affinity indicators can be used to quantify Ca2+ levels in the cytosol while lower affinity indicators can be optimized for measuring Ca2+ in subcellular compartments with higher concentrations. Indicators can be classified into either single wavelength or ratiometric dyes. Both classes require specific lasers, filters, and/or detection methods that are dependent upon their spectral properties and both classes have advantages and limitations. Single wavelength indicators are generally very bright and optimal for Ca2+ detection when more than one fluorophore is being imaging. Ratiometric indicators can be calibrated very precisely and they minimize the most common problems associated with chemical Ca2+ indicators including uneven dye loading, leakage, photobleaching and changes in cell volume. Recent technical advances that permit in vivo Ca2+ measurements will also be discussed. PMID:18929663

  2. Optimum spectral windows to minimize quantum noise of ratiometric intracellular fluorescent probes.

    PubMed

    Stern, M D; Spurgeon, H A; Hansford, R; Lakatta, E G; Capogrossi, M C

    1989-01-01

    When fluorescent indicators are used to measure intracellular ligands in single cells, the quality of the data is usually limited by quantum (shot) noise. For indicators which shift excitation or emission wavelengths upon ligand binding, a ratiometric method is usually employed. In choosing the spectral windows for excitation or collection of fluorescence, there is a trade-off between maximum sensitivity to ligand binding, and maximum collection of light. We show that there is a well-defined optimum choice of windows which minimizes the error caused by quantum noise in the estimated ligand concentration. An algorithm for determining these optimum windows is presented. As an example, we consider the measurement of intracellular calcium by indo-1 fluorescence emission ratio in cardiac myocytes. The optimum wavelength bands for collection of fluorescence are considerably wider than those commonly employed. The use of these windows in a pulsed-excitation time-resolved calcium measurement instrument resulted in improved signal to noise ratio of the calcium signal.

  3. An ICT-based strategy to a colorimetric and ratiometric fluorescence probe for hydrogen sulfide in living cells.

    PubMed

    Yu, Fabiao; Li, Peng; Song, Ping; Wang, Bingshuai; Zhao, Jianzhang; Han, Keli

    2012-03-18

    We present a colorimetric and ratiometric fluorescent probe Cy-N(3) that exhibits a selective response to H(2)S. The probe employs a near-infrared cyanine as a fluorophore, and is equipped with an operating azide unit. It is readily employed for assessing intracellular H(2)S levels, and confocal ratiometric imaging is achieved successfully.

  4. Highly Selective Two-Photon Fluorescent Probe for Ratiometric Sensing and Imaging Cysteine in Mitochondria.

    PubMed

    Niu, Weifen; Guo, Lei; Li, Yinhui; Shuang, Shaomin; Dong, Chuan; Wong, Man Shing

    2016-02-02

    A novel ratiometric mitochondrial cysteine (Cys)-selective two-photon fluorescence probe has been developed on the basis of a merocyanine as the fluorophore and an acrylate moiety as the biothiol reaction site. The biocompatible and photostable acrylate-functionalized merocyanine probe shows not only a mitochondria-targeting property but also highly selective detection and monitoring of Cys over other biothiols such as homocysteine (Hcy) and glutathione (GSH) and hydrogen sulfide (H2S) in live cells. In addition, this probe exhibits ratiometric fluorescence emission characteristics (F518/F452), which are linearly proportional to Cys concentrations in the range of 0.5-40 μM. More importantly, the probe and its released fluorophore, merocyanine, exhibit strong two-photon excited fluorescence (TPEF) with two-photon action cross-section (Φσmax) of 65.2 GM at 740 nm and 72.6 GM at 760 nm in aqueous medium, respectively, which is highly desirable for high contrast and brightness ratiometric two-photon fluorescence imaging of the living samples. The probe has been successfully applied to ratiometrically image and detect mitochondrial Cys in live cells and intact tissues down to a depth of 150 μm by two-photon fluorescence microscopy. Thus, this ratiometric two-photon fluorescent probe is practically useful for an investigation of Cys in living biological systems.

  5. Ratiometric fluorescence, electrochemiluminescence, and photoelectrochemical chemo/biosensing based on semiconductor quantum dots

    NASA Astrophysics Data System (ADS)

    Wu, Peng; Hou, Xiandeng; Xu, Jing-Juan; Chen, Hong-Yuan

    2016-04-01

    Ratiometric fluorescent sensors, which can provide built-in self-calibration for correction of a variety of analyte-independent factors, have attracted particular attention for analytical sensing and optical imaging with the potential to provide a precise and quantitative analysis. A wide variety of ratiometric sensing probes using small fluorescent molecules have been developed. Compared with organic dyes, exploiting semiconductor quantum dots (QDs) in ratiometric fluorescence sensing is even more intriguing, owing to their unique optical and photophysical properties that offer significant advantages over organic dyes. In this review, the main photophysical mechanism for generating dual-emission from QDs for ratiometry is discussed and categorized in detail. Typically, dual-emission can be obtained either with energy transfer from QDs to dyes or with independent dual fluorophores of QDs and dye/QDs. The recent discovery of intrinsic dual-emission from Mn-doped QDs offers new opportunities for ratiometric sensing. Particularly, the signal transduction of QDs is not restricted to fluorescence, and electrochemiluminescence and photoelectrochemistry from QDs are also promising for sensing, which can be made ratiometric for correction of interferences typically encountered in electrochemistry. All these unique photophysical properties of QDs lead to a new avenue of ratiometry, and the recent progress in this area is addressed and summarized here. Several interesting applications of QD-based ratiometry are presented for the determination of metal ions, temperature, and biomolecules, with specific emphasis on the design principles and photophysical mechanisms of these probes.

  6. Ratiometric fluorescent probe with AIE property for monitoring endogenous hydrogen peroxide in macrophages and cancer cells.

    PubMed

    Liu, Yong; Nie, Jing; Niu, Jie; Meng, Fangfang; Lin, Weiying

    2017-08-04

    Hydrogen peroxide (H2O2) plays a key role in the progression of human illnesses, such as autoimmune and auto-inflammatory diseases, infectious diseases, diabetes, and cancer, etc. In this work, we have discribed a novel probe, TPE-TLE, which remarkably displayed AIE property and ratiometric fluorescence emission profiles in the presence of H2O2. This ratiometric fluorescent probe with AIE property exhibits outstanding features such as the well-resolved emission peaks, high sensitivity, high selectivity, low cytotoxicity, and good cell-membrane permeability. These excellent attributes enable us to demonstrate the ratiometric imaging of endogenously produced H2O2 in macrophages and cancer cells based on the novel ratiometric probe with AIE property for the first time. By comparing two kinds of cells, it is firstly found that cancer cells should contain much more endogenous H2O2 than macrophages. We expect that TPE-TLE will be useful fluorescent platform for the development of a variety of ratiometric fluorescent probes with AIE property to achieve unique biological applications.

  7. Single-trial imaging of spikes and synaptic potentials in single neurons in brain slices with genetically encoded hybrid voltage sensor

    PubMed Central

    Ghitani, Nima; Bayguinov, Peter O.; Ma, Yihe

    2014-01-01

    Genetically encoded voltage sensors expand the optogenetics toolkit into the important realm of electrical recording, enabling researchers to study the dynamic activity of complex neural circuits in real time. However, these probes have thus far performed poorly when tested in intact neural circuits. Hybrid voltage sensors (hVOS) enable the imaging of voltage by harnessing the resonant energy transfer that occurs between a genetically encoded component, a membrane-tethered fluorescent protein that serves as a donor, and a small charged molecule, dipicrylamine, which serves as an acceptor. hVOS generates optical signals as a result of voltage-induced changes in donor-acceptor distance. We expressed the hVOS probe in mouse brain by in utero electroporation and in transgenic mice with a neuronal promoter. Under conditions favoring sparse labeling we could visualize single-labeled neurons. hVOS imaging reported electrically evoked fluorescence changes from individual neurons in slices from entorhinal cortex, somatosensory cortex, and hippocampus. These fluorescence signals tracked action potentials in individual neurons in a single trial with excellent temporal fidelity, producing changes that exceeded background noise by as much as 16-fold. Subthreshold synaptic potentials were detected in single trials in multiple distinct cells simultaneously. We followed signal propagation between different cells within one field of view and between dendrites and somata of the same cell. hVOS imaging thus provides a tool for high-resolution recording of electrical activity from genetically targeted cells in intact neuronal circuits. PMID:25411462

  8. Towards PDT with Genetically Encoded Photosensitizer KillerRed: A Comparison of Continuous and Pulsed Laser Regimens in an Animal Tumor Model.

    PubMed

    Shirmanova, Marina; Yuzhakova, Diana; Snopova, Ludmila; Perelman, Gregory; Serebrovskaya, Ekaterina; Lukyanov, Konstantin; Turchin, Ilya; Subochev, Pavel; Lukyanov, Sergey; Kamensky, Vladislav; Zagaynova, Elena

    2015-01-01

    The strong phototoxicity of the red fluorescent protein KillerRed allows it to be considered as a potential genetically encoded photosensitizer for the photodynamic therapy (PDT) of cancer. The advantages of KillerRed over chemical photosensitizers are its expression in tumor cells transduced with the appropriate gene and direct killing of cells through precise damage to any desired cell compartment. The ability of KillerRed to affect cell division and to induce cell death has already been demonstrated in cancer cell lines in vitro and HeLa tumor xenografts in vivo. However, the further development of this approach for PDT requires optimization of the method of treatment. In this study we tested the continuous wave (593 nm) and pulsed laser (584 nm, 10 Hz, 18 ns) modes to achieve an antitumor effect. The research was implemented on CT26 subcutaneous mouse tumors expressing KillerRed in fusion with histone H2B. The results showed that the pulsed mode provided a higher rate of photobleaching of KillerRed without any temperature increase on the tumor surface. PDT with the continuous wave laser was ineffective against CT26 tumors in mice, whereas the pulsed laser induced pronounced histopathological changes and inhibition of tumor growth. Therefore, we selected an effective regimen for PDT when using the genetically encoded photosensitizer KillerRed and pulsed laser irradiation.

  9. Towards PDT with Genetically Encoded Photosensitizer KillerRed: A Comparison of Continuous and Pulsed Laser Regimens in an Animal Tumor Model

    PubMed Central

    Shirmanova, Marina; Yuzhakova, Diana; Snopova, Ludmila; Perelman, Gregory; Serebrovskaya, Ekaterina; Lukyanov, Konstantin; Turchin, Ilya; Subochev, Pavel; Lukyanov, Sergey; Kamensky, Vladislav; Zagaynova, Elena

    2015-01-01

    The strong phototoxicity of the red fluorescent protein KillerRed allows it to be considered as a potential genetically encoded photosensitizer for the photodynamic therapy (PDT) of cancer. The advantages of KillerRed over chemical photosensitizers are its expression in tumor cells transduced with the appropriate gene and direct killing of cells through precise damage to any desired cell compartment. The ability of KillerRed to affect cell division and to induce cell death has already been demonstrated in cancer cell lines in vitro and HeLa tumor xenografts in vivo. However, the further development of this approach for PDT requires optimization of the method of treatment. In this study we tested the continuous wave (593 nm) and pulsed laser (584 nm, 10 Hz, 18 ns) modes to achieve an antitumor effect. The research was implemented on CT26 subcutaneous mouse tumors expressing KillerRed in fusion with histone H2B. The results showed that the pulsed mode provided a higher rate of photobleaching of KillerRed without any temperature increase on the tumor surface. PDT with the continuous wave laser was ineffective against CT26 tumors in mice, whereas the pulsed laser induced pronounced histopathological changes and inhibition of tumor growth. Therefore, we selected an effective regimen for PDT when using the genetically encoded photosensitizer KillerRed and pulsed laser irradiation. PMID:26657001

  10. 2D ratiometric fluorescent pH sensor for tracking of cells proliferation and metabolism.

    PubMed

    Ma, Jun; Ding, Changqin; Zhou, Jie; Tian, Yang

    2015-08-15

    Extracellular pH plays a vital role no matter in physiological or pathological studies. In this work, a hydrogel, CD@Nile-FITC@Gel (Gel sensor), entrapping the ratiometric fluorescent probe CD@Nile-FITC was developed. The Gel sensor was successfully used for real-time extracellular pH monitoring. In the case of CD@Nile-FITC, pH-sensitive fluorescent dye fluorescein isothiocyanate (FITC) was chosen as the response signal for H(+) and Nile blue chloride (Nile) as the reference signal. The developed fluorescent probe exhibited high selectivity for pH over other metal ions and amino acids. Meanwhile, the carbon-dots-based inorganic-organic probe demonstrated excellent photostability against long-term light illumination. In order to study the extracellular pH change in processes of cell proliferation and metabolism, CD@Nile-FITC probe was entrapped in sodium alginate gel and consequently formed CD@Nile-FITC@Gel. The MTT assay showed low cytotoxicity of the Gel and the pH titration indicated that it could monitor the pH fluctuations linearly and rapidly within the pH range of 6.0-9.0, which is valuable for physiological pH determination. As expected, the real-time bioimaging of the probe was successfully achieved.

  11. Multicompartment Polymer Nanostructures with Ratiometric Dual-emission pH-Sensitivity

    PubMed Central

    Sun, Guorong; Cui, Honggang; Lin, Lily Yun; Lee, Nam S.; Yang, Chao; Neumann, William L.; Freskos, John N.; Shieh, Jeng J.; Dorshow, Richard B.; Wooley, Karen L.

    2011-01-01

    Pyrazine-labeled multi-compartment nanostructures are shown to exhibit enhanced pH-responsive blue-shifted fluorescence emission intensities than are their simpler core-shell spherical analogs. An amphiphilic linear triblock terpolymer of ethylene oxide, N-acryloxysuccinimide and styrene, PEO45-b-PNAS105-b-PS45, which lacks significant incompatibility for the hydrophobic block segments and undergoes gradual hydrolysis of the NAS units, underwent supramolecular assembly in mixtures of organic solvent and water to afford multicompartment micelles (MCMs) with narrow size distribution. The assembly process was followed over time and found to evolve from individual polymer nanodroplets containing internally-phase segregated domains, of increasing definition, and ultimately to dissociate into discrete micelles. Upon covalent cross-linking of the MCMs with pH-insensitive pyrazine-based diamino cross-linkers, pH-responsive, photonic multicompartment nanostructures (MCNs) were produced. These MCNs exhibited significant enhancement of overall structural stability, in comparison with the MCMs, and internal structural tunability through the cross-linking chemistry. Meanwhile, the complex compartmentalized morphology exerted unique pH-responsive fluorescence dual-emission properties, indicating promise in ratiometric pH-sensing applications. PMID:21574617

  12. Ratiometric near infrared luminescent thermometer based on lanthanide metal-organic frameworks

    SciTech Connect

    Yue, Dan; Zhang, Jun; Zhao, Dian; Lian, Xiusheng; Cui, Yuanjing Yang, Yu; Qian, Guodong

    2016-09-15

    A near infrared luminescent MOFs thermometer (Nd{sub 0.676}Yb{sub 0.324}BTC) was prepared via a simple solvothermal method using Ln{sup 3+} (Ln=Nd, Yb) ions and 1, 3, 5-benznenetricarboxylic acid (H{sub 3}BTC), and characterized by PXRD, TGA, ICP, and photoluminescence (PL) spectrum. These results indicate that the Nd{sub 0.676}Yb{sub 0.324}BTC displays high relative sensitivity and excellent repeatability in the physiological temperature range (288–323 K), and the maximum relative sensitivity is determined to be 1.187% K{sup −1} at 323 K. These NIR luminescent MOFs may have potential applications in physiological temperature sensing. - Graphical abstract: A near infrared luminescent MOFs thermometer (Nd{sub 0.054}Yb{sub 0.946}BTC ) displays high relative sensitivity and excellent repeatability in the physiological temperature range (288–323 K). Display Omitted - Highlights: • A ratiometric near infrared luminescent MOFs thermometer (Nd{sub 0.676}Yb{sub 0.324}BTC) was prepared via a simple solvothermal method. • The maximum relative sensitivity of Nd{sub 0.676}Yb{sub 0.324}BTC is determined to be 1.187% K{sup −1} at 323 K. • Nd{sub 0.676}Yb{sub 0.324}BTC showed excellent repeatability in the physiological temperature range (288–323 K).

  13. Multi-angle ratiometric approach to measure chemical exchange in amide proton transfer imaging.

    PubMed

    Zu, Zhongliang; Janve, Vaibhav A; Li, Ke; Does, Mark D; Gore, John C; Gochberg, Daniel F

    2012-09-01

    Amide proton transfer imaging, a specific form of chemical exchange saturation transfer imaging, has previously been applied to studies of acute ischemic acidosis, stroke, and cancer. However, interpreting the resulting contrast is complicated by its dependence on the exchange rate between amides and water, the amide concentration, amide and water relaxation, and macromolecular magnetization transfer. Hence, conventional chemical exchange saturation transfer contrast is not specific to changes such as reductions in pH due to tissue acidosis. In this article, a multi-angle ratiometric approach based on several pulsed-chemical exchange saturation transfer scans at different irradiation flip angles is proposed to specifically reflect exchange rates only. This separation of exchange effects in pulsed-chemical exchange saturation transfer experiments is based on isolating rotation vs. saturation contributions, and such methods form a new subclass of chemical exchange rotation transfer (CERT) experiments. Simulations and measurements of creatine/agar phantoms indicate that a newly proposed imaging metric isolates the effects of exchange rate changes, independent of other sample parameters.

  14. A ratiometric fluorescence probe for selective visual sensing of Zn2+.

    PubMed

    Ajayaghosh, Ayyappanpillai; Carol, Priya; Sreejith, Sivaramapanicker

    2005-11-02

    A simple ratiometric fluorescence probe based on vinylpyrrole end-capped bipyridine for the visual sensing of Zn2+ under aqueous physiological pH (6.8-7.4) is described. The fluorophores 3a-c showed strong emission around 537 nm in acetonitrile with a quantum yield of 0.4. In buffered (HEPES, pH 7.2) acetonitrile-water mixture (9:1 v/v), titration of transition metal salts to 3c showed strong quenching of the emission at 547 nm except in the case of Zn2+, which resulted in a red-shifted emission at 637 nm. Alkali and alkaline earth metal salts could not induce any considerable changes to the emission behavior of 3a-c. The binding of Zn2+ was highly selective in the presence of a variety of other metal ions. Though Cu2+ quenches the emission of 3c, in the presence of Zn2+, a red emission prevails, indicating the preference of 3c toward Zn2+. Job plot and Benesi-Hildebrand analysis revealed a 1:1 complexation between the probe and the metal ion. The selective visual sensing of Zn2+ with a red emission is ideally suited for the imaging of biological specimens.

  15. A fluorescence ratiometric sensor for hypochlorite based on a novel dual-fluorophore response approach.

    PubMed

    Long, Lingliang; Zhang, Dongdong; Li, Xiufen; Zhang, Jinfang; Zhang, Chi; Zhou, Liping

    2013-05-02

    A fluorescence ratiometric sensor for OCl(-) has been developed based on a novel dual fluorophore response approach. The sensor molecule contains a coumarin fluorophore and a rhodamine fluorophore, and the two fluorophores are directly linked to an OCl(-) recognition group. The structure of the sensor was characterized by ESI-MS, NMR, and X-ray crystallographic analysis. Upon treatment with OCl(-), both fluorophores in the sensor responded simultaneously at two separate optical windows, with large enhancement of the fluorescence ratio (I578/I501) from 0.01 to 39.55. The fluorescence ratios for the sensor showed a good linearity with the concentration of OCl(-) in the range of 0.2-40 μM and the detection limits is 0.024 μM (SN(-1)=3). Investigation of reaction products indicated that the sensor reaction with OCl(-) produced two new fluorescent molecules, which were responsible for the fluorescence changes in two optical windows. In addition, the sensor showed high selectivity to OCl(-) over other reactive oxygen species, reactive nitrogen species, cations, and anions. The sensor has also been successfully applied to detection of OCl(-) in natural water samples with satisfactory recovery.

  16. Ratiometric ultrasensitive electrochemical immunosensor based on redox substrate and immunoprobe

    NASA Astrophysics Data System (ADS)

    Tang, Zhongxue; Ma, Zhanfang

    2016-10-01

    In this work, we presented a ratiometric electrochemical immunosensor based on redox substrate and immunoprobe. Carboxymethyl cellulose-Au-Pb2+ (CMC-Au-Pb2+) and carbon-Au-Cu2+ (C-Au-Cu2+) nanocomposites were firstly synthesized and implemented as redox substrate and immunoprobe with strong current signals at ‑0.45 V and 0.15 V, respectively. Human immunoglobulin G (IgG) was used as a model analyte to examine the analytical performance of the proposed method. The current signals of CMC-Au-Pb2+ (Isubstrate) and C-Au-Cu2+ (Iprobe) were monitored. The effect of redox substrate and immunoprobe behaved as a better linear relationship between Iprobe/Isubstrate and Lg CIgG (ng mL‑1). By measuring the signal ratio Iprobe/Isubstrate, the sandwich immunosensor for IgG exhibited a wide linear range from 1 fg mL‑1 to 100 ng mL‑1, which was two orders of magnitude higher than other previous works. The limit of detection reached 0.26 fg mL‑1. Furthermore, for human serum samples, the results from this method were consistent with those of the enzyme linked immunosorbent assay (ELISA), demonstrating that the proposed immunoassay was of great potential in clinical diagnosis.

  17. Fluorescence ratiometric classifier for the detection of skin pathologies

    NASA Astrophysics Data System (ADS)

    Anand, Suresh; Cicchi, Riccardo; Cosci, Alessandro; Rossari, Susanna; Kapsokalyvas, Dimitrios; Baria, Enrico; Maio, Vincenza; Massi, Daniela; De Giorgi, Vincenzo; Pimpinelli, Nicola; Pavone, Francesco S.

    2015-07-01

    Detection of pre-malignant lesions in skin could help in reducing the 5 year patient mortality rates and greatly advancing the quality of life. Current gold standard for the detection of skin pathologies is a tissue biopsy and followed by a series of steps before it is examined under a light microscope by a pathologist. The disadvantage with this method is its invasiveness. Light based biomedical point spectroscopic techniques offers an adjunct technique to invasive tissue pathology. In this context, we have implemented a simple multiplexed ratiometric approach (F470/F560 and F510/F580) based on fluorescence at two excitation wavelengths 378 nm and 445 nm respectively. The emission profile at these excitation wavelengths showed a shift towards the longer wavelengths for melanoma when compared with normal and nevus. At both excitation wavelengths, we observed an increased intensity ratios for normal, followed by nevus and melanoma. This intensity ratios provide a good diagnostic capability in differentiating normal, nevus and melanocytic skin lesions. This method could be applied in vivo because of the simplicity involved in discriminating normal and pathological skin tissues.

  18. Ratiometric ultrasensitive electrochemical immunosensor based on redox substrate and immunoprobe

    PubMed Central

    Tang, Zhongxue; Ma, Zhanfang

    2016-01-01

    In this work, we presented a ratiometric electrochemical immunosensor based on redox substrate and immunoprobe. Carboxymethyl cellulose-Au-Pb2+ (CMC-Au-Pb2+) and carbon-Au-Cu2+ (C-Au-Cu2+) nanocomposites were firstly synthesized and implemented as redox substrate and immunoprobe with strong current signals at −0.45 V and 0.15 V, respectively. Human immunoglobulin G (IgG) was used as a model analyte to examine the analytical performance of the proposed method. The current signals of CMC-Au-Pb2+ (Isubstrate) and C-Au-Cu2+ (Iprobe) were monitored. The effect of redox substrate and immunoprobe behaved as a better linear relationship between Iprobe/Isubstrate and Lg CIgG (ng mL−1). By measuring the signal ratio Iprobe/Isubstrate, the sandwich immunosensor for IgG exhibited a wide linear range from 1 fg mL−1 to 100 ng mL−1, which was two orders of magnitude higher than other previous works. The limit of detection reached 0.26 fg mL−1. Furthermore, for human serum samples, the results from this method were consistent with those of the enzyme linked immunosorbent assay (ELISA), demonstrating that the proposed immunoassay was of great potential in clinical diagnosis. PMID:27739493

  19. Benzothiazole-Based Neutral Ratiometric Fluorescence Sensor for Amyloid Fibrils.

    PubMed

    Mora, Aruna K; Murudkar, Sushant; Alamelu, A; Singh, Prabhat K; Chattopadhyay, Subrata; Nath, Sukhendu

    2016-11-07

    Early detection of amyloid fibrils is very important for the timely diagnosis of several neurological diseases. Thioflavin-T (ThT) is a gold standard fluorescent probe for amyloid fibrils and has been used for the last few decades. However, due to its positive charge, ThT is incapable of crossing the blood-brain barrier and cannot be used for in vivo imaging of fibrils. In the present work, we synthesized a neutral ThT derivative, 2-[2'-Me,4'-(dimethylamino)phenyl]benzothiazole (2Me-DABT), which showed a strong affinity towards the amyloid fibrils. On association with the amyloid fibrils, 2Me-DABT not only showed a large increase in its emission intensity, but also, unlike ThT, a large blueshift in its emission spectrum was observed. Thus, unlike ThT, 2Me-DABT is a potential candidate for the ratiometric sensor of the amyloid fibrils. Detailed photophysical properties of 2Me-DABT in amyloid fibrils and different solvent media were studied to understand its sensory activity. Fluorescence resonance energy transfer (FRET) studies suggested that the sites of localization for ThT and 2Me-DABT in amyloid fibrils are not same and their average distance of separation in amyloid fibrils was determined. The experimental data was nicely supported by molecular docking studies, which confirmed the binding of 2Me-DABT in the inner core of the amyloid fibrils.

  20. Ratiometric CdSe/ZnS quantum dot protein sensor.

    PubMed

    Tyrakowski, Christina M; Snee, Preston T

    2014-03-04

    We have created a platform for the ratiometric fluorescent sensing of targeted proteins by conjugating conjoined protein binding agent/organic dye ligands to water-soluble, emissive semiconductor quantum dots (QDs). The QD emission is tuned such that it may serve as an energy transfer donor to the dye acceptor. Upon exposure to the target proteins, these analytes bind to the surfaces of the QDs and change the microenvironments of the QD-bound dyes such that the emissive properties of the dyes are perturbed. The resulting alteration in the QD and dye fluorescence spectra creates a readout that is fully quantitative. The advantage of our methodology is that the detection of proteins is very fast as the platform is fully homogeneous, whereas the heterogeneous ELISA assay involves multiple steps with blocking agents and secondary reporters that ultimately complicate the process. The calculated detection limits for the two QD protein-sensing examples reported here are also competitive with the ubiquitous ELISA assay.

  1. Ratiometric spectral imaging for fast tumor detection and chemotherapy monitoring in vivo

    NASA Astrophysics Data System (ADS)

    Hwang, Jae Youn; Gross, Zeev; Gray, Harry B.; Medina-Kauwe, Lali K.; Farkas, Daniel L.

    2011-06-01

    We report a novel in vivo spectral imaging approach to cancer detection and chemotherapy assessment. We describe and characterize a ratiometric spectral imaging and analysis method and evaluate its performance for tumor detection and delineation by quantitatively monitoring the specific accumulation of targeted gallium corrole (HerGa) into HER2-positive (HER2 +) breast tumors. HerGa temporal accumulation in nude mice bearing HER2 + breast tumors was monitored comparatively by a. this new ratiometric imaging and analysis method; b. established (reflectance and fluorescence) spectral imaging; c. more commonly used fluorescence intensity imaging. We also tested the feasibility of HerGa imaging in vivo using the ratiometric spectral imaging method for tumor detection and delineation. Our results show that the new method not only provides better quantitative information than typical spectral imaging, but also better specificity than standard fluorescence intensity imaging, thus allowing enhanced in vivo outlining of tumors and dynamic, quantitative monitoring of targeted chemotherapy agent accumulation into them.

  2. A Ratiometric Wavelength Measurement Based on a Silicon-on-Insulator Directional Coupler Integrated Device

    PubMed Central

    Wang, Pengfei; Hatta, Agus Muhamad; Zhao, Haoyu; Zheng, Jie; Farrell, Gerald; Brambilla, Gilberto

    2015-01-01

    A ratiometric wavelength measurement based on a Silicon-on-Insulator (SOI) integrated device is proposed and designed, which consists of directional couplers acting as two edge filters with opposite spectral responses. The optimal separation distance between two parallel silicon waveguides and the interaction length of the directional coupler are designed to meet the desired spectral response by using local supermodes. The wavelength discrimination ability of the designed ratiometric structure is demonstrated by a beam propagation method numerically and then is verified experimentally. The experimental results have shown a general agreement with the theoretical models. The ratiometric wavelength system demonstrates a resolution of better than 50 pm at a wavelength around 1550 nm with ease of assembly and calibration. PMID:26343668

  3. Thin-section ratiometric Ca2+ images obtained by optical sectioning of fura-2 loaded mast cells

    PubMed Central

    1992-01-01

    The availability of the ratiometric Ca2+ indicator dyes, fura-2, and indo-1, and advances in digital imaging and computer technology have made it possible to detect Ca2+ changes in single cells with high temporal and spatial resolution. However, the optical properties of the conventional epifluorescence microscope do not produce a perfect image of the specimen. Instead, the observed image is a spatial low pass filtered version of the object and is contaminated with out of focus information. As a result, the image has reduced contrast and an increased depth of field. This problem is especially important for measurements of localized Ca2+ concentrations. One solution to this problem is to use a scanning confocal microscope which only detects in focus information, but this approach has several disadvantages for low light fluorescence measurements in living cells. An alternative approach is to use digital image processing and a deblurring algorithm to remove the out of focus information by using a knowledge of the point spread function of the microscope. All of these algorithms require a stack of two-dimensional images taken at different focal planes, although the "nearest neighbor deblurring" algorithm only requires one image above and below the image plane. We have used a modification of this scheme to construct a simple inverse filter, which extracts optical sections comparable to those of the nearest neighbors scheme, but without the need for adjacent image sections. We have used this "no neighbors" processing scheme to deblur images of fura-2-loaded mast cells from beige mice and generate high resolution ratiometric Ca2+ images of thin sections through the cell. The shallow depth of field of these images is demonstrated by taking pairs of images at different focal planes, 0.5-microns apart. The secretory granules, which exclude the fura-2, appear in focus in all sections and distinct changes in their size and shape can be seen in adjacent sections. In addition, we

  4. Fluorescence ratiometric properties induced by nanoparticle plasmonics and nanoscale dye dynamics.

    PubMed

    Hakonen, Aron

    2013-01-01

    Nanoscale transport of merocyanine 540 within/near the plasmon field of gold nanoparticles was recognized as an effective inducer of single-excitation dual-emission ratiometric properties. With a high concentration of the signal transducer (ammonium), a 700% increase in fluorescence was observed at the new red-shifted emission maximum, compared to a nanoparticle free sensor membrane. A previously nonrecognized isosbestic point is demonstrated at 581.4 ± 0.1 nm. The mechanism can be utilized for enhanced and simplified ratiometric optical chemical sensors and potentially for thin film engineering to make solar cells more effective and stable by a broader and more regulated absorption.

  5. Real-time and high-throughput analysis of mitochondrial metabolic states in living cells using genetically encoded NAD(+)/NADH sensors.

    PubMed

    Zhao, Yuzheng; Yang, Yi

    2016-11-01

    Mitochondria are central organelles that regulate cellular bioenergetics, biosynthesis, and signaling processes. NADH, a key player in cell metabolism, is often considered as a marker of mitochondrial function. However, traditional methods for NADH measurements are either destructive or unable to distinguish between NADH and NADPH. In contrast to traditional methods, genetically encoded NADH sensors can be used for the real-time tracking and quantitative measurement of subcellular NADH levels in living cells. Therefore, these sensors provide innovative tools and address the limitations of current techniques. We herein summarize the properties of different types of recently developed NADH biosensors, discuss their advantages and disadvantages, and focus on the high-throughput analysis of mitochondrial function by using highly responsive NAD(+)/NADH sensors.

  6. Dual-Emissive Cyclometalated Iridium(III) Polypyridine Complexes as Ratiometric Biological Probes and Organelle-Selective Bioimaging Reagents.

    PubMed

    Zhang, Kenneth Yin; Liu, Hua-Wei; Tang, Man-Chung; Choi, Alex Wing-Tat; Zhu, Nianyong; Wei, Xi-Guang; Lau, Kai-Chung; Lo, Kenneth Kam-Wing

    2015-07-06

    In this Article, we present a series of cyclometalated iridium(III) polypyridine complexes of the formula [Ir(N^C)2(N^N)](PF6) that showed dual emission under ambient conditions. The structures of the cyclometalating and diimine ligands were changed systematically to investigate the effects of the substituents on the dual-emission properties of the complexes. On the basis of the photophysical data, the high-energy (HE) and low-energy (LE) emission features of the complexes were assigned to triplet intraligand ((3)IL) and triplet charge-transfer ((3)CT) excited states, respectively. Time-dependent density functional theory (TD-DFT) calculations supported these assignments and indicated that the dual emission resulted from the interruption of the communication between the higher-lying (3)IL and the lower-lying (3)CT states by a triplet amine-to-ligand charge-transfer ((3)NLCT) state. Also, the avidin-binding properties of the biotin complexes were studied by emission titrations, and the results showed that the dual-emissive complexes can be utilized as ratiometric probes for avidin. Additionally, all the complexes exhibited efficient cellular uptake by live HeLa cells. The MTT and Annexin V assays confirmed that no cell death and early apoptosis occurred during the cell imaging experiments. Interestingly, laser-scanning confocal microscopy revealed that the complexes were selectively localized on the cell membrane, mitochondria, or both, depending on the nature of the substituents of the ligands. The results of this work will contribute to the future development of dual-emissive transition metal complexes as ratiometric probes and organelle-selective bioimaging reagents.

  7. Ratiometric Imaging of Tissue by Two-Photon Microscopy: Observation of a High Level of Formaldehyde around Mouse Intestinal Crypts.

    PubMed

    Singha, Subhankar; Jun, Yong Woong; Bae, Juryang; Ahn, Kyo Han

    2017-03-21

    Ratiometric imaging by two-photon microscopy can offer a viable tool for the relative quantification of biological analytes inside tissue with minimal influence from environmental factors that affect fluorescence signal. We demonstrate the ratiometric imaging of formaldehyde at the suborgan level using a two-photon fluorescent probe, which involves pixel-to-pixel ratiometric data transformation. This study reveals for the first time a high level of formaldehyde around the crypts of mouse small intestine, implicating its possible protective role along with the released antimicrobials from the Paneth cells.

  8. Magnetic and fluorescent core-shell nanoparticles for ratiometric pH sensing.

    PubMed

    Lapresta-Fernández, Alejandro; Doussineau, Tristan; Dutz, Silvio; Steiniger, Frank; Moro, Artur J; Mohr, Gerhard J

    2011-10-14

    This paper describes the preparation of nanoparticles composed of a magnetic core surrounded by two successive silica shells embedding two fluorophores, showing uniform nanoparticle size (50-60 nm in diameter) and shape, which allow ratiometric pH measurements in the pH range 5-8. Uncoated iron oxide magnetic nanoparticles (∼10 nm in diameter) were formed by the coprecipitation reaction of ferrous and ferric salts. Then, they were added to a water-in-oil microemulsion where the hydrophilic silica shells were obtained through hydrolysis and condensation of tetraethoxyorthosilicate together with the corresponding silylated dye derivatives-a sulforhodamine was embedded in the inner silica shell and used as the reference dye while a pH-sensitive fluorescein was incorporated in the outer shell as the pH indicator. The magnetic nanoparticles were characterized using vibrating sample magnetometry, dynamic light scattering, transmission electron microscopy, x-ray diffraction and Fourier transform infrared spectroscopy. The relationship between the analytical parameter, that is, the ratio of fluorescence between the sensing and reference dyes versus the pH was adjusted to a sigmoidal fit using a Boltzmann type equation giving an apparent pK(a) value of 6.8. The fluorescence intensity of the reference dye did not change significantly (∼3.0%) on modifying the pH of the nanoparticle dispersion. Finally, the proposed method was statistically validated against a reference procedure using samples of water and physiological buffer with 2% of horse serum, indicating that there are no significant statistical differences at a 95% confidence level.

  9. A cysteamine-selective two-photon fluorescent probe for ratiometric bioimaging.

    PubMed

    Sarkar, Avik R; Heo, Cheol Ho; Kim, Eunjin; Lee, Hyo Won; Singh, Hardev; Kim, Jeong Jin; Kang, Hyuk; Kang, Chulhun; Kim, Hwan Myung

    2015-02-11

    We report a two-photon fluorescent probe for ratiometric imaging of cysteamine in situ. This probe can detect the levels of endogenous cysteamine with statistical significance in live cells and brain hippocampal tissues, revealing that cysteamine is localized mainly in the perikaria of the pyramidal neurons and the granule cells.

  10. Detection of toxic mercury ions using a ratiometric CdSe/ZnS nanocrystal sensor.

    PubMed

    Page, Leah E; Zhang, Xi; Jawaid, Ali M; Snee, Preston T

    2011-07-21

    We have developed a strategy for the ratiometric detection of toxic Hg(2+) ions using a semiconductor nanocrystal energy-transfer donor coupled to a mercury-sensitive "turn-on" dye acceptor. The results demonstrate a new paradigm of toxic metal sensing that resolves the difficulties with the use of semiconductor nanotechnology for this purpose.

  11. pHluorin2: an enhanced, ratiometric, pH-sensitive green florescent protein.

    PubMed

    Mahon, Matthew J

    2011-06-01

    Green florescent protein (GFP) variants that are sensitive to changes in pH are invaluable reagents for the analysis of protein dynamics associated with both endo- and exocytotic vesicular trafficking. Ratiometric pHluorin is a GFP variant that displays a bimodal excitation spectrum with peaks at 395 and 475 nm and an emission maximum at 509 nm. Upon acidification, pHluorin excitation at 395 nm decreases with a corresponding increase in the excitation at 475 nm. GFP2, a GFP variant that contains mammalianized codons and the folding enhancing mutation F64L, displays ~8-fold higher florescence compared to pHluorin upon excitation at 395 nm. Using GFP2 as a template, an enhanced ratiometric pHluorin (pHluorin2) construct was developed to contain fully mammalianized codons, the F64L mutation and ten of the thirteen pHluorin-specific mutations. As a result, pHluorin2 displays markedly higher florescence when compared to pHluorin while maintaining the ratiometric pH-sensitivity. Unlike native pHluorin, pHluorin2 expressed in the ligand-binding domain of the parathyroid hormone 1 receptor is readily detectable by confocal microscopy and displays a marked increase in florescence upon ligand-induced endocytosis to intracellular vesicles. Thus, pHluorin2's enhanced florescence while sustaining ratiometric pH-sensitivity represents a significant improvement for this methodological approach.

  12. Visualizing BPA by molecularly imprinted ratiometric fluorescence sensor based on dual emission nanoparticles.

    PubMed

    Lu, Hongzhi; Xu, Shoufang

    2017-06-15

    Construction of ratiometric fluorescent probe often involved in tedious multistep preparation or complicated coupling or chemical modification process. The emergence of dual emission fluorescent nanoparticles would simplify the construction process and avoids the tedious chemical coupling. Herein, we reported a facile strategy to prepare ratiometric fluorescence molecularly imprinted sensor based on dual emission nanoparticles (d-NPs) which comprised of carbon dots and gold nanoclusters for detection of Bisphenol A (BPA). D-NPs emission at 460nm and 580nm were first prepared by seed growth co-microwave method using gold nanoparticles as seeds and glucose as precursor for carbon dots. When they were applied to propose ratiometric fluorescence molecularly imprinted sensor, the preparation process was simplified, and the sensitivity of sensor was improved with detection limit of 29nM, and visualizing BPA was feasible based on the distinguish fluorescence color change. The feasibility of the developed method in real samples was successfully evaluated through the analysis of BPA in water samples with satisfactory recoveries of 95.9-98.9% and recoveries ranging from 92.6% to 98.6% in canned food samples. When detection BPA in positive feeding bottles, the results agree well with those obtained by accredited method. The developed method proposed in this work to prepare ratiometric fluorescence molecularly imprinted sensor based on dual emission nanoparticles proved to be a convenient, reliable and practical way to prepared high sensitive and selective fluorescence sensors.

  13. Ratiometric detection of oligonucleotide stoichiometry on multifunctional gold nanoparticles by whispering gallery mode biosensing.

    PubMed

    Wu, F C; Wu, Y; Niu, Z; Vollmer, F

    2015-05-07

    A label-free method is developed to ratiometrically determine the stoichiometry of oligonucleotides attached to the surface of gold nanoparticle (GNP) by whispering gallery mode biosensing. Utilizing this scheme, it is furthermore shown that the stoichiometric ratio of GNP attached oligonucleotide species can be controlled by varying the concentration ratio of thiolated oligonucleotides that are used to modify the GNP.

  14. Development of microscopic systems for high-speed dual-excitation ratiometric Ca2+ imaging.

    PubMed

    Fukano, Takashi; Shimozono, Satoshi; Miyawaki, Atsushi

    2008-08-01

    For quantitative measurements of Ca(2+) concentration ([Ca(2+)]), ratiometric dyes are preferable, because the use of such dyes allows for correction of uneven loading or partitioning of dye within the cell as well as variations in cell thickness. Although dual-excitation ratiometric dyes for measuring [Ca(2+)], such as Fura-2, Fura-Red, and ratiometric-pericam, are widely used for a variety of applications, it has been difficult to use them for monitoring very fast Ca(2+) dynamics or Ca(2+) changes in highly motile cells. To overcome this problem, we have developed three new dual-excitation ratiometry systems. (1) A system in which two laser beams are alternated on every scanning line, allowing us to obtain confocal images using dual-excitation ratiometric dyes. This system increases the rate at which ratio measurements can be made to 200 Hz and provides confocal images at 1-10 Hz depending on the image size. (2) A truly simultaneous dual-excitation ratiometry system that used linearly polarized excitation light and polarization detection, allowing us to obtain ratiometric images without any time lag. This system, however, is based on statistical features of the fluorescence polarization and is limited to samples that contain a large number of fluorophores. In addition, this method requires complicated calculations. (3) An efficient, nearly simultaneous dual-excitation ratiometry system that allows us to rapidly switch between two synchronized excitation-detection components by employing two high-power light-emitting diodes (LEDs) and two high-speed liquid crystal shutters. The open/close operation of the two shutters is synchronized with the on/off switching of the two LEDs. This system increases the rate at which ratio measurements are made to 1 kHz, and provides ratio images at 10-100 Hz depending on the signal intensity.

  15. A FRET-based ratiometric fluorescent aptasensor for rapid and onsite visual detection of ochratoxin A.

    PubMed

    Qian, Jing; Wang, Kan; Wang, Chengquan; Hua, Mengjuan; Yang, Zhenting; Liu, Qian; Mao, Hanping; Wang, Kun

    2015-11-07

    A color change observable by the naked eye to indicate the content of an analyte is considered to be the most conceivable way of various sensing protocols. By taking advantage of the Förster resonance energy transfer (FRET) principles, we herein designed a dual-emission ratiometric fluorescent aptasensor for ochratoxin A (OTA) detection via a dual mode of fluorescent sensing and onsite visual screening. Amino group-modified OTA's aptamer was firstly labeled with the green-emitting CdTe quantum dots (gQDs) donor. The red-emitting CdTe QDs (rQDs) which were wrapped in the silica sphere could serve as the reference signal, while the gold nanoparticle (AuNP) acceptors were attached on the silica surface to bind with the thiolated complementary DNA (cDNA). The hybridization reaction between the aptamer and the cDNA brought gQD-AuNP pair close enough, thereby making the FRET occur in the aptasensor fabrication, while the subsequent fluorescence recovery induced by OTA was obtained in the detection procedure. Based on the red background of the wrapped rQDs, the aptasensor in response to increasing OTA displayed a distinguishable color change from red to yellow-green, which could be conveniently readout in solution even by the naked eye. Since the bioconjugations used as the aptasensor can be produced at large scale, this method can be used for in situ, rapid, or high-throughput OTA detection after only an incubation step in a homogeneous mode. We believe that this novel aptasensing strategy provides not only a promising method for OTA detection but also a universal model for detecting diverse targets by changing the corresponding aptamer.

  16. Ratiometric imaging of gastrodermal lipid bodies in coral-dinoflagellate endosymbiosis

    NASA Astrophysics Data System (ADS)

    Luo, Y.-J.; Wang, L.-H.; Chen, W.-N. U.; Peng, S.-E.; Tzen, J. T.-C.; Hsiao, Y.-Y.; Huang, H.-J.; Fang, L.-S.; Chen, C.-S.

    2009-03-01

    Cnidaria-dinoflagellate endosymbiosis is the phenomenon of autotrophic symbionts living inside the gastrodermal cells of their animal hosts. The molecular mechanism that regulates this association remains unclear. Using quantitative microscopy, we now provide evidence that the dynamic lipid changes in gastrodermal “lipid bodies” (LBs) reflect the symbiotic status of the host cell and its symbiont in the hermatypic coral Euphyllia glabrescens. By dual-emission ratiometric imaging with a solvatochromic fluorescent probe, Nile red (9-diethylamino-5H-benzo[α]phenoxazine-5-one), we showed that the in situ distribution of polar versus neutral lipids in LBs in living gastrodermal cells and symbionts can be analyzed. The ratio of Nile red fluorescence at red (R) versus green (G) wavelength region (i.e., R/G ratio) correlated with the relative molar ratio of polar (P) versus neutral (NP) lipids (i.e., P/NP ratio). The R/G ratio in host LBs increased after bleaching, indicating a decrease in neutral lipid accumulation in gastrodermal cells. On the other hand, neutral lipid accumulation inside the symbiont LBs resulted in gradual decreases of the R/G ratio as a result of bleaching. In comparison with the bleaching event, there was no relative lipid concentration change in host LBs under continual light or dark treatments as shown by insignificant R/G ratio shift. Patterns of R/G ratio shift in symbiont LBs were also different between corals undergoing bleaching and continual light/dark treatment. In the latter, there was little lipid accumulation in symbionts, with no resulting R/G ratio decrease. These results, demonstrating that the symbiotic status positively correlated with morphological and compositional changes of lipid bodies, not only highlight the pivotal role of LBs, but also implicate an involvement of lipid trafficking in regulating the endosymbiosis.

  17. A two-photon fluorescent probe for ratiometric imaging of endogenous hypochlorous acid in live cells and tissues.

    PubMed

    Jun, Yong Woong; Sarkar, Sourav; Singha, Subhankar; Reo, Ye Jin; Kim, Hye Rim; Kim, Jong-Jin; Chang, Young-Tae; Ahn, Kyo Han

    2017-09-28

    A fluorescent probe that enables ratiometric imaging of endogenous hypochlorous acid (HOCl) in cells and tissues by two-photon microscopy is developed based on a red-emitting acetyl-benzocoumarin (AcBC) dye. An oxathiolane group in the probe reacts with HOCl to generate the AcBC dye, which involves a ratiometric fluorescence change only toward HOCl along with high sensitivity.

  18. A new fluorescent probe for colorimetric and ratiometric detection of sulfur dioxide derivatives in liver cancer cells

    NASA Astrophysics Data System (ADS)

    Li, Dong-Peng; Wang, Zhao-Yang; Cui, Jie; Wang, Xin; Miao, Jun-Ying; Zhao, Bao-Xiang

    2017-03-01

    A new ratiometric fluorescent probe was constructed with hemicyanine and 7-nitrobenzofurazan for detection of sulfur dioxide derivatives (HSO3-/SO32-). The ratiometric response mode could be attributed to the efficient FRET (Förster resonance energy transfer) platform. The probe exbihited some desirable properties including fast response (within 2 minutes), good selectivity and high sensitivity. Moreover, the probe could detect endogenous HSO3- in liver cancer cells rather than normal liver cells, implying the diagnosal potential of the probe.

  19. Ratiometric Visualization of NO/H2S Cross-Talk in Living Cells and Tissues Using a Nitroxyl-Responsive Two-Photon Fluorescence Probe.

    PubMed

    Zhou, Yibo; Zhang, Xiufang; Yang, Sheng; Li, Yuan; Qing, Zhihe; Zheng, Jing; Li, Jishan; Yang, Ronghua

    2017-03-27

    It is of scientific significance to explore the intricate relationship between two crucial gasotransmitters nitric oxide (NO) and hydrogen sulfide (H2S), because they exert similar and interdependent biological actions within the living organisms. Nevertheless, visualization of the NO/H2S crosstalk using effective molecular imaging tools remains challenging. To address this issue, and given that nitroxyl (HNO) has been implicated as the interdependent production of NO and H2S via a network of cascading chemical reactions, we herein design a ratiometric two-photon fluorescent probe for HNO, termed TP-Rho-HNO, which consists of benzo[h]chromene-rhodol scaffold as two-photon energy transfer cassette with phosphine moiety as specific HNO recognition unit. The newly proposed probe has been successfully applied in ratiometric two-photon bioimaging of endogenous HNO derived from NO and H2S interaction in the human umbilical vein cells (HUVECs) and as well as in rat brain tissues. Intriguingly, the imaging results consistently demonstrate that the mutually dependent upgeneration of H2S and NO are present in living biosystems, indicating that this molecular probe would provide a powerful approach to elucidate the chemical foundation for the anfractuous cross-talk between the NO and H2S signaling pathways in biology.

  20. Calcium imaging with genetically encoded sensor Case12: Facile analysis of α7/α9 nAChR mutants.

    PubMed

    Shelukhina, Irina; Spirova, Ekaterina; Kudryavtsev, Denis; Ojomoko, Lucy; Werner, Markus; Methfessel, Christoph; Hollmann, Michael; Tsetlin, Victor

    2017-01-01

    Elucidation of the structural basis of pharmacological differences for highly homologous α7 and α9 nicotinic acetylcholine receptors (nAChRs) may shed light on their involvement in different physiological functions and diseases. Combination of site-directed mutagenesis and electrophysiology is a powerful tool to pinpoint the key amino-acid residues in the receptor ligand-binding site, but for α7 and α9 nAChRs it is complicated by their poor expression and fast desensitization. Here, we probed the ligand-binding properties of α7/α9 nAChR mutants by a proposed simple and fast calcium imaging method. The method is based on transient co-expression of α7/α9 nAChR mutants in neuroblastoma cells together with Ric-3 or NACHO chaperones and Case12 fluorescent calcium ion sensor followed by analysis of their pharmacology using a fluorescence microscope or a fluorometric imaging plate reader (FLIPR) with a GFP filter set. The results obtained were confirmed by electrophysiology and by calcium imaging with the conventional calcium indicator Fluo-4. The affinities for acetylcholine and epibatidine were determined for human and rat α7 nAChRs, and for their mutants with homologous residues of α9 nAChR incorporated at positions 117-119, 184, 185, 187, and 189, which are anticipated to be involved in ligand binding. The strongest decrease in the affinity was observed for mutations at positions 187 and 119. The L119D mutation of α7 nAChR, showing a larger effect for epibatidine than for acetylcholine, may implicate this position in pharmacological differences between α7 and α9 nAChRs.

  1. Calcium imaging with genetically encoded sensor Case12: Facile analysis of α7/α9 nAChR mutants

    PubMed Central

    Kudryavtsev, Denis; Ojomoko, Lucy; Werner, Markus; Methfessel, Christoph; Hollmann, Michael; Tsetlin, Victor

    2017-01-01

    Elucidation of the structural basis of pharmacological differences for highly homologous α7 and α9 nicotinic acetylcholine receptors (nAChRs) may shed light on their involvement in different physiological functions and diseases. Combination of site-directed mutagenesis and electrophysiology is a powerful tool to pinpoint the key amino-acid residues in the receptor ligand-binding site, but for α7 and α9 nAChRs it is complicated by their poor expression and fast desensitization. Here, we probed the ligand-binding properties of α7/α9 nAChR mutants by a proposed simple and fast calcium imaging method. The method is based on transient co-expression of α7/α9 nAChR mutants in neuroblastoma cells together with Ric-3 or NACHO chaperones and Case12 fluorescent calcium ion sensor followed by analysis of their pharmacology using a fluorescence microscope or a fluorometric imaging plate reader (FLIPR) with a GFP filter set. The results obtained were confirmed by electrophysiology and by calcium imaging with the conventional calcium indicator Fluo-4. The affinities for acetylcholine and epibatidine were determined for human and rat α7 nAChRs, and for their mutants with homologous residues of α9 nAChR incorporated at positions 117–119, 184, 185, 187, and 189, which are anticipated to be involved in ligand binding. The strongest decrease in the affinity was observed for mutations at positions 187 and 119. The L119D mutation of α7 nAChR, showing a larger effect for epibatidine than for acetylcholine, may implicate this position in pharmacological differences between α7 and α9 nAChRs. PMID:28797116

  2. The Use of Mn(II) Bound to His-tags as Genetically Encodable Spin-Label for Nanometric Distance Determination in Proteins.

    PubMed

    Ching, H Y Vincent; Mascali, Florencia C; Bertrand, Hélène C; Bruch, Eduardo M; Demay-Drouhard, Paul; Rasia, Rodolfo M; Policar, Clotilde; Tabares, Leandro C; Un, Sun

    2016-03-17

    A genetically encodable paramagnetic spin-label capable of self-assembly from naturally available components would offer a means for studying the in-cell structure and interactions of a protein by electron paramagnetic resonance (EPR). Here, we demonstrate pulse electron-electron double resonance (DEER) measurements on spin-labels consisting of Mn(II) ions coordinated to a sequence of histidines, so-called His-tags, that are ubiquitously added by genetic engineering to facilitate protein purification. Although the affinity of His-tags for Mn(II) was low (800 μM), Mn(II)-bound His-tags yielded readily detectable DEER time traces even at concentrations expected in cells. We were able to determine accurately the distance between two His-tag Mn(II) spin-labels at the ends of a rigid helical polyproline peptide of known structure, as well as at the ends of a completely cell-synthesized 3-helix bundle. This approach not only greatly simplifies the labeling procedure but also represents a first step towards using self-assembling metal spin-labels for in-cell distance measurements.

  3. A genetically encoded probe for the identification of proteins that form sulfenic acid in response to H2O2 in Saccharomyces cerevisiae.

    PubMed

    Takanishi, Christina L; Wood, Matthew J

    2011-06-03

    It is widely known that reactive oxygen species (ROS), such as hydrogen peroxide, play important roles in cellular signaling and initiation of oxidative stress responses via thiol modifications. Identification of the targets of these modifications will provide a better understanding of the relationship between ROS and human diseases, such as cancer and atherosclerosis. Sulfenic acid is the principle product of a reaction between hydrogen peroxide and a reactive protein cysteine. This reversible post-translational modification plays an important role in enzyme active sites, signaling transduction via disulfide bond formation, as well as an intermediate to overoxidation products during oxidative stress. By re-engineering the C-terminal cysteine rich domain (cCRD) of the Yap1 transcription factor, we were able to create a genetically encoded probe for the general detection and identification of proteins that form sulfenic acid in vivo. The Yap1-cCRD probe has been used previously in the identification of proteins that form sulfenic acid in Escherichia coli. Here we demonstrate the successful use of the Yap1-cCRD probe in the identification of proteins that form sulfenic acid in response to hydrogen peroxide in Saccharomyces cerevisiae.

  4. Engineering a genetically encoded competitive inhibitor of the KEAP1–NRF2 interaction via structure-based design and phage display

    PubMed Central

    Guntas, Gurkan; Lewis, Steven M.; Mulvaney, Kathleen M.; Cloer, Erica W.; Tripathy, Ashutosh; Lane, Thomas R.; Major, Michael B.; Kuhlman, Brian

    2016-01-01

    In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1–NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1–NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions. PMID:26489878

  5. Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions.

    PubMed

    Lang, Kathrin; Davis, Lloyd; Wallace, Stephen; Mahesh, Mohan; Cox, Daniel J; Blackman, Melissa L; Fox, Joseph M; Chin, Jason W

    2012-06-27

    Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.

  6. HcRed, a Genetically Encoded Fluorescent Binary Cross-Linking Agent for Cross-Linking of Mitochondrial ATP Synthase in Saccharomyces cerevisiae

    PubMed Central

    Gong, Lan; Ramm, Georg; Devenish, Rodney J.; Prescott, Mark

    2012-01-01

    Genetically encoded fluorescent cross-linking agents represent powerful tools useful both for visualising and modulating protein interactions in living cells. The far-red fluorescent protein HcRed, which is fluorescent only in a dimer form, can be used to promote the homo-dimerisation of target proteins, and thereby yield useful information about biological processes. We have in yeast cells expressed HcRed fused to a subunit of mitochondrial ATP synthase (mtATPase). This resulted in cross-linking of the large multi-subunit mtATPase complex within the inner-membrane of the mitochondrion. Fluorescence microscopy revealed aberrant mitochondrial morphology, and mtATPase complexes isolated from mitochondria were recovered as fluorescent dimers under conditions where complexes from control mitochondria were recovered as monomers. When viewed by electron microscopy normal cristae were absent from mitochondria in cells in which mATPase complexes were cross-linked. mtATPase dimers are believed to be the building blocks that are assembled into supramolecular mtATPase ribbons that promote the formation of mitochondrial cristae. We propose that HcRed cross-links mATPase complexes in the mitochondrial membrane hindering the normal assembly/disassembly of the supramolecular forms of mtATPase. PMID:22496895

  7. Monitoring cytosolic and ER Zn2+ in stimulated breast cancer cells using genetically encoded FRET sensors† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5mt00257e Click here for additional data file.

    PubMed Central

    Hessels, Anne M.; Taylor, Kathryn M.

    2016-01-01

    The Zn2+-specific ion channel ZIP7 has been implicated to play an important role in releasing Zn2+ from the ER. External stimulation of breast cancer cells has been proposed to induce phosphorylation of ZIP7 by CK2α, resulting in ZIP7-mediated Zn2+ release from the ER into the cytosol. Here, we examined whether changes in cytosolic and ER Zn2+ concentrations can be detected upon such external stimuli. Two previously developed FRET sensors for Zn2+, eZinCh-2 (K d = 1 nM at pH 7.1) and eCALWY-4 (K d = 0.63 nM at pH 7.1), were expressed in both the cytosol and the ER of wild-type MCF-7 and TamR cells. Treatment of MCF-7 and TamR cells with external Zn2+ and pyrithione, one of the previously used triggers, resulted in an immediate increase in free Zn2+ in both cytosol and ER, suggesting that Zn2+ was directly transferred across the cellular membranes by pyrithione. Cells treated with a second trigger, EGF/ionomycin, showed no changes in intracellular Zn2+ levels, neither in multicolor imaging experiments that allowed simultaneous imaging of cytosolic and ER Zn2+, nor in experiments in which cytosolic and ER Zn2+ were monitored separately. In contrast to previous work using small-molecule fluorescent dyes, these results indicate that EGF–ionomycin treatment does not result in significant changes in cytosolic Zn2+ levels as a result from Zn2+ release from the ER. These results underline the importance of using genetically encoded fluorescent sensors to complement and verify intracellular imaging experiments with synthetic fluorescent Zn2+ dyes. PMID:26739447

  8. A Genetically-Encoded YFP Sensor with Enhanced Chloride Sensitivity, Photostability and Reduced pH Interference Demonstrates Augmented Transmembrane Chloride Movement by Gerbil Prestin (SLC26a5)

    PubMed Central

    Zhong, Sheng; Navaratnam, Dhasakumar; Santos-Sacchi, Joseph

    2014-01-01

    Background Chloride is the major anion in cells, with many diseases arising from disordered Cl− regulation. For the non-invasive investigation of Cl− flux, YFP-H148Q and its derivatives chameleon and Cl-Sensor previously were introduced as genetically encoded chloride indicators. Neither the Cl− sensitivity nor the pH-susceptibility of these modifications to YFP is optimal for precise measurements of Cl− under physiological conditions. Furthermore, the relatively poor photostability of YFP derivatives hinders their application for dynamic and quantitative Cl− measurements. Dynamic and accurate measurement of physiological concentrations of chloride would significantly affect our ability to study effects of chloride on cellular events. Methodology/Principal Findings In this study, we developed a series of YFP derivatives to remove pH interference, increase photostability and enhance chloride sensitivity. The final product, EYFP-F46L/Q69K/H148Q/I152L/V163S/S175G/S205V/A206K (monomeric Cl-YFP), has a chloride Kd of 14 mM and pKa of 5.9. The bleach time constant of 175 seconds is over 15-fold greater than wild-type EYFP. We have used the sensor fused to the transmembrane protein prestin (gerbil prestin, SLC26a5), and shown for the first time physiological (mM) chloride flux in HEK cells expressing this protein. This modified fluorescent protein will facilitate investigations of dynamics of chloride ions and their mediation of cell function. Conclusions Modifications to YFP (EYFP-F46L/Q69K/H148Q/I152L/V163S/S175G/S205V/A206K (monomeric Cl-YFP) results in a photostable fluorescent protein that allows measurement of physiological changes in chloride concentration while remaining minimally affected by changes in pH. PMID:24901231

  9. Ratiometric Ca²+ measurements using the FlexStation® Scanning Fluorometer.

    PubMed

    Marshall, Ian C B; Boyfield, Izzy; McNulty, Shaun

    2005-01-01

    Many commercial organizations currently use the Fluorometric Imaging Plate Reader (FLIPR®: Molecular Devices, Sunnyvale, CA) to conduct high-throughput measurements of intracellular Ca(2+) concentration (see Chapter 7 ), taking advantage of its rapid kinetics, reliability, and compatibility for automation. For the majority of industrial applications, the primary limitation of FLIPR (i.e., its requirement for single wavelength fluorescent probes using visible light excitation) is not a significant issue. Indeed, visible light probes offer certain benefits over their ultraviolet (UV)-excited ratiometric counterparts, such as reduced sample autofluorescence and higher absorbance, thereby allowing relatively low concentrations of dye to be used. However, under certain circumstances researchers may prefer to conduct high-throughput experiments with ratiometric dyes, particularly when issues of dye leakage, photobleaching, or signal-to-noise ratio become a concern.

  10. Ratiometric and near-infrared molecular probes for the detection and imaging of zinc ions.

    PubMed

    Carol, Priya; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai

    2007-03-05

    The detection and imaging of Zn2+ in biological samples are of paramount interest owing to the role of this cation in physiological functions. This is possible only with molecular probes that specifically bind to Zn2+ and result in changes in emission properties. A "turn-on" emission or shift in the emission color upon binding to Zn2+ should be ideal for in vivo imaging. In this context, ratiometric and near-IR probes are of particular interest. Therefore, in the area of chemosensors or molecular probes, the design of fluorophores that allow ratiometric sensing or imaging in the near-IR region is attracting the attention of chemists. The purpose of this Focus Review is to highlight recent developments in this area and stress the importance of further research for future applications.

  11. A near-Infrared Fluorescent Chemodosimeter for Ratiometric Detecting Fluoride Based on Desilylation Reaction.

    PubMed

    Xie, Puhui; Guo, Fengqi; Gao, Guangqin; Fan, Wei; Yang, Guoyu; Xie, Lixia

    2016-09-01

    A new chemodosimeter based on dicyanomethylene-4H-chromene chromophore (probe 1) was developed as a ratiometric fluorescent probe in near-infrared range for F(-) with good selectivity in acetonitrile. Probe 1 could be used to directly visualize F(-) by the naked eye and showed more than 621-fold fluorescence enhancement at 715 nm upon reaction with F(-) upon excitation at 625 nm. The recognition of probe 1 to fluoride was featured by F(-)-induced red-shifts of both absorption (185 nm) and fluorescence peaks (132 nm) based on internal charge transfer (ICT) in acetonitrile. The desilylation reaction of 1 by F(-) was proposed for its dual absorption and emission ratiometric detection of fluoride.

  12. Ratiometric sensing of CO2 in ionic liquid modified ethyl cellulose matrix.

    PubMed

    Oter, Ozlem; Ertekin, Kadriye; Derinkuyu, Sibel

    2008-07-30

    In this study emission-based ratiometric response of ion pair form of 1-hydroxy-3,6,8-pyrenetrisulfonate (HPTS) to gaseous CO(2) has been evaluated in ionic liquid (IL) containing ethyl cellulose (EC) matrix. The ionic liquid: 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIMBF(4)); provided longer storage time and highly stable microenvironment for the HPTS molecule due to the buffering effect. The utilization of ionic liquid in ethyl cellulose matrix resulted with superior spectral characteristics. The excitation spectra of HPTS exhibited an atypical isoemmissive point in modified EC matrix at 418 nm which allows ratiometric processing of the signal intensities. EMIMBF(4)-doped sensor films exhibited enhanced linear working range between 0 and 100% pCO(2). The signal changes were fully reversible and the shelf life of the EMIMBF(4)-doped films was extended from 15 to 95 days.

  13. Ratiometric Array of Conjugated Polymers-Fluorescent Protein Provides a Robust Mammalian Cell Sensor.

    PubMed

    Rana, Subinoy; Elci, S Gokhan; Mout, Rubul; Singla, Arvind K; Yazdani, Mahdieh; Bender, Markus; Bajaj, Avinash; Saha, Krishnendu; Bunz, Uwe H F; Jirik, Frank R; Rotello, Vincent M

    2016-04-06

    Supramolecular complexes of a family of positively charged conjugated polymers (CPs) and green fluorescent protein (GFP) create a fluorescence resonance energy transfer (FRET)-based ratiometric biosensor array. Selective multivalent interactions of the CPs with mammalian cell surfaces caused differential change in FRET signals, providing a fingerprint signature for each cell type. The resulting fluorescence signatures allowed the identification of 16 different cell types and discrimination between healthy, cancerous, and metastatic cells, with the same genetic background. While the CP-GFP sensor array completely differentiated between the cell types, only partial classification was achieved for the CPs alone, validating the effectiveness of the ratiometric sensor. The utility of the biosensor was further demonstrated in the detection of blinded unknown samples, where 121 of 128 samples were correctly identified. Notably, this selectivity-based sensor stratified diverse cell types in minutes, using only 2000 cells, without requiring specific biomarkers or cell labeling.

  14. Design and Fabrication of a Ratiometric Planar Optode for Simultaneous Imaging of pH and Oxygen.

    PubMed

    Jiang, Zike; Yu, Xinsheng; Hao, Yingyan

    2017-06-07

    This paper presents a simple, high resolution imaging approach utilizing ratiometric planar optode for simultaneous measurement of dissolved oxygen (DO) and pH. The planar optode comprises a plastic optical film coated with oxygen indicator Platinum(II) octaethylporphyrin (PtOEP) and reference quantum dots (QDs) embedded in polystyrene (PS), pH indicator 5-Hexadecanoylamino-fluorescein (5-Fluorescein) embedded in Hydromed D4 matrix. The indicator and reference dyes are excited by utilizing an LED (Light Emitting Diode) source with a central wavelength of 405 nm, the emission respectively matches the different channels (red, green, and blue) of a 3CCD camera after eliminating the excitation source by utilizing the color filter. The result shows that there is low cross-sensitivity between the two analytes dissolved oxygen and pH, and it shows good performance in the dynamic response ranges of 0-12 mg/L and a dynamic range of pH 6-8. The optode has been tested with regard to the response times, accuracy, photostability and stability. The applied experiment for detecting pH/Oxygen of sea-water under the influence of the rain drops is demonstrated. It is shown that the planar optode measuring system provides a simple method with low cross-talk for pH/Oxygen imaging in aqueous applications.

  15. Design and Fabrication of a Ratiometric Planar Optode for Simultaneous Imaging of pH and Oxygen

    PubMed Central

    Jiang, Zike; Yu, Xinsheng; Hao, Yingyan

    2017-01-01

    This paper presents a simple, high resolution imaging approach utilizing ratiometric planar optode for simultaneous measurement of dissolved oxygen (DO) and pH. The planar optode comprises a plastic optical film coated with oxygen indicator Platinum(II) octaethylporphyrin (PtOEP) and reference quantum dots (QDs) embedded in polystyrene (PS), pH indicator 5-Hexadecanoylamino-fluorescein (5-Fluorescein) embedded in Hydromed D4 matrix. The indicator and reference dyes are excited by utilizing an LED (Light Emitting Diode) source with a central wavelength of 405 nm, the emission respectively matches the different channels (red, green, and blue) of a 3CCD camera after eliminating the excitation source by utilizing the color filter. The result shows that there is low cross-sensitivity between the two analytes dissolved oxygen and pH, and it shows good performance in the dynamic response ranges of 0–12 mg/L and a dynamic range of pH 6−8. The optode has been tested with regard to the response times, accuracy, photostability and stability. The applied experiment for detecting pH/Oxygen of sea-water under the influence of the rain drops is demonstrated. It is shown that the planar optode measuring system provides a simple method with low cross-talk for pH/Oxygen imaging in aqueous applications. PMID:28590430

  16. A Ratiometric Luminescent Thermometer Co-doped with Lanthanide and Transition Metals.

    PubMed

    Li, Zhiqiang; Hou, Zhaohui; Ha, Denghui; Li, Huanrong

    2015-12-01

    Herein, we report the fabrication of a sensitive ratiometric and colorimetric luminescent thermometer with a wide operating-temperature range, from cryogenic temperatures up to high temperatures, through the combination of lanthanide and transition metal complexes. Benefiting from the transition metal complex as a self-reference, the lanthanide content in the mixed-coordination complex, Eu0.05(Mebip-mim bromine)0.15Zn0.95(Mebip-mim bromine)1.9, was lowered to 5%.

  17. Stimulus and network dynamics collide in a ratiometric model of the antennal lobe macroglomerular complex.

    PubMed

    Chong, Kwok Ying; Capurro, Alberto; Karout, Salah; Pearce, Timothy Charles

    2012-01-01

    Time is considered to be an important encoding dimension in olfaction, as neural populations generate odour-specific spatiotemporal responses to constant stimuli. However, during pheromone mediated anemotactic search insects must discriminate specific ratios of blend components from rapidly time varying input. The dynamics intrinsic to olfactory processing and those of naturalistic stimuli can therefore potentially collide, thereby confounding ratiometric information. In this paper we use a computational model of the macroglomerular complex of the insect antennal lobe to study the impact on ratiometric information of this potential collision between network and stimulus dynamics. We show that the model exhibits two different dynamical regimes depending upon the connectivity pattern between inhibitory interneurons (that we refer to as fixed point attractor and limit cycle attractor), which both generate ratio-specific trajectories in the projection neuron output population that are reminiscent of temporal patterning and periodic hyperpolarisation observed in olfactory antennal lobe neurons. We compare the performance of the two corresponding population codes for reporting ratiometric blend information to higher centres of the insect brain. Our key finding is that whilst the dynamically rich limit cycle attractor spatiotemporal code is faster and more efficient in transmitting blend information under certain conditions it is also more prone to interference between network and stimulus dynamics, thus degrading ratiometric information under naturalistic input conditions. Our results suggest that rich intrinsically generated network dynamics can provide a powerful means of encoding multidimensional stimuli with high accuracy and efficiency, but only when isolated from stimulus dynamics. This interference between temporal dynamics of the stimulus and temporal patterns of neural activity constitutes a real challenge that must be successfully solved by the nervous system

  18. Ratiometric Catalyzed-Assembly of NanoCluster Beacons: A Nonenzymatic Approach for Amplified DNA Detection.

    PubMed

    Ge, Lei; Sun, Ximei; Hong, Qing; Li, Feng

    2017-09-20

    In this work, a novel fluorescent transformation phenomenon of oligonucleotide-encapsulated silver nanoclusters (AgNCs) was demonstrated, in which green-emissive AgNCs effectively transformed to red-emissive AgNCs when placed in close proximity to a special DNA fragment (denoted as convertor here). Taking advantage of a catalyzed-hairpin-assembly (CHA) amplification strategy, we rationally and compatibly engineered a simple and sensitive AgNC-based fluorescent signal amplification strategy through the ratiometric catalyzed-assembly (RCA) of green-emissive NanoCluster Beacon (NCB) with a convertor modified DNA hairpin to induce the template transformation circularly. The proposed ratiometric fluorescent biosensing platform based on RCA-amplified NCB (RCA-NCB) emits intense green fluorescence in the absence of target DNA and will undergo consecutively fluorescent signal transformation from green emission to red emission upon exposure to its target DNA. The ratiometric adaptation of the NCB to CHA circuit advances their general usability as biosensing platform with great improvements in detection sensitivity. By measuring the fluorescence intensity ratio of the red emission and green emission, the proposed RCA-NCB platform exhibits sensitive and accurate analytical performance toward Werner Syndrome-relevant gene, the proof-of-concept target in this work. A low detection limit down to the pM level was achieved, which is lower than most of the reported AgNC-based fluorescent DNA biosensors, making the proposed RCA-NCB biosensing strategy appealing in amplifying the ratiometric fluorescent signal for sensitive DNA detection. Moreover, our proposed RCA-NCB platform shows good recovery toward the target DNA in real human serum samples, illustrating their potential promise for clinical and imaging applications in the future.

  19. A ratiometric near-infrared fluorescent probe for hydrazine and its in vivo applications.

    PubMed

    Hu, Chong; Sun, Wen; Cao, Jianfang; Gao, Pan; Wang, Jingyun; Fan, Jiangli; Song, Fengling; Sun, Shiguo; Peng, Xiaojun

    2013-08-02

    Based on modulation of the conjugated polymethine π-electron system of a cyanine dye derivative, a ratiometric near-infared fluorescent probe (Cy7A) for hydrazine (N2H4) has been designed and synthesized. Cy7A can be selectively hydrazinolysized with great changes in its fluorescent excitation/emission profiles, which makes it possible to detect N2H4 in water samples and living cells and, for the first time, visualize N2H4 in living mice.

  20. Ratiometric MRI sensors based on core-shell nanoparticles for quantitative pH imaging.

    PubMed

    Okada, Satoshi; Mizukami, Shin; Sakata, Takao; Matsumura, Yutaka; Yoshioka, Yoshichika; Kikuchi, Kazuya

    2014-05-21

    Ratiometric MRI sensors consist of paramagnetic cores and pH-sensitive polymer shells. The core-shell nanostructure enables the coexistence of two incompatible NMR relaxation properties in one particle. The sensors show pH sensitivity in transverse relaxivity (r2 ), but not in longitudinal relaxivity (r1 ). Quantitative pH imaging is achieved by measuring the r2 /r1 value with a clinical 3 T MRI scanner.

  1. A simple ratiometric and colorimetric chemosensor for the selective detection of fluoride in DMSO buffered solution

    NASA Astrophysics Data System (ADS)

    Niu, Hu; Shu, Qinghai; Jin, Shaohua; Li, Bingjun; Zhu, Jiaping; Li, Lijie; Chen, Shusen

    2016-01-01

    A derivative of squaramide (cyclobuta[b]quinoxaline-1, 2(3H, 8H)-dione) has been synthesized for the ratiometric and colorimetric sensing of F- in aqueous solution in competitive fashion. With F-, probe 1 showed a highly selective naked-eye detectable color change along with a characteristic UV-Vis absorbance over other tested ions, which probably originates from the deprotonation occurred between 1 and F-, as proved by the 1H NMR titration experiments and DFT calculations.

  2. Errors in confocal fluorescence ratiometric imaging microscopy due to chromatic aberration.

    PubMed

    Lin, Yuxiang; Gmitro, Arthur F

    2011-01-01

    Confocal fluorescence ratiometric imaging is an optical technique used to measure a variety of important biological parameters. A small amount of chromatic aberration in the microscope system can introduce a variation in the signal ratio dependent on the fluorophore concentration gradient along the optical axis and lead to bias in the measurement. We present a theoretical model of this effect. Experimental results and simulations clearly demonstrate that this error can be significant and should not be ignored.

  3. Green fluorescent protein variants as ratiometric dual emission pH sensors. 3. Temperature dependence of proton transfer.

    PubMed

    McAnaney, Tim B; Shi, Xinghua; Abbyad, Paul; Jung, Henry; Remington, S James; Boxer, Steven G

    2005-06-21

    In parts 1 and 2 of this series [Hanson, G. T., McAnaney, T. B., Park, E. S., Rendell, M. E. P., Yarbrough, D. K., Chu, S. Y., Xi, L. X., Boxer, S. G., Montrose, M. H., and Remington, S. J. (2002) Biochemistry 41, 15477-15488; McAnaney, T. B., Park, E. S., Hanson, G. T., Remington, S. J., and Boxer, S. G. (2002) Biochemistry 41, 15489-15494], we described the structure, excited-state dynamics, and applications of pH-sensitive, ratiometric dual emission green fluorescent protein (deGFP) variants with fluorescence emission that is modulated between blue (lambda(max) approximately equal 465 nm) and green (lambda(max) approximately equal 515 nm) depending on the pH of the bulk solvent. In this paper, we consider the energetic origin of the dual emission properties of these GFP variants by examining the temperature dependence of the steady-state absorption and fluorescence emission. In most cases, the quantum yield of the green emission decreased as the temperature was lowered, indicating that the excited-state proton transfer (ESPT) which produces the green emitting form is an activated process. The activation energies of ESPT, determined by modeling the quantum yields of both blue and green emissions between 260 and 298 K in the context of a simple photocycle, were found to be larger at low pH than at high pH. These results indicate that the ratiometric dual emission properties of deGFP mutants are due to this pH-sensitive ESPT rate, combined with a modulation of the ground-state neutral and anionic chromophore populations with pH. The time-resolved fluorescence of one of the deGFP mutants was studied in detail. The time-resolved emission spectra of this mutant are the first ultrafast spectra obtained for a GFP. These spectra demonstrate that the rising kinetics for green emission, considered a hallmark of ESPT, is the sum of the contribution from both the neutral and intermediate anionic forms of the chromophore at the probe wavelength and may not be observed in all

  4. Ratiometric fluorescent sensor based on inhibition of resonance for detection of cadmium in aqueous solution and living cells.

    PubMed

    Xue, Lin; Li, Guoping; Liu, Qing; Wang, Huanhuan; Liu, Chun; Ding, Xunlei; He, Shenggui; Jiang, Hua

    2011-04-18

    Although cadmium has been recognized as a highly toxic heavy metal and poses many detrimental effects on human health, the Cd(2+)-uptake and nosogenesis mechanisms are still insufficiently understood, mainly because of the lack of facile analytical methods for monitoring changes in the environmental and intracellular Cd(2+) concentrations with high spatial and temporal reliability. To this end, we present the design, synthesis, and photophysical properties of a cadmium sensor, DQCd1 based on the fluorophore 4-isobutoxy-6-(dimethylamino)-8-methoxyquinaldine (model compound 1). Preliminary investigations indicate that 1 could be protonated under neutral media and yield a resonance process over the quinoline fluorophore. Upon excitation at 405 nm, 1 shows a strong fluorescence emission at 554 nm with a quantum yield of 0.17. Similarly, DQCd1 bears properties comparable to its precursor. It exhibits fluorescence emission at 558 nm (Φ(f) = 0.15) originating from the monocationic species under physiological conditions. Coordination with Cd(2+) causes quenching of the emission at 558 nm and simultaneously yields a significant hypsochromic shift of the emission maximum to 495 nm (Φ(f) = 0.11) due to inhibition of the resonance process. Thus, a single-excitation, dual-emission ratiometric measurement with a large blue shift in emission (Δλ = 63 nm) and remarkable changes in the ratio (F(495 nm)/F(558 nm)) of the emission intensity (R/R(0) up to 15-fold) is established. Moreover, the sensor DQCd1 exhibits very high sensitivity for Cd(2+) (K(d) = 41 pM) and excellent selectivity response for Cd(2+) over other heavy- and transition-metal ions and Na(+), K(+), Mg(2+), and Ca(2+) at the millimolar level. Therefore, DQCd1 can act as a ratiometric fluorescent sensor for Cd(2+) through inhibition of the resonance process. Confocal microscopy and cytotoxicity experiments indicate that DQCd1 is cell-permeable and noncytotoxic under our experimental conditions. It can indeed

  5. An FITC-BODIPY FRET couple: application to selective, ratiometric detection and bioimaging of cysteine.

    PubMed

    Ma, Dong Hee; Kim, Dokyoung; Akisawa, Takuya; Lee, Kyung-Ha; Kim, Kyong-Tai; Ahn, Kyo Han

    2015-04-01

    A novel FRET couple of fluorescein is disclosed, and it was readily constructed by conjugating an amino-BODIPY dye, a new FRET donor, with fluorescein isocyanate. Its potential was demonstrated by a fluorescence sensing system for cysteine, which was prepared by introducing acryloyl groups to the fluorescein moiety. The FRET probe exhibited promising ratiometric response to cysteine with high selectivity and sensitivity in a buffer solution containing acetonitrile at a physiological pH of 7.4, but showed slow reactivity. This slow response was solved by addition of a surfactant, thus allowing ratiometric imaging and determination of the endogenous level of cysteine in cells in HEPES buffer, by confocal fluorescence microscopy. Imaging experiments toward various cells suggested that such aryl acrylate type probes are vulnerable to the ubiquitous esterase activity. For the selected C6 cell line, in which the esterase activity was minimal, the ratiometric quantification of cysteine level was demonstrated. The FRET probe was also applied to determine the level of cysteine in human blood plasma.

  6. Ratiometric fluorescence imaging of cellular polarity: decrease in mitochondrial polarity in cancer cells.

    PubMed

    Jiang, Na; Fan, Jiangli; Xu, Feng; Peng, Xiaojun; Mu, Huiying; Wang, Jingyun; Xiong, Xiaoqing

    2015-02-16

    Mitochondrial polarity strongly influences the intracellular transportation of proteins and interactions between biomacromolecules. The first fluorescent probe capable of the ratiometric imaging of mitochondrial polarity is reported. The probe, termed BOB, has two absorption maxima (λabs = 426 and 561 nm) and two emission maxima--a strong green emission (λem = 467 nm) and a weak red emission (642 nm in methanol)--when excited at 405 nm. However, only the green emission is markedly sensitive to polarity changes, thus providing a ratiometric fluorescence response with a good linear relationship in both extensive and narrow ranges of solution polarity. BOB possesses high specificity to mitochondria (Rr =0.96) that is independent of the mitochondrial membrane potential. The mitochondrial polarity in cancer cells was found to be lower than that of normal cells by ratiometric fluorescence imaging with BOB. The difference in mitochondrial polarity might be used to distinguish cancer cells from normal cells.

  7. Ratiometric Tension Probes for Mapping Receptor Forces and Clustering at Intermembrane Junctions.

    PubMed

    Ma, Victor Pui-Yan; Liu, Yang; Blanchfield, Lori; Su, Hanquan; Evavold, Brian D; Salaita, Khalid

    2016-07-13

    Short-range communication between cells is required for the survival of multicellular organisms. One mechanism of chemical signaling between adjacent cells employs surface displayed ligands and receptors that only bind when two cells make physical contact. Ligand-receptor complexes that form at the cell-cell junction and physically bridge two cells likely experience mechanical forces. A fundamental challenge in this area pertains to mapping the mechanical forces experienced by ligand-receptor complexes within such a fluid intermembrane junction. Herein, we describe the development of ratiometric tension probes for direct imaging of receptor tension, clustering, and lateral transport within a model cell-cell junction. These probes employ two fluorescent reporters that quantify both the ligand density and the ligand tension and thus generate a tension signal independent of clustering. As a proof-of-concept, we applied the ratiometric tension probes to map the forces experienced by the T-cell receptor (TCR) during activation and showed the first direct evidence that the TCR-ligand complex experiences sustained pN forces within a fluid membrane junction. We envision that the ratiometric tension probes will be broadly useful for investigating mechanotransduction in juxtacrine signaling pathways.

  8. Rational design of polymeric core shell ratiometric oxygen-sensing nanostructures.

    PubMed

    Byrne, Aisling; Jacobs, Jaco; Burke, Christopher S; Martin, Aaron; Heise, Andreas; Keyes, Tia E

    2017-09-08

    A new approach for the fabrication of luminescent ratiometric sensing nanosensors is described using core-shell nanoparticles in which the probe and reference are spatially separated into the shell and core of the nanostructure respectively. The isolation of the reference in the core of the particle ensures a stable emission reference signal unaffected by the external environment. The core shell structure was prepared by engineering structurally well-defined Ru-conjugated block copolymers which acted as emulsifiers in the miniemulsion polymerisation of BODIPY loaded styrene nanoparticles. The resulting particles are highly stable and show excellent size monodispersity. The nanosensors exhibit dual emission under a single excitation wavelength with a reversible and quantitative ratiometric response to the O2 content in aqueous media. In the presence of a low concentration of CTAB, the particles cross the cell membrane and the particles show negligible cytotoxicity. Such an approach to sensor nanoparticles should be of value across a range of applications where a stable ratiometric signal in diverse environments is required.

  9. SRpHi ratiometric pH biosensors for super-resolution microscopy.

    PubMed

    Richardson, Douglas S; Gregor, Carola; Winter, Franziska R; Urban, Nicolai T; Sahl, Steffen J; Willig, Katrin I; Hell, Stefan W

    2017-09-18

    Fluorescence-based biosensors have become essential tools for modern biology, allowing real-time monitoring of biological processes within living cells. Intracellular fluorescent pH probes comprise one of the most widely used families of biosensors in microscopy. One key application of pH probes has been to monitor the acidification of vesicles during endocytosis, an essential function that aids in cargo sorting and degradation. Prior to the development of super-resolution fluorescence microscopy (nanoscopy), investigation of endosomal dynamics in live cells remained difficult as these structures lie at or below the ~250 nm diffraction limit of light microscopy. Therefore, to aid in investigations of pH dynamics during endocytosis at the nanoscale, we have specifically designed a family of ratiometric endosomal pH probes for use in live-cell STED nanoscopy.Ratiometric fluorescent pH probes are useful tools to monitor acidification of vesicles during endocytosis, but the size of vesicles is below the diffraction limit. Here the authors develop a family of ratiometric pH sensors for use in STED super-resolution microscopy, and optimize their delivery to endosomes.

  10. Label-free ratiometric DNA detection using two kinds of interaction-responsive emission dyes.

    PubMed

    Guo, Yahui; Chen, Qingmin; Qi, Yiting; Xie, Yunfei; Qian, He; Yao, Weirong; Pei, Renjun

    2017-01-15

    A novel ratiometric method with label-free and dual-wavelength signal outputs was developed for DNA detection by employing two kinds of structure-specific dyes that characterising interaction-responsive emission property. The ratiometric platform for the fluorescent detection of DNA was based on target-induced structural transformation from stem-loop structure incorporating split G-quadruplex (SISG) to doubule-strand DNA (dsDNA). The SISG conformation will be disrupted upon binding to the target DNA of perfect complementary sequence, resulting in fluorescence decrease at 610nm as NMM releases from SISG and fluorescence increase at 450nm as DAPI inserts into the dsDNA. The method demonstrated its simplicity in that it saved the trouble of expensive and cumbersome functionalization process compared with reported ratiometric methods, and that the two dyes could be excited at the same excitation wavelength. More intriguingly, the combinatorial employment of the two kinds of structure-selective dyes demonstrated a result of "heterosis", in that this sensor simultaneously inherits the sensitivity of DAPI-based signal and the selectivity of G4-based signal. Besides that, this proposed biosensor has been successfully applied in serum sample for DNA detection, and provided a simple and sensitive method for potential DNA detection in bioanalysis, food analysis and disease diagnostic. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Mapping of the Communication-Mediating Interface in Nonribosomal Peptide Synthetases Using a Genetically Encoded Photocrosslinker Supports an Upside-Down Helix-Hand Motif.

    PubMed

    Dehling, Eva; Volkmann, Gerrit; Matern, Julian C J; Dörner, Wolfgang; Alfermann, Jonas; Diecker, Julia; Mootz, Henning D

    2016-10-23

    Nonribosomal peptide synthetases (NRPSs) are large modular protein templates that assemble bioactive peptides, many of which possess therapeutic importance. Protein-protein interactions between subunits of bacterial NRPSs are essential for proper template formation. The structural basis of the typical subunit interface between epimerization (E) and condensation domains is only poorly understood. Conflicting helix-helix and helix-hand models were previously proposed. Here, the genetically encoded photocrosslinker p-benzoylphenylalanine (BpF) was incorporated into the C-terminal communication-mediating domain (COM) of GrsA. Using the partner elongation module TycB1 to form a dipeptide product, we could correlate the ability to form covalent crosslinks with the functional module interaction. Perturbation of the module interaction with the large side chain of BpF in a scan at 19 positions demonstrated the importance of three hydrophobic residues in an α-helical arrangement. Mapping of covalent crosslinks using tandem mass spectrometry revealed the residues from the interior of the condensation domain as part of the protein interface; a finding not predicted by the helix-helix model. The epimerization domain of GrsA was found to be important for the interaction. Together with multiple sequence analyses and structural modeling, our results suggest an upside-down helix-hand model in which the C-terminal COM-helix is embedded in a hand motif with a hydrophobic core in a reversed orientation compared to a previous proposal. Our results provide a more detailed and the first direct structural understanding of the COM domain interaction and will contribute to successful biocombinatorial engineering attempts in the design of artificial NRPS templates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag.

    PubMed

    Hirabayashi, Ai; Fukunaga, Yuko; Miyazawa, Atsuo

    2014-06-01

    Postsynaptic density-95 (PSD-95) accumulates at excitatory postsynapses and plays important roles in the clustering and anchoring of numerous proteins at the PSD. However, a detailed ultrastructural analysis of clusters exclusively consisting of PSD-95 has never been performed. Here, we employed a genetically encoded tag, three tandem repeats of metallothionein (3MT), to study the structure of PSD-95 clusters in cells by electron tomography and cryo-electron microscopy of vitreous sections. We also performed conventional transmission electron microscopy (TEM). Cultured hippocampal neurons expressing a fusion protein of PSD-95 coupled to 3MT (PDS-95-3MT) were incubated with CdCl2 to result in the formation of Cd-bound PSD-95-3MT. Two types of electron-dense deposits composed of Cd-bound PSD-95-3MT were observed in these cells by TEM, as reported previously. Electron tomography revealed the presence of membrane-shaped structures representing PSD-95 clusters at the PSD and an ellipsoidal structure located in the non-synaptic cytoplasm. By TEM, the PSD-95 clusters appeared to be composed of a number of dense cores. In frozen hydrated sections, these dense cores were also found beneath the postsynaptic membrane. Taken together, our findings suggest that dense cores of PSD-95 aggregate to form the larger clusters present in the PSD and the non-synaptic cytoplasm. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Application of a Genetically Encoded Biosensor for Live Cell Imaging of L-Valine Production in Pyruvate Dehydrogenase Complex-Deficient Corynebacterium glutamicum Strains

    PubMed Central

    Mahr, Regina; Helfrich, Stefan; Nöh, Katharina; Blombach, Bastian; Kohlheyer, Dietrich; Frunzke, Julia

    2014-01-01

    The majority of biotechnologically relevant metabolites do not impart a conspicuous phenotype to the producing cell. Consequently, the analysis of microbial metabolite production is still dominated by bulk techniques, which may obscure significant variation at the single-cell level. In this study, we have applied the recently developed Lrp-biosensor for monitoring of amino acid production in single cells of gradually engineered L-valine producing Corynebacterium glutamicum strains based on the pyruvate dehydrogenase complex-deficient (PDHC) strain C. glutamicum ΔaceE. Online monitoring of the sensor output (eYFP fluorescence) during batch cultivation proved the sensor's suitability for visualizing different production levels. In the following, we conducted live cell imaging studies on C. glutamicum sensor strains using microfluidic chip devices. As expected, the sensor output was higher in microcolonies of high-yield producers in comparison to the basic strain C. glutamicum ΔaceE. Microfluidic cultivation in minimal medium revealed a typical Gaussian distribution of single cell fluorescence during the production phase. Remarkably, low amounts of complex nutrients completely changed the observed phenotypic pattern of all strains, resulting in a phenotypic split of the population. Whereas some cells stopped growing and initiated L-valine production, others continued to grow or showed a delayed transition to production. Depending on the cultivation conditions, a considerable fraction of non-fluorescent cells was observed, suggesting a loss of metabolic activity. These studies demonstrate that genetically encoded biosensors are a valuable tool for monitoring single cell productivity and to study the phenotypic pattern of microbial production strains. PMID:24465669

  14. Imaging of cardiac movement using ratiometric and nonratiometric optical mapping: effects of ischemia and 2, 3-butaneodione monoxime.

    PubMed

    Himel, Herman D; Knisley, Stephen B

    2006-01-01

    Transmembrane voltage-sensitive fluorescent dyes are used to study electrical activity in hearts. Green and red fluorescence emissions from di-4-ANEPPS excited with 488 nm light indicate both transmembrane voltage changes and heart movement. We have previously shown that the ratio, green fluorescence divided by red fluorescence, indicates the transmembrane voltage without effects of movement. Here we examine the feasibility of measuring the movement, which is useful for the study of cardiac function, by subtracting this ratiometric signal from the red or green fluorescence signal. The results of this subtraction show tissue movement and its relative changes during cardiac ischemia and perfusion with an electromechanical uncoupling agent. By incorporating the spatial variations in fluorescence intensity from the heart, tissue movement can be qualitatively mapped to examine relative changes, however, with limited ability to quantify absolute displacement. Since these maps are obtained simultaneously with corresponding transmembrane potentials, the method allows study of spatiotemporal cardiac movement patterns and their relationship to the action potential.

  15. Metal-Enhanced Ratiometric Fluorescence/Naked Eye Bimodal Biosensor for Lead Ions Analysis with Bifunctional Nanocomposite Probes.

    PubMed

    Liang, Linlin; Lan, Feifei; Ge, Shenguang; Yu, Jinghua; Ren, Na; Yan, Mei

    2017-03-21

    A novel metal-enhanced ratiometric fluorescence/naked eye bimodal biosensor based on ZnFe2O4@Au-Ag bifunctional nanocomposite and DNA/CeO2 complex for lead ions (Pb(2+)) has been successfully developed. The nanocomposite probe was composed of a magnetic ZnFe2O4 core and a Au-Ag hollow nanocube shell. Upon bioconjugation, bifunctional magnetic nanocomposites could not only make the probe possess excellent recyclability but also provide an enrichment of "hot spots" for surface enhanced fluorescence detection of Pb(2+) by a metal-enhanced fluorescence effect. Typically, the bifunctional nanocomposites conjugated with double-stranded DNA (included Pb(2+)-specific DNAzyme strand and corresponding substrate strand) to form a Pb(2+) biosensor. Nanoceria as a fluorescence quencher strongly adsorbed DNA. Therefore, the formation of double-stranded DNA brought the labeled nitrogen sulfur doped carbon dots (N,S-CDs) and CeO2 into close proximity, which significantly quenched the fluorescence of N,S-CDs. The presence of Pb(2+) led to the breakage of the DNAzyme strand, resulting in the fluorescence signal of Cy3 decreasing, while the fluorescence intensity of N,S-CDs aggrandized. First, a preliminary test of Pb(2+) was performed by the naked eye. The disengaged DNA/CeO2 complex could result in color change after adding H2O2 because of autocatalysis of CeO2, resulting in real-time visual detection of Pb(2+). If further accurate determination was required, the fluorescence intensity ratio of these two fluorescence indicators was measured at 562 and 424 nm (I562/I424). A good linear correlation exists between the log(I562/I424) and the logarithm of Pb(2+) concentrations ranging from 10(-12) to 3 × 10(-6) M. Remarkably, the detection limit of this ratiometric biosensor was 3 × 10(-13) M, which ascribed to its superior fluorescence enhancement. Interestingly, the developed bifunctional nanocomposite probe manifests good recyclability and selectivity. More importantly, the

  16. Ratiometric fluorescence and mesoporous structured imprinting nanoparticles for rapid and sensitive detection 2,4,6-trinitrophenol.

    PubMed

    Li, Ming; Liu, Haijian; Ren, Xueqin

    2017-03-15

    The present study reports the fabrication of mesoporous-structured ratiometric molecularly imprinted sensors using a combined surface-imprinted and ratiometric fluorescence method. The sensors were subsequently examined in the selective and sensitive determination of 2,4,6-trinitrophenol (TNP). In the preparation of the ratiometric system, the reference dye CdTe quantum dots were embedded in silica core particles via the Stöber method; the functional target sensitive dye AAMBT&SiO2, which was obtained via polymerization of 2-acrylamide-6-methoxybenzothiazole (AAMBT) with allyltriethoxysilane, was embedded in the mesoporous silica shell. In the surface imprinting process, cetyltrimethylammonium bromide was employed to create mesoporous-structured silica to promote quenching of AAMBT by TNP via resonance energy transfer, thereby enhancing the sensitivity of the sensor. Under optimum conditions, the ratiometric fluorescence molecularly imprinted polymer sensors achieved a detection limit of 43nM within 3min. The practical application of the developed sensor in real water samples was successfully demonstrated through analysis of TNP in water samples, achieving satisfactory recoveries of 92-104%. Thus, a convenient and practical method for preparing highly selective and sensitive ratiometric fluorescence sensors is presented herein, providing a prospective method for rapid trace pollutants analysis in complex water samples.

  17. Ratiometric optical temperature sensor using two fluorescent dyes dissolved in an ionic liquid encapsulated by Parylene film.

    PubMed

    Kan, Tetsuo; Aoki, Hironori; Binh-Khiem, Nguyen; Matsumoto, Kiyoshi; Shimoyama, Isao

    2013-03-27

    A temperature sensor that uses temperature-sensitive fluorescent dyes is developed. The droplet sensor has a diameter of 40 µm and uses 1 g/L of Rhodamine B (RhB) and 0.5 g/L of Rhodamine 110 (Rh110), which are fluorescent dyes that are dissolved in an ionic liquid (1-ethyl-3-methylimidazolium ethyl sulfate) to function as temperature indicators. This ionic liquid is encapsulated using vacuum Parylene film deposition (which is known as the Parylene-on-liquid-deposition (PoLD) method). The droplet is sealed by the chemically stable and impermeable Parylene film, which prevents the dye from interacting with the molecules in the solution and keeps the volume and concentration of the fluorescent material fixed. The two fluorescent dyes enable the temperature to be measured ratiometrically such that the droplet sensor can be used in various applications, such as the wireless temperature measurement of microregions. The sensor can measure the temperature of such microregions with an accuracy of 1.9 °C, a precision of 3.7 °C, and a fluorescence intensity change sensitivity of 1.0%/K. The sensor can measure temperatures at different sensor depths in water, ranging from 0 to 850 µm. The droplet sensor is fabricated using microelectromechanical system (MEMS) technology and is highly applicable to lab-on-a-chip devices.

  18. Ratiometric Optical Temperature Sensor Using Two Fluorescent Dyes Dissolved in an Ionic Liquid Encapsulated by Parylene Film

    PubMed Central

    Kan, Tetsuo; Aoki, Hironori; Binh-Khiem, Nguyen; Matsumoto, Kiyoshi; Shimoyama, Isao

    2013-01-01

    A temperature sensor that uses temperature-sensitive fluorescent dyes is developed. The droplet sensor has a diameter of 40 μm and uses 1 g/L of Rhodamine B (RhB) and 0.5 g/L of Rhodamine 110 (Rh110), which are fluorescent dyes that are dissolved in an ionic liquid (1-ethyl-3-methylimidazolium ethyl sulfate) to function as temperature indicators. This ionic liquid is encapsulated using vacuum Parylene film deposition (which is known as the Parylene-on-liquid-deposition (PoLD) method). The droplet is sealed by the chemically stable and impermeable Parylene film, which prevents the dye from interacting with the molecules in the solution and keeps the volume and concentration of the fluorescent material fixed. The two fluorescent dyes enable the temperature to be measured ratiometrically such that the droplet sensor can be used in various applications, such as the wireless temperature measurement of microregions. The sensor can measure the temperature of such microregions with an accuracy of 1.9 °C, a precision of 3.7 °C, and a fluorescence intensity change sensitivity of 1.0%/K. The sensor can measure temperatures at different sensor depths in water, ranging from 0 to 850 μm. The droplet sensor is fabricated using microelectromechanical system (MEMS) technology and is highly applicable to lab-on-a-chip devices. PMID:23535716

  19. Development of a coumarin-furan conjugate as Zn2 + ratiometric fluorescent probe in ethanol-water system

    NASA Astrophysics Data System (ADS)

    Li, Chao-rui; Li, Si-liang; Yang, Zheng-yin

    2017-03-01

    In this study, a novel coumarin-derived compound bearing the furan moiety called 7-diethylamino-3-formylcoumarin (2‧-furan formyl) hydrazone (1) has been designed, synthesized and evaluated as a Zn2 + ratiometric fluorescent probe in ethanol-water system. This probe 1 showed good selectivity and high sensitivity towards Zn2 + over other metal ions investigated, and a decrease in fluorescence emission intensity at 511 nm accompanied by an enhancement in fluorescence emission intensity at 520 nm of this probe 1 was observed in the presence of Zn2 + in ethanol-water (V : V = 9 : 1) solution, which provided ratiometric fluorescence detection of Zn2 +. Additionally, the ratiometric fluorescence response of 1 to Zn2 + was nearly completed within 0.5 min, which suggested that this probe 1 could be utilized for sensing and monitoring Zn2 + in environmental and biological systems for real-time detection.

  20. One-step synthesis of nitrogen-doped carbon nanodots for ratiometric pH sensing by femtosecond laser ablation method

    NASA Astrophysics Data System (ADS)

    Xu, Huanhuan; Yan, Lihe; Nguyen, Vanthan; Yu, Yang; Xu, Yanmin

    2017-08-01

    Nitrogen-doped carbon nanodots (CDs) are synthesized by one-step femtosecond laser ablation of graphite powder in aminotoluene at room temperature. The as-prepared CDs have the average diameter of 2.87 nm and possess an excitation-independent emission covering nearly the whole visible light region at a single excitation wavelength. The X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) analysis indicate that there are a huge number of multiple oxygen groups and amine groups on the surface of the CDs. As their different fluorescence peaks originated from different emission surface groups on the nanodots show different pH dependence, these CDs can be used for ratiometric pH sensing.

  1. Water-soluble colorimetric and ratiometric fluorescent probe for selective imaging of palladium species in living cells.

    PubMed

    Liu, Wei; Jiang, Jie; Chen, Chunyang; Tang, Xiaoliang; Shi, Jinmin; Zhang, Peng; Zhang, Kaiming; Li, Zhiqi; Dou, Wei; Yang, Lizi; Liu, Weisheng

    2014-12-01

    A novel water-soluble colorimetric and ratiometric fluorescent probe was synthesized and applied to imaging palladium species under physiological conditions in phosphate buffered saline (PBS) containing less than 1% organic cosolvent without adding any additional reagents. Based on palladium triggered terminal propargyl ethers cleavage reaction, the probe exhibited a high selectivity and sensitivity for palladium species of all the typical oxidation states (0, +2, +4), with a low detection limit (25 nM, 2.7 μg/L) and an obvious color change. Furthermore, the probe was successfully used for ratiometric fluorescence imaging of palladium in living cells.

  2. A new fluorescent probe for colorimetric and ratiometric detection of sulfur dioxide derivatives in liver cancer cells

    PubMed Central

    Li, Dong-Peng; Wang, Zhao-Yang; Cui, Jie; Wang, Xin; Miao, Jun-Ying; Zhao, Bao-Xiang

    2017-01-01

    A new ratiometric fluorescent probe was constructed with hemicyanine and 7-nitrobenzofurazan for detection of sulfur dioxide derivatives (HSO3−/SO32−). The ratiometric response mode could be attributed to the efficient FRET (Förster resonance energy transfer) platform. The probe exbihited some desirable properties including fast response (within 2 minutes), good selectivity and high sensitivity. Moreover, the probe could detect endogenous HSO3− in liver cancer cells rather than normal liver cells, implying the diagnosal potential of the probe. PMID:28349998

  3. A Three-Photon Active Organic Fluorophore for Deep Tissue Ratiometric Imaging of Intracellular Divalent Zinc.

    PubMed

    Philips, Divya Susan; Sreejith, Sivaramapanicker; He, Tingchao; Menon, Nishanth Venugopal; Anees, Palapuravan; Mathew, Jomon; Sajikumar, Sreedharan; Kang, Yuejun; Stuparu, Mihaiela Corina; Sun, Handong; Zhao, Yanli; Ajayaghosh, Ayyappanpillai

    2016-05-20

    Deep tissue bioimaging with three-photon (3P) excitation using near-infrared (NIR) light in the second IR window (1.0-1.4 μm) could provide high resolution images with an improved signal-to-noise ratio. Herein, we report a photostable and nontoxic 3P excitable donor-π-acceptor system (GMP) having 3P cross-section (σ3 ) of 1.78×10(-80)  cm(6)  s(2)  photon(-2) and action cross-section (σ3 η3 ) of 2.31×10(-81)  cm(6)  s(2)  photon(-2) , which provides ratiometric fluorescence response with divalent zinc ions in aqueous conditions. The probe signals the Zn(2+) binding at 530 and 600 nm, respectively, upon 1150 nm excitation with enhanced σ3 of 1.85×10(-80)  cm(6)  s(2)  photon(-2) and σ3 η3 of 3.33×10(-81)  cm(6)  s(2)  photon(-2) . The application of this probe is demonstrated for ratiometric 3P imaging of Zn(2+) in vitro using HuH-7 cell lines. Furthermore, the Zn(2+) concentration in rat hippocampal slices was imaged at 1150 nm excitation after incubation with GMP, illustrating its potential as a 3P ratiometric probe for deep tissue Zn(2+) ion imaging.

  4. A cationic fluorescent polymeric thermometer for the ratiometric sensing of intracellular temperature.

    PubMed

    Uchiyama, Seiichi; Tsuji, Toshikazu; Ikado, Kumiko; Yoshida, Aruto; Kawamoto, Kyoko; Hayashi, Teruyuki; Inada, Noriko

    2015-07-07

    We developed new cationic fluorescent polymeric thermometers containing both benzothiadiazole and BODIPY units as an environment-sensitive fluorophore and as a reference fluorophore, respectively. The temperature-dependent fluorescence spectra of the thermometers enabled us to perform highly sensitive and practical ratiometric temperature sensing inside living mammalian cells. Intracellular temperatures of non-adherent MOLT-4 (human acute lymphoblastic leukaemia) and adherent HEK293T (human embryonic kidney) cells could be monitored with high temperature resolutions (0.01-1.0 °C) using the new cationic fluorescent polymeric thermometer.

  5. A Nanocrystal-based Ratiometric pH Sensor for Natural pH Ranges

    PubMed Central

    Somers, Rebecca C.; Lanning, Ryan M.; Snee, Preston T.; Greytak, Andrew B.; Jain, Rakesh K.

    2014-01-01

    Summary A ratiometric fluorescent pH sensor based on CdSe/CdZnS nanocrystal quantum dots (NCs) has been designed for biological pH ranges. The construct is formed from the conjugation of a pH dye (SNARF) to NCs coated with a poly(amido amine) (PAMAM) dendrimer. The sensor exhibits a well–resolved ratio response at pH values between 6 and 8 under linear or two–photon excitation, and in the presence of a 4% bovine serum albumin (BSA) solution. PMID:26413260

  6. Small quinolinium-based enzymatic probes via blue-to-red ratiometric fluorescence.

    PubMed

    Wang, Pan; Du, Jiajun; Liu, Huijing; Bi, Guoqiang; Zhang, Guoqing

    2016-02-21

    A small fluorescence ratiometric probe consisting of a single dye species, N-methyl-6-hydroxyquinolinium (MHQ), and coupled enzymatic substrates, exhibits a dramatic colour change (deep blue to red) and possesses a huge response ratio (over 2000 fold) upon specific recognition of target enzymes. Such dramatic responses are attributed to the excited-state proton transfer processes of MHQ molecules in water. Here the detection of β-galactosidase and porcine pancreatic lipase is successfully demonstrated and this class of molecules has the potential to be developed as a "naked-eye" probe in vitro.

  7. Latent pH-responsive ratiometric fluorescent cluster based on self-assembled photoactivated SNARF derivatives

    PubMed Central

    Nakata, Eiji; Yukimachi, Yoshihiro; Uto, Yoshihiro; Hori, Hitoshi; Morii, Takashi

    2016-01-01

    Abstract We have developed a self-assembled fluorescent cluster comprising a seminaphthorhodafluor (SNARF) derivative protected by a photoremovable o-nitrobenzyl group. Prior to UV irradiation, a colorless and nonfluorescent cluster was spontaneously assembled in aqueous solution. After UV irradiation, the self-assembled cluster remained intact and showed a large enhancement in pH-responsive fluorescence. The unique pH responsive fluorescent cluster could be used as a dual-emissive ratiometric fluorescent pH probe not only in the test tube but also in HeLa cell cultures. PMID:27877893

  8. A Sensitive Ratiometric Fluorescent Sensor for Zinc(II) with High Selectivity

    PubMed Central

    Lv, Yuanyuan; Cao, Mingda; Li, Jiakai; Wang, Junbo

    2013-01-01

    A new fluorescent Zn2+ chemosensor (P1) based on a functionalized porphyrin was synthesized and characterized. P1 displayed dramatic ratiometric variations in absorption and fluorescent emission spectra upon exposure to Zn2+ due to the formation of a 1:1 Zn2+/P1 complex. The sensor also exhibited high selectivity and sensitivity toward Zn2+ over other common metal ions in the physiological pH range with a detection limit of 1.8 μM. The sensor showed fast response times and excellent reproducibility, thus confirming its potential applicability as a fluorescent sensor for Zn2+ sensing. PMID:23467028

  9. A Nanocrystal-based Ratiometric pH Sensor for Natural pH Ranges.

    PubMed

    Somers, Rebecca C; Lanning, Ryan M; Snee, Preston T; Greytak, Andrew B; Jain, Rakesh K; Bawendi, Moungi G; Nocera, Daniel G

    A ratiometric fluorescent pH sensor based on CdSe/CdZnS nanocrystal quantum dots (NCs) has been designed for biological pH ranges. The construct is formed from the conjugation of a pH dye (SNARF) to NCs coated with a poly(amido amine) (PAMAM) dendrimer. The sensor exhibits a well-resolved ratio response at pH values between 6 and 8 under linear or two-photon excitation, and in the presence of a 4% bovine serum albumin (BSA) solution.

  10. Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients

    NASA Astrophysics Data System (ADS)

    Castelló Serrano, Iván; Stoica, Georgiana; Matas Adams, Alba; Palomares, Emilio

    2014-10-01

    We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for

  11. Terbium(III)/gold nanocluster conjugates: the development of a novel ratiometric fluorescent probe for mercury(II) and a paper-based visual sensor.

    PubMed

    Qi, Yan-Xia; Zhang, Min; Zhu, Anwei; Shi, Guoyue

    2015-08-21

    In this work, a novel ratiometric fluorescent probe was developed for rapid, highly accurate, sensitive and selective detection of mercury(II) (Hg(2+)) based on terbium(III)/gold nanocluster conjugates (Tb(3+)/BSA-AuNCs), in which bovine serum albumin capped gold nanoclusters (BSA-AuNCs) acted as the signal indicator and terbium(III) (Tb(3+)) was used as the build-in reference. Our proposed ratiometric fluorescent probe exhibited unique specificity toward Hg(2+) against other common environmentally and biologically important metal ions, and had high accuracy and sensitivity with a low detection limit of 1 nM. In addition, our proposed probe was effectively employed to detect Hg(2+) in the biological samples from the artificial Hg(2+)-infected rats. More significantly, an appealing paper-based visual sensor for Hg(2+) was designed by using filter paper embedded with Tb(3+)/BSA-AuNC conjugates, and we have further demonstrated its feasibility for facile fluorescent sensing of Hg(2+) in a visual format, in which only a handheld UV lamp is used. In the presence of Hg(2+), the paper-based visual sensor, illuminated by a handheld UV lamp, would undergo a distinct fluorescence color change from red to green, which can be readily observed with naked eyes even in trace Hg(2+) concentrations. The Tb(3+)/BSA-AuNC-derived paper-based visual sensor is cost-effective, portable, disposable and easy-to-use. This work unveiled a facile approach for accurate, sensitive and selective measuring of Hg(2+) with self-calibration.

  12. Ratiometric Matryoshka biosensors from a nested cassette of green- and orange-emitting fluorescent proteins.

    PubMed

    Ast, Cindy; Foret, Jessica; Oltrogge, Luke M; De Michele, Roberto; Kleist, Thomas J; Ho, Cheng-Hsun; Frommer, Wolf B

    2017-09-05

    Sensitivity, dynamic and detection range as well as exclusion of expression and instrumental artifacts are critical for the quantitation of data obtained with fluorescent protein (FP)-based biosensors in vivo. Current biosensors designs are, in general, unable to simultaneously meet all these criteria. Here, we describe a generalizable platform to create dual-FP biosensors with large dynamic ranges by employing a single FP-cassette, named GO-(Green-Orange) Matryoshka. The cassette nests a stable reference FP (large Stokes shift LSSmOrange) within a reporter FP (circularly permuted green FP). GO- Matryoshka yields green and orange fluorescence upon blue excitation. As proof of concept, we converted existing, single-emission biosensors into a series of ratiometric calcium sensors (MatryoshCaMP6s) and ammonium transport activity sensors (AmTryoshka1;3). We additionally identified the internal acid-base equilibrium as a key determinant of the GCaMP dynamic range. Matryoshka technology promises flexibility in the design of a wide spectrum of ratiometric biosensors and expanded in vivo applications.Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.

  13. Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis.

    PubMed

    Kumar, Srividya; Verma, Taru; Mukherjee, Ria; Ariese, Freek; Somasundaram, Kumaravel; Umapathy, Siva

    2016-04-07

    Biomolecular structure elucidation is one of the major techniques for studying the basic processes of life. These processes get modulated, hindered or altered due to various causes like diseases, which is why biomolecular analysis and imaging play an important role in diagnosis, treatment prognosis and monitoring. Vibrational spectroscopy (IR and Raman), which is a molecular bond specific technique, can assist the researcher in chemical structure interpretation. Based on the combination with microscopy, vibrational microspectroscopy is currently emerging as an important tool for biomedical research, with a spatial resolution at the cellular and sub-cellular level. These techniques offer various advantages, enabling label-free, biomolecular fingerprinting in the native state. However, the complexity involved in deciphering the required information from a spectrum hampered their entry into the clinic. Today with the advent of automated algorithms, vibrational microspectroscopy excels in the field of spectropathology. However, researchers should be aware of how quantification based on absolute band intensities may be affected by instrumental parameters, sample thickness, water content, substrate backgrounds and other possible artefacts. In this review these practical issues and their effects on the quantification of biomolecules will be discussed in detail. In many cases ratiometric analysis can help to circumvent these problems and enable the quantitative study of biological samples, including ratiometric imaging in 1D, 2D and 3D. We provide an extensive overview from the recent scientific literature on IR and Raman band ratios used for studying biological systems and for disease diagnosis and treatment prognosis.

  14. Near-infrared-light mediated ratiometric luminescent sensor for multimode visualized assays of explosives.

    PubMed

    Hu, Xiaoxia; Wei, Ting; Wang, Jie; Liu, Zi-En; Li, Xinyang; Zhang, Binhao; Li, Zhihao; Li, Lele; Yuan, Quan

    2014-10-21

    The development of a portable and easy-to-use device for the detection of explosives with high sensitivity and selectivity is in high demand for homeland security and public safety. In this study, we demonstrate miniaturized devices depending on the upconversion ratiometric luminescent probe for point-of-care (POC) assay of explosives with the naked-eye. When the PEI-coated upconversion nanoparticles (UCNPs) selectively bonded to 2,4,6-trinitrotoluene (TNT) explosives by the formation of Meisenheimer complex, the formed of UCNP-Meisenheimer complexes show turned visible multicolor upconversion luminescence (UCL) on account of TNT-modulating Förster resonance energy transfer process under near-infrared excitation. With UCL emission at 808 nm as internal standard and ratiometric UCL at 477 nm to that at 808 nm (I477/I808) as output signal, the probe can simultaneously meet the accuracy for TNT explosives quantitative analysis. In addition, this easy-to-use visual technique provides a powerful tool for convenient POC assay of rapid explosives identification.

  15. Low-cost optical lifetime assisted ratiometric glutamine sensor based on glutamine binding protein.

    PubMed

    Lam, Hung; Kostov, Yordan; Rao, Govind; Tolosa, Leah

    2008-12-01

    Here we report a reagentless fluorescence sensing technique for glutamine in the submicromolar range based on the glutamine binding protein (QBP). The S179C mutant is labeled with the short-lived acrylodan (lifetime<5ns) and the long-lived tris(dibenzoylmethane) mono(5-amino-1,10-phenanthroline)europium(III) (lifetime > 300 micros) at the -SH and the N-terminal positions, respectively. In the presence of glutamine the fluorescence of acrylodan is quenched, while the fluorescence of europium complex remains constant. In this report we describe an innovative technique, the so called lifetime assisted ratiometric sensing to discriminate the two fluorescence signals using minimal optics and power requirements. This method exploits the large difference between the fluorescence lifetimes of the two fluorophores to isolate the individual fluorescence from each other by alternating the modulation frequency of the excitation light between 300 Hz and 10 kHz. The result is a ratiometric optical method that does not require expensive and highly attenuating band pass filters for each of the dyes, but only one long pass filter for both. Thus, the signal to noise ratio is enhanced, and at the same time, the optical setup is simplified. The end product is a simple sensing device suitable for low-cost applications such as point-of-care diagnostics or in-the-field analysis.

  16. A Two-Photon Ratiometric Fluorescent Probe for Imaging Carboxylesterase 2 in Living Cells and Tissues.

    PubMed

    Jin, Qiang; Feng, Lei; Wang, Dan-Dan; Dai, Zi-Ru; Wang, Ping; Zou, Li-Wei; Liu, Zhi-Hong; Wang, Jia-Yue; Yu, Yang; Ge, Guang-Bo; Cui, Jing-Nan; Yang, Ling

    2015-12-30

    In this study, a two-photon ratiometric fluorescent probe NCEN has been designed and developed for highly selective and sensitive sensing of human carboxylesterase 2 (hCE2) based on the catalytic properties and substrate preference of hCE2. Upon addition of hCE2, the probe could be readily hydrolyzed to release 4-amino-1,8-naphthalimide (NAH), which brings remarkable red-shift in fluorescence (90 nm) spectrum. The newly developed probe exhibits good specificity, ultrahigh sensitivity, and has been successfully applied to determine the real activities of hCE2 in complex biological samples such as cell and tissue preparations. NCEN has also been used for two-photon imaging of intracellular hCE2 in living cells as well as in deep-tissues for the first time, and the results showed that the probe exhibited high ratiometric imaging resolution and deep-tissue imaging depth. All these findings suggested that this probe holds great promise for applications in bioimaging of endogenous hCE2 in living cells and in exploring the biological functions of hCE2 in complex biological systems.

  17. Ratiometric Temperature Imaging Using Environment-Insensitive Luminescence of Mn-Doped Core/Shell Nanocrystals

    PubMed Central

    Park, Yerok; Koo, Chiwan; Chen, Hsiang-Yun; Han, Arum; Son, Dong Hee

    2013-01-01

    We report a ratiometric temperature imaging method based on Mn luminescence from Mn-doped CdS/ZnS nanocrystals (NCs) with controlled doping location, which is designed to exhibit strong temperature dependence of the spectral lineshape while being insensitive to the surrounding chemical environment. Ratiometric thermometry on Mn luminescence spectrum was performed by using Mn-doped CdS/ZnS core/shell NCs that have a large local lattice strain on Mn site, which results in the enhanced temperature dependence of the bandwidth and peak position. Mn luminescence spectral lineshape is highly robust with respect to the change in the polarity, phase and pH of the surrounding medium and aggregation of the NCs, showing great potential in temperature imaging under chemically heterogeneous environment. The temperature sensitivity (ΔIR/IR = 0.5%/K at 293 K, IR = intensity ratio at two different wavelengths) is highly linear in a wide range of temperatures from cryogenic to above-ambient temperatures. We demonstrate the surface temperature imaging of a cyro-cooling device showing the temperature variation of >200 K by imaging the luminescence of the NC film formed by simple spin coating, taking advantage of the environment-insensitive luminescence. PMID:23629731

  18. A Novel Ratiometric Fluorescent Mercury Probe Based on Deprotonation-ICT Mechanism.

    PubMed

    Xie, Puhui; Guo, Fengqi; Yang, Sen; Yao, Denghui; Yang, Guoyu; Xie, Lixia

    2014-03-01

    A new NBD-rhodamine dye (1) was developed as a colorimetric and ratiometric fluorescent chemosensor for Hg(2+) with good selectivity in aqueous ethanol solutions under neutral to basic conditions. Sensor 1 showed absorption at 468 nm and a weak emission at 529 nm (ϕ F  = 0.063) in ethanol/aqueous tris buffer (9:1, v/v) of pH 9.17 solution. Bathochromic shifts in both absorption (492 nm) and fluorescence spectra (569 nm, ϕ F  = 0.129), respectively upon addition of 2 equiv. of Hg(2+) were observed. The ring-opening reaction of the spirolactam form to the corresponding xanthene form was not found. The interaction of Hg(2+) with chemosensor 1 resulted in the deprotonation of the secondary amine conjugated to the NBD component so that the electron-donating ability of the N atom was enhanced. Deprotonation-ICT mechanism of secondary amines was suggested for the ratiometric fluorescent chemosensing for Hg(2+).

  19. A new ditopic ratiometric receptor for detecting zinc and fluoride ions in living cells.

    PubMed

    Li, Ya-Ping; Zhao, Qiang; Yang, Hua-Rong; Liu, Sui-Jun; Liu, Xiu-Ming; Zhang, Ying-Hui; Hu, Tong-Liang; Chen, Jia-Tong; Chang, Ze; Bu, Xian-He

    2013-09-21

    The synthesis, characterization and ion binding properties of a new ditopic ratiometric receptor (1), based on 2-(4,5-dihydro-1H-imidazol-2-yl)phenol and crown ether moieties, have been described. The ditopic ratiometric receptor has been studied in sensing both F(-) and Zn(2+) ions, exhibiting different fluorescent colour changes from cyan green to blue/black observable by the naked eye under UV-light. The addition of Zn(2+) to the solution of 1 induced the formation of a 2 : 2 ligand-metal complex 1-Zn(2+), which displays a remarkable blue shift of the emission maxima of 1 from 455 nm to 400 nm due to the inhibition of excited-state intramolecular proton transfer (ESIPT) mechanism. The sensing processes were monitored by fluorescence/absorption titrations, and further confirmed by Job's plot and (1)H NMR titrations. The crystal structure of 1-Zn(2+) reveals that 1 binds Zn(2+) in four-coordinated modes. Furthermore, 1 is cell permeable and may be applied to detect trace Zn(2+) and F(-) during the development of a living organism.

  20. Design and biosensing of Mg²⁺-dependent DNAzyme-triggered ratiometric electrochemiluminescence.

    PubMed

    Cheng, Yan; Huang, Yin; Lei, Jianping; Zhang, Lei; Ju, Huangxian

    2014-05-20

    A dual-potential ratiometric electrochemiluminescence (ECL) sensing approach based on Mg(2+)-dependent DNAzyme-regulated ECL signals of luminol and CdS quantum dots (QDs) is designed. The system consists of DNAzyme strand functionalized QDs as capture probes and cathode ECL emitters, luminol-reduced gold nanoparticles (Au@luminol) as anode ECL emitters, and a Mg(2+) substrate strand modified with a cyanine dye (Cy5) fluorophore as the quencher. In the absence of Mg(2+) ions, the cathode ECL of the QDs is quenched by electrochemiluminescence resonance energy transfer between CdS QDs and Cy5 molecule, while the anode ECL from Au@luminol is introduced into the system. On the other hand, in the presence of Mg(2+) ions, the DNAzyme cleaves the substrate strand, and then releases the Cy5 and Au@luminol, which results in the recovery of the cathode ECL of the QDs and the decrease of the anode ECL simultaneously. On the basis of the ratio of ECL intensities at two excitation potentials, this approach was demonstrated to yield a linear calibration range from 10 to 10,000 μM Mg(2+) before it was applied to Mg(2+) detection in Hela cell extract. DNAzyme-triggered ratiometric ECL strategy with potential resolution would provide a reliable and sensitive method in biosensing and clinical diagnosis.

  1. A nanoparticle-based ratiometric and self-calibrated fluorescent thermometer for single living cells.

    PubMed

    Takei, Yoshiaki; Arai, Satoshi; Murata, Atsushi; Takabayashi, Masao; Oyama, Kotaro; Ishiwata, Shin'ichi; Takeoka, Shinji; Suzuki, Madoka

    2014-01-28

    The homeostasis of body temperature and energy balance is one of the major principles in biology. Nanoscale thermometry of aqueous solutions is a challenging but crucial technique to understand the molecular basis of this essential process. Here, we developed a ratiometric nanothermometer (RNT) for intracellular temperature measurement in real time. Both the thermosensitive fluorophore, β-diketonate chelate europium(III) thenoyltrifluoroacetonate, and the thermoinsensitive fluorophore, rhodamine 101, which was used as a self-reference, are embedded in a polymeric particle that protects the fluorophores from intracellular conditions. The ratiometric measurement of single RNT spots is independent of the displacement of the RNT along the z-axis. The temperature is therefore determined at the location of each RNT under an optical microscope regardless of the dynamic movement of living cells. As a demonstration of the spot-by-spot intracellular thermometry, we successfully followed the temperature change in individual RNT spots in a single cell together with the Ca(2+) burst induced by the Ca(2+) ionophore ionomycin. The temperature increases differently among different spots, implying heterogeneous heat production in the cell. We then show that, in some spots, the temperature gradually decreases, while in others it remains high. The average temperature elevation within a cell is positively correlated to the increase in Ca(2+), suggesting that the activity and/or number of heat sources are dependent on the Ca(2+) concentration.

  2. A ratiometric fluorescent probe for oxalate based on alkyne-conjugated carboxamidoquinolines in aqueous solution and imaging in living cells.

    PubMed

    He, Chunsheng; Qian, Xuhong; Xu, Yufang; Yang, Chunmei; Yin, Liyan; Zhu, Weiping

    2011-02-07

    A novel ratiometric fluorescent probe for oxalic acid was designed and synthesized, based on the zinc-containing [DAQZ@2Zn(2+)] complex. It shows highly selective "on-off" fluorescence changes with a more than 20 nm blue shift in wavelength for oxalic acids in aqueous solution. Moreover, it can fluorescently respond to oxalic acid in living cells.

  3. Rapid and ratiometric detection of hypochlorite with real application in tap water: molecules to low cost devices (TLC sticks).

    PubMed

    Goswami, Shyamaprosad; Manna, Abhishek; Paul, Sima; Quah, Ching Kheng; Fun, Hoong-Kun

    2013-12-25

    We have designed a chemodosimeter DPNO (weak fluorescence) which can be oxidized to HPNO (strong blue fluorescence) by OCl(-) with high selectivity and sensitivity in a ratiometric approach with a noticeably lower detection limit. The sensor could be useful for the detection of hypochlorites in tap water.

  4. A ratiometric two-photon probe for Ca(2+) in live tissues and its application to spinal cord injury model.

    PubMed

    Kim, Hyung Joong; Lim, Chang Su; Lee, Hyo Won; Lee, Hye Sue; Um, Yun Ju; Kumar, Hemant; Han, Inbo; Kim, Hwan Myung

    2017-10-01

    Ratiometric imaging with a small-molecule probe is important for the in-situ quantitative analysis of chemical events. We developed a ratiometric two-photon fluorescent probe (SCa1-IREF) derived from dual dyes with different Stokes shifts. This probe has two identical windows: a Ca(2+)-sensing window and an internal reference window, with eliminated FRET interference. SCa1-IREF shows a marked change in the ratio upon response with Ca(2+), significant two-photon brightness, considerable selectivity for Ca(2+), and cell loading ability with low cytotoxicity. The ratiometric two-photon microscopy images revealed that this probe could directly and quantitatively estimate Ca(2+) in live neurons and various tissues including rat spinal cord tissue. The studies of spinal cord injury model revealed that the Ca(2+) level was significantly affected by elapsed time after injury. These results will provide useful applications for in-situ [Ca(2+)]i imaging and for the development of effective ratiometric probes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. A ratiometric fluorescent nanoprobe based on terbium functionalized carbon dots for highly sensitive detection of an anthrax biomarker.

    PubMed

    Chen, Hao; Xie, Yujie; Kirillov, Alexander M; Liu, Liangliang; Yu, Minghui; Liu, Weisheng; Tang, Yu

    2015-03-25

    A ratiometric fluorescent nanoprobe based on terbium functionalized carbon dots (CDs) was designed to detect dipicolinic acid (DPA) as an anthrax biomarker with high selectivity and sensitivity. CDs were generated by one-step synthesis using an ethylenediaminetetraacetic acid precursor, and served as a scaffold for coordination with Tb(3+) and a fluorescence reference.

  6. A ratiometric fluorescent chemosensor for selective and visual detection of phosgene in solutions and in the gas phase.

    PubMed

    Wang, Shao-Lin; Zhong, Lin; Song, Qin-Hua

    2017-01-26

    A ratiometric fluorescent chemosensor, Phos-1, was constructed with 4,5-diaminonaphthalimide as a fluorophore for selective and visual detection of phosgene. The sensing mechanism was demonstrated to be the phosgene molecule acylating both amine groups of Phos-1. A test paper with Phos-1 was fabricated for facile, selective and visual detection of phosgene gas.

  7. Molecular engineering of a TBET-based two-photon fluorescent probe for ratiometric imaging of living cells and tissues.

    PubMed

    Zhou, Liyi; Zhang, Xiaobing; Wang, Qianqian; Lv, Yifan; Mao, Guojiang; Luo, Aili; Wu, Yongxiang; Wu, Yuan; Zhang, Jing; Tan, Weihong

    2014-07-16

    In contrast to one-photon microscopy, two-photon probe-based fluorescent imaging can provide improved three-dimensional spatial localization and increased imaging depth. Consequently, it has become one of the most attractive techniques for studying biological events in living cells and tissues. However, the quantitation of these probes is primarily based on single-emission intensity change, which tends to be affected by a variety of environmental factors. Ratiometric probes, on the other hand, can eliminate these interferences by the built-in correction of the dual emission bands, resulting in a more favorable system for imaging living cells and tissues. Herein, for the first time, we adopted a through-bond energy transfer (TBET) strategy to design and synthesize a small molecular ratiometric two-photon fluorescent probe for imaging living cells and tissues in real time. Specifically, a two-photon fluorophore (D-π-A-structured naphthalene derivative) and a rhodamine B fluorophore are directly connected by electronically conjugated bond to form a TBET probe, or Np-Rh, which shows a target-modulated ratiometric two-photon fluorescence response with highly efficient energy transfer (93.7%) and two well-resolved emission peaks separated by 100 nm. This novel probe was then applied for two-photon imaging of living cells and tissues and showed high ratiometric imaging resolution and deep-tissue imaging depth of 180 μm, thus demonstrating its practical application in biological systems.

  8. A water-soluble two-photon ratiometric triarylboron probe with nucleolar targeting by preferential RNA binding.

    PubMed

    Liu, Jun; Zhang, Shilu; Zhang, Chenghua; Dong, Jun; Shen, Chengyi; Zhu, Jiang; Xu, Huajun; Fu, Mingkai; Yang, Guoqiang; Zhang, Xiaoming

    2017-10-06

    By functionalizing triarylboron with cyclen, we developed a two-photon fluorescence probe, TAB-2, which can selectively bind RNA with a ratiometric readout. We tested TAB-2 in NIH/3T3 fibroblast cells, and demonstrated its capability in visualizing nucleoli and analyzing microenvironment polarity by two-photon and fluorescence-lifetime imaging microscopy.

  9. A Ratiometric Sensor Using Single Chirality Near-Infrared Fluorescent Carbon Nanotubes: Application to In Vivo Monitoring.

    PubMed

    Giraldo, Juan P; Landry, Markita P; Kwak, Seon-Yeong; Jain, Rishabh M; Wong, Min Hao; Iverson, Nicole M; Ben-Naim, Micha; Strano, Michael S

    2015-08-26

    Advances in the separation and functionalization of single walled carbon nanotubes (SWCNT) by their electronic type have enabled the development of ratiometric fluorescent SWCNT sensors for the first time. Herein, single chirality SWCNT are independently functionalized to recognize either nitric oxide (NO), hydrogen peroxide (H(2)O(2)), or no analyte (remaining invariant) to create optical sensor responses from the ratio of distinct emission peaks. This ratiometric approach provides a measure of analyte concentration, invariant to the absolute intensity emitted from the sensors and hence, more stable to external noise and detection geometry. Two distinct ratiometric sensors are demonstrated: one version for H(2)O(2), the other for NO, each using 7,6 emission, and each containing an invariant 6,5 emission wavelength. To functionalize these sensors from SWCNT isolated from the gel separation technique, a method for rapid and efficient coating exchange of single chirality sodium dodecyl sulfate-SWCNT is introduced. As a proof of concept, spatial and temporal patterns of the ratio sensor response to H(2)O(2) and, separately, NO, are monitored in leaves of living plants in real time. This ratiometric optical sensing platform can enable the detection of trace analytes in complex environments such as strongly scattering media and biological tissues.

  10. A ratiometric nanosensor based on conjugated polyelectrolyte-stabilized AgNPs for ultrasensitive fluorescent and colorimetric sensing of melamine.

    PubMed

    Zhu, Xixi; Xiao, Yi; Jiang, Xiaoying; Li, Jiahui; Qin, Hongling; Huang, Hongmei; Zhang, Youyu; He, Xiaoxiao; Wang, Kemin

    2016-05-01

    A new ratiometric nanosensor is developed for selective and ultrasensitive detection of melamine based on conjugated polyelectrolyte (CPE)-stabilized silver nanoparticles (P1-AgNPs) by perfectly combining the advantages of CPE and AgNPs. P1 featuring a π-delocalized backbone bearing pyridinyl groups can act as an excellent dual-emission fluorescent probe as well as a polymer localizer for AgNPs. In the presence of melamine, the fluorescence intensity at 386nm increases owing to the turn-on of the fluorescence of P1, whereas FL intensity at 488nm decreases due to the melamine-induced aggregation and subsequent aggregation-enhanced emission quenching of P1-AgNPs, therefore leading to the ratiometric fluorescent sensing of analyte. Moreover, analyte-induced aggregation of P1-AgNPs also allows the ratiometric colorimetric measurement of melamine. Under the optimum conditions, this facile ratiometric nanosensor favors the fluorescent and colorimetric determination of melamine in liquid milk products with the detection limit as low as 0.1 and 0.45nM, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Through bond energy transfer: a convenient and universal strategy toward efficient ratiometric fluorescent probe for bioimaging applications.

    PubMed

    Gong, Yi-Jun; Zhang, Xiao-Bing; Zhang, Cui-Cui; Luo, Ai-Li; Fu, Ting; Tan, Weihong; Shen, Guo-Li; Yu, Ru-Qin

    2012-12-18

    Fluorescence resonance energy transfer (FRET) strategy has been widely applied in designing ratiometric probes for bioimaging applications. Unfortunately, for FRET systems, sufficiently large spectral overlap is necessary between the donor emission and the acceptor absorption, which would limit the resolution of double-channel images. The through-bond energy transfer (TBET) system does not need spectral overlap between donor and acceptor and could afford large wavelength difference between the two emissions with improved imaging resolution and higher energy transfer efficiency than that of the classical FRET system. It seems to be more favorable for designing ratiometric probes for bioimaging applications. In this paper, we have designed and synthesized a coumarin-rhodamine (CR) TBET system and demonstrated that TBET is a convenient strategy to design an efficient ratiometric fluorescent bioimaging probe for metal ions. Such TBET strategy is also universal, since no spectral overlap between the donor and the acceptor is necessary, and many more dye pairs than that of FRET could be chosen for probe design. As a proof-of-concept, Hg(2+) was chosen as a model metal ion. By combining TBET strategy with dual-switch design, the proposed sensing platform shows two well-separated emission peaks with a wavelength difference of 110 nm, high energy transfer efficiency, and a large signal-to-background ratio, which affords a high sensitivity for the probe with a detection limit of 7 nM for Hg(2+). Moreover, by employing an Hg(2+)-promoted desulfurization reaction as recognition unit, the probe also shows a high selectivity to Hg(2+). All these unique features make it particularly favorable for ratiometric Hg(2+) sensing and bioimaging applications. It has been preliminarily used for a ratiometric image of Hg(2+) in living cells and practical detection of Hg(2+) in river water samples with satisfying results.

  12. Ratiometric detection of copper ions and alkaline phosphatase activity based on semiconducting polymer dots assembled with rhodamine B hydrazide.

    PubMed

    Sun, Junyong; Mei, Han; Gao, Feng

    2017-05-15

    The rational surface functionalization of semiconducting polymer dots (Pdots) has attracted much attention to extend their applications in fabricating chemo/biosensing platform. In this study, a novel ratiometric fluorescent sensing platform using functionalized Pdots as probes for fluorescence signal transmission has been designed for sensing Cu(Ⅱ) and activity of alkaline phosphatase (ALP) with high selectivity and enhanced sensitivity. The highly fluorescent Pdots were firstly prepared with Poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(1,4-benzo-{2,1',3}-thiadiazole)] (PFBT) via nanoprecipitation method, and then assembled with non-fluorescent rhodamine B hydrazide (RB-hy), which shows special binding activity to Cu(Ⅱ), through adsorption process to obtain functionalized nanohybrids, Pdots@RB-hy. As thus, a FRET donors/acceptors pair, in which PFBT Pdots act as energy donors while RB-hy-Cu(II) complexes act as energy acceptors were constructed. On the basis of the varies in fluorescence intensities of donors/acceptors in the presence of different amounts of Cu(II), a ratiometric method for sensing Cu(II) has been proposed. The proposed ratiometric Cu(II) sensor shows a good linear detection range from 0.05 to 5μM with a detection limit of 15nM. Furthermore, using the Pdots@RB-hy-Cu(II) system as signal transducer, a ratiometric sensing for alkaline phosphatase (ALP) activity has also been established with pyrophosphate (PPi) as substrates. The constructed ratiometric sensor of ALP activity displays a linear detection range from 0.005 to 15UL(-1) with a detection limit of 0.0018UL(-1). The sensor was further successfully used for ALP activity detection in human serum with satisfactory results.

  13. Quantum dot-DNA aptamer conjugates coupled with capillary electrophoresis: A universal strategy for ratiometric detection of organophosphorus pesticides.

    PubMed

    Tang, Tingting; Deng, Jingjing; Zhang, Min; Shi, Guoyue; Zhou, Tianshu

    2016-01-01

    Based on the highly sensitivity and stable-fluorescence of water-soluble CdTe/CdS core-shell quantum dots (QDs) with broad-specificity DNA aptamers, a novel ratiometric detection strategy was proposed for the sensitive detection of organophosphorus pesticides by capillary electrophoresis with laser-induced fluorescence (CE-LIF). The as-prepared QDs were first conjugated with the amino-modified oligonucleotide (AMO) by amidation reaction, which is partial complementary to the DNA aptamer of organophosphorus pesticides. Then QD-labeled AMO (QD-AMO) was incubated with the DNA aptamer to form QD-AMO-aptamer duplex. When the target organophosphorus pesticides were added, they could specifically bind the DNA aptamer, leading to the cleavage of QD-AMO-aptamer duplex, accompany with the release of QD-AMO. As a result, the ratio of peak height between QD-AMO and QD-AMO-aptamer duplex changed in the detection process of CE-LIF. This strategy was subsequently applied for the detection of phorate, profenofos, isocarbophos, and omethoate with the detection limits of 0.20, 0.10, 0.17, and 0.23μM, respectively. This is the first report about using QDs as the signal indicators for organophosphorus pesticides detection based on broad-specificity DNA aptamers by CE-LIF, thus contributing to extend the scope of application of QDs in different fields. The proposed method has great potential to be a universal strategy for rapid detection of aptamer-specific small molecule targets by simply changing the types of aptamer sequences. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. A cyclization-induced emission enhancement (CIEE)-based ratiometric fluorogenic and chromogenic probe for the facile detection of a nerve agent simulant DCP.

    PubMed

    Mahapatra, Ajit Kumar; Maiti, Kalipada; Manna, Saikat Kumar; Maji, Rajkishor; Mondal, Sanchita; Das Mukhopadhyay, Chitrangada; Sahoo, Prithidipa; Mandal, Debasish

    2015-06-14

    The first ratiometric fluorescent probe for the detection of a nerve agent simulant was developed based on tandem phosphorylation and intramolecular cyclization, by which high sensitivity as well as large emission shift could be achieved.

  15. Fluorescent zinc indicators for neurobiology.

    PubMed

    Thompson, R B; Peterson, Dwight; Mahoney, William; Cramer, Michele; Maliwal, Badri P; Suh, Sang Won; Frederickson, Chris; Fierke, Carol; Herman, Petr

    2002-07-30

    Mounting evidence indicates that zinc has multiple roles in cell biology, viz. as a part of metalloenzyme catalytic sites, as a structural component of gene regulatory proteins, and (like calcium) as a free signal ion, particularly in the cortex of the brain. While most Zn(II) in the brain is tightly bound, such that free Zn(II) levels extracellularly and intracellularly are likely to be picomolar, a subset of glutamatergic neurons possess weakly bound zinc in presynaptic boutons which is released at micromolar levels in response to a variety of stimuli. Key to further progress in understanding the multiple roles of zinc will be the availability of fluorescent indicator systems that will permit quantitative determination and imaging of zinc fluxes and levels over a broad concentration range both intracellularly and extracellularly using fluorescence microscopy. Towards that end, we have compared a variety of fluorescent indicators for their sensitivity to Zn(II) and Cu(II), selectivity for Zn(II) in the presence of potential interferents such as Ca(II) or Mg(II), and potential for quantitative imaging. The commercially available probes Fura-2, Mag-Fura-5, Newport Green DCF, and FuraZin-1 were compared with the carbonic anhydrase-based indicator systems for selectivity and sensitivity. In addition, intracellular levels of Zn following excitotoxic insult were determined by single pixel fluorescence lifetime microscopy of Newport Green DCF, and extracellular levels of free zinc following stimulus of rat hippocampal slices were determined ratiometrically with a carbonic anhydrase-based indicator system. These results suggest that zinc ion at high nM to microM levels can be accurately quantitated by FuraZin-1 ratiometrically or by Newport Green DCF by fluorescence lifetime; and at levels down to pM by intensity ratio, lifetime, or polarization using carbonic anhydrase-based systems. Copyright 2002 Elsevier Science B.V.

  16. Norharmane: old yet highly selective dual channel ratiometric fluoride and hydrogen sulfate ion sensor.

    PubMed

    Mallick, Arabinda; Katayama, Tetsuro; Ishibasi, Yukihide; Yasuda, Masakazu; Miyasaka, Hiroshi

    2011-01-21

    Norharmane provides a simple unexplored class of anion receptor, that allows for the ratiometric selective detection of F(-) and HSO(4)(-) ions. The presence of a strong base can easily form hydrogen bonds with the acidic hydrogen bond donor moiety and the relatively strong acid can easily protonate the basic hydrogen bond acceptor moiety, which can modulate the optical response and can detect the anions efficiently with high selectivity. In view of that, it is promising to conceive the use of these systems in various sensing applications as well as in other situations, such as anion transport and purification, where the availability of cheap and easy-to-make anion receptors, would be advantageous.

  17. A colorimetric and absorption ratiometric anion sensor based on indole & hydrazide binding units

    NASA Astrophysics Data System (ADS)

    Zou, Linbo; Yan, Boren; Pan, Dingwu; Tan, Zan; Bao, Xiaoping

    2015-09-01

    A colorimetric and absorption ratiometric anion sensor (L) based on indole and hydrazide binding units was designed and synthesized, and its recognition & sensing properties towards different anions were studied by naked-eye observations, UV-vis and 1H NMR titration spectra. Sensor L could selectively recognize biologically important F-, AcO- and H2PO4- in DMSO over other anions, along with a significant change in its color and absorption spectrum, resulting from the formation of corresponding 1:2 (L/F-) and 1:1 (L/AcO- and L/H2PO4-) complexes. The 1H NMR titration experiments proved that sensor L experienced deprotonation of NH fragment and produced [HF2]- species, whereas a stable H-bonding complex was formed in the presence of AcO- and H2PO4-.

  18. A colorimetric and absorption ratiometric anion sensor based on indole & hydrazide binding units.

    PubMed

    Zou, Linbo; Yan, Boren; Pan, Dingwu; Tan, Zan; Bao, Xiaoping

    2015-09-05

    A colorimetric and absorption ratiometric anion sensor (L) based on indole and hydrazide binding units was designed and synthesized, and its recognition & sensing properties towards different anions were studied by naked-eye observations, UV-vis and (1)H NMR titration spectra. Sensor L could selectively recognize biologically important F(-), AcO(-) and H2PO4(-) in DMSO over other anions, along with a significant change in its color and absorption spectrum, resulting from the formation of corresponding 1:2 (L/F(-)) and 1:1 (L/AcO(-) and L/H2PO4(-)) complexes. The (1)H NMR titration experiments proved that sensor L experienced deprotonation of NH fragment and produced [HF2](-) species, whereas a stable H-bonding complex was formed in the presence of AcO(-) and H2PO4(-).

  19. Resolution of lysosomes in living cells with a ratiometric molecular pH-meter.

    PubMed

    Li, Zhu; Wu, Shuqi; Han, Jiahuai; Yang, Liu; Han, Shoufa

    2013-09-30

    Intracellular acidic vesicles, constituted mostly by lysosomes, mediated a variety of biological events ranging from endocytosis, apoptosis, to cancer metastasis, etc. A chimeric molecular pH-meter (Lyso-DR), comprised of a dansyl fluorophore and proton activatable rhodamine-lactam, was prepared for ratiometric reporting of intralysosomal acidity. Exclusively confined in lysosomes, Lyso-DR exhibited pH dependent dual fluorescence emission bands which enable resolution of individual lysosomes in terms of acidity and quantitation of the overall intracellular lysosomal acidity, e.g. the lysosomal pH of HeLa cells is around pH 5.0 whereas that of L929 cells is around pH 6.2. Lyso-DR effectively differentiated the lysosomal pH changes of cells undergoing apoptosis vs necrosis, suggesting its utility in investigations on lysosome involved biomedical processes. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. A Ratiometric Near Infrared Fluorogen for the Real Time Visualization of Intracellular Redox Status during Apoptosis.

    PubMed

    Saranya, Giridharan; Anees, Palapuravan; Joseph, Manu M; Maiti, Kaustabh K; Ajayaghosh, Ayyappanpillai

    2017-04-04

    Direct monitoring of apoptotic progression is a major step forward to the early detection of therapeutic efficacy and evaluation of disease condition. Herein, we explore the regulatory role of glutathione (GSH) as a potential biomarker for tracking apoptosis. For this purpose, we introduced a near-infrared (NIR) squaraine dye that is capable of sensing GSH in a ratiometric manner by switching its emission from NIR (690 nm) to visible region (560 nm). The favourable biocompatible attributes of the probe facilitated the real time monitoring of apoptotic process in line with the conventional apoptotic assay. Furthermore, the robust nature of the probe was utilized for the quantitative estimation of GSH during different stages of apoptosis. Through this study, we demonstrate an easy and reliable method of assaying apoptosis which can provide valuable insights in translational clinical research.

  1. Synthesis of an azido-tagged low affinity ratiometric calcium sensor

    PubMed Central

    Caldwell, Stuart T.; Cairns, Andrew G.; Olson, Marnie; Chalmers, Susan; Sandison, Mairi; Mullen, William; McCarron, John G.; Hartley, Richard C.

    2015-01-01

    Changes in high localised concentrations of Ca2+ ions are fundamental to cell signalling. The synthesis of a dual excitation, ratiometric calcium ion sensor with a Kd of 90 μM, is described. It is tagged with an azido group for bioconjugation, and absorbs in the blue/green and emits in the red region of the visible spectrum with a large Stokes shift. The binding modulating nitro group is introduced to the BAPTA core prior to construction of a benzofuran-2-yl carboxaldehyde by an allylation–oxidation–cyclisation sequence, which is followed by condensation with an azido-tagged thiohydantoin. The thiohydantoin unit has to be protected with an acetoxymethyl (AM) caging group to allow CuAAC click reaction and incorporation of the KDEL peptide endoplasmic reticulum (ER) retention sequence. PMID:26709317

  2. Mixed-Lanthanoid Metal-Organic Framework for Ratiometric Cryogenic Temperature Sensing.

    PubMed

    Liu, Xue; Akerboom, Sebastiaan; de Jong, Mathijs; Mutikainen, Ilpo; Tanase, Stefania; Meijerink, Andries; Bouwman, Elisabeth

    2015-12-07

    A ratiometric thermometer based on a mixed-metal Ln(III) metal-organic framework is reported that has good sensitivity in a wide temperature range from 4 to 290 K and a quantum yield of 22% at room temperature. The sensing mechanism in the europium-doped compound Tb0.95Eu0.05HL (H4L = 5-hydroxy-1,2,4-benzenetricarboxylic acid) is based not only on phonon-assisted energy transfer from Tb(III) to Eu(III) centers, but also on phonon-assisted energy migration between neighboring Tb(III) ions. It shows good performance in a wide temperature range, especially in the range 4-50 K, reaching a sensitivity up to 31% K(-1) at 4 K.

  3. Numerical Study of Novel Ratiometric Sensors Based on Plasmon-Exciton Coupling.

    PubMed

    Tang, Yuankai; Yu, Xiantong; Pan, Haifeng; Chen, Jinquan; Audit, Benjamin; Argoul, Françoise; Zhang, Sanjun; Xu, Jianhua

    2017-10-01

    We numerically studied the optical properties of spherical nanostructures made of an emitter core coated by a silver shell through the generalized Mie theory. When there is a strong coupling between the localized surface plasmon in the metallic shell and the emitter exciton in the core, the extinction spectra exhibit two peaks. Upon adsorption of analytes on these core-shell nanostructures, the intensities of the two peaks change with opposite trends. This property makes them potential sensitive ratiometric sensors. Molecule adsorption on these nanostructures can be quantified through a very simple optical configuration likely resulting in a much faster acquisition time compared with systems based on the traditional metal nanoparticle surface plasmon resonance (SPR) biosensors.

  4. Fabrication strategies, sensing modes and analytical applications of ratiometric electrochemical biosensors.

    PubMed

    Jin, Hui; Gui, Rijun; Yu, Jianbo; Lv, Wei; Wang, Zonghua

    2017-05-15

    Previously developed electrochemical biosensors with single-electric signal output are probably affected by intrinsic and extrinsic factors. In contrast, the ratiometric electrochemical biosensors (RECBSs) with dual-electric signal outputs have an intrinsic built-in correction to the effects from system or background electric signals, and therefore exhibit a significant potential to improve the accuracy and sensitivity in electrochemical sensing applications. In this review, we systematically summarize the fabrication strategies, sensing modes and analytical applications of RECBSs. First, the different fabrication strategies of RECBSs were introduced, referring to the analytes-induced single- and dual-dependent electrochemical signal strategies for RECBSs. Second, the different sensing modes of RECBSs were illustrated, such as differential pulse voltammetry, square wave voltammetry, cyclic voltammetry, alternating current voltammetry, electrochemiluminescence, and so forth. Third, the analytical applications of RECBSs were discussed based on the types of target analytes. Finally, the forthcoming development and future prospects in the research field of RECBSs were also highlighted.

  5. In vitro and in vivo imaging of peroxynitrite by a ratiometric boronate-based fluorescent probe.

    PubMed

    Palanisamy, Sathyadevi; Wu, Pei-Yu; Wu, Shou-Cheng; Chen, Yu-Jen; Tzou, Shey-Cherng; Wang, Chih-Hong; Chen, Chiao-Yun; Wang, Yun-Ming

    2017-05-15

    Peroxynitrite (ONOO(-)) is an important species involved in many physiopathological processes. Progresses have been made in developing novel fluorescent probes to detect peroxynitrite with relatively high sensitivity and specificity. Herein, we report the synthesis, characterization and biological applications of a new boronate-based fluorescent probe, 4-MB. The studies showed that 4-MB exhibits a dual ratiometric and calorimetric response toward peroxynitrite due to ONOO(-)-triggered oxidative reaction. A possible mechanism of the oxidation reaction was proposed and the reaction product was isolated and characterized using different spectroscopic methods. We have thoroughly demonstrated the utility of 4-MB for intracellular peroxynitrite imaging. Further, we showed that 4-MB can be potentially employed to visualize exogenous and endogenous peroxynitrite in RAW264.7 macrophages, EAhy926 cells, zebrafish and in live tissues from a high-fat diet-induced obese mouse model. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Measurement of intracellular Ca2+ concentration in single cells using ratiometric calcium dyes.

    PubMed

    Srikanth, Sonal; Gwack, Yousang

    2013-01-01

    Measurement of intracellular Ca(2+) concentration ([Ca(2+)](i)) is useful to study the upstream and downstream events of Ca(2+) signaling. Ca(2+)-binding proteins including EF-hand-containing proteins are important downstream effector molecules after an increase of [Ca(2+)](i). Conversely, these proteins can also act as key modulators for regulation of [Ca(2+)](i) by sensing the Ca(2+) levels in the intracellular organelles and cytoplasm. Here we describe a single-cell Ca(2+) imaging technique that was used to measure the intracellular Ca(2+) levels to examine the function of Ca(2+)-binding proteins, STIM1 and Calcium release-activated Calcium channel regulator 2A (CRACR2A), using ratiometric Ca(2+) dye Fura-2 in adherent and non-adherent cells.

  7. Ratiometric Chemical Blend Processing with a Neuromorphic Model of the Insect Macroglomerular Complex

    NASA Astrophysics Data System (ADS)

    Karout, Salah; Rácz, Zoltán; Capurro, Alberto; Cole, Marina; Gardner, Julian W.; Pearce, Tim C.

    2011-09-01

    We present a dynamical spiking neuromorphic model constrained by the known biology of the insect antennal lobe (AL) macroglomerular complex (MGC) implemented in a field programmable gate array (FPGA). When driven by polymer coated quartz-crystal microbalance (QCM) chemosensors at its input, the dynamical trajectories of the model's projection neuron (PN) output population activity encode the concentration ratios of binary odour mixtures. We demonstrate that it is possible to recover blend ratio information from the early transient phase of QCM responses that would otherwise be difficult to separate directly from chemosensor data using classical approaches. Our results demonstrate the potential of insect-based neuromorphic signal processing methods for the rapid and efficient classification of ratiometrically encoded chemical blends.

  8. Novel pH-sensitive probes with a ratiometric detection for intracellular pH

    NASA Astrophysics Data System (ADS)

    Ipuy, Martin; Billon, Cyrielle; Micouin, Guillaume; Samarut, Jacques; Andraud, Chantal; Bretonnière, Yann

    2014-08-01

    The development of new pH-sensitive fluorescent probes based on a push-pull architecture is presented with a 2- dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofurane as strong electron acceptor group. With a small structural change, it is possible to obtain a large range of phenolic pKa from 4.8 to 8.6 with some close to neutrality, underlining the role of the electron density modulation on the acidic properties. Remarkable changes in the optical properties (both absorption and fluorescence) were observed as a function of the pH. Ratiometric imaging of intracellular pH was carried out with the most promising probes and highlighted the possibility to distinguish near-neutral minor pH fluctuations in cells.

  9. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

    PubMed Central

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-01-01

    Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0–7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems. PMID:27934889

  10. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

    NASA Astrophysics Data System (ADS)

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-12-01

    Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0–7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.

  11. Electrochemical OFF-ON ratiometric chemodosimeters for the selective and rapid detection of fluoride.

    PubMed

    Mani, Veerappan; Li, Wen-Yung; Gu, Jiun-An; Lin, Chun-Mao; Huang, Sheng-Tung

    2015-01-01

    We have described two "OFF-ON electrochemical latent ratiometric redox chemodosimeters", 1,4-Bis(tert-butyldimethylsiloxy)benzene (H2Q') and 1,4-Bis (tert-butyldimet hylsiloxy)-2-methoxybenzene (MH2Q') for the selective detection of inorganic fluoride. The electrochemical signals of hydroquinone (H2Q) and o-methoxy hydroquinone (MH2Q) within this latent redox probes (H2Q' and MH2Q') were completely masked by protecting their hydroxyl group as silylether (OFF state). The externally added fluoride ions triggered the deprotection of H2Q' and MH2Q' and unmasked the electrochemical properties of H2Q and MH2Q respectively. The electrochemical reporters (H2Q and MH2Q) presented a pair of redox peaks at the electrode surface (ON state) and the peak currents are linearly dependent with the concentration of fluoride which leading to the ratiometric detection of fluoride. The limit of detection (signal-to-noise ratio=3) observed for the probes are 23.8 µM and 2.38 µM for H2Q' and MH2Q' respectively. The deprotection is highly selective for fluoride over other anions investigated. The probes are highly stable and the proposed approach offers rapid response time and promising practical applicability. The proposed strategy holds great promise for the commencement of new H2Q based electrochemical probes by tuning the electrochemical behavior of H2Q. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Dansyl-anthracene dyads for ratiometric fluorescence recognition of Cu2+.

    PubMed

    Kaur, Kuljit; Kumar, Subodh

    2011-03-21

    Dansyl-anthracene dyads 1 and 2 in CH(3)CN-H(2)O (7:3) selectively recognize Cu(2+) ions amongst alkali, alkaline earth and other heavy metal ions using both absorbance and fluorescence spectroscopy. In absorbance, the addition of Cu(2+) to the solution of dyads 1 or 2 results in appearance of broad absorption band from 200 nm to 725 nm for dyad 1 and from 200 nm to 520 nm for dyad 2. This is associated with color change from colorless to blue (for 1) and fluorescent green (for 2). This bathochromic shift of the spectrum could be assigned to internal charge transfer from sulfonamide nitrogen to anthracene moiety. In fluorescence, under similar conditions dyads 1 and 2 on addition of Cu(2+) selectively quench fluorescence due to dansyl moiety between 520-570 nm (for 1)/555-650 nm (for 2) with simultaneous fluorescence enhancement at 470 nm and 505 nm for dyads 1 and 2, respectively. Hence these dyads provide opportunity for ratiometric analysis of 1-50 μM Cu(2+). The other metal ions viz. Fe(3+), Co(2+), Ni(2+), Cd(2+), Zn(2+), Hg(2+), Ag(+), Pb(2+), Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ba(2+) do not interfere in the estimation of Cu(2+) except Cr(3+) in case of dyad 1. The coordination of dimethylamino group of dansyl unit with Cu(2+) causes quenching of fluorescence due to dansyl moiety between 520-600 nm and also restricts the photoinduced electron transfer from dimethylamino to anthracene moiety to release fluorescence between 450-510 nm. This simultaneous quenching and release of fluorescence respectively due to dansyl and anthracene moieties emulates into Cu(2+) induced ratiometric change.

  13. Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor.

    PubMed

    Gao, Fenglei; Du, Lili; Zhang, Yu; Tang, Daoquan; Du, Yan

    2015-07-09

    A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the "signal-off" of Fc and the "signal-on" of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10(-13) to 10(-8) mol L(-1) with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

  14. Fluorescence spectroscopy incorporating a ratiometric approach for the diagnosis and classification of urothelial carcinoma

    NASA Astrophysics Data System (ADS)

    Anand, Suresh; Cicchi, Riccardo; Crisci, Alfonso; Nesi, Gabriella; Carini, Marco; Pavone, Francesco S.

    2016-02-01

    The current most popular clinical method for the screening of urothelial carcinoma is white light cystoscopy. This method has inherent disadvantages making a strong genesis towards developing more powerful diagnostic techniques. Laser induced intrinsic fluorescence spectroscopy has been studied as an adjunct to current methods for the detection of tumors. This technique allows real time results based on the changes in spectral profile between normal and tumor tissues. We conducted a pilot study based on fluorescence spectroscopy at two wavelengths 378 and 445 nm excitation for the differentiation of urothelial carcinoma. At both the excitation wavelengths, the measured fluorescence signal showed an increased intensity at wavelengths greater than 520 nm. In addition, the emission profile showed modulation at 580 nm which is due to the reabsorption of emitted fluo- rescence due to hemoglobin. Additionally, we developed a tissue characterizing algorithm, based on fluorescence intensity ratios, F510/F600 and F520/F580 at 378 and 445 nm excitation wavelengths respectively. Further, the results were correlated with the pathologists assessment of urothelial carcinoma. This ratiometric classification algorithm yielded 81% sensitivity and 83% specificity at 378 nm and while at 445 nm excitation we achieved a sensitivity and specificity of 85% and 86% for classifying normal and tumor bladder tissues. In this study we have demonstrated the potential of a simple ratiometric algorithm based on fluorescence spectroscopy could be an alternative tool to tissue biopsy. Furthermore, this technique based fiber-based fluorescence spectroscopy could be integrated into an endoscopy system for use in the operating room.

  15. A novel ratiometric fluorescent probe based on 1, 8-naphthalimide for the detection of Ho3 + and its bioimaging

    NASA Astrophysics Data System (ADS)

    Zhang, Huifang; Liu, Tao; Yin, Caixia; Wen, Yin; Chao, Jianbin; Zhang, Yongbin; Huo, Fangjun

    2017-03-01

    A ratiometric fluorescent probe for the detection of Ho3 + in DMSO-aqueous medium was designed and synthesized based on 1, 8-naphthalimide. The probe displayed response to Ho3 + with a fluorescence decrease at 512 nm and enhancement at 480 nm, accompanying with a distinct fluorescence change from bright yellow-green to cyan. Besides, the probe exhibited a lower detection limit (6 × 10- 8 M) and could be used in intracellular fluorescence imaging. To the best of the knowledge, it was the first ratiometric fluorescent probe for Ho3 + detection. This probe was expected to be a useful tool for further elucidating the roles of Ho3 + in materials, biology and environment.

  16. A simple ratiometric fluorescent sensor for fructose based on complexation of 10-hydroxybenzo[h]quinoline with boronic acid

    NASA Astrophysics Data System (ADS)

    Li, Huihui; Yang, Cailing; Zhu, Xinyue; Zhang, Haixia

    2017-06-01

    A simple ratiometric fluorescent sensor for fructose was presented. It consisted of 10-hydroxybenzo[h]quinoline (HBQ) which showed emission at 572 nm and 3-pyridylboronic acid (PDBA) whose complex with HBQ gave emission at 500 nm. The reaction of fructose with PDBA inhibited the complexation of HBQ with PDBA, resulting in the change of dual-emission intensity ratio. The sensor well quantified fructose in the range of 0.015-2.5 mM with detection limit of 0.005 mM. Besides, this sensor exhibited excellent selectivity and was successfully applied to fructose detection in food. This work provides a simple ratiometric sensing platform for sensitive and selective detection of fructose.

  17. Carbon-dot-based dual-emission silica nanoparticles as a ratiometric fluorescent probe for Bisphenol A

    NASA Astrophysics Data System (ADS)

    Xiang, Guo-Qiang; Ren, Yue; Xia, Yin; Mao, Wenjie; Fan, Chao; Guo, Si-Yu; Wang, Pan-Pan; Yang, Deng-Hui; He, Lijun; Jiang, Xiuming

    2017-04-01

    A simple and effective strategy for designing a ratiometric fluorescent nanosensor is described in this work. A carbon dots (CDs) based dual-emission nanosensor for Bisphenol A (BPA) was prepared by coating CDs on the surface of dye-doped silica nanoparticles. The fluorescence of dual-emission silica nanoparticles was quenched in hydrochloric acid by potassium bromate (KBrO3) oxidation; BPA inhibited KBrO3 oxidation, resulting in the ratiometric fluorescence response of dual-emission silica nanoparticles. Several important parameters affecting the performance of the nanosensor were investigated and optimized. The detection limit of this nanosensor was 0.80 ng mL- 1 with a linear range from 10 to 500 ng mL- 1. This was applied successfully to determine BPA in the leached solution of different plastic products with satisfactory results.

  18. A fiber optic ammonia sensor using a universal pH indicator.

    PubMed

    Rodríguez, Adolfo J; Zamarreño, Carlos R; Matías, Ignacio R; Arregui, Francisco J; Cruz, Rene F Domínguez; May-Arrioja, Daniel A

    2014-02-27

    A universal pH indicator is used to fabricate a fiber optic ammonia sensor. The advantage of this pH indicator is that it exhibits sensitivity to ammonia over a broad wavelength range. This provides a differential response, with a valley around 500 nm and a peak around 650 nm, which allows us to perform ratiometric measurements. The ratiometric measurements provide not only an enhanced signal, but can also eliminate any external disturbance due to humidity or temperature fluctuations. In addition, the indicator is embedded in a hydrophobic and gas permeable polyurethane film named Tecoflex®. The film provides additional advantages to the sensor, such as operation in dry environments, efficient transport of the element to be measured to the sensitive area of the sensor, and prevent leakage or detachment of the indicator. The combination of the universal pH indicator and Tecoflex® film provides a reliable and robust fiber optic ammonia sensor.

  19. A Fiber Optic Ammonia Sensor Using a Universal pH Indicator

    PubMed Central

    Rodríguez, Adolfo J.; Zamarreño, Carlos R.; Matías, Ignacio R.; Arregui, Francisco. J.; Domínguez Cruz, Rene F.; May-Arrioja, Daniel. A.

    2014-01-01

    A universal pH indicator is used to fabricate a fiber optic ammonia sensor. The advantage of this pH indicator is that it exhibits sensitivity to ammonia over a broad wavelength range. This provides a differential response, with a valley around 500 nm and a peak around 650 nm, which allows us to perform ratiometric measurements. The ratiometric measurements provide not only an enhanced signal, but can also eliminate any external disturbance due to humidity or temperature fluctuations. In addition, the indicator is embedded in a hydrophobic and gas permeable polyurethane film named Tecoflex®. The film provides additional advantages to the sensor, such as operation in dry environments, efficient transport of the element to be measured to the sensitive area of the sensor, and prevent leakage or detachment of the indicator. The combination of the universal pH indicator and Tecoflex® film provides a reliable and robust fiber optic ammonia sensor. PMID:24583969

  20. Novel Double-Potential Electrochemiluminescence Ratiometric Strategy in Enzyme-Based Inhibition Biosensing for Sensitive Detection of Organophosphorus Pesticides.

    PubMed

    Chen, Hongmei; Zhang, Han; Yuan, Ruo; Chen, Shihong

    2017-03-07

    Generally, electrochemiluminescence (ECL) ratiometric assays were based on the energy transfer (ET) between an emitter and a metal nanomaterial or between two different emitters. The choice of suitable energy donor-acceptor pair and the distance dependence of ET would greatly limit the practical application of ratiometric assays. This work explored a novel double-potential ECL ratiometry without the ET for organophosphorus pesticides (OPs) analysis, in which, reduced graphene oxide-CdTe quantum dots (RGO-CdTe QDs) and carboxyl-conjugated polymer dots (PFO dots) were chosen as cathodic and anodic ECL emitters, and the reactant (dissolved O2) and the product (H2O2) in enzymatic reactions served as their coreactants, respectively. With the occurrence of the enzymatic reactions induced by the acetylcholinesterase (AChE) and choline oxidase (ChOx), the cathodic ECL signal from RGO-CdTe QDs was at "signal off" state due to the consumption of dissolved O2. Meanwhile, the anodic ECL signal from PFO dots was at "signal on" state due to the in situ generation of H2O2. In the presence of OPs, the cathodic ECL signal would increase while the anodic ECL signal would decline correspondingly due to the inhibition of OPs on the activity of AChE. Using the reactant and the product in enzymatic reactions as the coreactants of two different ECL emitters, we conveniently achieved the opposite change trend in two ECL signals for the ratiometric detection of OPs, which exhibited a greatly improved accuracy, reliability and sensitivity, thus, showing a great attraction for developing ECL ratiometric systems for the bioanalysis.

  1. A FRET-based ratiometric fluorescent and colorimetric probe for the facile detection of organophosphonate nerve agent mimic DCP.

    PubMed

    Xuan, Weimin; Cao, Yanting; Zhou, Jiahong; Wang, Wei

    2013-11-18

    A FRET ratiometric fluorescent probe enabling a fast and highly sensitive response to OP nerve agent mimic DCP within 1 min and with as low as 0.17 ppm concentration detection limit has been developed. Moreover, the probe exhibits noticeable color changes under UV light and even with the naked eye. It is also demonstrated that it can detect both liquid and gas nerve agents.

  2. AIEgens for dark through-bond energy transfer: design, synthesis, theoretical study and application in ratiometric Hg(2+) sensing.

    PubMed

    Chen, Yuncong; Zhang, Weijie; Cai, Yuanjing; Kwok, Ryan T K; Hu, Yubing; Lam, Jacky W Y; Gu, Xinggui; He, Zikai; Zhao, Zheng; Zheng, Xiaoyan; Chen, Bin; Gui, Chen; Tang, Ben Zhong

    2017-03-01

    A novel dark through-bond energy transfer (DTBET) strategy is proposed and applied as the design strategy to develop ratiometric Hg(2+) sensors with high performance. Tetraphenylethene (TPE) derivatives with aggregation-induced emission (AIE) characteristics are selected as dark donors to eliminate emission leakage from the donors. The TBET mechanism has been adopted since it experiences less influence from spectral overlapping than Förster resonance energy transfer (FRET), making it more flexible for developing cassettes with large pseudo-Stokes shifts. In this work, energy transfer from the TPE derivatives (dark donor) to a rhodamine moiety (acceptor) was illustrated through photophysical spectroscopic studies and the energy transfer efficiency (ETE) was found to be up to 99%. In the solution state, no emission from the donors was observed and large pseudo-Stokes shifts were achieved (>280 nm), which are beneficial for biological imaging. Theoretical calculations were performed to gain a deeper mechanistic insight into the DTBET process and the structure-property relationship of the DTBET cassettes. Ratiometric Hg(2+) sensors were rationally constructed based on the DTBET mechanism by taking advantage of the intense emission of TPE aggregates. The Hg(2+) sensors exhibited well resolved emission peaks. >6000-fold ratiometric fluorescent enhancement is also achieved and the detection limit was found to be as low as 0.3 ppb. This newly proposed DTBET mechanism could be used to develop novel ratiometric sensors for various analytes and AIEgens with DTBET characteristics will have great potential in various areas including light harvesting materials, environmental science, chemical sensing, biological imaging and diagnostics.

  3. A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids.

    PubMed

    Maity, Debabrata; Jiang, Juanjuan; Ehlers, Martin; Wu, Junchen; Schmuck, Carsten

    2016-05-04

    A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.

  4. Protein-templated gold nanoclusters sequestered within sol-gel thin films for the selective and ratiometric luminescence recognition of Hg2+

    NASA Astrophysics Data System (ADS)

    Hofmann, Carrie M.; Essner, Jeremy B.; Baker, Gary A.; Baker, Sheila N.

    2014-04-01

    Sequestration of bovine serum albumin (BSA)-stabilized gold nanoclusters (AuNCs@BSA) prepared using microwave assistance within sol-gel-derived mesoporous silica films permits the selective and highly sensitive quenchometric detection of aqueous Hg2+ (limit of detection = 600 pM) with luminescence signal arising from oxidized BSA allowing for an analytically robust and reliable ratiometric detection. Overall, this work highlights a number of important advances, including the highest luminescence quantum yield reported to date for a protein-templated luminescent noble metal nanocluster (13%) made possible using a microwave-mediated synthesis followed by cold incubation. We also demonstrate the clear advantage of exploiting the luminescence signal arising from oxidized BSA as an internal reference to generate selectivity of response to Hg2+. A careful Stern-Volmer quenching analysis reveals the persistence of two unique quenching sites for AuNCs@BSA entrapped within a sol-gel-derived glass, a minor population of which is unquenchable. Finally, based on these AuNCs@BSA nanosensors, we advise a path forward for paper-based indicator strip detection of heavy metals in aqueous streams, the implementation of which can be performed using the unaided eye, making it a meaningful approach for routine screening and in resource-limited situations.Sequestration of bovine serum albumin (BSA)-stabilized gold nanoclusters (AuNCs@BSA) prepared using microwave assistance within sol-gel-derived mesoporous silica films permits the selective and highly sensitive quenchometric detection of aqueous Hg2+ (limit of detection = 600 pM) with luminescence signal arising from oxidized BSA allowing for an analytically robust and reliable ratiometric detection. Overall, this work highlights a number of important advances, including the highest luminescence quantum yield reported to date for a protein-templated luminescent noble metal nanocluster (13%) made possible using a microwave

  5. Rhodamine 6G conjugated-quantum dots used for highly sensitive and selective ratiometric fluorescence sensor of glutathione.

    PubMed

    Gui, Rijun; An, Xueqin; Su, Hongjuan; Shen, Weiguo; Zhu, Linyong; Ma, Xingyuan; Chen, Zhiyun; Wang, Xiaoyong

    2012-05-30

    Rhodamine 6G (R6G) and 3-mercaptopropionic acid (MPA) capped-CdTe quantum dots (QDs) were conjugated by electrostatic interactions in aqueous solution. The R6G-QDs conjugate was utilized as a photoluminescence (PL) ratiometric sensor for the detection of glutathione (GSH). In this method, intentional introduction of GSH destroyed the conjugation of R6G and QDs, and induced regular PL change of R6G-QDs conjugates due to the competitive chelation between GSH and MPA ligand on the surface of QDs. The ratio of PL intensity of R6G (I(R6G)) to that of QDs (I(QDs)) in this conjugate was near linear toward the concentration of GSH in the range from 0.05 to 80 μM, and corresponding regression equation showed a good linear coefficient of 0.9954. The limit of detection of 15 nM in this proposed method was about 40-fold lower than that of other QDs-based PL sensors. Interferential experiments testified that R6G-QDs conjugates-based ratiometric PL sensor of GSH showed high selectivity over other related thiols and amino acids. Real sample assays further verified perfect analysis performance of the PL sensor of GSH. In comparison with conventional analytical techniques for the measurement of GSH, this ratiometric PL sensor was facile, economic, highly sensitive and selective.

  6. A sensitive ratiometric electrochemical biosensor based on DNA four-way junction formation and enzyme-assisted recycling amplification.

    PubMed

    Cui, Lin; Lu, Mengfei; Yang, Xiao-Yun; Tang, Bo; Zhang, Chun-Yang

    2017-05-02

    A simple ratiometric electrochemical biosensor is developed for sensitive detection of target DNA based on DNA four-way junction (DNA-4WJ) formation and enzyme-assisted recycling amplification. This biosensor can be easily fabricated by a one-step assembly of ratiometric probes and simply performed by a one-step incubation procedure. In the presence of target DNA, two unmodified DNA oligonucleotides may cooperatively hybridize with a hairpin probe in the triple-helix molecular beacon (THMB) to form a DNA-4WJ, which may cause conformational transduction and induce the change in the distance between two redox labeling probes and the electrode surface. The subsequent recognition and cleavage of DNA-4WJ quadripartite complexes by RNase HII may result in significant signal amplification. Due to the introduction of DNA-4WJ formation, enzyme-assisted recycling amplification and ratiometric measurement, this biosensor exhibits high sensitivity with a detection limit as low as 0.063 pM and a long dynamic range from 0.1 pM to 100 nM. Moreover, this biosensor demonstrates good performance with excellent selectivity, high reliability and good reproducibility, holding great potential for further applications in biomedical research and clinical diagnostics.

  7. Surgical molecular navigation with a Ratiometric Activatable Cell Penetrating Peptide improves intraoperative identification and resection of small salivary gland cancers

    PubMed Central

    Hussain, Timon; Savariar, Elamprakash N.; Diaz-Perez, Julio A.; Messer, Karen; Pu, Minya; Tsien, Roger Y.; Nguyen, Quyen T.

    2015-01-01

    Background We evaluated the use of intraoperative fluorescence guidance by enzymatically cleavable ratiometric activatable cell-penetrating peptide (RACPPPLGC(Me)AG) containing Cy5 as a fluorescent donor and Cy7 as a fluorescent acceptor for salivary gland cancer surgery in a mouse model. Methods Surgical resection of small parotid gland cancers in mice was performed with fluorescence guidance or white light (WL) imaging alone. Tumor identification accuracy, operating time and tumor free survival were compared. Results RACPP guidance aided tumor detection (positive histology in 90% (27/30) vs. 48% (15/31) for WL, p<0.001). A ~25% ratiometric signal increase as the threshold to distinguish between tumor and adjacent tissue, yielded >90% detection sensitivity and specificity. Operating time was reduced by 54% (p<0.001), tumor free survival was increased with RACPP guidance (p=0.025). Conclusions RACPP provides real-time intraoperative guidance leading to improved survival. Ratiometric signal thresholds can be set according to desired detection accuracy levels for future RACPP applications. PMID:25521629

  8. Ultraefficient Cap-Exchange Protocol To Compact Biofunctional Quantum Dots for Sensitive Ratiometric Biosensing and Cell Imaging

    PubMed Central

    2017-01-01

    An ultraefficient cap-exchange protocol (UCEP) that can convert hydrophobic quantum dots (QDs) into stable, biocompatible, and aggregation-free water-dispersed ones at a ligand:QD molar ratio (LQMR) as low as 500, some 20–200-fold less than most literature methods, has been developed. The UCEP works conveniently with air-stable lipoic acid (LA)-based ligands by exploiting tris(2-carboxylethyl phosphine)-based rapid in situ reduction. The resulting QDs are compact (hydrodynamic radius, Rh, < 4.5 nm) and bright (retaining > 90% of original fluorescence), resist nonspecific adsorption of proteins, and display good stability in biological buffers even with high salt content (e.g., 2 M NaCl). These advantageous properties make them well suited for cellular imaging and ratiometric biosensing applications. The QDs prepared by UCEP using dihydrolipoic acid (DHLA)-zwitterion ligand can be readily conjugated with octa-histidine (His8)-tagged antibody mimetic proteins (known as Affimers). These QDs allow rapid, ratiometric detection of the Affimer target protein down to 10 pM via a QD-sensitized Förster resonance energy transfer (FRET) readout signal. Moreover, compact biotinylated QDs can be readily prepared by UCEP in a facile, one-step process. The resulting QDs have been further employed for ratiometric detection of protein, exemplified by neutravidin, down to 5 pM, as well as for fluorescence imaging of target cancer cells. PMID:28421739

  9. Design of a Modular DNA Triangular-Prism Sensor Enabling Ratiometric and Multiplexed Biomolecule Detection on a Single Microbead.

    PubMed

    Liu, Yu; Chen, Qiaoshu; Liu, Jianbo; Yang, Xiaohai; Guo, Qiuping; Li, Li; Liu, Wei; Wang, Kemin

    2017-03-21

    DNA nanostructures have emerged as powerful and versatile building blocks for the construction of programmable nanoscale structures and functional sensors for biomarker detection, disease diagnostics, and therapy. Here we integrated multiple sensing modules into a single DNA three-dimensional (3D) nanoarchitecture with a triangular-prism (TP) structure for ratiometric and multiplexed biomolecule detection on a single microbead. In our design, the complementary hybridization of three clip sequences formed TP nanoassemblies in which the six single-strand regions in the top and bottom faces act as binding sites for different sensing modules, including an anchor module, reference sequence module, and capture sequence module. The multifunctional modular TP nanostructures were thus exploited for ratiometric and multiplexed biomolecule detection on microbeads. Microbead imaging demonstrated that, after ratiometric self-calibration analysis, the imaging deviations resulting from uneven fluorescence intensity distribution and differing probe concentrations were greatly reduced. The rigid nanostructure also conferred the TP as a framework for geometric positioning of different capture sequences. The inclusion of multiple targets led to the formation of sandwich hybridization structures that gave a readily detectable optical response at different fluorescence channels and distinct fingerprint-like pattern arrays. This approach allowed us to discriminate multiplexed biomolecule targets in a simple and efficient fashion. In this module-designed strategy, the diversity of the controlled DNA assembly coupled with the geometrically well-defined rigid nanostructures of the TP assembly provides a flexible and reliable biosensing approach that shows great promise for biomedical applications.

  10. Construction of single fluorophore ratiometric pH sensors using dual-emission Mn(2+)-doped quantum dots.

    PubMed

    Pratiwi, Feby Wijaya; Hsia, Chih-Hao; Kuo, Chiung Wen; Yang, Shun-Min; Hwu, Yeu-Kuang; Chen, Peilin

    2016-10-15

    We present a novel ratiometric pH sensor design using water-soluble, dual-emission, Mn(2+)-doped quantum dots (Qdots) decorated with D-penicillamine (DPA-MnQdots). In contrast to more commonly used ratiometric pH sensors that rely on the coupling of two fluorophores, our design uses only a single emitter, which simplifies ratiometric sensing and broadens the applications of the sensor. Our single-emitter DPA-MnQdots exhibit two emission bands, at 510nm (green) and 610nm (red), which are, respectively, attributable to exciton recombination and emission of the Mn(2+) dopants. The emission intensity ratio (I510/I610) of the DPA-MnQdots depends linearly on surrounding pH values within physiological conditions (from pH 4.5 to 8.5). Moreover, the biocompatible DPA-MnQdots were used for long-term monitoring of local pH values in HeLa cells.

  11. Neuronal acid-induced [Zn²⁺]i elevations calibrated using the low-affinity ratiometric probe FuraZin-1.

    PubMed

    Kiedrowski, Lech

    2015-11-01

    The experiments were carried out on primary cultures of murine cortical neurons from cryopreserved preparations obtained from embryonic-day-16 fetuses. To calibrate acid-induced intracelluar [Zn(2+) ] ([Zn(2+) ]i ) elevations, a low affinity (Kd = 39 μM at pH 6.1) ratiometric Zn(2+) probe, FuraZin-1, was used. A pHi drop from 7.2 to 6.1 caused [Zn(2+) ]i elevations reaching 2 μM; when the thiol-reactive agent N-ethylmaleimide (NEM) was subsequently applied, [Zn(2+) ]i increased further to 5.6 μM; analogous acid- and NEM-induced [Zn(2+) ]i elevations could also be detected but not calibrated, using the high affinity Zn(2+) probe FluoZin-3. The data indicate that NEM causes Zn(2+) release from ligands that chelate Zn(2+) at pH 6.1. ATP could also chelate Zn(2+) at pH 6.1 because its pKa is about 6.8. Therefore, it was tested whether an ATP depletion affects the acid-induced [Zn(2+) ]i elevations. The ATP depletion was induced by inhibiting mitochondrial and glycolytic ATP production. Interestingly, an almost complete ATP depletion (confirmed using a luciferin/luciferase assay) failed to affect the acid-induced [Zn(2+) ]i increases. These data suggest that the total amount of Zn(2+) accumulated in intracellular ATP-dependent stores (Zn(2+) -ATP complexes and organelles that accumulate Zn(2+) in an ATP-dependent manner) is negligible compared to the amount of Zn(2+) accumulated in the acid-sensitive intracellular ligands. In vitro, upon acidification, Zn(2+) -cysteine complexes release Zn(2+) and ATP chelates the released Zn(2+) . However, in vivo (cultured neurons), an ATP depletion failed to enhance acid-induced [Zn(2+) ]i elevations. These [Zn(2+) ]i elevations were calibrated using a low affinity ratiometric probe FuraZin-1; they reached 2 µM levels and increased to 5 µM when a thiol-reactive agent, N-ethylmaleimide, compromised Zn(2+) binding by cysteines. © 2015 International Society for Neurochemistry.

  12. A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

    NASA Astrophysics Data System (ADS)

    Del Bonis-O'Donnell, Jackson Travis; Vong, Daniel; Pennathur, Sumita; Fygenson, Deborah Kuchnir

    2016-07-01

    DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag+ ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the

  13. Highly-sensitive Eu3+ ratiometric thermometers based on excited state absorption with predictable calibration

    NASA Astrophysics Data System (ADS)

    Souza, Adelmo S.; Nunes, Luiz A. O.; Silva, Ivan G. N.; Oliveira, Fernando A. M.; da Luz, Leonis L.; Brito, Hermi F.; Felinto, Maria C. F. C.; Ferreira, Rute A. S.; Júnior, Severino A.; Carlos, Luís D.; Malta, Oscar L.

    2016-02-01

    Temperature measurements ranging from a few degrees to a few hundreds of Kelvin are of great interest in the fields of nanomedicine and nanotechnology. Here, we report a new ratiometric luminescent thermometer using thermally excited state absorption of the Eu3+ ion. The thermometer is based on the simple Eu3+ energy level structure and can operate between 180 and 323 K with a relative sensitivity ranging from 0.7 to 1.7% K-1. The thermometric parameter is defined as the ratio between the emission intensities of the 5D0 --> 7F4 transition when the 5D0 emitting level is excited through the 7F2 (physiological range) or 7F1 (down to 180 K) level. Nano and microcrystals of Y2O3:Eu3+ were chosen as a proof of concept of the operational principles in which both excitation and detection are within the first biological transparent window. A novel and of paramount importance aspect is that the calibration factor can be calculated from the Eu3+ emission spectrum avoiding the need for new calibration procedures whenever the thermometer operates in different media.Temperature measurements ranging from a few degrees to a few hundreds of Kelvin are of great interest in the fields of nanomedicine and nanotechnology. Here, we report a new ratiometric luminescent thermometer using thermally excited state absorption of the Eu3+ ion. The thermometer is based on the simple Eu3+ energy level structure and can operate between 180 and 323 K with a relative sensitivity ranging from 0.7 to 1.7% K-1. The thermometric parameter is defined as the ratio between the emission intensities of the 5D0 --> 7F4 transition when the 5D0 emitting level is excited through the 7F2 (physiological range) or 7F1 (down to 180 K) level. Nano and microcrystals of Y2O3:Eu3+ were chosen as a proof of concept of the operational principles in which both excitation and detection are within the first biological transparent window. A novel and of paramount importance aspect is that the calibration factor can be

  14. Engineering the metal sensitive sites in Macrolampis sp2 firefly luciferase and use as a novel bioluminescent ratiometric biosensor for heavy metals.

    PubMed

    Gabriel, Gabriele V M; Viviani, Vadim R

    2016-12-01

    Most luminescent biosensors for heavy metals are fluorescent and rely on intensity measurements, whereas a few are ratiometric and rely on spectral changes. Bioluminescent biosensors for heavy metals are less common. Firefly luciferases have been coupled to responsive promoters for mercury and arsenium, and used as light on biosensors. Firefly luciferase bioluminescence spectrum is naturally sensitive to heavy metal cations such as zinc and mercury and to pH. Although pH sensitivity of firefly luciferases was shown to be useful for ratiometric estimation of intracellular pH, its potential use for ratiometric estimation of heavy metals was never considered. Using the yellow-emitting Macrolampis sp2 firefly luciferase and site-directed mutagenesis, we show that the residues H310 and E354 constitute two critical sites for metal sensitivity that can be engineered to increase sensitivity to zinc, nickel, and mercury. A linear relationship between cation concentration and the ratio of bioluminescence intensities at 550 and 610 nm allowed, for the first time, the ratiometric estimation of heavy metals concentrations down to 0.10 mM, demonstrating the potential applicability of firefly luciferases as enzymatic and intracellular ratiometric metal biosensors.

  15. A general strategy to facilely design ratiometric electrochemical sensors in electrolyte solution by directly using a bare electrode for dual-signal sensing of analytes.

    PubMed

    Yu, Jianbo; Jin, Hui; Gui, Rijun; Wang, Zonghua; Ge, Feng

    2017-01-01

    In this paper, we have described a general strategy to facilely design ratiometric electrochemical sensors in electrolyte solutions, directly using a bare electrode for dual-signal sensing of analytes. Two types of substances (methylene blue/MB, doxorubicin/DOX) with different electrochemical signal peaks were added into electrolyte solutions (phosphate buffered saline, NaCl), where one was the analyte (DOX) and the other was used as a reference (MB). A linear plotting of DOX concentration [DOX] versus ratiometric electrochemical signal peak intensity (IDOX/IMB) was achieved, with a good linear coefficient and low detection limit of DOX (0.4nM). Experimental results implied that this ratiometric electrochemical sensor (ECS) of DOX enabled highly selective and sensitive detection of DOX in real samples, with high detection recoveries. In comparison with previous reports about ratiometric ECS, this as-proposed strategy can directly fabricate a ratiometric ECS in electrolyte solution (not on electrode), only using a bare electrode for dual- signal sensing of analytes. This strategy is not only novel and facile, but also flexible and general, as adequately confirmed in experiments, which would facilitate a further development in the facile fabrication and efficient applications of electrochemical sensors.

  16. Ratiometric Nanothermometer Based on Rhodamine Dye-Incorporated F127-Melamine-Formaldehyde Polymer Nanoparticle: Preparation, Characterization, Wide-Range Temperature Sensing, and Precise Intracellular Thermometry.

    PubMed

    Wu, Youshen; Liu, Jiajun; Ma, Jingwen; Liu, Yongchun; Wang, Ya; Wu, Daocheng

    2016-06-15

    A series of fluorescent nanothermometers (FTs) was prepared with Rhodamine dye-incorporated Pluronic F-127-melamine-formaldehyde composite polymer nanoparticles (R-F127-MF NPs). The highly soluble Rhodamine dye molecules were bound with Pluronic F127 micelles and subsequently incorporated in the cross-linked MF resin NPs during high-temperature cross-link treatment. The morphology and chemical structure of R-F127-MF NPs were characterized with dynamic light scattering, electron microscopy, and Fourier-transform infrared (FTIR) spectra. Fluorescence properties and thermoresponsivities were analyzed using fluorescence spectra. R-F127-MF NPs are found to be monodispersed, presenting a size range of 88-105 nm, and have bright fluorescence and high stability in severe treatments such as autoclave sterilization and lyophilization. By simultaneously incorporating Rhodamine B and Rhodamine 110 (as reference) dyes at a doping ratio of 1:400 in the NPs, ratiometric FTs with a high sensibility of 7.6%·°C(-1) and a wide temperature sensing range from -20 to 110 °C were obtained. The FTs exhibit good stability in solutions with varied pH, ionic strengths, and viscosities and have similar working curves in both intracellular and extracellular environments. Cellular temperature variations in Hela cells during microwave exposure were successfully monitored using the FTs, indicating their considerable potential applications in the biomedical field.

  17. Laser Induced Dual Fluorescence Ratiometric Technique for Mixing Characterization in Microfluidic Systems

    NASA Astrophysics Data System (ADS)

    Bedding, David; Hidrovo, Carlso

    2016-11-01

    Increasing the rate of mixing within microfluidic systems is vitally important in understanding biological and chemical reaction kinetics and mechanisms. The small length scales characteristic of these systems which translate into highly viscous, Stokes flows result in mixing that is primarily dominated by diffusion. In order to counteract this, an approach that utilizes inertial droplet collisions to promote chaotic advection between two mixing species has been developed. A Laser-Induced Dual Fluorescence (LIDF) system in conjunction with a high-speed camera and appropriate optics are used to capture two intensity fields providing information about the mixing process as well as the excitation intensity field over the volume of interest. The rate of mixing for the coalescing droplets was quantified by taking the standard deviation of the first intensity field over time, while the second intensity field provides information about the intensity field. A ratiometric imaging approach allows removal of mixing fluorescence signal noise in the form of variation in excitation intensity, primarily from the lasing patterns and lensing effects within the interrogation volume. NSF CAREER Award Grant CBET - 1151091.

  18. A ratiometric fluorescent probe for sensing hydrogen peroxide based on a hemicyanine-naphthol fluorophore.

    PubMed

    Lei, Yingjie; Xue, Cong; Zhang, Sichun; Sha, Yaowu

    2016-05-01

    The synthesis, properties and applications of a water-soluble boronate-functioned hemicyanine-naphthol hybrid as a novel ratiometric fluorescent sensor for hydrogen peroxide are presented. The dye displayed remarkable a colour change from pale orange (λ(em)  = 590 nm) to pink (λ(em)  = 690 nm) in the presence of H2O2, which could be rationalized by the chemoselective H2O2-mediated transformation of arylboronate to phenolate with high selectivity and a fast response (within 2 min). A good linear relationship (R(2)  = 0.9951) was obtained with the H2O2 concentration ranging from 0 to 25 μM, with a limit of detection of 0.09 μM according to the signal-to-noise ratio (S/N = 3). The advantages of this fluorophore include easy modification, excellent aqueous solubility and superior photostability, and it has been applied to the detection of trace amounts of hydrogen peroxide in water samples. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Ratiometric Dissolved Oxygen Sensors Based on Ruthenium Complex Doped with Silver Nanoparticles

    PubMed Central

    Jiang, Zike; Yu, Xinsheng; Zhai, Shikui; Hao, Yingyan

    2017-01-01

    A ratiometric optical sensor has been developed with electrospinning processing method for dissolved oxygen measurement. The sensing film is fabricated by using silver nano-particles (Ag NPs) doped with tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) dichloride complex (Ru(DPP)3Cl2) encapsulated in plasticized polymethyl methacrylate (PMMA). An insensitive 3-(2-benzothiazolyl)-7-(diethy lamino)-(6CI,7CI) (Coumarin6) is adopted as reference. The ratio of oxygenation is calculated at each image pixel of a 3CCD camera to quantify the oxygen concentration in aqueous environment. Compared to Ag-free film, the response time of Ag-containing films were improved from 1.5 s to 1.0 s upon switching from deoxygenated to air saturation and from 65 s to 45 s from air saturation to fully deoxygenated. The response times of the Ag-free film obtained by knifing was 2.0 s upon switching from deoxygenated to air saturation and 104 s from air saturation to fully deoxygenated. Results of the evaluation of accuracy, limit of detection, stability, and photostability are presented. An experiment measuring the spatiotemporal variation of oxygen distribution within the photosynthesis and respiration of Chlorella vulgaris is demonstrated. It is shown that the nanofiber-based optical sensor film could serve as a promising method for rapid oxygen monitoring in aqueous applications. PMID:28282946

  20. Peptide-Based, Two-Fluorophore, Ratiometric Probe for Quantifying Mobile Zinc in Biological Solutions

    PubMed Central

    2015-01-01

    Small-molecule fluorescent sensors are versatile agents for detecting mobile zinc in biology. Capitalizing on the abundance of validated mobile zinc probes, we devised a strategy for repurposing existing intensity-based sensors for quantitative applications. Using solid-phase peptide synthesis, we conjugated a zinc-sensitive Zinpyr-1 derivative and a zinc-insensitive 7-hydroxycoumarin derivative onto opposite ends of a rigid P9K peptide scaffold to create HcZ9, a ratiometric fluorescent probe for mobile zinc. A plate reader-based assay using HcZ9 was developed, the accuracy of which is comparable to that of atomic absorption spectroscopy. We investigated zinc accumulation in prostatic cells and zinc levels in human seminal fluid. When normal and tumorigenic cells are bathed in zinc-enriched media, cellular mobile zinc is buffered and changes slightly, but total zinc levels increase significantly. Quantification of mobile and total zinc levels in human seminal plasma revealed that the two are positively correlated with a Pearson’s coefficient of 0.73. PMID:25382858

  1. Ratiometric optical PEBBLE nanosensors for real-time magnesium ion concentrations inside viable cells.

    PubMed

    Park, Edwin J; Brasuel, Murphy; Behrend, Caleb; Philbert, Martin A; Kopelman, Raoul

    2003-08-01

    This paper presents the development and characterization of a highly selective magnesium fluorescent optical nanosensor, made possible by PEBBLE (probe encapsulated by biologically localized embedding) technology. A ratiometric sensor has been developed by co-immobilizing a dye that is sensitive to and highly selective for magnesium, with a reference dye in a matrix. The sensors are prepared via a microemulsion polymerization process, which entraps the sensing components inside a polymer matrix. The resultant spherical sensors are approximately 40 nm in diameter. The Coumarin 343 (C343) dye, which by itself does not enter the cell, when immobilized in a PEBBLE is used as the magnesium-selective agent that provides the high and necessary selectivity over other intracellular ions, such as Ca2+, Na+, and K+. The dynamic range of these sensors was 1-30 mM, with a linear range from 1 to 10 mM, with a response time of <4 s. In contrast to free dye, these nano-optodes are not perturbed by proteins. They are fully reversible and exhibit minimal leaching and photobleaching over extended periods of time. In vitro intracellular changes in Mg2+ concentration were monitored in C6 glioma cells, which remained viable after PEBBLE delivery via gene gun injection. The selectivity for Mg2+ along with the biocompatibility of the matrix provides a new and reliable tool for intracellular magnesium measurements.

  2. A two-photon ratiometric fluorescence probe for Cupric Ions in Live Cells and Tissues

    PubMed Central

    Zhu, Anwei; Ding, Changqin; Tian, Yang

    2013-01-01

    Development of sensitive and selective probes for cupric ions (Cu2+) at cell and tissue level is a challenging work for progress in understanding the biological effects of Cu2+. Here, we report a ratiometric two-photon probe for Cu2+ based on the organic-inorganic hybrids of graphene quantum dots (GQDs) and Nile Blue dye. Meanwhile, Cu-free derivative of copper-zinc superoxide dismutase (SOD) – E2Zn2SOD is designed as the unique receptor for Cu2+ and conjugated on the surface of GQDs. This probe shows a blue-to-yellow color change in repose to Cu2+, good selectivity, low cytotoxicity, long-term photostability, and insensitivity to pH over the biologically relevant pH range. The developed probe allows the direct visualization of Cu2+ levels in live cells as well as in deep-tissues at 90–180 μm depth through the use of two-photon microscopy. Furthermore, the effect of ascorbic acid is also evaluated on intracellular Cu2+ binding to E2Zn2SOD by this probe. PMID:24121717

  3. A novel, rapid method to quantify intraplatelet calcium dynamics by ratiometric flow cytometry.

    PubMed

    Assinger, Alice; Volf, Ivo; Schmid, Diethart

    2015-01-01

    Cytosolic free calcium ions represent important second-messengers in platelets. Therefore, quantitative measurement of intraplatelet calcium provides a popular and very sensitive tool to evaluate platelet activation and reactivity. Current protocols for determination of intracellular calcium concentrations in platelets have a number of limitations. Cuvette-based methods do not allow measurement of calcium flux in complex systems, such as whole blood, and therefore require isolation steps that potentially interfere with platelet activation. Flow cytometry has the potential to overcome this limitation, but to date the application of calibrated, quantitative readout of calcium kinetics has only been described for Indo-1. As excitation of Indo-1 requires a laser in the ultraviolet range, such measurements cannot be performed with a standard flow cytometer. Here, we describe a novel, rapid calibration method for ratiometric calcium measurement in platelets using both Ar(+)-laser excited fluorescence dyes Fluo-4 and Fura Red. We provide appropriate equations that allow rapid quantification of intraplatelet calcium fluxes by measurement of only two standardisation buffers. We demonstrate that this method allows quantitative calcium measurement in platelet rich plasma as well as in whole blood. Further, we show that this method prevents artefacts due to platelet aggregate formation and is therefore an ideal tool to determine basal and agonist induced calcium kinetics.

  4. Ratiometric fluorescence detection of silver ions using thioflavin T-based organic/inorganic hybrid supraparticles.

    PubMed

    Li, Yan-Yun; Zhang, Min; Lu, Ling-Fei; Zhu, Anwei; Xia, Fei; Zhou, Tianshu; Shi, Guoyue

    2015-09-07

    In this work, we present a new type of functional organic/inorganic hybrid supraparticle that spontaneously assembles from silver ions (Ag(+)), iodide ions (I(-)) and thioflavin T (ThT) under aqueous solution conditions. ThT alone in aqueous solution was weakly fluorescent with an emission band at 494 nm, which was related to the monomer. However, in the above-mentioned hybrid supraparticle (i.e., ThT@AgI SP) structure, the ThT monomer can form a dimer with a new emission band. The new band shifted to 546 nm and the emission intensity increased. We further present a facile strategy of reversible fluorescence switching of ThT by a simple cation (Ag(+)) and anions (I(-) and S(2-)), which can be employed for the ratiometric fluorescence detection of Ag(+) with high sensitivity and selectivity. The linear range of detecting Ag(+) was from 100 nM to 10 μM, with a limit of detection as low as approximately 50 nM. Moreover, it can be successfully applied for the operation of a logic gate system and to the sensing of Ag(+) in real water samples.

  5. Optical tweezers and non-ratiometric fluorescent-dye-based studies of respiration in sperm mitochondria

    NASA Astrophysics Data System (ADS)

    Chen, Timothy; Shi, Linda Z.; Zhu, Qingyuan; Chandsawangbhuwana, Charlie; Berns, Michael W.

    2011-04-01

    The purpose of this study is to investigate how the mitochondrial membrane potential affects sperm motility using laser tweezers and a non-ratiometric fluorescent probe, DiOC6(3). A 1064 nm Nd:YVO4 continuous wave laser was used to trap motile sperm at a power of 450 mW in the trap spot. Using customized tracking software, the curvilinear velocity (VCL) and the escape force from the laser tweezers were measured. Human (Homo sapiens), dog (Canis lupis familiaris) and drill (Mandrillus leucophaeus) sperm were treated with DiOC6(3) to measure the membrane potential in the mitochondria-rich sperm midpieces. Sperm from all three species exhibited an increase in fluorescence when treated with the DiOC6(3). When a cyanide inhibitor (CCCP) of aerobic respiration was applied, sperm of all three species exhibited a reduction in fluorescence to pre-dye levels. With respect to VCL and escape force, the CCCP had no effect on dog or human sperm, suggesting a major reliance upon anaerobic respiration (glycolysis) for ATP in these two species. Based on the preliminary study on drill sperm, CCCP caused a drop in the VCL, suggesting potential reliance on both glycolysis and aerobic respiration for motility. The results demonstrate that optical trapping in combination with DiOC6(3) is an effective way to study sperm motility and energetics.

  6. Highly sensitive ratiometric quantification of cyanide in water with gold nanoparticles via Resonance Rayleigh Scattering.

    PubMed

    Hernández, Yulán; Coello, Yves; Fratila, Raluca M; de la Fuente, Jesús M; Lionberger, Troy A

    2017-05-15

    A highly sensitive and selective ratiometric sensor for the quantification of cyanide (CN(-)) in aqueous samples has been developed using spherical gold nanoparticles (AuNPs) stabilized by polysorbate 40 (PS-40). Three different AuNP sizes (14, 40 and 80nm mean diameters) were used to evaluate the response of the sensor using both colorimetric and Resonance Rayleigh Scattering (RRS) detection schemes. The best results were obtained for the sensor using 40nm AuNPs, for which the limits of detection (LODs) were found to be 100nmolL(-1) in a benchtop instrument and 500nmolL(-1) by the naked eye, values well below the maximum acceptable level for drinking water (1.9µmolL(-1)) set by the World Health Organization (WHO). The practical use of the 40nm-AuNPs RRS sensor was demonstrated with the determination of CN(-) in drinking and fresh waters. Finally, the sensor was successfully implemented in a compact portable device consisting of two light-emitting diodes (LEDs) and a miniature spectrometer, turning this sensor into a very potent tool for its application as a quick routine field-deployable analytical method.

  7. Ratiometric Dissolved Oxygen Sensors Based on Ruthenium Complex Doped with Silver Nanoparticles.

    PubMed

    Jiang, Zike; Yu, Xinsheng; Zhai, Shikui; Hao, Yingyan

    2017-03-09

    A ratiometric optical sensor has been developed with electrospinning processing method for dissolved oxygen measurement. The sensing film is fabricated by using silver nano-particles (Ag NPs) doped with tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) dichloride complex (Ru(DPP)₃Cl₂) encapsulated in plasticized polymethyl methacrylate (PMMA). An insensitive 3-(2-benzothiazolyl)-7-(diethy lamino)-(6CI,7CI) (Coumarin6) is adopted as reference. The ratio of oxygenation is calculated at each image pixel of a 3CCD camera to quantify the oxygen concentration in aqueous environment. Compared to Ag-free film, the response time of Ag-containing films were improved from 1.5 s to 1.0 s upon switching from deoxygenated to air saturation and from 65 s to 45 s from air saturation to fully deoxygenated. The response times of the Ag-free film obtained by knifing was 2.0 s upon switching from deoxygenated to air saturation and 104 s from air saturation to fully deoxygenated. Results of the evaluation of accuracy, limit of detection, stability, and photostability are presented. An experiment measuring the spatiotemporal variation of oxygen distribution within the photosynthesis and respiration of Chlorella vulgaris is demonstrated. It is shown that the nanofiber-based optical sensor film could serve as a promising method for rapid oxygen monitoring in aqueous applications.

  8. A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters.

    PubMed

    Del Bonis-O'Donnell, Jackson Travis; Vong, Daniel; Pennathur, Sumita; Fygenson, Deborah Kuchnir

    2016-08-14

    DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag(+) ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.

  9. Quantitative ratiometric discrimination between noncancerous and cancerous prostate cells based on neuropilin-1 overexpression.

    PubMed

    Pallaoro, Alessia; Braun, Gary B; Moskovits, Martin

    2011-10-04

    A multiplexed, ratiometric method is described that can confidently distinguish between cancerous and noncancerous epithelial prostate cells in vitro. The technique is based on bright surface-enhanced resonance Raman scattering (SERRS) biotags (SBTs) infused with unique Raman reporter molecules, and carrying cell-specific peptides. Two sets of SBTs were used. One targets the neuropilin-1 (NRP-1) receptors of cancer cells through the RPARPAR peptide. The other functions as a positive control (PC) and binds to both noncancerous and cancer cells through the HIV-derived TAT peptide. Point-by-point 2D Raman maps of the spatial distribution of the two tags were constructed with subcellular resolution from cells simultaneously incubated with the two sets of SBTs. Averaging the SERRS signal over a given cell yielded an NRP/PC ratio from which a robust quantitative measure of the overexpression of the NRP-1 by the cancer cell line was extracted. The use of a local, on-cell reference produces quantitative, statistically robust measures of overexpression independent of such sources of uncertainty as variations in the location of the focal plane, the local cell concentration, and turbidity.

  10. A ratiometric fluorescent probe for alkaline phosphatase via regulation of excited-state intramolecular proton transfer.

    PubMed

    Fan, Chunlei; Luo, Shengxu; Qi, Haiping

    2016-03-01

    A ratiometric fluorescent probe 2-(benzimidazol-2-yl)phenyl phosphoric acid (1) for alkaline phosphatase (ALP) is designed and synthesized. The method employs the modulation of the excited-state intramolecular proton transfer (ESIPT) process of 2-(2'-hydroxyphenyl)benzimidazole (HPBI) through the hydroxyl group protection/deprotection reaction. Upon phosphorylated with POCl3 , HPBI shows only an emission peak at 363 nm due to the blockage of ESIPT. However, once selective enzymatic hydrolysis with alkaline phosphatase (ALP) in Tris-HCl buffer occurs, the probe 1 is returned to HPBI and the ESIPT process is switched on, which results in a decrease in the emission band at 363 nm and an increase in a new fluorescence peak around 430 nm. The fluorescence intensity ratio at 430 and 360 nm (I430/I360) increases linearly with the activity of ALP up to 0.050 U/mL and the detection limit is 0.0013 U/mL. The proposed probe shows excellent specificity toward ALP.

  11. Ratiometric coumarin-neutral red (CONER) nanoprobe for detection of hydroxyl radicals.

    PubMed

    Ganea, Gabriela M; Kolic, Paulina E; El-Zahab, Bilal; Warner, Isiah M

    2011-04-01

    Excessive production of reactive oxygen species can lead to alteration of cellular functions responsible for many diseases including cardiovascular diseases, neurodegenerative diseases, cancer, and aging. Hydroxyl radical is a short-lived radical which is considered very aggressive due to its high reactivity toward biological molecules. In this study, a COumarin-NEutral Red (CONER) nanoprobe was developed for detection of hydroxyl radical based on the ratiometric fluorescence signal between 7-hydroxy coumarin 3-carboxylic acid and neutral red dyes. Biocompatible poly lactide-co-glycolide (PLGA) nanoparticles containing encapsulated neutral red were produced using a coumarin 3-carboxylic acid conjugated poly(sodium N-undecylenyl-Nε-lysinate) (C3C-poly-Nε-SUK) as moiety reactive to hydroxyl radicals. The response of the CONER nanoprobe was dependent on various parameters such as reaction time and nanoparticle concentration. The probe was selective for hydroxyl radicals as compared with other reactive oxygen species including O(2)(•-), H(2)O(2), (1)O(2), and OCl(-). Furthermore, the CONER nanoprobe was used to detect hydroxyl radicals in vitro using viable breast cancer cells exposed to oxidative stress. The results suggest that this nanoprobe represents a promising approach for detection of hydroxyl radicals in biological systems.

  12. A real-time single sperm tracking, laser trapping, and ratiometric fluorescent imaging system

    NASA Astrophysics Data System (ADS)

    Shi, Linda Z.; Botvinick, Elliot L.; Nascimento, Jaclyn; Chandsawangbhuwana, Charlie; Berns, Michael W.

    2006-08-01

    Sperm cells from a domestic dog were treated with oxacarbocyanine DiOC II(3), a ratiometrically-encoded membrane potential fluorescent probe in order to monitor the mitochondria stored in an individual sperm's midpiece. This dye normally emits a red fluorescence near 610 nm as well as a green fluorescence near 515 nm. The ratio of red to green fluorescence provides a substantially accurate and precise measurement of sperm midpiece membrane potential. A two-level computer system has been developed to quantify the motility and energetics of sperm using video rate tracking, automated laser trapping (done by the upper-level system) and fluorescent imaging (done by the lower-level system). The communication between these two systems is achieved by a networked gigabit TCP/IP cat5e crossover connection. This allows for the curvilinear velocity (VCL) and ratio of the red to green fluorescent images of individual sperm to be written to the hard drive at video rates. This two-level automatic system has increased experimental throughput over our previous single-level system (Mei et al., 2005) by an order of magnitude.

  13. Dual wavelength fluorescent ratiometric pH measurement by scanning near-field optical microscopy

    NASA Astrophysics Data System (ADS)

    Li, Yongbo; Shinohara, Ryosuke; Iwami, Kentaro; Ohta, Yoshihiro; Umeda, Norihiro

    2010-08-01

    A novel method to observe pH distribution by dual wavelength fluorescent ratiometric pH measurement by scanning near-field optical microscopy (SNOM) is developed. In this method, in order to investigate not only the pH of mitochondrial membrane but also its distribution in the vicinity, a pH sensitive fluorescent reagent covers mitochondria instead of injecting it to mitochondria. This method utilizes a dual-emission pH sensitive dye and SNOM with a themally-pulled and metal-coated optical fiber to improve the spatial resolution. Time-dependence of Fluorescent intensity ratio (FIR) under acid addition is investigated. As the distances between the dropped point and the SNOM probe becomes closer, the time when FIR changes becomes earlier. The response of mitochondria under supplement of nutrition is studied by using this method. While the probe is near to mitochondria, the ratio quickly becomes to increase. In conclusion, it was confirmed that the temporal variation of pH can be detected by this method, and pH distribution in the vicinity of mitochondria is able to be measured by this method.

  14. UV-Vis Ratiometric Resonance Synchronous Spectroscopy for Determination of Nanoparticle and Molecular Optical Cross Sections.

    PubMed

    Nettles, Charles B; Zhou, Yadong; Zou, Shengli; Zhang, Dongmao

    2016-03-01

    Demonstrated herein is a UV-vis Ratiometric Resonance Synchronous Spectroscopic (R2S2, pronounced as "R-two-S-two" for simplicity) technique where the R2S2 spectrum is obtained by dividing the resonance synchronous spectrum of a NP-containing solution by the solvent resonance synchronous spectrum. Combined with conventional UV-vis measurements, this R2S2 method enables experimental quantification of the absolute optical cross sections for a wide range of molecular and nanoparticle (NP) materials that range optically from pure photon absorbers or scatterers to simultaneous photon absorbers and scatterers, simultaneous photon absorbers and emitters, and all the way to simultaneous photon absorbers, scatterers, and emitters in the UV-vis wavelength region. Example applications of this R2S2 method were demonstrated for quantifying the Rayleigh scattering cross sections of solvents including water and toluene, absorption and resonance light scattering cross sections for plasmonic gold nanoparticles, and absorption, scattering, and on-resonance fluorescence cross sections for semiconductor quantum dots (Qdots). On-resonance fluorescence quantum yields were quantified for the model molecular fluorophore Eosin Y and fluorescent Qdots CdSe and CdSe/ZnS. The insights and methodology presented in this work should be of broad significance in physical and biological science research that involves photon/matter interactions.

  15. Reaction-based probe for hydrogen sulfite: dual-channel and good ratiometric response.

    PubMed

    Cheng, Xiaohong; He, Ping; Zhong, Zhicheng; Liang, Guijie

    2016-11-01

    We designed and synthesized a new series of intramolecular charge transfer (ICT) molecules (compounds T1, T2 and T3) by attaching various electron-donating thiophene groups to the triphenylamine backbone with aldehyde group as the electron acceptor. Based on the nucleophilic addition reaction between hydrogen sulfite and aldehyde, all compounds could act as ratiometric optical probe for hydrogen sulfite and displayed efficient chromogenic and fluorogenic signaling. Upon the addition of hydrogen sulfite anions, probe T3 displayed apparent fluorescent color changes from yellowish-green to blue, with a large emission wavelength shift (Δλ = 120 nm). T3 responded to hydrogen sulfite with high sensitivity and the detection limit was determined to be as low as 0.9 μM. At the same time, apparent changes in UV-vis spectra could also be observed. By virtue of the special nucleophilic addition reaction with aldehyde, T3 displayed high selectivity over other anions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin.

    PubMed

    Wang, Xiaoyan; Yu, Jialuo; Kang, Qi; Shen, Dazhong; Li, Jinhua; Chen, Lingxin

    2016-03-15

    A facile strategy was developed to prepare molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin (PC) based on fluorescence resonance energy transfer (FRET), via a sol-gel polymerization process using nitrobenzoxadiazole (NBD) as fluorescent signal source. The ratio of two fluorescence peak emission intensities of NBD and PC was utilized to determine the concentration of PC, which could effectively reduce the background interference and fluctuation of diverse conditions. As a result, this sensor obtained high sensitivity with a low detection limit of 0.14 nM within 6 min, and excellent recognition specificity for PC over its analogues with a high imprinting factor of 9.1. Furthermore, the sensor attained high recoveries in the range of 93.8-110.2% at three spiking levels of PC, with precisions below 4.7% in seawater and lake water samples. The developed sensor strategy demonstrated simplicity, reliability, rapidity, high selectivity and high sensitivity, proving to be a feasible way to develop high efficient fluorescence sensors and thus potentially applicable for ultratrace analysis of complicated matrices.

  17. The synthesis of new fluorescent bichromophoric compounds as ratiometric pH probes for intracellular measurements.

    PubMed

    Saura, A Vanessa; Marín, María J; Burguete, M Isabel; Russell, David A; Galindo, Francisco; Luis, Santiago V

    2015-07-28

    Three different bichromophoric compounds (1-3) containing an aminomethyl anthracene moiety linked to a second chromophore (pyrene, 4-nitrobenzo-2-oxa-1,3-diazole (NBD) and dansyl) through a valine-derived pseudopeptidic spacer have been prepared and their fluorescent properties studied. The results obtained show that upon irradiation the photophysical behavior of these probes involves electronic energy transfer from the excited anthracene to the second chromophore and also intramolecular photoinduced electron transfer. The X-ray structure obtained for 3 reveals that the folding associated with the pseudopeptidic spacer favours a close proximity of the two chromophores. The emissive response of 3 is clearly dependent on the pH of the medium, hence this bichromophoric compound was shown to be an excellent ratiometric pH fluorescent sensor. The emission intensity due to the anthracene moiety exhibits a decrease at neutral-basic pH values that is concomitant with an increase in the intensity arising from the dansyl fluorophore. These properties make this compound a good candidate for biological pH sensing as has been confirmed by preliminary studies with RAW 264.7 macrophage cells imaged by means of confocal fluorescence microscopy with an average pH estimation of 5.4-5.8 for acidic organelles.

  18. A Novel, Rapid Method to Quantify Intraplatelet Calcium Dynamics by Ratiometric Flow Cytometry

    PubMed Central

    Assinger, Alice; Volf, Ivo; Schmid, Diethart

    2015-01-01

    Cytosolic free calcium ions represent important second-messengers in platelets. Therefore, quantitative measurement of intraplatelet calcium provides a popular and very sensitive tool to evaluate platelet activation and reactivity. Current protocols for determination of intracellular calcium concentrations in platelets have a number of limitations. Cuvette-based methods do not allow measurement of calcium flux in complex systems, such as whole blood, and therefore require isolation steps that potentially interfere with platelet activation. Flow cytometry has the potential to overcome this limitation, but to date the application of calibrated, quantitative readout of calcium kinetics has only been described for Indo-1. As excitation of Indo-1 requires a laser in the ultraviolet range, such measurements cannot be performed with a standard flow cytometer. Here, we describe a novel, rapid calibration method for ratiometric calcium measurement in platelets using both Ar+-laser excited fluorescence dyes Fluo-4 and Fura Red. We provide appropriate equations that allow rapid quantification of intraplatelet calcium fluxes by measurement of only two standardisation buffers. We demonstrate that this method allows quantitative calcium measurement in platelet rich plasma as well as in whole blood. Further, we show that this method prevents artefacts due to platelet aggregate formation and is therefore an ideal tool to determine basal and agonist induced calcium kinetics. PMID:25849642

  19. A ratiometric chemodosimeter for highly selective naked-eye and fluorogenic detection of cyanide.

    PubMed

    Lin, Wei-Chi; Hu, Jiun-Wei; Chen, Kew-Yu

    2015-09-17

    A simple indole-based chemosensor (1) with a very low molecular weight of 207 g mol(-1) has been synthesized for the highly reactive and selective detection of CN(-) in aqueous media, even in the presence of other anions, such as F(-), Cl(-), Br(-), AcO(-), [Formula: see text] , SCN(-), [Formula: see text] , [Formula: see text] , [Formula: see text] , BzO(-), [Formula: see text] , and [Formula: see text] . The sensor achieves rapid detection of cyanide anion in 2 min, and the pseudo-first-order rate constant is estimated as 1.576 min(-1). The colorimetric and ratiometric fluorescent response of the sensor to CN(-) is attributable to the addition of CN(-) to the electron-deficient dicyanovinyl group of 1, which prevents intramolecular charge transfer. The sensing mechanism is supported by density functional theory and time-dependent density functional theory calculations. Moreover, sensor 1 exhibits both high accuracy in determining the concentration of CN(-) in real samples and 1-based test strips can conveniently detect CN(-) without any additional equipment. The detection limit of the sensor 1 (1.1 μM) for cyanide is lower than the maximum permissible level of CN(-) (1.9 μM) in drinking water. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Ratiometric near-infrared chemosensor for trivalent chromium ion based on tricarboyanine in living cells.

    PubMed

    Li, Chun-Yan; Kong, Xue-Fei; Li, Yong-Fei; Weng, Chao; Tang, Jia-Liang; Liu, Dan; Zhu, Wei-Guo

    2014-05-08

    A tricarboyanine derivative (IRPP) is applied as a ratiometric near-infrared chemosensor for detecting trivalent chromium ions (Cr(3+)) in living cells. Upon the addition of Cr(3+) to a solution of IRPP, large-scale shifts in the emission spectrum (from 755 nm to 561 nm) are observed. In the newly developed sensing system, these well-resolved emission peaks yield a sensing system that covers a linear range from 1.0×10(-7) to 1.0×10(-5) M with a detection limit of 2.5×10(-8) M. The experimental results show the response behavior of IRPP towards Cr(3+) is pH independent under neutral conditions (6.0-7.5). Most importantly, the fast response time (less than 3 min) and selectivity for Cr(3+) over other common metal ions provide a strong argument for the use of this sensor in real world applications. As a proof of concept, the proposed chemosensor has been used to detect and quantify Cr(3+) in river water samples and to image Cr(3+) in living cells with encouraging results. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Ratiometric analysis of Acridine Orange staining in the study of acidic organelles and autophagy.

    PubMed

    Thomé, Marcos P; Filippi-Chiela, Eduardo C; Villodre, Emilly S; Migliavaca, Celina B; Onzi, Giovana R; Felipe, Karina B; Lenz, Guido

    2016-12-15

    Acridine Orange is a cell-permeable green fluorophore that can be protonated and trapped in acidic vesicular organelles (AVOs). Its metachromatic shift to red fluorescence is concentration-dependent and, therefore, Acridine Orange fluoresces red in AVOs, such as autolysosomes. This makes Acridine Orange staining a quick, accessible and reliable method to assess the volume of AVOs, which increases upon autophagy induction. Here, we describe a ratiometric analysis of autophagy using Acridine Orange, considering the red-to-green fluorescence intensity ratio (R/GFIR) to quantify flow cytometry and fluorescence microscopy data of Acridine-Orange-stained cells. This method measured with accuracy the increase in autophagy induced by starvation or rapamycin, and the reduction in autophagy produced by bafilomycin A1 or the knockdown of Beclin1 or ATG7. Results obtained with Acridine Orange, considering R/GFIR, correlated with the conversion of the unlipidated form of LC3 (LC3-I) into the lipidated form (LC3-II), SQSTM1 degradation and GFP-LC3 puncta formation, thus validating this assay to be used as an initial and quantitative method for evaluating the late step of autophagy in individual cells, complementing other methods. © 2016. Published by The Company of Biologists Ltd.

  2. Highly-sensitive Eu(3+) ratiometric thermometers based on excited state absorption with predictable calibration.

    PubMed

    Souza, Adelmo S; Nunes, Luiz A O; Silva, Ivan G N; Oliveira, Fernando A M; da Luz, Leonis L; Brito, Hermi F; Felinto, Maria C F C; Ferreira, Rute A S; Júnior, Severino A; Carlos, Luís D; Malta, Oscar L

    2016-03-07

    Temperature measurements ranging from a few degrees to a few hundreds of Kelvin are of great interest in the fields of nanomedicine and nanotechnology. Here, we report a new ratiometric luminescent thermometer using thermally excited state absorption of the Eu(3+) ion. The thermometer is based on the simple Eu(3+) energy level structure and can operate between 180 and 323 K with a relative sensitivity ranging from 0.7 to 1.7% K(-1). The thermometric parameter is defined as the ratio between the emission intensities of the (5)D0 → (7)F4 transition when the (5)D0 emitting level is excited through the (7)F2 (physiological range) or (7)F1 (down to 180 K) level. Nano and microcrystals of Y2O3:Eu(3+) were chosen as a proof of concept of the operational principles in which both excitation and detection are within the first biological transparent window. A novel and of paramount importance aspect is that the calibration factor can be calculated from the Eu(3+) emission spectrum avoiding the need for new calibration procedures whenever the thermometer operates in different media.

  3. Lanthanoid-Doped Phosphate/Vanadate Mixed Hollow Particles as Ratiometric Luminescent Sensors.

    PubMed

    de Sousa Filho, Paulo C; Larquet, Eric; Dragoë, Diana; Serra, Osvaldo A; Gacoin, Thierry

    2017-01-18

    Rare earth (RE) phosphates and vanadates are structurally similar compositions that display distinct but complementary luminescent properties. The properties of these phosphors can be combined in REPO4-REVO4 heterostructures during the development of new sensing technologies for biological applications. This work presents the synthesis of hollow RE phosphate/vanadate colloidal particles and evaluates their applicability as luminescent markers. Hydrothermal treatments of RE hydroxycarbonate particles in the presence of the PO4(3-) and VO4(3-) precursors afforded the final REPO4-REVO4 solids in a two-step template synthesis. We converted precursor hydroxycarbonate particles into the final heterostructures and characterized their structure and morphology. According to our detailed study into the spectroscopic properties of Eu(3+)-doped particles and their luminescence response to several species, the presence of the phosphate and vanadate phases in a single particle provided different chemical environments and enabled the design of a ratiometric approach to detect H2O2. These results open new perspectives for the development of new intracellular luminescent markers.

  4. Polycation-induced benzoperylene probe excimer formation and the ratiometric detection of heparin and heparinase.

    PubMed

    Yang, Meiding; Chen, Jian; Zhou, Huipeng; Li, Wenying; Wang, Yan; Li, Juanmin; Zhang, Cuiyun; Zhou, Chuibei; Yu, Cong

    2016-01-15

    A benzoperylene probe excimer emission in an aqueous buffer solution is observed for the first time, and a novel ratiometric fluorescence method based on the probe excimer emission for the sensitive detection of heparin and heparinase is demonstrated. A negatively charged benzoperylene derivative, 6-(benzo[ghi]perylene-1,2-dicarboxylic imide-yl)hexanoic acid (BPDI), was employed. A polycation, poly(diallyldimethylammonium) chloride (poly-DDA), could induce aggregation of BPDI through noncovalent interactions. A decrease of BPDI monomer emission and a simultaneous increase of BPDI excimer emission were observed. Upon the addition of heparin, the strong binding between heparin and poly-DDA caused release of BPDI monomer molecules, and an excimer-monomer emission signal transition was detected. However, after the enzymatic hydrolysis of heparin by heparinase, heparin was hydrolyzed into small fragments, which weakened the competitive binding of heparin to poly-DDA. Poly-DDA induced aggregation of BPDI, and a monomer-excimer emission signal transition was detected. Our assay is simple, rapid, inexpensive, sensitive and selective, which could facilitate the heparin and heparinase related biochemical and biomedical research.

  5. Real-time ratiometric fluorescent assay for alkaline phosphatase activity with stimulus responsive infinite coordination polymer nanoparticles.

    PubMed

    Deng, Jingjing; Yu, Ping; Wang, Yuexiang; Mao, Lanqun

    2015-03-03

    This study demonstrates a novel ratiometric fluorescent method for real-time alkaline phosphatase (ALP) activity assay with stimulus responsive infinite coordination polymer (ICP) nanoparticles as the probe. The ICP nanoparticles used in this study are composed of two components; one is the supramolecular ICP network formed with guanine monophosphate (GMP) as the ligand and Tb(3+) as the central metal ion, and the other is a fluorescent dye, i.e., 7-amino-4-methyl coumarin (coumarin) encapsulated into the ICP network. Upon being excited at 315 nm, the ICP network itself emits green fluorescence at 552 nm. Coumarin dye encapsulated in the ICP network emits weak fluorescence at 450 nm upon excitation at the same wavelength (315 nm), and this fluorescence emission becomes strong when the encapsulated dye is released from the network into the solution phase. Hence, we develop a ratiometric fluorescent assay based on the ALP-induced destruction of the supramolecular ICP network and the release of coumarin. This mechanism can be used for real-time ratiometric fluorescent monitoring of ALP activity by continuously measuring the ratio of fluorescent intensity at the wavelength of 552 nm (F552) to that at 450 nm (F450) (F552/F450) in the time-dependent fluorescent spectra of the coumarin@Tb-GMP suspension containing ALP with different activities. Under the experimental conditions employed here, the F552/F450 value is linear with the ALP activity within a range from 0.025 U/mL to 0.2 U/mL. The detection limit is down to 0.010 U/mL (S/N = 3). Moreover, the assay developed here is employed for ALP inhibitor evaluation. This study offers a simple yet sensitive method for real-time ALP activity assay.

  6. Electro-Grafted Electrode with Graphene-oxide-Like DNA Affinity for Ratiometric Homogeneous Electrochemical Biosensing of MicroRNA.

    PubMed

    Ge, Lei; Wang, Wenxiao; Li, Feng

    2017-10-10

    This work demonstrated for the first time a simple and rapid approach to endow the electrode with the excellent discrimination ability over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) through the robust electrochemical grafting of in-situ generated 1-naphthalenesulfonate (NS(-)) diazonium salt onto the surface of indium tin oxide (ITO) electrode. On the basis of understanding the influence of sequence and length on the binding affinity of ssDNA and dsDNA toward NS(-) grafted ITO (NS(-)-ITO) electrode, these interesting findings were successfully employed to rationally develop a ratiometric homogeneous electrochemical biosensing platform for microRNA based on the affinity-mediated signal transduction. The achievement of ultrasensitive detection of microRNA lies in a compatibly designed T7 exonuclease-assisted isothermal amplification strategy, in which the presence of target microRNA initiated the continual and opposite affinity-inversion of two rationally engineered electrochemical signal reporters, methylene blue (MB) labeled hairpin reporter and ferrocene (Fc) labeled dsDNA reporter, toward NS(-)-ITO electrode, thereby providing the ratiometric transduction and amplification of the homogeneous electrochemical output signal. By measuring the distinct variation in the peak current intensity ratios of Fc and MB tags, this ratiometric homogeneous electrochemical microRNA biosensing platform showed a detection limit of 25 aM, which is much lower than that of the reported homogeneous electrochemical biosensors. Therefore, we envision that the proposed approach will find useful applications in disease molecular diagnoses and biomedicine.

  7. Graphitic Carbon Nitride Nanosheets-Based Ratiometric Fluorescent Probe for Highly Sensitive Detection of H2O2 and Glucose.

    PubMed

    Liu, Jin-Wen; Luo, Ying; Wang, Yu-Min; Duan, Lu-Ying; Jiang, Jian-Hui; Yu, Ru-Qin

    2016-12-14

    Graphitic carbon nitride (g-C3N4) nanosheets, an emerging graphene-like carbon-based nanomaterial with high fluorescence and large specific surface areas, hold great potential for biosensor applications. Current g-C3N4 nanosheets based fluorescent biosensors majorly rely on single fluorescent intensity reading through fluorescence quenching interactions between the nanosheets and metal ions. Here we report for the first time the development of a novel g-C3N4 nanosheets-based ratiometric fluorescence sensing strategy for highly sensitive detection of H2O2 and glucose. With o-phenylenediamine (OPD) oxidized by H2O2 in the presence of horseradish peroxidase (HRP), the oxidization product can assemble on the g-C3N4 nanosheets through hydrogen bonding and π-π stacking, which effectively quenches the fluorescence of g-C3N4 while delivering a new emission peak. The ratiometric signal variations enable robust and sensitive detection of H2O2. On the basis of the glucose converting into H2O2 through the catalysis of glucose oxidase, the g-C3N4-based ratiometric fluorescence sensing platform is also exploited for glucose assay. The developed strategy is demonstrated to give a detection limit of 50 nM for H2O2 and 0.4 μM for glucose, at the same time, it has been successfully used for glucose levels detection in human serum. This strategy may provide a cost-efficient, robust, and high-throughput platform for detecting various species involving H2O2-generation reactions for biomedical applications.

  8. FITC Doped Rattle-Type Silica Colloidal Particle-Based Ratiometric Fluorescent Sensor for Biosensing and Imaging of Superoxide Anion.

    PubMed

    Zhou, Ying; Ding, Jie; Liang, Tingxizi; Abdel-Halim, E S; Jiang, Liping; Zhu, Jun-Jie

    2016-03-01

    Fluorescent nanosensors have been widely applied in recognition and imaging of bioactive small molecules; however, the complicated surface modification process and background interference limit their applications in practical biological samples. Here, a simple, universal method was developed for ratiometric fluorescent determination of general small molecules. Taking superoxide anion (O2(•-)) as an example, the designed sensor was composed of three main moieties: probe carrier, rattle-type silica colloidal particles (mSiO2@hmSiO2 NPs); reference fluorophore doped into the core of NPs, fluorescein isothiocyanate (FITC); fluorescent probe for superoxide anion, hydroethidine (HE). In the absence of O2(•-), the sensor just emitted green fluorescence of FITC at 518 nm. When released HE was oxidized by O2(•-), the oxidation product exhibited red fluorescence at 570 nm and the intensity was linearly associated with the concentration of O2(•-), while that of reference element remained constant. Accordingly, ratiometric determination of O2(•-) was sensitively and selectively achieved with a linear range of 0.2-20 μM, and the detection limit was calculated as low as 80 nM. Besides, the technique was also successfully applied for dual-emission imaging of O2(•-) in live cells and realized visual recognition with obvious fluorescence color change in normal conditions or under oxidative stress. As long as appropriate reference dyes and sensing probes are selected, ratiometric biosensing and imaging of bioactive small molecules would be achieved. Therefore, the design could provide a simple, accurate, universal platform for biological applications.

  9. An Nd3+-sensitized upconversion nanophosphor modified with a cyanine dye for the ratiometric upconversion luminescence bioimaging of hypochlorite

    NASA Astrophysics Data System (ADS)

    Zou, Xianmei; Liu, Yi; Zhu, Xingjun; Chen, Min; Yao, Liming; Feng, Wei; Li, Fuyou

    2015-02-01

    Excessive or misplaced production of ClO- in living systems is usually associated with many human diseases. Therefore, it is of great importance to develop an effective and sensitive method to detect ClO- in living systems. Herein, we designed an 808 nm excited upconversion luminescence nanosystem, composed of the Nd3+-sensitized core-shell upconversion nanophosphor NaYF4:30%Yb,1%Nd,0.5%Er@NaYF4:20%Nd, which serves as an energy donor, and the ClO--responsive cyanine dye hCy3, which acts as an energy acceptor, for ratiometric upconversion luminescence (UCL) monitoring of ClO-. The detection limit of ClO- for this nanoprobe in aqueous solution is 27 ppb and the nanoprobe was successfully used to detect the ClO- in the living cells by ratiometric upconversion luminescence. Importantly, the nanoprobe realized the detection of ClO- in a mouse model of arthritis, which produced an excess of ROS, under 808 nm irradiation in vivo. The excitation laser efficiently reduced the heating effect, compared to the commonly used 980 nm laser for upconversion systems.Excessive or misplaced production of ClO- in living systems is usually associated with many human diseases. Therefore, it is of great importance to develop an effective and sensitive method to detect ClO- in living systems. Herein, we designed an 808 nm excited upconversion luminescence nanosystem, composed of the Nd3+-sensitized core-shell upconversion nanophosphor NaYF4:30%Yb,1%Nd,0.5%Er@NaYF4:20%Nd, which serves as an energy donor, and the ClO--responsive cyanine dye hCy3, which acts as an energy acceptor, for ratiometric upconversion luminescence (UCL) monitoring of ClO-. The detection limit of ClO- for this nanoprobe in aqueous solution is 27 ppb and the nanoprobe was successfully used to detect the ClO- in the living cells by ratiometric upconversion luminescence. Importantly, the nanoprobe realized the detection of ClO- in a mouse model of arthritis, which produced an excess of ROS, under 808 nm irradiation in

  10. Ratiometric fluorescent probe for rapid detection of bisulfite through 1,4-addition reaction in aqueous solution.

    PubMed

    Sun, Yue; Zhao, Dong; Fan, Shanwei; Duan, Lian; Li, Ruifeng

    2014-04-16

    A ratiometric fluorescent probe based on a positively charged benzo[e]indolium moiety for bisulfite is reported. The bisulfite underwent a 1,4-addition reaction with the C-4 atom in the ethylene group. This reaction resulted in a large emission wavelength shift (Δλ = 106 nm) and an observable fluorescent color change from orange to cyan. The reaction could be completed in 90 s in a PBS buffer solution and displayed high selectivity and sensitivity for bisulfite. A simple paper test strip system was developed to detect bisulfite rapidly. Probe 1 was used to detect bisulfite in real samples with good recovery.

  11. Ratiometric fluorescent paper sensor utilizing hybrid carbon dots-quantum dots for the visual determination of copper ions

    NASA Astrophysics Data System (ADS)

    Wang, Yahui; Zhang, Cheng; Chen, Xiaochun; Yang, Bo; Yang, Liang; Jiang, Changlong; Zhang, Zhongping

    2016-03-01

    A simple and effective ratiometric fluorescence nanosensor for the selective detection of Cu2+ has been developed by covalently connecting the carboxyl-modified red fluorescent cadmium telluride (CdTe) quantum dots (QDs) to the amino-functionalized blue fluorescent carbon nanodots (CDs). The sensor exhibits the dual-emissions peaked at 437 and 654 nm, under a single excitation wavelength of 340 nm. The red fluorescence can be selectively quenched by Cu2+, while the blue fluorescence is a internal reference, resulting in a distinguishable fluorescence color change from pink to blue under a UV lamp. The detection limit of this highly sensitive ratiometric probe is as low as 0.36 nM, which is lower than the U.S. Environmental Protection Agency (EPA) defined limit (20 μM). Moreover, a paper-based sensor has been prepared by printing the hybrid carbon dots-quantum dots probe on a microporous membrane, which provides a convenient and simple approach for the visual detection of Cu2+. Therefore, the as-synthesized probe shows great potential application for the determination of Cu2+ in real samples.A simple and effective ratiometric fluorescence nanosensor for the selective detection of Cu2+ has been developed by covalently connecting the carboxyl-modified red fluorescent cadmium telluride (CdTe) quantum dots (QDs) to the amino-functionalized blue fluorescent carbon nanodots (CDs). The sensor exhibits the dual-emissions peaked at 437 and 654 nm, under a single excitation wavelength of 340 nm. The red fluorescence can be selectively quenched by Cu2+, while the blue fluorescence is a internal reference, resulting in a distinguishable fluorescence color change from pink to blue under a UV lamp. The detection limit of this highly sensitive ratiometric probe is as low as 0.36 nM, which is lower than the U.S. Environmental Protection Agency (EPA) defined limit (20 μM). Moreover, a paper-based sensor has been prepared by printing the hybrid carbon dots-quantum dots probe on a

  12. Genetically encoded and post-translationally modified forms of a major histocompatibility complex class I-restricted antigen bearing a glycosylation motif are independently processed and co-presented to cytotoxic T lymphocytes.

    PubMed

    Hudrisier, D; Riond, J; Mazarguil, H; Oldstone, M B; Gairin, J E

    1999-12-17

    The mechanisms by which antigenic peptides bearing a glycosylation site may be processed from viral glycoproteins, post-translationally modified, and presented by major histocompatibility complex class I molecules remain poorly understood. With the aim of exploring these processes, we have dissected the structural and functional properties of the MHC-restricted peptide GP92-101 (CSANNSHHYI) generated from the lymphocytic choriomeningitis virus (LCMV) GP1 glycoprotein. LCMV GP92-101 bears a glycosylation motif -NXS- that is naturally N-glycosylated in the mature viral glycoprotein, displays high affinity for H-2D(b) molecules, and elicits a CD8(+) cytotoxic T lymphocyte response. By analyzing the functional properties of natural and synthetic peptides and by identifying the viral sequence(s) from the pool of naturally occurring peptides, we demonstrated that multiple forms of LCMV GP92-101 were generated from the viral glycoprotein and co-presented at the surface of LCMV-infected cells. They corresponded to non-glycosylated and post-translationally modified sequences (conversion of Asn-95 to Asp or alteration of Cys-92). The glycosylated form, despite its potential immunogenicity, was not detected. These data illustrate that distinct, non-mutually exclusive antigen presentation pathways may occur simultaneously within a cell to generate structurally and functionally different peptides from a single genetically encoded sequence, thus contributing to increasing the diversity of the T cell repertoire.

  13. Triple-Helix Molecular Switch Electrochemical Ratiometric Biosensor for Ultrasensitive Detection of Nucleic Acids.

    PubMed

    Xiong, Erhu; Li, Zhenzhen; Zhang, Xiaohua; Zhou, Jiawan; Yan, Xiaoxia; Liu, Yunqing; Chen, Jinhua

    2017-09-05

    Biomolecular receptors such as nucleic acids that switch between two or more conformations upon binding to a specific target can be used to build specific and sensitive biosensors. In this work, based on the electrochemical dual-signaling ratiometric strategy and triple-helix molecular switch, we developed a selective, reusable, and simple electrochemical DNA (E-DNA) biosensor for target DNA (T-DNA) detection. A hairpin DNA capture probe labeled with methylene blue (MB-DNA) self-assembles on the surface of a gold electrode (GE) through Au-S bond, and then a single-strand DNA modified with two ferrocenes (Fc-DNA) on each end to enhance the oxidation signal hybridizes with the MB-DNA to form a triple-helix conformation. When T-DNA exists, the Fc-DNA hybridizes with T-DNA disassembling the triple-helix stem and allowing the MB-DNA to revert to its hairpin structure. Hence, the Fc tags diffuse away from the GE surface while the MB tags remain affixed close to it, resulting in a decrease in the peak current of Fc (IFc) and an increase in that of MB (IMB). The linear relationship between the value of IMB/IFc and the T-DNA concentration is observed from 0.5 to 80 pM, and the limit of detection is as low as 0.12 pM. The developed E-DNA biosensor may have great potential in the electrochemical detection of a wide range of analytes and be a biosensing platform for early clinical diagnosis and biomedical research.

  14. Intracellular cascade FRET for temperature imaging of living cells with polymeric ratiometric fluorescent thermometers.

    PubMed

    Hu, Xianglong; Li, Yang; Liu, Tao; Zhang, Guoying; Liu, Shiyong

    2015-07-22

    Intracellular temperature plays a prominent role in cellular functions and biochemical activities inside living cells, but effective intracellular temperature sensing and imaging is still in its infancy. Herein, thermoresponsive double hydrophilic block copolymers (DHBCs)-based fluorescent thermometers were fabricated to investigate their application in intracellular temperature imaging. Blue-emitting coumarin monomer, CMA, green-emitting 7-nitro-2,1,3-benzoxadiazole (NBD) monomer, NBDAE, and red-emitting rhodamine B monomer, RhBEA, were copolymerized separately with N-isopropylacrylamide (NIPAM) to afford dye-labeled PEG-b-P(NIPAM-co-CMA), PEG-b-P(NIPAM-co-NBDAE), and PEG-b-P(NIPAM-co-RhBEA). Because of the favorable fluorescence resonance energy transfer (FRET) potentials between CMA and NBDAE, NBDAE and RhBEA, as well as the slight tendency between CMA and RhBEA fluorophore pairs, three polymeric thermometers based on traditional one-step FRET were fabricated by facile mixing two of these three fluorescent DHBCs, whereas exhibiting limited advantages. Thus, two-step cascade FRET among three polymeric fluorophores was further interrogated, in which NBD acted as a bridging dye by transferring energy from CMA to RhBEA. Through the delicate optimization of the molar contents of three polymeric components, a ∼8.4-fold ratio change occurred in the temperature range of 20-44 °C, and the detection sensitivity improved significantly, reached as low as ∼0.4 °C, which definitely outperformed other one-step FRET thermometers in the intracellular temperature imaging of living cells. To our knowledge, this work represents the first example of polymeric ratiometric thermometer employing thermoresponsive polymer-based cascade FRET mechanism.

  15. Ratiometric imaging of extracellular pH in bacterial biofilms with C-SNARF-4.

    PubMed

    Schlafer, Sebastian; Garcia, Javier E; Greve, Matilde; Raarup, Merete K; Nyvad, Bente; Dige, Irene

    2015-02-01

    pH in the extracellular matrix of bacterial biofilms is of central importance for microbial metabolism. Biofilms possess a complex three-dimensional architecture characterized by chemically different microenvironments in close proximity. For decades, pH measurements in biofilms have been limited to monitoring bulk pH with electrodes. Although pH microelectrodes with a better spatial resolution have been developed, they do not permit the monitoring of horizontal pH gradients in biofilms in real time. Quantitative fluorescence microscopy can overcome these problems, but none of the hitherto employed methods differentiated accurately between extracellular and intracellular microbial pH and visualized extracellular pH in all areas of the biofilms. Here, we developed a method to reliably monitor extracellular biofilm pH microscopically with the ratiometric pH-sensitive dye C-SNARF-4, choosing dental biofilms as an example. Fluorescent emissions of C-SNARF-4 can be used to calculate extracellular pH irrespective of the dye concentration. We showed that at pH values of <6, C-SNARF-4 stained 15 bacterial species frequently isolated from dental biofilm and visualized the entire bacterial biomass in in vivo-grown dental biofilms with unknown species composition. We then employed digital image analysis to remove the bacterial biomass from the microscopic images and adequately calculate extracellular pH values. As a proof of concept, we monitored the extracellular pH drop in in vivo-grown dental biofilms fermenting glucose. The combination of pH ratiometry with C-SNARF-4 and digital image analysis allows the accurate monitoring of extracellular pH in bacterial biofilms in three dimensions in real time and represents a significant improvement to previously employed methods of biofilm pH measurement.

  16. Genetically-Encoded Reporters of Signal Transduction

    DTIC Science & Technology

    2006-07-17

    the substrate by phosphorylation or methylation allows it to form an intramolecular complex with the modification-specific binding domain, increasing... hydrazide or hydroxylamine functionalized probes. Irwin labeled AP fusion proteins in vitro, in cell lysate, and on the surface of live mammalian cells...cytotoxicity of the labeling conditions, in cells or complex mixtures has never been reported. we monitored the intracellular Ca2 ÷ levels using calcium Green

  17. Genetically encoded fluorescent coumarin amino acids

    DOEpatents

    Wang, Jiangyun [San Diego, CA; Xie, Jianming [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2012-06-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  18. Genetically encoded fluorescent coumarin amino acids

    DOEpatents

    Wang, Jiangyun; Xie, Jianming; Schultz, Peter G.

    2010-10-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl) ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  19. A high-resolution mitochondria-targeting ratiometric fluorescent probe for detection of the endogenous hypochlorous acid

    NASA Astrophysics Data System (ADS)

    Zhou, Liyi; Lu, Dan-Qing; Wang, Qianqian; Hu, Shunqin; Wang, Haifei; Sun, Hongyan; Zhang, Xiaobing

    2016-09-01

    Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (Cdbnd C) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210 nm) and the two well-resolved emission peaks separated by 140 nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50 s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

  20. Label-free silicon nanodots featured ratiometric fluorescent aptasensor for lysosomal imaging and pH measurement.

    PubMed

    Zhang, Yanan; Guo, Shan; Cheng, Shibo; Ji, Xinghu; He, Zhike

    2017-03-22

    The homeostasis of lysosomal pH is crucial in cell physiology. Developing small fluorescent nanosensors for lysosome imaging and ratiometric measurement of pH is highly demanded yet challenging. Herein, a pH-sensitive fluorescein tagged aptamer AS1411 has been utilized to covalently modify the label-free fluorescent silicon nanodots via a crosslinker for construction of a ratiometric pH biosensor. The established aptasensor exhibits the advantages of ultrasmall size, hypotoxicity, excellent pH reversibility and good photostability, which favors its application in an intracellular environment. Using human breast MCF-7 cancer cells and MCF-10A normal cells as the model, this aptasensor shows cell specificity for cancer cells and displays a wide pH response range of 4.5-8.0 in living cells. The results demonstrate that the pH of MCF-7 cells is 5.1, which is the expected value for acidic organelles. Lysosome imaging and accurate measurement of pH in MCF-7 cells have been successfully conducted based on this nanosensor via fluorescent microscopy and flow cytometry.

  1. Ratiometric fluorescence sensor based on a pyrene derivative and quantification detection of heparin in aqueous solution and serum.

    PubMed

    Dai, Qing; Liu, Weimin; Zhuang, Xiaoqing; Wu, Jiasheng; Zhang, Hongyan; Wang, Pengfei

    2011-09-01

    A ratiometric fluorescence sensor based on pyrene was designed for selective detection of heparin in HEPES (N-(2-hydroxyethyl)piperazine-N'-ethanesulfonic acid) buffer and serum sample. Pyrene and long-chain alkanes were linked through bisquaternary functionality in the sensor which could interact with heparin via supramolecular assembly. A ratiometric fluorescent signal change of the sensor can be observed because of the specific monomer-excimer conversion of pyrene which is modulated by the supramolecular self-assembly of sensor and heparin. Upon addition of heparin, the excimer emission of the sensor at 489 nm is observed and the monomer emission intensity at 395 nm decreases concomitantly. Addition of heparin derivatives with very similar structure such as chondroitin 4-sulfate or hyaluronic acid to the same sensor solution only leads to very smaller changes in intensity ratios probably because of lower charge density and more distant spatial distribution of anions (or disadvantageous spatial orientation of anions) as compared to those of heparin. The novel sensor can effectively differentiate heparin from its derivatives with relatively low background interference and wide linear response in HEPES and serum. A linear calibration curve is obtained from 0 to 3.4 μM for heparin quantification in serum.

  2. Selective detection of endogenous H2S in living cells and the mouse hippocampus using a ratiometric fluorescent probe

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Meng, Wen-Qi; Lu, Liang; Xue, Yun-Sheng; Li, Cheng; Zou, Fang; Liu, Yi; Zhao, Jing

    2014-07-01

    As one of three gasotransmitters, the fundamental signalling roles of hydrogen sulphide are receiving increasing attention. New tools for the accurate detection of hydrogen sulphide in cells and tissues are in demand to probe its biological functions. We report the p-nitrobenzyl-based ratiometric fluorescent probe RHP-2, which features a low detection limit, high selectivity and good photostability. The emission intensity ratios had a good linear relationship with the sulphide concentrations in PBS buffer and bovine serum. Our probe was applied to the ratiometric determination and imaging of endogenous H2S in living cells. Furthermore, RHP-2 was used as an effective tool to measure endogenous H2S in the mouse hippocampus. We observed a significant reduction in sulphide concentrations and downregulated expression of cystathionine β-synthetase (CBS) mRNA and CBS protein in the mouse hippocampus in a chronic unpredictable mild stress (CUMS)-induced depression model. These data suggested that decreased concentrations of endogenous H2S may be involved in the pathogenesis of chronic stress depression.

  3. Visual & reversible sensing of cyanide in real samples by an effective ratiometric colorimetric probe & logic gate application.

    PubMed

    Bhardwaj, Shubhrajyotsna; Singh, Ashok Kumar

    2015-10-15

    A novel anion probe 3 (2,4-di-tert-butyl-6-((2(2,4-dinitrophenyl) hydrazono) methyl) phenol) has been unveiled as an effective ratiometric and colorimetric sensor for selective and rapid detection of cyanide. The sensing behavior was demonstrated by UV-vis experiments and NMR studies. This sensory system exhibited prominent visual color change toward cyanide ion over other testing anions in DMSO (90%) solvent, with a 1:1 binding stoichiometry and a detection limit down to 3.6×10(-8) mol L(-1). Sensor reveals specific anti-jamming activity and reversible in the presence of Cu(2+) ions. This concept has been applied to design a logic gate circuit at the molecular level. Further we developed coated graphite electrode using probe 3 as ionophore and studied the performance characteristics of electrode. The sensitivity of ratiometric-based colorimetric assay is below the 1.9 μM, accepted by the World Health Organization as the highest permissible cyanide concentration in drinking water. So it can be applied for both quantitative determination and qualitative supervising of cyanide concentrations in real samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Molecular Targeting of Papillary Thyroid Carcinoma With Fluorescently Labeled Ratiometric Activatable Cell Penetrating Peptides in a Transgenic Murine Model

    PubMed Central

    OROSCO, RYAN K.; SAVARIAR, ELAMPRAKASH N.; WEISSBROD, PHILIP A.; DIAZ-PEREZ, JULIO A.; BOUVET, MICHAEL; TSIEN, ROGER Y.; NGUYEN, QUYEN T.

    2016-01-01

    Background and Objectives Molecularly targeted fluorescent molecules may help detect tumors that are unseen by traditional white-light surgical techniques. We sought to evaluate a fluorescent ratiometric activatable cell penetrating peptide (RACPP) for tumor detection in a transgenic model of PTC. Methods Thirteen BRAFV600E mice with PTC were studied—seven injected intravenously with RACPP, four controls with saline. Total thyroidectomy was performed with microscopic white-light visualization. Fluorescent imaging of post-thyroidectomy fields was performed, and tissue with increased signal was removed and evaluated for PTC. Final samples were analyzed by a pathologist blinded to conditions. Vocal cord function was evaluated postoperatively with video laryngoscopy. Results The average in situ ratiometric (Cy5/Cy7) thyroid tumor-to-background contrast ratio was 2.27 +/−0.91. Fluorescence-guided clean-up following thyroidectomy identified additional tumor in 2 of 7 RACPP animals (smallest dimension 1.2 mm), and decreased the number of animals with residual tumor from 4 to 3. All retained tumor foci on final pathology were smaller than 0.76 mm. Intact vocal abduction was present in all of the RACPP animals. Conclusions RACPPs successfully targeted PTC in a transgenic thyroidectomy model, and allowed for residual tumor detection that reduced positive margins beyond what was possible with white-light surgery alone. PMID:26799257

  5. Rhodamine-modified upconversion nanophosphors for ratiometric detection of hypochlorous acid in aqueous solution and living cells.

    PubMed

    Zhou, Yi; Pei, Wenbo; Wang, Chenyuan; Zhu, Jixin; Wu, Jiansheng; Yan, Qinyu; Huang, Ling; Huang, Wei; Yao, Cheng; Loo, Joachim Say Chye; Zhang, Qichun

    2014-09-10

    Hypochlorous acid (HOCl), a reactive oxygen species (ROS) produced by myeloperoxidase (MPO) enzyme-mediated peroxidation of chloride ions, acts as a key microbicidal agent in immune systems. However, misregulated production of HOCl could damage host tissues and cause many inflammation-related diseases. Due to its biological importance, many efforts have been focused on developing fluorescent probes to image HOCl in living system. Compared with those conventional fluorescent probes, up-conversion luminescence (UCL) detection system has been proven to exhibit a lot of advantages including no photo-bleaching, higher light penetration depth, no autofluorescence and less damage to biosamples. Herein, we report a novel water-soluble organic-nano detection system based on rhodamine-modified UCNPs for UCL-sensing HOCl. Upon the interaction with HOCl, the green UCL emission intensity in the detection system were gradually decreased, but the emissions in the NIR region almost have no change, which is very important for the ratiometric UCL detection of HOCl in aqueous solution. More importantly, RBH1-UCNPs could be used for the ratiometric UCL visualization of HOCl released by MPO-mediated peroxidation of chloride ions in living cells. This organic-nano system could be further developed into a novel next-generation imaging technique for bio-imaging HOCl in living system without background noise.

  6. New chemodosimetric reagents as ratiometric probes for cysteine and homocysteine and possible detection in living cells and in blood plasma.

    PubMed

    Das, Priyadip; Mandal, Amal Kumar; Chandar, Nellore Bhanu; Baidya, Mithu; Bhatt, Harshad B; Ganguly, Bishwajit; Ghosh, Sudip K; Das, Amitava

    2012-11-26

    In this work, we have rationally designed and synthesized two new reagents (L(1) and L(2)), each bearing a pendant aldehyde functionality. This aldehyde group can take part in cyclization reactions with β- or γ-amino thiols to yield the corresponding thiazolidine and thiazinane derivatives, respectively. The intramolecular charge-transfer (ICT) bands of these thiazolidine and thiazinane derivatives are distinctly different from those of the molecular probes (L(1) and L(2)). Such changes could serve as a potential platform for using L(1) and L(2) as new colorimetric/fluorogenic as well as ratiometric sensors for cysteine (Cys) and homocysteine (Hcy) under physiological conditions. Both reagents proved to be specific towards Cys and Hcy even in the presence of various amino acids, glucose, and DNA. Importantly, these two chemodosimetric reagents could be used for the quantitative detection of Cys present in blood plasma by using a pre-column HPLC technique. Such examples are not common in contemporary literature. MTT assay studies have revealed that these probes have low cytotoxicity. Confocal laser scanning micrographs of cells demonstrated that these probes could penetrate cell membranes and could be used to detect intracellular Cys/Hcy present within living cells. Thus, the results presented in this article not only demonstrate the efficiency and specificity of two ratiometric chemodosimeter molecules for the quantitative detection of Cys and Hcy, but also provide a strategy for developing reagents for analysis of these vital amino acids in biological samples.

  7. Self-Assembled Fluorescent Bovine Serum Albumin Nanoprobes for Ratiometric pH Measurement inside Living Cells.

    PubMed

    Yang, Qiaoyu; Ye, Zhongju; Zhong, Meile; Chen, Bo; Chen, Jian; Zeng, Rongjin; Wei, Lin; Li, Hung-wing; Xiao, Lehui

    2016-04-20

    In this work, we demonstrated a new ratiometric method for the quantitative analysis of pH inside living cells. The structure of the nanosensor comprises a biofriendly fluorescent bovine serum albumin (BSA) matrix, acting as a pH probe, and pH-insensitive reference dye Alexa 594 enabling ratiometric quantitative pH measurement. The fluorescent BSA matrix was synthesized by cross-linking of the denatured BSA proteins in ethanol with glutaraldehyde. The size of the as-synthesized BSA nanoparticles can be readily manipulated from 30 to 90 nm, which exhibit decent fluorescence at the peak wavelength of 535 nm with a pH response range of 6-8. The potential of this pH sensor for intracellular pH monitoring was demonstrated inside living HeLa cells, whereby a significant change in fluorescence ratio was observed when the pH of the cell was switched from normal to acidic with anticancer drug treatment. The fast response of the nanosensor makes it a very powerful tool in monitoring the processes occurring within the cytosol.

  8. Ratiometric fluorescence detection of superoxide anion based on AuNPs-BSA@Tb/GMP nanoscale coordination polymers.

    PubMed

    Liu, Nan; Hao, Juan; Cai, Keying; Zeng, Mulan; Huang, Zhenzhong; Chen, Lili; Peng, Bingxian; Li, Ping; Wang, Li; Song, Yonghai

    2017-08-03

    A novel ratiometric fluorescence nanosensor for superoxide anion (O2(•-) ) detection was designed with gold nanoparticles-bovine serum albumin (AuNPs-BSA)@terbium/guanosine monophosphate disodium (Tb/GMP) nanoscale coordination polymers (NCPs) (AuNPs-BSA@Tb/GMP NCPs). The abundant hydroxyl and amino groups of AuNPs-BSA acted as binding points for the self-assembly of Tb(3+) and GMP to form core-shell AuNPs-BSA@Tb/GMP NCP nanosensors. The obtained probe exhibited the characteristic fluorescence emission of both AuNPs-BSA and Tb/GMP NCPs. The AuNPs-BSA not only acted as a template to accelerate the growth of Tb/GMP NCPs, but also could be used as the reference fluorescence for the detection of O2(•-) . The resulting AuNPs-BSA@Tb/GMP NCP ratiometric fluorescence nanosensor for the detection of O2(•-) demonstrated high sensitivity and selectivity with a wide linear response range (14 nM-10 μM) and a low detection limit (4.7 nM). Copyright © 2017 John Wiley & Sons, Ltd.

  9. Selective detection of endogenous H2S in living cells and the mouse hippocampus using a ratiometric fluorescent probe

    PubMed Central

    Zhang, Ling; Meng, Wen-qi; Lu, Liang; Xue, Yun-Sheng; Li, Cheng; Zou, Fang; Liu, Yi; Zhao, Jing

    2014-01-01

    As one of three gasotransmitters, the fundamental signalling roles of hydrogen sulphide are receiving increasing attention. New tools for the accurate detection of hydrogen sulphide in cells and tissues are in demand to probe its biological functions. We report the p-nitrobenzyl-based ratiometric fluorescent probe RHP-2, which features a low detection limit, high selectivity and good photostability. The emission intensity ratios had a good linear relationship with the sulphide concentrations in PBS buffer and bovine serum. Our probe was applied to the ratiometric determination and imaging of endogenous H2S in living cells. Furthermore, RHP-2 was used as an effective tool to measure endogenous H2S in the mouse hippocampus. We observed a significant reduction in sulphide concentrations and downregulated expression of cystathionine β-synthetase (CBS) mRNA and CBS protein in the mouse hippocampus in a chronic unpredictable mild stress (CUMS)-induced depression model. These data suggested that decreased concentrations of endogenous H2S may be involved in the pathogenesis of chronic stress depression. PMID:25070356

  10. Rapid and facile ratiometric detection of an anthrax biomarker by regulating energy transfer process in bio-metal-organic framework.

    PubMed

    Zhang, Yihe; Li, Bin; Ma, Heping; Zhang, Liming; Zheng, Youxuan

    2016-11-15

    A ratiometric fluorescent sensor based on luminescent bio-metal-organic framework was prepared by exchanging both Tb(3+) and Eu(3+) cations into anionic bio-MOF-1. Due to a highly efficient energy transfer from Tb(3+) to Eu(3+) (>89%), emission color of Tb/Eu@bio-MOF-1 was orange-red even though Tb(3+) was the dominant content in this Tb/Eu co-doping material. More interestingly, this energy transfer process could be modulated by dipicolinic acid (DPA), an unique biomarker for bacillus spores. With DPA addition, corresponding DPA-to-Tb(3+) energy transfer was gradually enhanced while the energy transfer from Tb(3+) to Eu(3+) was significantly weakened. By regulating the energy transfer process in Tb/Eu@bio-MOF-1, visual colorimetric sensing of DPA in porous MOF was realized for the first time. Detection limit of Tb/Eu@bio-MOF-1 for DPA was 34nM, which was much lower than an infectious dosage of Bacillus anthracis spores (60μM) for human being. Besides, Tb/Eu@bio-MOF-1 showed a remarkable selectivity over other aromatic ligands and amino acids. More importantly, this porous ratiometric sensor worked equally well in human serum. These particularly attractive features of Tb/Eu@bio-MOF-1 made the direct, rapid and naked-eye detection of DPA for practical application possible. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Ratiometric Molecular Probes Based on Dual Emission of a Blue Fluorescent Coumarin and a Red Phosphorescent Cationic Iridium(III) Complex for Intracellular Oxygen Sensing

    PubMed Central

    Yoshihara, Toshitada; Murayama, Saori; Tobita, Seiji

    2015-01-01

    Ratiometric molecular probes RP1 and RP2 consisting of a blue fluorescent coumarin and a red phosphorescent cationic iridium complex connected by a tetra- or octaproline linker, respectively, were designed and synthesized for sensing oxygen levels in living cells. These probes exhibited dual emission with good spectral separation in acetonitrile. The photorelaxation processes, including intramolecular energy transfer, were revealed by emission quantum yield and lifetime measurements. The ratios (RI=(Ip/If)) between the phosphorescence (Ip) and fluorescence (If) intensities showed excellent oxygen responses; the ratio of RI under degassed and aerated conditions (RI0/RI) was 20.3 and 19.6 for RP1 and RP2. The introduction of the cationic Ir (III) complex improved the cellular uptake efficiency compared to that of a neutral analogue with a tetraproline linker. The emission spectra of the ratiometric probes internalized into living HeLa or MCF-7 cells could be obtained using a conventional microplate reader. The complex RP2 with an octaproline linker provided ratios comparable to the ratiometric measurements obtained using a microplate reader: the ratio of the RI value of RP2 under hypoxia (2.5% O2) to that under normoxia (21% O2) was 1.5 and 1.7 for HeLa and MCF-7 cells, respectively. Thus, the intracellular oxygen levels of MCF-7 cells could be imaged by ratiometric emission measurements using the complex RP2. PMID:26066988

  12. A dual-potential electrochemiluminescence ratiometric approach based on graphene quantum dots and luminol for highly sensitive detection of protein kinase activity.

    PubMed

    Zhao, Hui-Fang; Liang, Ru-Ping; Wang, Jing-Wu; Qiu, Jian-Ding

    2015-08-14

    A novel Au NP mediated dual-potential ECL ratiometric approach for highly sensitive protein kinase activity and inhibition assay has been developed based on the simultaneous decrease of cathodic ECL from GQDs and enhancement of anodic ECL from luminol in the same bioanalysis.

  13. Ratiometric Fluorescent Probe for Vicinal Dithiol-Containing Proteins in Living Cells Designed via Modulating the Intramolecular Charge Transfer-Twisted Intramolecular Charge Transfer Conversion Process.

    PubMed

    Wang, Yuanyuan; Zhong, Yaogang; Wang, Qin; Yang, Xiao-Feng; Li, Zheng; Li, Hua

    2016-10-18

    Vicinal dithiol-containing proteins (VDPs) play a significant role in maintaining the cellular redox homeostasis and are implicated in many diseases. To provide new chemical tools for VDPs imaging, we report here a ratiometric fluorescent probe CAsH2 for VDPs using 7-diethylaminiocoumarin as the fluorescent reporter and cyclic 1,3,2-dithiarsenolane as the specific ligand. CAsH2 shows peculiar dual fluorescence emission from the excited intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) states in aqueous media. However, upon selective binding of protein vicinal dithiols to the trivalent arsenical of CAsH2, the probe was brought from the polar water media into the hydrophobic protein domain, causing the excited state ICT to TICT conversion to be restricted; as a result, an increase from the ICT emission band and a decrease from the TICT emission band were observed simultaneously. The designed probe shows high selectivity toward VDPs over other proteins and biological thiols. Preliminary experiments show that CAsH2 can be used for the ratiometric imaging of endogenous VDPs in living cells. So far as we know, this is a rare example of the ratiometric fluorescent probe designed via modulating the ICT-TICT conversion process, which provides a new way to construct various protein-specific ratiometric fluorescent probes.

  14. Ratiometric Molecular Probes Based on Dual Emission of a Blue Fluorescent Coumarin and a Red Phosphorescent Cationic Iridium(III) Complex for Intracellular Oxygen Sensing.

    PubMed

    Yoshihara, Toshitada; Murayama, Saori; Tobita, Seiji

    2015-06-09

    Ratiometric molecular probes RP1 and RP2 consisting of a blue fluorescent coumarin and a red phosphorescent cationic iridium complex connected by a tetra- or octaproline linker, respectively, were designed and synthesized for sensing oxygen levels in living cells. These probes exhibited dual emission with good spectral separation in acetonitrile. The photorelaxation processes, including intramolecular energy transfer, were revealed by emission quantum yield and lifetime measurements. The ratios (R(I) = (I(p)/I(f))) between the phosphorescence (I(p)) and fluorescence (I(f)) intensities showed excellent oxygen responses; the ratio of R(I) under degassed and aerated conditions ( R(I)(0) was 20.3 and 19.6 for RP1 and RP2. The introduction of the cationic Ir (III) complex improved the cellular uptake efficiency compared to that of a neutral analogue with a tetraproline linker. The emission spectra of the ratiometric probes internalized into living HeLa or MCF-7 cells could be obtained using a conventional microplate reader. The complex RP2 with an octaproline linker provided ratios comparable to the ratiometric measurements obtained using a microplate reader: the ratio of the R(I)) value of RP2 under hypoxia (2.5% O2) to that under normoxia (21% O2) was 1.5 and 1.7 for HeLa and MCF-7 cells, respectively. Thus, the intracellular oxygen levels of MCF-7 cells could be imaged by ratiometric emission measurements using the complex RP2.

  15. FRET based ratiometric Ca(2+) imaging to investigate immune-mediated neuronal and axonal damage processes in experimental autoimmune encephalomyelitis.

    PubMed

    Siffrin, Volker; Birkenstock, Jérôme; Luchtman, Dirk W; Gollan, René; Baumgart, Jan; Niesner, Raluca A; Griesbeck, Oliver; Zipp, Frauke

    2015-07-15

    Irreversible axonal and neuronal damage are the correlate of disability in patients suffering from multiple sclerosis (MS). A sustained increase of cytoplasmic free [Ca(2+)] is a common upstream event of many neuronal and axonal damage processes and could represent an early and potentially reversible step. We propose a method to specifically analyze the neurodegenerative aspects of experimental autoimmune encephalomyelitis by Förster Resonance Energy Transfer (FRET) imaging of neuronal and axonal Ca(2+) dynamics by two-photon laser scanning microscopy (TPLSM). Using the genetically encoded Ca(2+) sensor TN-XXL expressed in neurons and their corresponding axons, we confirm the increase of cytoplasmic free [Ca(2+)] in axons and neurons of autoimmune inflammatory lesions compared to those in non-inflamed brains. We show that these relative [Ca(2+)] increases were associated with immune-neuronal interactions. In contrast to Ca(2+)-sensitive dyes the use of a genetically encoded Ca(2+) sensor allows reliable intraaxonal free [Ca(2+)] measurements in living anesthetized mice in health and disease. This method detects early axonal damage processes in contrast to e.g. cell/axon morphology analysis, that rather detects late signs of neurodegeneration. Thus, we describe a method to analyze and monitor early neuronal damage processes in the brain in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Chemical Etching of Bovine Serum Albumin-Protected Au25 Nanoclusters for Label-Free and Separation-Free Ratiometric Fluorescent Detection of Tris(2-carboxyethyl)phosphine.

    PubMed

    Shu, Tong; Wang, Jianxing; Su, Lei; Zhang, Xueji

    2016-11-15

    This study describes a novel ratiometric fluorescent sensor based on chemical etching of gold nanocluster (GNCs) for label-free, separation-free determination of tris(2-carboxyethyl)phosphine (TCEP). TCEP was discovered to exhibit unusual chemical behavior toward fluorescent gold nanoclusters: it quenched the red fluorescent emission of the bovine serum album (BSA)-protected GNCs (GNCs@BSA) and simultaneously restored the blue fluorescent emission of the dityrosine (diTyr) residues of the BSA ligand. The TCEP-induced quenching of the fluorescent GNCs@BSA was investigated with the UV-vis adsorption spectrum, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), inductively coupled plasma-mass spectrometry (ICP-MS) and X-ray photoelectron spectroscopy (XPS), revealing the chemical etching of the gold(0) core of the GNCs@BSA by TCEP. Furthermore, the ratio of the blue fluorescence intensity of the diTyr to the red fluorescence intensity of the GNCs@BSA was found to be dependent on TCEP concentration and showed a linear relationship in the TCEP concentration range of 500 nM to 50, 000 nM (R(2) = 0.9943) with a limit of detection (LOD) of 130 nM, achieving the higher sensitivity over previous reports. This ratiometric sensor also showed superior selectivity for TCEP over certain common interferences including glutathione, 20 kinds of natural amino acids, and the oxidized form of TCEP. With the developed ratiometric method, the deproteinized human serum samples spiked with TCEP were analyzed with satisfactory results. In addition, it is worth noting that compared with conventional ratiometric fluorescent sensors, the ratiometric sensor developed in this study does not require external fluorophores, avoiding the additional derivation procedures.

  17. A versatile ratiometric nanosensing approach for sensitive and accurate detection of Hg(2+) and biological thiols based on new fluorescent carbon quantum dots.

    PubMed

    Fu, Huili; Ji, Zhongyin; Chen, Xuejie; Cheng, Anwei; Liu, Shucheng; Gong, Peiwei; Li, Guoliang; Chen, Guang; Sun, Zhiwei; Zhao, Xianen; Cheng, Feng; You, Jinmao

    2017-03-01

    Herein, we first reported a facile synthesis method for fabrication of highly photoluminescent carbon quantum dots (CQDs) using sodium alginate as the carbon source and histidine as both the nitrogen source and functional monomer by one-pot hydrothermal synthesis. The as-prepared CQDs gave a high quantum yield of 32%. By employing the new CQDs and rhodamine B (RhB), we demonstrated a simple, facile, sensitive, and accurate ratiometric sensor for detection of Hg(2+) and biological thiols. The photoluminescence of CQDs in the ratiometric sensor can be selectively and intensively suppressed by Hg(2+) due to strong electrostatic interaction between the surface functional groups of the CQDs and Hg(2+). When glutathione (GSH) was introduced into the "Turn Off" CQDs-RhB-Hg(2+) sensing system, the fluorescence of the CQDs can be recovered rapidly due to the stronger affinity between thiol and Hg(2+), while the fluorescence of the RhB remained constant in this sensing process. Based on the above principle, the ratiometric strategy for detecting Hg(2+) and GSH can be achieved readily, and gives satisfactory limit of detections (LODs) of 30 and 20 nM for Hg(2+) and GSH, respectively. The dual-emission fluorescent CQDs-RhB sensor does not need the complicated molecular design and the synthesis of dual-emission fluorophores. Meanwhile, the feasibility of the proposed method for analysis of water samples, food samples, and biological samples (plasma from mice oxidative stress study) was investigated. The developed ratiometric nanosensor is proven to be facile, with less sample consumption, rapid, lost cost, highly sensitive, and very selective for Hg(2+) and biological thiol detection, which offers a new approach for environmental, food, and biological analysis. Graphical abstract Ratiometric nanosensing approach detection of Hg(2+) and biological thiols.

  18. Imaging the nanomolar range of nitric oxide with an amplifier-coupled fluorescent indicator in living cells

    NASA Astrophysics Data System (ADS)

    Sato, Moritoshi; Hida, Naoki; Umezawa, Yoshio

    2005-10-01

    Nitric oxide (NO) is a small uncharged free radical that is involved in diverse physiological and pathophysiological mechanisms. NO is generated by three isoforms of NO synthase, endothelial, neuronal, and inducible ones. When generated in vascular endothelial cells, NO plays a key role in vascular tone regulation, in particular. Here, we describe an amplifier-coupled fluorescent indicator for NO to visualize physiological nanomolar dynamics of NO in living cells (detection limit of 0.1 nM). This genetically encoded high-sensitive indicator revealed that 1 nM of NO, which is enough to relax blood vessels, is generated in vascular endothelial cells even in the absence of shear stress. The nanomolar range of basal endothelial NO thus revealed appears to be fundamental to vascular homeostasis. fluorescence resonance energy transfer | genetic encoding

  19. A ratiometric method of autofluorescence correction used for the quantification of Evans blue dye fluorescence in rabbit arterial tissues.

    PubMed

    Murphy, Christopher L; Lever, M John

    2002-03-01

    Evans blue dye (EBD) conjugates with albumin in the circulation and is frequently used to measure vascular protein leakage. The fluorescence of the dye from tissue sections can be used to measure its uptake at very specific anatomical locations, but problems arise with dye quantification because tissue components also fluoresce; so-called autofluorescence. We have measured uptake of EBD by blood vessel walls at various points around the aorto-renal branch of rabbits. High resolution, digitised, fluorescence images of histological sections of artery wall allowed detailed microscopic analysis of EBD accumulation; and a ratiometric method was developed to enable autofluorescence to be separated from EBD fluorescence. When EBD-free tissue sections were illuminated with blue light, the ratio of red to green fluorescence was constant throughout the tissue (0.59 +/- 0.03, mean +/- S.D., n = 32). Therefore, at each individual pixel, the level of red autofluorescence could be determined by multiplying the green intensity at that pixel by the calculated red to green ratio. Since EBD fluorescence was detected only in the red region of the spectrum, intensity values of the dye alone were obtained from EBD-exposed tissue by subtracting the red autofluorescence estimated by this ratiometric method. In such cases the red to green fluorescence ratio was measured from adjacent sites known to be free of EDB (0.59 +/- 0.02, mean +/- S.D., n = 56). We were therefore able to increase the sensitivity of tracer quantification by complete elimination of background autofluorescence on a pixel-by-pixel basis. Use of EBD standards allowed calibration of corrected fluorescence intensities and calculation of mass transfer coefficients for albumin into the artery wall. Spatial variations in the permeability of the artery wall around the renal ostium were detected with the present high resolution technique, with an average mass transfer coefficient of (6.8 +/- 0.9) x 10(-8) cm s(-1) for all

  20. Theoretical investigation on ratiometric two-photon fluorescent probe for Zn2+ detection based on ICT mechanism

    NASA Astrophysics Data System (ADS)

    Huang, Shuang; Yang, Bao-Zhu; Ren, Ai-Min

    2016-06-01

    OPA (one-photon absorption), TPA (two-photon absorption) and fluorescence properties of a free ligand L upon coordination with Zn2+, and the regeneration with CN- were investigated in theory. According to our research, OPA spectra of ligand L show red-shift binding with Zn2+ while blue-shift with CN-. The fluorescence spectra and TPA wavelength are shifted in the same situation as those of OPA spectra. The value of TPA cross-section decreased at first, and then increased to 1813 GM for [L-Zn(CN)4]2-. Intramolecular charge transfer (ICT) mechanism was investigated by natural bond orbital (NBO) analysis. It demonstrates that L is hopeful to be a good ratiometric fluorescent probe for zinc ion detection in solution, and it can regenerate after CN- was introduced.

  1. FRET based ratio-metric sensing of hyaluronidase in synthetic urine as a biomarker for bladder and prostate cancer.

    PubMed

    Chib, Rahul; Raut, Sangram; Fudala, Rafal; Chang, Aaron; Mummert, Mark; Rich, Ryan; Gryczynski, Zygmunt; Gryczynski, Ignacy

    2013-01-01

    Elevated hyaluronidase levels are found in the urine of bladder and prostate cancer patients. Therefore, HA-ase is regarded as an important biomarker for the detection of these cancers. In this report, we use a FRET based ratiometric sensing approach to detect the level of HA-ase in synthetic urine. For this, we have used a HA-FRET probe (hyaluronan) labeled with fluorescein as a donor and rhodamine as an acceptor. We monitor the digestion of our HA-FRET probe with different concentrations of HA-ase in synthetic urine via fluorescence emission. The extent to which FRET is released depends on the concentration of HA-ase. Our fluorescence intensity results are also supported with time resolved fluorescence decay data. This assay can be used to develop a non-invasive technique for the detection of bladder and/or prostate cancer progression.

  2. A triterpene oleanolic acid conjugate with 3-hydroxyflavone derivative as a new membrane probe with two-color ratiometric response.

    PubMed

    Turkmen, Zeynep; Klymchenko, Andrey S; Oncul, Sule; Duportail, Guy; Topcu, Gulacti; Demchenko, Alexander P

    2005-07-29

    We report on the synthesis by coupling of a triterpenoid oleanolic acid with 4'-diethylamino-3-hydroxyflavone (FE) to produce an environment-sensitive biomembrane probe with two-band ratiometric response in fluorescence emission. The synthesized compound (probe FOT) was tested in a series of model solvents and demonstrated the response to solvent polarity and intermolecular hydrogen bonding very similar to that of parent probe FE. Meantime when incorporated into lipid bilayer membranes, it showed new features differing in response between lipids of different surface charges as well as between glycerophospholipids and sphingomyelin. We observed that in the conditions of coexistence of rafts and non-raft structures the probe is excluded from the rafts.

  3. Facile and high spatial resolution ratio-metric luminescence thermal mapping in microfluidics by near infrared excited upconversion nanoparticles

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Cao, Wenbin; Li, Shunbo; Wen, Weijia

    2016-02-01

    A local area temperature monitor is important for precise control of chemical and biological processes in microfluidics. In this work, we developed a facile method to realize micron spatial resolution of temperature mapping in a microfluidic channel quickly and cost effectively. Based on the temperature dependent fluorescence emission of NaYF4:Yb3+, Er3+ upconversion nanoparticles (UCNPs) under near-infrared irradiation, ratio-metric imaging of UCNPs doped polydimethylsiloxane can map detailed temperature distribution in the channel. Unlike some reported strategies that utilize temperature sensitive organic dye (such as Rhodamine) to achieve thermal sensing, our method is highly chemically inert and physically stable without any performance degradation in long term operation. Moreover, this method can be easily scaled up or down, since the spatial and temperature resolution is determined by an optical imaging system. Our method supplied a simple and efficient solution for temperature mapping on a heterogeneous surface where usage of an infrared thermal camera was limited.

  4. Design of ratiometric emission probe with visible light excitation for determination of Ca2+ in living cells.

    PubMed

    Liu, Qiaoling; Du, Huizhi; Ren, Xiaoze; Bian, Wei; Fan, Li; Shuang, Shaomin; Dong, Chuan; Hu, Qin; Choi, Martin M F

    2014-08-19

    An organic salt as a fluorescent probe based on intramolecular charge transfer for Ca(2+) determination is developed. Ca(2+) can be detected by ratiometric emission at 490 and 594 nm with an excitation wavelength of 405 nm. This probe is highly selective for Ca(2+) over other divalent metal cations and displays a large Stokes shift of 189 nm that can avoid interference of the excitation light beam and autofluorescence of biological samples. The dissociation constant for Ca(2+) is 2.25 ± 0.47 μM and pertinent to Ca(2+) detection in cellular resting and dynamic states. The probe demonstrates its application in monitoring Ca(2+) in living cells under confocal microscopic imaging.

  5. ZnS:Mn nanoparticles functionalized by PAMAM-OH dendrimer based fluorescence ratiometric probe for cadmium.

    PubMed

    Campos, Bruno B; Algarra, Manuel; Radotić, Ksenija; Mutavdžić, Dragosav; Rodríguez-Castellón, Enrique; Jiménez-Jiménez, José; Alonso, Beatriz; Casado, Carmen M; Esteves da Silva, Joaquim C G

    2015-03-01

    We report a nanocomposite of ZnS:Mn quantum dots and a third generation PAMAM-OH dendrimer (ZnS:Mn@PAMAM-OH(G=3)) which was rationalized to be used as ratiometric nanosensor for Cd(2+) in aqueous solution. The nanoparticles exhibited a bright yellow-orange emission with peaks at 448 and 595 nm. The structure of ZnS:Mn was not changed after coupling with PAMAM-OH, which was evidenced by the analysis of the emission spectra of the compounds. The results confirm that the prepared fluorescence nanoparticles could selectively detect Cd(2+) in aqueous solution with a limit of detection of 24.34 μM and RSD 4.07%, obtained by using the ratio I448/I595. The method was applied to different water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. An Interactive Quantum Dot and Carbon Dot Conjugate for pH-Sensitive and Ratiometric Cu(2+) Sensing.

    PubMed

    Ahmad, Kafeel; Gogoi, Sonit Kumar; Begum, Raihana; Sk, Md Palashuddin; Paul, Anumita; Chattopadhyay, Arun

    2017-03-17

    Herein we report the photoinduced electron transfer from Mn(2+) -doped ZnS quantum dots (Qdots) to carbon dots (Cdots) in an aqueous dispersion. We also report that the electron transfer was observed for low pH values, at which the oppositely charged nanoparticles (NPs) interacted with each other. Conversely, at higher pH values the NPs were both negatively charged and thus not in contact with each other, so the electron transfer was absent. Steady-state and time-resolved photoluminescence studies revealed that interacting particle conjugates were responsible for the electron transfer. The phenomenon could be used to detect the presence of Cu(2+) ions, which preferentially, ratiometrically, and efficiently quenched the luminescence of the Qdots.

  7. Synthesis and characterization of DNA-quantum dot conjugates for the fluorescence ratiometric detection of unlabelled DNA.

    PubMed

    Page, Leah Elizabeth; Zhang, Xi; Tyrakowski, Christina Marie; Ho, Chiun-Teh; Snee, Preston Todd

    2016-11-21

    A quantum dot-based ratiometrically responsive fluorescent sensor for unlabeled single-stranded DNA (ssDNA) is reported. Several technical issues concerning the development of high yield ssDNA-QD conjugation chemistry were addressed. The DNA sensor was synthesized by conjugating methacrylic phosphoramidite-functional oligonucleotides to water-soluble cadmium zinc sulfide core/zinc sulfide shell quantum dots (CdZnS/ZnS QDs). Duplex DNA was formed when the QD-bound ssDNA was incubated with its complement. Next, titration with PicoGreen resulted in FRET energy transfer from the dot to the dsDNA intercalating dye. The resulting ratio of the dye to QD integrated emissions is a calibratable metric for label-free DNA detection with a LOD of 3.8 nmol.

  8. A new FRET ratiometric fluorescent chemosensor for Hg2+ and its application in living EC 109 cells

    NASA Astrophysics Data System (ADS)

    Song, Jianhua; Huai, Manxiu; Wang, Cuicui; Xu, Zhanhui; Zhao, Yufen; Ye, Yong

    2015-03-01

    On the basis of fluorescent resonance energy transfer, a new fluorophore dyad (L) bearing rhodamine B and naphthalimide was developed as fluorescent ratiometric chemosensor for Hg2+ in aqueous solution. L exhibited high selectivity and excellent sensitivity towards Hg2+ with a broad pH span (1.0-8.0) and the detection limit of L was 2.11 × 10-8 M. Sensor L for the detection of Hg2+ was rapid and the recognizing event could complete in 2.5 min. A significant change in the color could be used for naked-eye detection. The selective fluorescence response of L to Hg2+ is due to the Hg2+-promoted ring opening of spirolactam of rhodamine moiety, leading to a cyclization reaction of thiourea moiety. In addition, fluorescence imaging experiments of Hg2+ in living EC 109 cells demonstrated its value of practical applications in biological systems.

  9. Ratiometric and turn-on monitoring for heavy and transition metal ions in aqueous solution with a fluorescent peptide sensor.

    PubMed

    Joshi, Bishnu Prasad; Park, Junwon; Lee, Wan In; Lee, Keun-Hyeung

    2009-05-15

    A novel fluorescent peptide sensor containing tryptophan (donor) and dansyl fluorophore (acceptor) was synthesized for monitoring heavy and transition metal (HTM) ions on the basis of metal ion binding motif (Cys-X-X-X-Cys). The peptide probe successfully exhibited a turn on and ratiometric response for several heavy metal ions such as Hg(2+), Cd(2+), Pb(2+), Zn(2+), and Ag(+) in aqueous solution. The enhancements of emission intensity were achieved in the presence of the HTM ions by fluorescent resonance energy transfer (FRET) and chelation enhanced fluorescence (CHEF) effects. The detection limits of the sensor for Cd(2+), Pb(2+), Zn(2+), and Ag(+) were lower than the EPA's drinking water maximum contaminant levels (MCL). We described the fluorescent enhancement, binding affinity, and detection limit of the peptide probe for HTM ions.

  10. Ratiometric biosensor array for multiplexed detection of microRNAs based on electrochemiluminescence coupled with cyclic voltammetry.

    PubMed

    Feng, Xiaobin; Gan, Ning; Zhang, Huairong; Li, Tianhua; Cao, Yuting; Hu, Futao; Jiang, Qianli

    2016-01-15

    A novel multiplexed ratiometric biosensor array was fabricated on a homemade screen-printed carbon electrode (SPCE) for near-simultaneous detection of microRNA (miRNA)-21 and miRNA-141 based on electrochemiluminescence (ECL) coupled with cyclic voltammetry (CV) method. In the detection system, the ECL signal tags (Ru-SiO2@PLL-Au) were fabricated using poly-l-lysine (PLL) as bridging agent and co-reactant to connect Ru-SiO2 (Ru(bpy)3(2+)-doped silica) and gold nanoparticles (Au NPs), which were respectively modified on two spatial resolved working electrodes (WE1 and WE2) of SPCE. Then the ferrocene (Fc)-labeled hairpin DNA (Fc-HDNA1 and Fc-HDNA2) as CV signal tags and ECL quenching material were immobilized on Ru-SiO2@PLL-Au. Upon miRNA-21 and miRNA-141 adding, the target miRNAs could hybridize with corresponding Fc-HDNA, which could lead to Fc away from Ru-SiO2@PLL-Au. Such conformational changes could recover the ECL of Ru-SiO2@PLL-Au and decreased the CV current of Fc, respectively. This "signal-on" of ECL and "signal-off" of CV were employed for dual-signal ratiometric readout. With the help of a multiplexed switch, two dual-signals from WE1 and WE2 were used for multiplexed detection of miRNA-21 and miRNA-141 down to 6.3 and 8.6fM, respectively. This approach was used in real sample analysis and has significant potential for miRNA biomarkers detection in a clinical laboratory setting. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Integrity of lipid nanocarriers in bloodstream and tumor quantified by near-infrared ratiometric FRET imaging in living mice.

    PubMed

    Bouchaala, Redouane; Mercier, Luc; Andreiuk, Bohdan; Mély, Yves; Vandamme, Thierry; Anton, Nicolas; Goetz, Jacky G; Klymchenko, Andrey S

    2016-08-28

    Lipid nanocarriers are considered as promising candidates for drug delivery and cancer targeting because of their low toxicity, biodegradability and capacity to encapsulate drugs and/or contrasting agents. However, their biomedical applications are currently limited because of a poor understanding of their integrity in vivo. To address this problem, we report on fluorescent nano-emulsion droplets of 100nm size encapsulating lipophilic near-infrared cyanine 5.5 and 7.5 dyes with a help of bulky hydrophobic counterion tetraphenylborate. Excellent brightness and efficient Förster Resonance Energy Transfer (FRET) inside lipid NCs enabled for the first time quantitative fluorescence ratiometric imaging of NCs integrity directly in the blood circulation, liver and tumor xenografts of living mice using a whole-animal imaging set-up. This unique methodology revealed that the integrity of our FRET NCs in the blood circulation of healthy mice is preserved at 93% at 6h of post-administration, while it drops to 66% in the liver (half-life is 8.2h). Moreover, these NCs show fast and efficient accumulation in tumors, where they enter in nearly intact form (77% integrity at 2h) before losing their integrity to 40% at 6h (half-life is 4.4h). Thus, we propose a simple and robust methodology based on ratiometric FRET imaging in vivo to evaluate quantitatively nanocarrier integrity in small animals. We also demonstrate that nano-emulsion droplets are remarkably stable nano-objects that remain nearly intact in the blood circulation and release their content mainly after entering tumors. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  12. Silver enhanced ratiometric nanosensor based on two adjustable Fluorescence Resonance Energy Transfer modes for quantitative protein sensing.

    PubMed

    Li, Hui; Zhao, Yaju; Chen, Zhu; Xu, Danke

    2017-01-15

    We developed a silver decahedral nanoparticles (Ag10NPs)-enhanced ratiometric Fluorescence Resonance Energy Transfer (FRET) nanosensor based on two adjustable FRET modes. Alexa Fluor 488 (Alexa) and Cyanine3 (Cy3)-aptamer-Black hole quencher-2 (BHQ-2) were bound with Ag10NPs to form the ratiometric FRET nanosensor (Ag-Alexa/Cy3/BHQ-2). Alexa act as donor and Cy3 as acceptor in the FRET mode 1 while Cy3 was donor and BHQ-2 was acceptor in the FRET mode 2. In the absence of platelet-derived growth factor (PDGF-BB), the fluorescence intensity of Alexa was lowest while that of Cy3 was highest. Upon the addition of PDGF-BB, Cy3-aptamer-BHQ-2 binds with PDGF-BB resulting in the change of structure of aptamer. The fluorescence intensity of Alexa increased while that of Cy3 decreased. In addition, the fluorescence intensity ratio of Alexa to Cy3 increased remarkably with PDGF-BB concentration in the range of 0.4-400ng/mL. A good linear response was obtained when the PDGF-BB concentrations were in the range o