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1

Single molecule electronics and devices.  

PubMed

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

2

Single Molecule Electron Paramagnetic Resonance  

NASA Astrophysics Data System (ADS)

Electron paramagnetic resonance (EPR) is a powerful spectroscopic tool for studying the dynamics of biomolecular systems. EPR measurements on bulk samples using a commercial X-band spectrometer provide insight into atomic-scale structure and dynamics of ensembles of biomolecules. Separately, single molecule measurements of biomolecular systems allow researchers to capture heterogeneous behaviors that have revealed the molecular mechanisms behind many biological processes. We are merging these two powerful techniques to perform single molecule EPR. In this experiment, we selectively label double-stranded DNA molecules with nitrogen-vacancy (NV) center nanodiamonds and optically detect the magnetic resonance of the NV probe. Shifts and broadening of our EPR peaks indicate the changing position of the attached DNA relative to the applied magnetic field. Using this new technique, we have successfully measured the first EPR spectrum of a single biomolecule. By controlling the geometry of the diamond and the applied magnetic field, we will quantitatively determine the rotational and translational dynamics of single biomolecules. This research provides the foundation for an advanced single molecule magnetic resonance approach to studies of complex biomolecular systems.

Teeling-Smith, Richelle M.; Johnston-Halperin, Ezekiel; Poirier, Michael G.; Hammel, P. Chris

2013-03-01

3

Single-molecule junctions beyond electronic transport.  

PubMed

The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications. PMID:23736215

Aradhya, Sriharsha V; Venkataraman, Latha

2013-06-01

4

Electron Transport in Single Molecule Transistors Jiwoong Park  

E-print Network

Electron Transport in Single Molecule Transistors by Jiwoong Park B.S. (Seoul National University. Paul Alivisatos Fall 2003 #12;Electron Transport in Single Molecule Transistors Copyright © 2003 by Jiwoong Park #12;1 Abstract Electron Transport in Single Molecule Transistors by Jiwoong Park Doctor

McEuen, Paul L.

5

Single-molecule electronics: from chemical design to functional devices.  

PubMed

The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable us to continue the trend of aggressive downscaling of silicon-based electronic devices. More significantly, the fabrication, understanding and control of fully functional circuits at the single-molecule level could also open up the possibility of using molecules as devices with novel, not-foreseen functionalities beyond complementary metal-oxide semiconductor technology (CMOS). This review aims at highlighting the chemical design and synthesis of single molecule devices as well as their electrical and structural characterization, including a historical overview and the developments during the last 5 years. We discuss experimental techniques for fabrication of single-molecule junctions, the potential application of single-molecule junctions as molecular switches, and general physical phenomena in single-molecule electronic devices. PMID:25099384

Sun, Lanlan; Diaz-Fernandez, Yuri A; Gschneidtner, Tina A; Westerlund, Fredrik; Lara-Avila, Samuel; Moth-Poulsen, Kasper

2014-11-01

6

Quantum-mechanical analysis of single molecule quantum electronic devices  

Microsoft Academic Search

This paper documents the need to coherently apply quantum mechanics in order to analyze microscopic devices. We examine device physics and study characteristics of single-molecule processing devices. The device physics of the proposed single-molecule device is based on the controlled propagation of electrons. By applying quantum mechanics and advanced numeric schemes, we perform the device-level analysis researching electron propagation (motion),

Sergey Edward Lyshevski

2011-01-01

7

Electron Transfer-Based Single Molecule Fluorescence as a Probe for Nano-Environment Dynamics  

PubMed Central

Electron transfer (ET) is one of the most important elementary processes that takes place in fundamental aspects of biology, chemistry, and physics. In this review, we discuss recent research on single molecule probes based on ET. We review some applications, including the dynamics of glass-forming systems, surface binding events, interfacial ET on semiconductors, and the external field-induced dynamics of polymers. All these examples show that the ET-induced changes of fluorescence trajectory and lifetime of single molecules can be used to sensitively probe the surrounding nano-environments. PMID:24496314

Chen, Ruiyun; Wu, Ruixiang; Zhang, Guofeng; Gao, Yan; Xiao, Liantuan; Jia, Suotang

2014-01-01

8

Single-Molecule Electronic Measurements with Metal Electrodes  

ERIC Educational Resources Information Center

A review of concepts like tunneling through a metal-molecule-metal-junction, contrast with electrochemical and optical-charge injection, strong-coupling limit, calculations of tunnel transport, electron transfer through Redox-active molecules is presented. This is followed by a discussion of experimental approaches for single-molecule measurements.

Lindsay, Stuart

2005-01-01

9

Tracking electrons in biological macromolecules: from ensemble to single molecule.  

PubMed

Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level. PMID:25102116

Tabares, Leandro C; Gupta, Ankur; Aartsma, Thijs J; Canters, Gerard W

2014-01-01

10

Interfacial charge transfer events of BODIPY molecules: single molecule spectroelectrochemistry and substrate effects.  

PubMed

We present single molecule fluorescence and spectroelectrochemistry characteristics of 4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) bearing two carboxylic acid groups at its 2 and 6 positions. Our study shows a heterogeneous half redox potential distribution for the BODIPY molecules embedded in polystyrene film because of the heterogeneity in their charge transfer rates. Single molecules adsorbed onto a TiO2 surface with ordered nanostructures show surprising fluorescence blinking activity with the shortest ON duration time in comparison to bare glass and indium-tin oxide (ITO) surfaces. Single molecule stability tests show longer ON duration time and a stable fluorescence feature when dispersed in polystyrene thin film than molecules exposed to air. Shorter ON times are observed for molecules. In intimate contact with ITO in comparison to glass substrates. Such a decrease in their fluorescence stability or intensity is explained by charge transfer activities from the dye molecules to the metal oxide surface. Electron transfer and back transfer rates are calculated to illustrate the substrate effects by using a well-established model. PMID:25252244

Liu, Jia; Hill, Caleb M; Pan, Shanlin; Liu, Haiying

2014-10-01

11

Molecular electronics--resonant transport through single molecules.  

PubMed

The mechanically controllable break-junction technique (MCBJ) enables us to investigate charge transport through an individually contacted and addressed molecule in ultra-high vacuum (UHV) environment at variable temperature ranging from room temperature down to 4 K. Using a statistical measurement and analysis approach, we acquire current-voltage (I-V) characteristics during the repeated formation, manipulation, and breaking of a molecular junction. At low temperatures, voltages accessing the first molecular orbitals in resonance can be applied, providing spectroscopic information about the junction's energy landscape, in particular about the molecular level alignment in respect to the Fermi energy of the electrodes. Thereby, we can investigate the non-linear transport properties of various types of functional molecules and explore their potential use as functional building blocks for future nano-electronics. An example will be given by the reversible and controllable switching between two distinct conductive states of a single molecule. As a proof-of-principle for functional molecular devices, a single-molecule memory element will be demonstrated. PMID:21137712

Lörtscher, Emanuel; Riel, Heike

2010-01-01

12

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions  

NASA Astrophysics Data System (ADS)

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

Widawsky, Jonathan R.

13

Single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces  

PubMed Central

A method was developed to monitor dynamic changes in protein structure and interfacial behavior on surfaces by single-molecule Förster resonance energy transfer. This method entails the incorporation of unnatural amino acids to site-specifically label proteins with single-molecule Förster resonance energy transfer probes for high-throughput dynamic fluorescence tracking microscopy on surfaces. Structural changes in the enzyme organophosphorus hydrolase (OPH) were monitored upon adsorption to fused silica (FS) surfaces in the presence of BSA on a molecule-by-molecule basis. Analysis of >30,000 individual trajectories enabled the observation of heterogeneities in the kinetics of surface-induced OPH unfolding with unprecedented resolution. In particular, two distinct pathways were observed: a majority population (? 85%) unfolded with a characteristic time scale of 0.10 s, and the remainder unfolded more slowly with a time scale of 0.7 s. Importantly, even after unfolding, OPH readily desorbed from FS surfaces, challenging the common notion that surface-induced unfolding leads to irreversible protein binding. This suggests that protein fouling of surfaces is a highly dynamic process because of subtle differences in the adsorption/desorption rates of folded and unfolded species. Moreover, such observations imply that surfaces may act as a source of unfolded (i.e., aggregation-prone) protein back into solution. Continuing study of other proteins and surfaces will examine whether these conclusions are general or specific to OPH in contact with FS. Ultimately, this method, which is widely applicable to virtually any protein, provides the framework to develop surfaces and surface modifications with improved biocompatibility. PMID:24235137

McLoughlin, Sean Yu; Kastantin, Mark; Schwartz, Daniel K.; Kaar, Joel L.

2013-01-01

14

Carbon tips for all-carbon single-molecule electronics  

NASA Astrophysics Data System (ADS)

We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution.

Dappe, Y. J.; González, C.; Cuevas, J. C.

2014-05-01

15

Electron-vibration interaction in multichannel single-molecule junctions.  

PubMed

The effect of electron-vibration interaction in atomic-scale junctions with a single conduction channel was widely investigated both theoretically and experimentally. However, the more general case of junctions with several conduction channels has received very little attention. Here we study electron-vibration interaction in multichannel molecular junctions, formed by introduction of either benzene or carbon dioxide between platinum electrodes. By combining shot noise and differential conductance measurements, we analyze the effect of vibration activation on conductance in view of the distribution of conduction channels. Based on the shift of vibration energy while the junction is stretched, we identify vibration modes with transverse and longitudinal symmetry. The detection of different vibration modes is ascribed to efficient vibration coupling to different conduction channels according to symmetry considerations. While most of our observations can be explained in view of the theoretical models for a single conduction channel, the appearance of conductance enhancement, induced by electron-vibration interaction, at high conductance values indicates either unexpected high electron-vibration coupling or interchannel scattering. PMID:24252112

Ben-Zvi, Regev; Vardimon, Ran; Yelin, Tamar; Tal, Oren

2013-12-23

16

Electronic Measurements of Single-Molecule Catalysis by cAMP-Dependent Protein Kinase A  

E-print Network

Electronic Measurements of Single-Molecule Catalysis by cAMP- Dependent Protein Kinase A Patrick C and Biochemistry, and Chemistry, University of California, Irvine, California 92697, United States *S Supporting-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate

Weiss, Gregory A.

17

Controlled chain polymerisation and chemical soldering for single-molecule electronics.  

PubMed

Single functional molecules offer great potential for the development of novel nanoelectronic devices with capabilities beyond today's silicon-based devices. To realise single-molecule electronics, the development of a viable method for connecting functional molecules to each other using single conductive polymer chains is required. The method of initiating chain polymerisation using the tip of a scanning tunnelling microscope (STM) is very useful for fabricating single conductive polymer chains at designated positions and thereby wiring single molecules. In this feature article, developments in the controlled chain polymerisation of diacetylene compounds and the properties of polydiacetylene chains are summarised. Recent studies of "chemical soldering", a technique enabling the covalent connection of single polydiacetylene chains to single functional molecules, are also introduced. This represents a key step in advancing the development of single-molecule electronics. PMID:22517409

Okawa, Yuji; Akai-Kasaya, Megumi; Kuwahara, Yuji; Mandal, Swapan K; Aono, Masakazu

2012-05-21

18

Single Molecule Dissociation by Tunneling Electrons B. C. Stipe, M. A. Rezaei, and W. Ho  

E-print Network

constants apart. The dissociation rate as a function of current was found to vary as I 0:8\\Sigma0:2 , I 1Single Molecule Dissociation by Tunneling Electrons B. C. Stipe, M. A. Rezaei, and W. Ho Laboratory­ scope was used to image and dissociate single O2 molecules on the Pt(111) surface in the temperature

Persson, Mats

19

Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?  

SciTech Connect

X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

Fratalocchi, A. [PRIMALIGHT, Faculty of Electrical Engineering, Applied Mathematics and Computational Science, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia)] [Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185, Rome (Italy); Ruocco, G. [Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185, Rome (Italy)] [IPCF-CNR, c/o Department of Physics, Sapienza University, P.le Aldo Moro 2, 00185, Rome (Italy)

2011-03-11

20

Localization accuracy in single molecule microscopy using electron-multiplying charge-coupled device cameras  

PubMed Central

The electron-multiplying charge-coupled device (EMCCD) is a popular technology for imaging under extremely low light conditions. It has become widely used, for example, in single molecule microscopy experiments where few photons can be detected from the individual molecules of interest. Despite its important role in low light microscopy, however, little has been done in the way of determining how accurately parameters of interest (e.g., location of a single molecule) can be estimated from an image that it produces. Here, we develop the theory for calculating the Fisher information matrix, and hence the Cramer-Rao lower bound-based limit of the accuracy, for estimating parameters from an EMCCD image. An EMCCD operates by amplifying a weak signal that would otherwise be drowned out by the detector’s readout noise as in the case of a conventional charge-coupled device (CCD). The signal amplification is a stochastic electron multiplication process, and is modeled here as a geometrically multiplied branching process. In developing our theory, we also introduce a “noise coefficient” which enables the comparison of the Fisher information of different data models via a scalar quantity. This coefficient importantly allows the selection of the best detector (e.g., EMCCD or CCD), based on factors such as the signal level, and regardless of the specific estimation problem at hand. We apply our theory to the problem of localizing a single molecule, and compare the calculated limits of the localization accuracy with the standard deviations of maximum likelihood location estimates obtained from simulated images of a single molecule. PMID:24379939

Chao, Jerry; Ward, E. Sally; Ober, Raimund J.

2012-01-01

21

Research Update: Molecular electronics: The single-molecule switch and transistor  

SciTech Connect

In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

Sotthewes, Kai; Heimbuch, René, E-mail: r.heimbuch@utwente.nl; Kumar, Avijit; Zandvliet, Harold J. W. [Physics of Interfaces and Nanomaterials, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands); Geskin, Victor [Service de Chimie des Materiaux Nouveaux, University of Mons, Mons (Belgium)

2014-01-01

22

Conformation-controlled electron transport in single-molecule junctions containing oligo(phenylene ethynylene) derivatives.  

PubMed

Understanding the relationships between the molecular structure and electronic transport characteristics of single-molecule junctions is of fundamental and technological importance for future molecular electronics. Herein, we report a combined experimental and theoretical study on the single-molecule conductance of a series of oligo(phenylene ethynylene) (OPE) molecular wires, which consist of two phenyl-ethynyl-phenyl ? units with different dihedral angles. The molecular conductance was studied by scanning tunneling microscopy (STM)-based break-junction techniques under different conditions, including variable temperature and bias potential, which suggested that a coherent tunneling mechanism takes place in the OPE molecular wires with a length of 2.5 nm. The conductance of OPE molecular junctions are strongly affected by the coupling strength between the two ? systems, which can be tuned by controlling their intramolecular conformation. A cos(2)? dependence was revealed between the molecular conductance and dihedral angles between the two conjugated units. Theoretical investigations on the basis of density functional theory and nonequilibrium Green's functions (NEGF) gave consistent results with the experimental observations and provided insights into the conformation-dominated molecular conductance. PMID:23729379

Wang, Le-Jia; Yong, Ai; Zhou, Kai-Ge; Tan, Lin; Ye, Jian; Wu, Guo-Ping; Xu, Zhu-Guo; Zhang, Hao-Li

2013-08-01

23

Fast electron transfer through a single molecule natively structured redox protein  

NASA Astrophysics Data System (ADS)

The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent.The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent. Electronic supplementary information (ESI) available: Experimental methods, DNA and protein sequences, additional STM statistical analysis and images, electrochemical data and It-z data analysis. See DOI: 10.1039/c2nr32131a

Della Pia, Eduardo Antonio; Chi, Qijin; MacDonald, J. Emyr; Ulstrup, Jens; Jones, D. Dafydd; Elliott, Martin

2012-10-01

24

Electron Transport, Energy Transfer, and Optical Response in Single Molecule Junctions  

NASA Astrophysics Data System (ADS)

The last decade has seen incredible growth in the quality of experiments being done on single molecule junctions. Contemporary experimental measurements have expanded far beyond simple electron transport. Measurement of vibronic eects, quantum interference and decoherence eects, molecular optical response (Raman spectroscopy), and molecular spintronics are just some of the continuing areas of research in single molecule junctions. Experimental advancements demand advanced theoretical treatments, which can be used accurately within appropriate physical regimes, in order to understand measured phenomena and predict interesting directions for future study. In this dissertation we will study systems with strong intra-system interactions using a many-body states based approach. We will be focused on three related processes in molecular junctions: electron transport, electronic energy transfer, and molecular excitation. Inelastic electron transport in the regime of strong and nonlinear electron-vibration coupling within and outside of the Born-Oppenheimer regime will be investigated. To understand their appropriateness, we will compare simple semi-classical approximations in molecular redox junctions and electron-counting devices to fully quantum calculations based on many-body system states. The role of coherence and quantum interference in energy and electron transfer in molecular junctions is explored. Experiments that simultaneously measure surface enhanced Raman scattering and electron conduction have revealed a strong interaction between conducting electrons and molecular excitation. We investigate the role of the molecular response to a classical surface plasmon enhanced electric eld considering the back action of the oscillating molecular dipole. Raman scattering is quantum mechanical by nature and involves strong interaction between surface plasmons in the contacts and the molecular excitation. We develop a scheme for treating strong plasmon-molecular excitation interactions quantum mechanically within nonequilibrium molecular junctions. Finally we perform preliminary calculations of the Raman spectrum of a three-ring oligophenylene vinylene terminating in amine functional groups molecule in a molecular junction and compare our results to experimental measurements. This work is the rst steps towards full calculations of the optical response of current-carrying molecular junction, which should combine classical calculations of the plasmon enhanced electric field with quantum calculations for the plasmon-molecular exciton interaction and nonequilibrium Raman scattering.

White, Alexander James

25

All-optical sensing of a single-molecule electron spin  

E-print Network

We demonstrate an all-optical method for magnetic sensing of individual molecules in ambient conditions at room temperature. Our approach is based on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV centers is all-optical and provides a sensitive probe of the magnetic field fluctuations stemming from the dynamics of the electronic spins of the attached molecules. As a specific example, we demonstrate detection of a single paramagnetic molecule containing a gadolinium (Gd$^{3+}$) ion. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to co-localize one NV center and one Gd$^{3+}$-containing molecule. Possible applications include nanoscale and in vivo magnetic spectroscopy and imaging of individual molecules.

Sushkov, A O; Lovchinsky, I; Kubo, M; Lo, P K; Bennett, S D; Hunger, D; Akimov, A; Walsworth, R L; Park, H; Lukin, M D

2013-01-01

26

All-optical sensing of a single-molecule electron spin.  

PubMed

We demonstrate an all-optical method for magnetic sensing of individual molecules in ambient conditions at room temperature. Our approach is based on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV centers is all-optical and provides a sensitive probe of the magnetic field fluctuations stemming from the dynamics of the electronic spins of the attached molecules. As a specific example, we demonstrate detection of a single paramagnetic molecule containing a gadolinium (Gd(3+)) ion. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to colocalize one NV center and one Gd(3+)-containing molecule. Possible applications include nanoscale and in vivo magnetic spectroscopy and imaging of individual molecules. PMID:25333198

Sushkov, A O; Chisholm, N; Lovchinsky, I; Kubo, M; Lo, P K; Bennett, S D; Hunger, D; Akimov, A; Walsworth, R L; Park, H; Lukin, M D

2014-11-12

27

All-optical sensing of a single-molecule electron spin  

E-print Network

We demonstrate an all-optical method for magnetic sensing of individual molecules in ambient conditions at room temperature. Our approach is based on shallow nitrogen-vacancy (NV) centers near the surface of a diamond crystal, which we use to detect single paramagnetic molecules covalently attached to the diamond surface. The manipulation and readout of the NV centers is all-optical and provides a sensitive probe of the magnetic field fluctuations stemming from the dynamics of the electronic spins of the attached molecules. As a specific example, we demonstrate detection of a single paramagnetic molecule containing a gadolinium (Gd$^{3+}$) ion. We confirm single-molecule resolution using optical fluorescence and atomic force microscopy to co-localize one NV center and one Gd$^{3+}$-containing molecule. Possible applications include nanoscale and in vivo magnetic spectroscopy and imaging of individual molecules.

A. O. Sushkov; N. Chisholm; I. Lovchinsky; M. Kubo; P. K. Lo; S. D. Bennett; D. Hunger; A. Akimov; R. L. Walsworth; H. Park; M. D. Lukin

2013-11-07

28

A study of planar anchor groups for graphene-based single-molecule electronics  

NASA Astrophysics Data System (ADS)

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

Bailey, Steven; Visontai, David; Lambert, Colin J.; Bryce, Martin R.; Frampton, Harry; Chappell, David

2014-02-01

29

Electronic coherences and vibrational wave-packets in single molecules studied with femtosecond phase-controlled spectroscopy.  

PubMed

Employing femtosecond pulse-shaping techniques we investigate ultrafast, coherent and incoherent dynamics in single molecules at room temperature. In first experiments single molecules are excited into their purely electronic 0-0 transition by phase-locked double-pulse sequences with pulse durations of 75 fs and 20 nm spectral band width. Their femtosecond kinetics can then be understood in terms of a 2-level system and modelled with the optical Bloch equations. We find that we observe the coherence decay in single molecules, and the purely electronic dephasing times can be retrieved directly in the time domain. In addition, the Rabi-frequencies and thus the transition dipole moments of single molecules are determined from these data. Upon excitation of single molecules into a vibrational level of the electronically excited state also incoherent intra-molecular vibrational relaxation is recorded. Increasing the spectral band width of the excitation pulses to up to 120 nm (resulting in a transform-limited pulse width of 15 fs) coherent superpositions of excited state vibrational modes, i.e. vibrational wave packets, are excited. The wave-packet oscillations in the excited state potential energy surface are followed in time by a phase-controlled pump-probe scheme, which permits to record wave packet interference, and to determine the energies of vibrational modes and their coupling strengths to the electronic transition. PMID:21240402

Hildner, Richard; Brinks, Daan; Stefani, Fernando D; van Hulst, Niek F

2011-02-01

30

Manipulation and characterization of thin-film interfacial chemistry: Sol-gel deposition and single molecule tracking experiments  

NASA Astrophysics Data System (ADS)

Single molecule trajectories of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbo - cyanine perchlorate (DiI) fluorophores diffusing on planar supported 1,2-dimyristoyl-snglycero- 3-phosphocholine (DMPC) lipid bilayers imaged through total internal reflection fluorescence (TIRF) microscopy at different temperatures are investigated. The spatial resolution limit for detecting molecular motion is evaluated by characterizing the apparent motion which arises from the limited signal-to-noise ratio (S/N) of imaged and simulated stationary DiI molecules. Statistical criteria for reliably distinguishing molecular motion from stationary molecules using F-test statistics, including the computation of local signal-to-noise ratios are then established and used for reliably detecting subdiffraction motion of DiI molecules on DMPC. The same single molecule tracking concept is used in investigating the temperature dependence of subdiffraction diffusional confinement of single Rhodamine 6G molecules in polymer brushes of poly (N-isopropylacrylamide), pNIPAAm, above and below its lower critical solution temperature (LCST) of 32°C. Reliably distinguishing subdiffraction molecular motion from stationary events is crucial in validating the application of single molecule tracking experiment in probing nanometersized hydrophobic environments of polymer structure. A versatile and rapid sol-gel technique for the fabrication of high quality one-dimensional photonic bandgap materials was developed. Silica/titania multilayer materials are fabricated by a sol-gel chemistry route combined with dip-coating onto planar or curved substrate. A shock-cooling step immediately following the thin film heat-treatment process is introduced. The versatility of this sol-gel method is demonstrated by the fabrication of various Bragg stack-type materials with fine-tuned optical properties. Measured optical properties show good agreement with theoretical simulations confirming the high quality of these sol-gel fabricated optical materials. Finally, magnetic functionalization studies of sol-gel derived Co-ion doped titania thin films using superconducting quantum interference device (SQUID) magnetometry and an attempt to measure their magneto-optical properties using a home-built Faraday rotation setup are discussed. The experimental limitations in reliably measuring magnetization responses of these thin films are introduced and discussed in detail. The summary and outlook chapters summarize the scientific significance of each research project and briefly introduce ongoing research based on the work and the results presented in this dissertation.

Barhoum, Moussa

31

Quantum master equation for electron transport through quantum dots and single molecules Upendra Harbola, Massimiliano Esposito,* and Shaul Mukamel  

E-print Network

Quantum master equation for electron transport through quantum dots and single molecules Upendra s : 73.63. b, 03.65.Yz, 05.60.Gg I. INTRODUCTION Electron transport through a quantum dot QD or a single in the fabrication of devices such as quantum dots whose size and geometry can be controlled with high precision14

Mukamel, Shaul

32

Single-molecule-mediated heat current between an electronic and a bosonic bath  

NASA Astrophysics Data System (ADS)

In molecular devices, electronic degrees of freedom are coupled to vibrational modes of the molecule, offering an opportunity to study fundamental aspects of this coupling at the nanoscale. To this end, we consider the nonequilibrium heat exchange between a conduction band and a bosonic bath mediated by a single molecule. For molecules large enough so that onsite Coulomb repulsion can be dropped, we carry out an asymptotically exact calculation of the heat current, governed by the smallness of the electron-phonon coupling, and obtain the steady-state heat current driven by a finite-temperature drop. At low temperatures, the heat current is found to have a power-law behavior with respect to the temperature difference with the power depending on the nature of the bosonic bath. At high temperatures, on the other hand, the current is linear in the temperature difference for all types of bosonic baths. The crossover between these behaviors is described. Some of the results are given a physical explanation by comparing to a perturbative master-equation calculation (the limitation of which we examine).

Vinkler-Aviv, Yuval; Schiller, Avraham; Andrei, Natan

2014-01-01

33

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology  

PubMed Central

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

2011-01-01

34

Electronic Measurements of Single-Molecule Processing by DNA Polymerase I (Klenow Fragment)  

PubMed Central

Bioconjugating single molecules of the Klenow fragment of DNA polymerase I into electronic nanocircuits allowed electrical recordings of enzymatic function and dynamic variability with the resolution of individual nucleotide incorporation events. Continuous recordings of DNA polymerase processing multiple homopolymeric DNA templates extended over 600 s and through >10,000 bond forming events. An enzymatic processivity of 42 nucleotides for a template of the same length was directly observed. Statistical analysis determined key kinetic parameters for the enzyme’s open and closed conformations. Consistent with these nanocircuit-based observations, the enzyme closed complex forms a phosphodiester bond in a highly efficient process >99.8% of the time with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for catalysis occurs during the enzyme open state, but with a nearly two-fold longer duration for dATP or dTTP incorporation than for dCTP or dGTP into complementary, homopolymeric DNA templates. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase I. PMID:23631761

Olsen, Tivoli J.; Choi, Yongki; Sims, Patrick C.; Gul, O. Tolga; Corso, Brad L.; Dong, Chengjun; Brown, William A.; Collins, Philip G.; Weiss, Gregory A.

2013-01-01

35

Wiring up Single Molecules  

NSDL National Science Digital Library

In recent years, circuit design has advanced to achieve extremely small feature sizes -- literally tens of millions of transistors can be integrated in a single chip. This progress has given rise to molecular electronics, the notion of creating electronic devices with single molecules as circuit elements. In this paper, the authors "discuss transistors, where electrons flow through discrete quantum states of a single molecule." Fabrication considerations are outlined, and the current-voltage responses of several such transistors that were fabricated by the authors are shown. The paper concludes by looking ahead to future possibilities of chemically-tailored transistors that could be designed with specific properties.

36

Fabrication of nanogapped single-electron transistors for transport studies of individual single-molecule magnets  

E-print Network

Fabrication of nanogapped single-electron transistors for transport studies of individual single of optical and electron beam lithography. Electromigration induced breaking of the nanowires reliably. Conduction through a molecular SET only occurs when a molecular electronic level lies between the Fermi

del Barco, Enrique

37

Single-Molecule Electron Tunneling Spectroscopy of the Higher Plant Light-Harvesting Complex LHC II  

Microsoft Academic Search

Electronic spectroscopy of a single biological molecule is demonstrated with ?4 Å spatial resolution. The light-harvesting complex II (LHC II), in the ground and photo-excited states, was studied using scanning tunneling microscopy and spectroscopy of intact Photosystem II complexes. Analysis of the spectra indicates that the main mechanisms of tunneling between the STM tip and the surface involve delocalized electronic

Philip B. Lukins

1999-01-01

38

Holography and Coherent Diffraction with Low-Energy Electrons: A Route towards Structural Biology at the Single Molecule Level  

E-print Network

The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2 Angstrom has been achieved revealing the 660.000 unit cells of the graphene sheet from one data set at once. Applied to individual biomolecules the method allows for non-destructive imaging and imports the potential to distinguish between di...

Latychevskaia, Tatiana; Escher, Conrad; Fink, Hans-Werner

2014-01-01

39

Site-dependent electronic structures of a single molecule on a metal surface studied by scanning tunneling microscopy and spectroscopy  

NASA Astrophysics Data System (ADS)

Single-molecule observation of the electronic structures of para-cyanobenzoate (pCB) adsorbed on Cu(1 1 0) has been performed using scanning tunneling microscopy (STM) and spectroscopy (STS). We found that pCB has two types of the adsorption site on Cu(1 1 0); i.e., two oxygen atoms of pCB are bridged between adjacent Cu atoms at the short- or long-bridge sites. STS and STS mapping revealed that the pCB adsorbed at the short-bridge site has a resonant peak at 2.0 V above the Fermi level, which is assigned to the lowest unoccupied molecular orbital (LUMO) of pCB. However, the LUMO state is shifted toward lower voltage (1.2 V) when the pCB molecule is adsorbed at the long-bridge site. The energy levels of the LUMO state, depending on the adsorption site of pCB, can thus be ascribed to the degree of the electronic interaction between pCB and the Cu substrate. The site transformation of pCB induced by the injection of tunneling electrons from the STM tip has also been presented.

Katano, Satoshi; Hori, Masafumi; Kim, Yousoo; Kawai, Maki

2014-10-01

40

Yeast cytochrome c integrated with electronic elements: a nanoscopic and spectroscopic study down to single-molecule level  

NASA Astrophysics Data System (ADS)

Various aspects of redox protein integration with nano-electronic elements are addressed by a multi-technique investigation of different yeast cytochrome c (YCC)-based hybrid systems. Three different immobilization strategies on gold via organic linkers are explored, involving either covalent bonding or electrostatic interaction. Specifically, Au surfaces are chemically modified by self-assembled monolayers (SAMs) exposing thiol-reactive groups, or by acid-oxidized single-wall carbon nanotubes (SWNTs). Atomic force microscopy and scanning tunnelling microscopy are employed to characterize the morphology and the electronic properties of single YCC molecules adsorbed on the modified gold surfaces. In each hybrid system, the protein molecules are stably assembled, in a native configuration. A standing-up arrangement of YCC on SAMs is suggested, together with an enhancement of the molecular conduction, as compared to YCC directly assembled on gold. The electrostatic interaction with functionalized SWNTs allows several YCC adsorption geometries, with a preferential high-spin haem configuration, as outlined by Raman spectroscopy. Moreover, the conduction properties of YCC, explored in different YCC nanojunctions by conductive atomic force microscopy, indicate the effectiveness of electrical conduction through the molecule and its dependence on the electrode material. The joint employment of several techniques confirms the key role of a well-designed immobilization strategy, for optimizing biorecognition capabilities and electrical coupling with conductive substrates at the single-molecule level, as a starting point for advanced applications in nano-biotechnology.

Delfino, I.; Bonanni, B.; Andolfi, L.; Baldacchini, C.; Bizzarri, A. R.; Cannistraro, S.

2007-06-01

41

Single molecule laser spectroscopy.  

PubMed

In this article, we discussed some single molecule spectroscopy techniques and methods. We have chosen the simplicity in this survey based on our laboratory experience in this field. We concentrated on the imaging by both techniques the wide field and the scanning microscopes. Other imaging enhancements on the technique like extended resolution wide field, the total internal reflection imaging, and its derivatives are also reviewed. In addition to the imaging techniques, some diffusion techniques also are discussed like fluorescence correlation spectroscopy. The related methods like Forester resonance transfer, photo-induced electron transfer and anisotropy (steady state and time decay) are also discussed. In addition, we elucidated some simple details about the theory behind the FCS and its resulting curve fitting. This review is preceded by general introduction and ended with the conclusion. PMID:25156641

Atta, Diaa; Okasha, Ali

2015-01-25

42

Single-Molecule Magnets on Gold Direct Observation of Single-Molecule Magnets  

E-print Network

,2] In the last decade, it was discovered that single molecules can, in principle, be used to store magneticSingle-Molecule Magnets on Gold Direct Observation of Single-Molecule Magnets Organized on Gold, and Herre S. J. Van der Zant An aim of molecular electronics is to use single (or a few) molecules as active

43

Nanophotonics and Single Molecules  

Microsoft Academic Search

Single emitting molecules are currently providing a new window into nanoscale systems ranging from biology to materials science.\\u000a The amount of information that can be extracted from each single molecule depends upon the specific photophysical properties\\u000a of the fluorophore and how these properties are affected by the nearby environment. For this reason, it is necessary to develop\\u000a single-molecule emitters with

W. E. Moerner; P. James Schuck; David P. Fromm; Anika Kinkhabwala; Samuel J. Lord; Stefanie Y. Nishimura; Katherine A. Willets; Arvind Sundaramurthy; Gordon Kino; Meng He; Zhikuan Lu; Robert J. Twieg

44

Multiplexed single molecule immunoassays.  

PubMed

We have developed a method that enables the multiplexed detection of proteins based on counting single molecules. Paramagnetic beads were labeled with fluorescent dyes to create optically distinct subpopulations of beads, and antibodies to specific proteins were then immobilized to individual subpopulations. Mixtures of subpopulations of beads were then incubated with a sample, and specific proteins were captured on their specific beads; these proteins were then labeled with enzymes via immunocomplex formation. The beads were suspended in enzyme substrate, loaded into arrays of femtoliter wells--or Single Molecule Arrays (Simoa)--that were integrated into a microfluidic device (the Simoa disc). The wells were then sealed with oil, and imaged fluorescently to determine: a) the location and subpopulation identity of individual beads in the femtoliter wells, and b) the presence or absence of a single enzyme associated with each bead. The images were analyzed to determine the average enzyme per bead (AEB) for each bead subpopulation that provide a quantitative parameter for determining the concentration of each protein. We used this approach to simultaneously detect TNF-?, IL-6, IL-1?, and IL-1? in human plasma with single molecule resolution at subfemtomolar concentrations, i.e., 200- to 1000-fold more sensitive than current multiplexed immunoassays. The simultaneous, specific, and sensitive measurement of several proteins using multiplexed digital ELISA could enable more reliable diagnoses of disease. PMID:23719780

Rissin, David M; Kan, Cheuk W; Song, Linan; Rivnak, Andrew J; Fishburn, Matthew W; Shao, Qichao; Piech, Tomasz; Ferrell, Evan P; Meyer, Raymond E; Campbell, Todd G; Fournier, David R; Duffy, David C

2013-08-01

45

Electronic transport, transition-voltage spectroscopy, and the Fano effect in single molecule junctions composed of a biphenyl molecule attached to metallic and semiconducting carbon nanotube electrodes.  

PubMed

We have investigated electronic transport in a single-molecule junction composed of a biphenyl molecule attached to a p-doped semiconductor and metallic carbon nanotube leads. We find that the current-voltage characteristics are asymmetric as a result of the different electronic natures of the right and left leads, which are metallic and semiconducting, respectively. We provide an analysis of transition voltage spectroscopy in such a system by means of both Fowler-Nordheim and Lauritsen-Millikan plots; this analysis allows one to identify the positions of resonances and the regions where the negative differential conductance occurs. We show that transmittance curves are well described by the Fano lineshape, for both direct and reverse bias, demonstrating that the frontier molecular orbitals are effectively involved in the transport process. This result gives support to the interpretation of transition voltage spectroscopy based on the coherent transport model. PMID:25109887

Brito da Silva Júnior, Carlos Alberto; Leal, José Fernando Pereira; Aleixo, Vicente Ferrer Pureza; Pinheiro, Felipe A; Del Nero, Jordan

2014-09-28

46

Ultrafast Interfacial Proton-Coupled Electron Transfer  

SciTech Connect

Interfaces between metallic or semiconducting solids and protic solvent adsorbates or liquids represent one of the most important, and yet hardly explored material environments for proton coupled electron transfer (PCET) processes. PCET mediated dynamical phenomena driven by light, electron, and chemical potentials are central in energy transduction processes of vast economic and environmental importance including the photocatalytic splitting of H?O, the photo and electrochemical reduction of CO?, and the conversion of chemical to electrical energy in fuel cells. Experimental and theoretical investigations of the dynamical aspects of PCET at solid surfaces are particularly challenging because relatively localized charges within a solvent couple in the presence of strong interfacial potentials to delocalized states of electronic continua of semiconductor or metal electrodes. Moreover, the localized charges are never the bare protons and electrons that balance chemical equations, but rather are dressed particles with associated polarization clouds inhomogeneously distributed and comprised variously of free electrons, lattice ions, and solvent molecules. The polarization clouds screen the Coulomb potential on the medium specific time scales and impose energetic costs associated with transport through the inhomogeneous region of interfaces between the solid and molecular environments. We introduce some recent theoretical studies aimed at providing an atomistic description on metal-protic solvent interface and modeling of simple processes such as the discharge of H? at a metal interface. Because of the paucity of experimental research and embryonic stage of theory, our goal is to present some key theoretical concepts and early experimental efforts based primarily on a surface science approach to ultrafast electron induced dynamics. In order to introduce some key features of interfacial PCET in the strong and intermediate coupling regimes, we discuss specific examples of photoinduced dissociation of alkanes on metals and photoinduced PCET dynamics of methanol covered TiO? surfaces.

Petek, Hrvoje; Zhao, Jin

2010-12-08

47

Towards single molecule DNA sequencing  

NASA Astrophysics Data System (ADS)

Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.

Liu, Hao

48

Single Molecule Recordings of Lysozyme Activity  

PubMed Central

Single molecule bioelectronic circuits provide an opportunity to study chemical kinetics and kinetic variability with bond-by-bond resolution. To demonstrate this approach, we examined the catalytic activity of T4 lysozyme processing peptidoglycan substrates. Monitoring a single lysozyme molecule through changes in a circuit’s conductance helped elucidate unexplored and previously invisible aspects of lysozyme’s catalytic mechanism and demonstrated lysozyme to be a processive enzyme governed by 9 independent time constants. The variation of each time constant with pH or substrate crosslinking provided different insights into catalytic activity and dynamic disorder. Overall, ten lysozyme variants were synthesized and tested in single molecule circuits to dissect the transduction of chemical activity into electronic signals. Measurements show that a single amino acid with the appropriate properties is sufficient for good signal generation, proving that the single molecule circuit technique can be easily extended to other proteins. PMID:23752924

Choi, Yongki; Weiss, Gregory A.

2013-01-01

49

Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies  

PubMed Central

SpoIIIE/FtsK are a family of ring-shaped, membrane-anchored, ATP-fuelled motors required to segregate DNA across bacterial membranes. This process is directional and requires that SpoIIIE/FtsK recognize highly skewed octameric sequences (SRS/KOPS for SpoIIIE/FtsK) distributed along the chromosome. Two models have been proposed to explain the mechanism by which SpoIIIE/FtsK interact with DNA. The loading model proposes that SpoIIIE/FtsK oligomerize exclusively on SpoIIIE recognition sequence/orienting polar sequences (SRS/KOPS) to accomplish directional DNA translocation, whereas the target search and activation mechanism proposes that pre-assembled SpoIIIE/FtsK hexamers bind to non-specific DNA, reach SRS/KOPS by diffusion/3d hopping and activate at SRS/KOPS. Here, we employ single-molecule total internal reflection imaging, atomic force and electron microscopies and ensemble biochemical methods to test these predictions and obtain further insight into the SpoIIIE–DNA mechanism of interaction. First, we find that SpoIIIE binds DNA as a homo-hexamer with neither ATP binding nor hydrolysis affecting the binding mechanism or affinity. Second, we show that hexameric SpoIIIE directly binds to double-stranded DNA without requiring the presence of SRS or free DNA ends. Finally, we find that SpoIIIE hexamers can show open and closed conformations in solution, with open-ring conformations most likely resembling a state poised to load to non-specific, double-stranded DNA. These results suggest how SpoIIIE and related ring-shaped motors may be split open to bind topologically closed DNA. PMID:24297254

Cattoni, Diego I.; Thakur, Shreyasi; Godefroy, Cedric; Le Gall, Antoine; Lai-Kee-Him, Josephine; Milhiet, Pierre-Emmanuel; Bron, Patrick; Nöllmann, Marcelo

2014-01-01

50

IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.  

PubMed

The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a "focused electron tomography reconstruction" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single "snapshot" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. PMID:22291925

Zhang, Lei; Ren, Gang

2012-01-01

51

Quantum phase transition in a single-molecule quantum dot  

E-print Network

LETTERS Quantum phase transition in a single-molecule quantum dot Nicolas Roch1 , Serge Florens1 demonstrate this possibility in a single-molecule quantum dot, where a gate voltage induces a crossing of two dif- ferent types of electron spin state (singlet and triplet) at zero magnetic field. The quantum dot

Canet, Léonie

52

Single-molecule spectroscopy using nanoporous membranes.  

PubMed

We describe a novel approach for optically detecting DNA translocation events through an array of solid-state nanopores that potentially allows for ultra high-throughput, parallel detection at the single-molecule level. The approach functions by electrokinetically driving DNA strands through sub micrometer-sized holes on an aluminum/silicon nitride membrane. During the translocation process, the molecules are confined to the walls of the nanofluidic channels, allowing 100% detection efficiency. Importantly, the opaque aluminum layer acts as an optical barrier between the illuminated region and the analyte reservoir. In these conditions, high-contrast imaging of single-molecule events can be performed. To demonstrate the efficiency of the approach, a 10 pM fluorescently labeled lambda-DNA solution was used as a model system to detect simultaneous translocation events using electron multiplying CCD imaging. Single-pore translocation events are also successfully detected using single-point confocal spectroscopy. PMID:17718589

Chansin, Guillaume A T; Mulero, Rafael; Hong, Jongin; Kim, Min Jun; DeMello, Andrew J; Edel, Joshua B

2007-09-01

53

Single-molecule mechanics of mussel adhesion  

NASA Astrophysics Data System (ADS)

The glue proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces in aqueous environments in which most adhesives function poorly. Studies of these functionally unique proteins have revealed the presence of the unusual amino acid 3,4-dihydroxy-L-phenylalanine (dopa), which is formed by posttranslational modification of tyrosine. However, the detailed binding mechanisms of dopa remain unknown, and the chemical basis for mussels' ability to adhere to both inorganic and organic surfaces has never been fully explained. Herein, we report a single-molecule study of the substrate and oxidation-dependent adhesive properties of dopa. Atomic force microscopy (AFM) measurements of a single dopa residue contacting a wet metal oxide surface reveal a surprisingly high strength yet fully reversible, noncovalent interaction. The magnitude of the bond dissociation energy as well as the inability to observe this interaction with tyrosine suggests that dopa is critical to adhesion and that the binding mechanism is not hydrogen bond formation. Oxidation of dopa, as occurs during curing of the secreted mussel glue, dramatically reduces the strength of the interaction to metal oxide but results in high strength irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role of dopa emerges from these studies, in which dopa exploits a remarkable combination of high strength and chemical multifunctionality to accomplish adhesion to substrates of widely varying composition from organic to metallic. 3,4-dihydroxylphenylalanine | atomic force microscopy | mussel adhesive protein

Lee, Haeshin; Scherer, Norbert F.; Messersmith, Phillip B.

2006-08-01

54

Single-molecule electric revolving door.  

PubMed

This work proposes a new type of molecular machine, the single-molecule electric revolving door, which utilizes conductance dependence upon molecular conformation as well as destructive quantum interference. We perform electron transport simulations in the zero-bias limit using the Landauer formalism together with density functional theory. The simulations show that the open- and closed-door states, accompanied by significant conductance variation, can be operated by an external electric field. The large on-off conductance ratio (~10(5)) implies that the molecular machine can also serve as an effective switching device. The simultaneous control and detection of the door states can function at the nanosecond scale, thereby offering a new capability for molecular-scale devices. PMID:24127690

Hsu, Liang-Yan; Li, Elise Y; Rabitz, Herschel

2013-11-13

55

RICE UNIVERSITY Transport in Single Molecule Transistors  

E-print Network

RICE UNIVERSITY Transport in Single Molecule Transistors by Lam H. Yu A Thesis Submitted in Partial Houston, Texas January, 2006 #12;Abstract Transport in Single Molecule Transistors by Lam H. Yu molecule transistors (SMTs), nanometer-scale transistors in which charge transport occurs through

Natelson, Douglas

56

Single Molecule Approaches Embrace Molecular Cohorts  

PubMed Central

Enormous mechanistic insight has been gained by studying the behavior of single molecules. The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. PMID:23953107

Ha, Taekjip

2013-01-01

57

Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data  

E-print Network

Molecule Data Max Greenfeld1,2. , Dmitri S. Pavlichin3. , Hideo Mabuchi4 *, Daniel Herschlag1,2 * 1 Single Molecule Data. PLoS ONE 7(2): e30024. doi:10.1371/journal.pone.0030024 Editor: Daniel J. Muller at the single molecule level have greatly expanded the types of biological systems amenable to single molecule

Herschlag, Dan

58

Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level  

NASA Astrophysics Data System (ADS)

Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)-, (M-O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm2. To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm2 at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.

Keller, Adrian; Kopyra, Janina; Gothelf, Kurt V.; Bald, Ilko

2013-08-01

59

Grafting single molecule magnets on gold nanoparticles.  

PubMed

The chemical synthesis and characterization of the first hybrid material composed by gold nanoparticles and single molecule magnets (SMMs) are described. Gold nanoparticles are functionalized via ligand exchange using a tetrairon(III) SMM containing two 1,2-dithiolane end groups. The grafting is evidenced by the shift of the plasmon resonance peak recorded with a UV-vis spectrometer, by the suppression of nuclear magnetic resonance signals, by X-ray photoemission spectroscopy peaks, and by transmission electron microscopy images. The latter evidence the formation of aggregates of nanoparticles as a consequence of the cross-linking ability of Fe4 through the two 1,2-dithiolane rings located on opposite sides of the metal core. The presence of intact Fe4 molecules is directly proven by synchrotron-based X-ray absorption spectroscopy and X-ray magnetic circular dichroism spectroscopy, while a detailed magnetic characterization, obtained using electron paramagnetic resonance and alternating-current susceptibility, confirms the persistence of SMM behavior in this new hybrid nanostructure. PMID:23996936

Perfetti, Mauro; Pineider, Francesco; Poggini, Lorenzo; Otero, Edwige; Mannini, Matteo; Sorace, Lorenzo; Sangregorio, Claudio; Cornia, Andrea; Sessoli, Roberta

2014-01-29

60

Single Molecule Probes of Lipid Membrane Structure  

E-print Network

-M) using p-polarized excitation can reveal single-molecule orientations when spherical aberrations are introduced into the optics train. This approach was used here to measure the orientation of fluorescent lipid analogs doped into Langmuir...

Livanec, Philip W.

2009-12-14

61

Low-energy cross-section calculations of single molecules by electron impact: a classical Monte Carlo transport approach with quantum mechanical description  

NASA Astrophysics Data System (ADS)

The present state of modeling radio-induced effects at the cellular level does not account for the microscopic inhomogeneity of the nucleus from the non-aqueous contents (i.e. proteins, DNA) by approximating the entire cellular nucleus as a homogenous medium of water. Charged particle track-structure calculations utilizing this approximation are therefore neglecting to account for approximately 30% of the molecular variation within the nucleus. To truly understand what happens when biological matter is irradiated, charged particle track-structure calculations need detailed knowledge of the secondary electron cascade, resulting from interactions with not only the primary biological component—water--but also the non-aqueous contents, down to very low energies. This paper presents our work on a generic approach for calculating low-energy interaction cross-sections between incident charged particles and individual molecules. The purpose of our work is to develop a self-consistent computational method for predicting molecule-specific interaction cross-sections, such as the component molecules of DNA and proteins (i.e. nucleotides and amino acids), in the very low-energy regime. These results would then be applied in a track-structure code and thereby reduce the homogenous water approximation. The present methodology—inspired by seeking a combination of the accuracy of quantum mechanics and the scalability, robustness, and flexibility of Monte Carlo methods—begins with the calculation of a solution to the many-body Schrödinger equation and proceeds to use Monte Carlo methods to calculate the perturbations in the internal electron field to determine the interaction processes, such as ionization and excitation. As a test of our model, the approach is applied to a water molecule in the same method as it would be applied to a nucleotide or amino acid and compared with the low-energy cross-sections from the GEANT4-DNA physics package of the Geant4 simulation toolkit for the energy ranges of 7 eV to 1 keV.

Madsen, J. R.; Akabani, G.

2014-05-01

62

Single-Molecule X-Ray Interferometry: Controlling Coupled Electron-Nuclear Quantum Dynamics and Imaging Molecular Potentials by Ultrahigh-Resolution Resonant Photoemission and Ab Initio Calculations  

NASA Astrophysics Data System (ADS)

This paper reports an advanced study of the excited ionic states of the gas-phase nitrogen molecule in the binding-energy region of 22-34 eV, combining ultrahigh-resolution resonant photoemission (RPE) and ab initio configuration-interaction calculations. The RPE spectra are recorded for nine photon energies within the N 1s??* absorption resonance of N2 by using a photon bandwidth that is considerably smaller than lifetime broadening, and the dependence on excitation energy of the decay spectra is analyzed and used for the first assignment of 12 highly overlapped molecular states. The effect on the RPE profile of avoided curve crossings between the final N2+ ionic states is discussed, based on theoretical simulations that account for vibronic coupling, and compared with the experimental data. By use of synchrotron radiation with high spectral brightness, it is possible to selectively promote the molecule to highly excited vibrational sublevels of a core-excited electronic state, thereby controlling the spatial distribution of the vibrational wave packets, and to accurately image the ionic molecular potentials. In addition, the mapping of the vibrational wave functions of the core-excited states using the bound final states with far-from-equilibrium bond lengths has been achieved experimentally for the first time. Theoretical analysis has revealed the rich femtosecond nuclear dynamics underlying the mapping phenomenon.

Kimberg, V.; Lindblad, A.; Söderström, J.; Travnikova, O.; Nicolas, C.; Sun, Y. P.; Gel'mukhanov, F.; Kosugi, N.; Miron, C.

2013-01-01

63

Pair Tunneling through Single Molecules  

NASA Astrophysics Data System (ADS)

Coupling to molecular vibrations induces a polaronic shift, and can lead to a negative charging energy, U. For negative U, the occupation of the ground state of the molecule is even. In this situation, virtual pair transitions between the molecule and the leads can dominate electron transport. At low temperature, T, these transitions give rise to the charge-Kondo effect [1]. We developed the electron transport theory through the negative-U molecule [2] at relatively high T, when the Kondo correlations are suppressed. Two physical ingredients distinguish our theory from the transport through a superconducting grain coupled to the normal leads [3]: (i) in parallel with sequential pair-tunneling processes, single-particle cotunneling processes take place; (ii) the electron pair on the molecule can be created (or annihilated) by two electrons tunneling in from (or out to) opposite leads. We found that, even within the rate-equation description, the behavior of differential conductance through the negative-U molecule as function of the gate voltage is quite peculiar: the height of the peak near the degeneracy point is independent of temperature, while its width is proportional to T. This is in contrast to the ordinary Coulomb-blockade conductance peak, whose integral strength is T-independent. At finite source-drain bias, V>>T, the width of the conductance peak is ˜V, whereas the conventional Coulomb-blockade peak at finite V splits into two sharp peaks at detunings V/2, and -V/2. Possible applications to the gate-controlled current rectification and switching will be discussed. [1] A. Taraphder and P. Coleman, Phys. Rev. Lett. 66, 2814 (1991). [2] J. Koch, M. E. Raikh, and F. von Oppen, Phys. Rev. Lett. 96, 056803 (2006). [3] F. W. J. Hekking, L. I. Glazman, K. A. Matveev, and R. I. Shekhter, Phys. Rev. Lett. 70, 4138 (1993).

Raikh, Mikhail

2007-03-01

64

A single-molecule diode  

PubMed Central

We have designed and synthesized a molecular rod that consists of two weakly coupled electronic ? -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical ? -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hanisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

2005-01-01

65

A single-molecule diode  

NASA Astrophysics Data System (ADS)

We have designed and synthesized a molecular rod that consists of two weakly coupled electronic ? -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical ? -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode. Author contributions: F.E., H.B.W., and M.M. designed research; M.E., R.O., M.K., M.F., F.E., H.B.W., and M.M. performed research; M.E., R.O., M.K., M.F., C.v.H., F.W., F.E., H.B.W., and M.M. contributed new reagents/analytic tools; M.E., R.O., M.K., C.v.H., F.E., H.B.W., and M.M. analyzed data; and F.E., H.B.W., and M.M. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: A, acceptor; D, donor; MCB, mechanically controlled break junction.Data deposition: The atomic coordinates have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, United Kingdom (CSD reference no. 241632).

Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

2005-06-01

66

Origin of discrete current fluctuations in a single molecule junction.  

PubMed

A series of fresh molecular junctions at a single molecule level were created and the current fluctuations were studied as electrons passed through them. Our results indicate that telegraph-like current fluctuations at room temperature neither originate from electron trapping/detrapping processes nor from molecule re-conformation. Our results will be helpful in better understanding the mechanism of current fluctuations. PMID:25271483

Xiang, Dong; Lee, Takhee; Kim, Youngsang; Mei, Tingting; Wang, Qingling

2014-10-24

67

Electronic structures of interfacial states formed at polymeric semiconductor heterojunctions.  

PubMed

Heterojunctions between organic semiconductors are central to the operation of light-emitting and photovoltaic diodes, providing respectively for electron-hole capture and separation. However, relatively little is known about the character of electronic excitations stable at the heterojunction. We have developed molecular models to study such interfacial excited electronic excitations that form at the heterojunction between model polymer donor and polymer acceptor systems: poly(9,9-dioctylfluorene-co-bis-N,N-(4-butylphenyl)-bis-N,N-phenyl-1,4-phenylenediamine) (PFB) with poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT), and poly(9,9-dioctylfluorene-co-N-(4-butylphenyl)diphenylamine) (TFB) with F8BT. We find that for stable ground-state geometries the excited state has a strong charge-transfer character. Furthermore, when partly covalent, modelled radiative lifetimes (approximately 10(-7) s) and off-chain axis polarization (30 degrees) match observed 'exciplex' emission. Additionally for the PFB:F8BT blend, geometries with fully ionic character are also found, thus accounting for the low electroluminescence efficiency of this system. PMID:18438413

Huang, Ya-shih; Westenhoff, Sebastian; Avilov, Igor; Sreearunothai, Paiboon; Hodgkiss, Justin M; Deleener, Caroline; Friend, Richard H; Beljonne, David

2008-06-01

68

Single-molecule spectroelectrochemistry (SMS-EC).  

PubMed

We introduce single-molecule spectroelectrochemistry (SMS-EC), a powerful new technique for studying electrochemical kinetics in highly heterogeneous systems. This technique uses fluorescence single-molecule spectroscopy to indirectly measure electrochemical kinetics one molecule at a time, offering for the first time the distribution of key electrochemical variables, such as the half-wave potential, E1/2, not just the ensemble averages. In SMS-EC, the potential of the working electrode of an electrochemical cell is linearly scanned while simultaneously measuring the florescence intensity, Ifl(t), of individual single molecules as a function of time in a wide-field microscope. SMS-EC is used herein to study the oxidation at an indium tin oxide (ITO) electrode of single molecules of the organic conjugated polymer F8BT. The results reveal both excited singlet state and ground state oxidation of F8BT. The latter process occurs over a narrow distribution of single-molecule half-wave potential values, indicating a relatively uniform electrochemical potential at the electrode. PMID:16834364

Palacios, Rodrigo E; Fan, Fu-Ren F; Bard, Allen J; Barbara, Paul F

2006-07-19

69

Single Molecule Measurements Using Correlation Force Spectroscopy  

NASA Astrophysics Data System (ADS)

Thermal noise represents a fundamental limit in force measurements. We describe single molecule measurements using two AFM cantilevers that have lower thermal noise than single-cantilever measurements. We achieve this by measuring the correlated thermal motions of two closely spaced cantilevers. Because only correlated thermal noise is measured, there is lower noise. In addition, the use of two cantilevers produces both decreased hydrodynamic fluid damping and decreased van der Waals forces acting on an AFM probe, both of which are interferences in single molecule measurements. Analysis of the correlated motions reveals molecular damping, a parameter that is not sensed with conventional (pulling) AFM single molecule force spectroscopy. When a molecule is straddled between the two cantilevers, the correlation arises from the solvent coupling as well as stiffness and damping of the molecule. We will describe the technique of correlation force spectroscopy and measurements of the mechanical properties of single polymer chains such as dextran.

Radiom, Milad; Robbins, Brian; Walz, John; Paul, Mark; Ducker, William

2013-03-01

70

A Practical Guide to Single Molecule FRET  

PubMed Central

Despite the explosive growth in the biological applications of single molecule methods over the last decade, these techniques have thus far been practiced mostly by researchers who are biophysically oriented. This is partly because of the lack of commercial instruments in many cases and also because of the perceived steep learning curve and need for expensive equipments. We wish to provide a practical guide to using Förster (or Fluorescence) Resonance Energy Transfer (FRET) at the single molecule level, focusing on the study of immobilized molecules that allow measurements of single molecule reaction trajectories from about 1 millisecond to many minutes. An instrument can be built at a reasonable cost using various off-the-shelf components and operated reliably using current well-established protocols and freely available software. PMID:18511918

Roy, Rahul; Hohng, Sungchul

2013-01-01

71

Incoherent x-ray scattering in single molecule imaging  

E-print Network

Imaging of the structure of single proteins or other biomolecules with atomic resolution would be enormously beneficial to structural biology. X-ray free-electron lasers generate highly intense and ultrashort x-ray pulses, providing a route towards imaging of single molecules with atomic resolution. The information on molecular structure is encoded in the coherent x-ray scattering signal. In contrast to crystallography there are no Bragg reflections in single molecule imaging, which means the coherent scattering is not enhanced. Consequently, a background signal from incoherent scattering deteriorates the quality of the coherent scattering signal. This background signal cannot be easily eliminated because the spectrum of incoherently scattered photons cannot be resolved by usual scattering detectors. We present an ab initio study of incoherent x-ray scattering from individual carbon atoms, including the electronic radiation damage caused by a highly intense x-ray pulse. We find that the coherent scattering pa...

Slowik, Jan Malte; Dixit, Gopal; Jurek, Zoltan; Santra, Robin

2014-01-01

72

Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data  

PubMed Central

Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data. PMID:22363412

Mabuchi, Hideo; Herschlag, Daniel

2012-01-01

73

Density Functional Theory with Dissipation: Transport through Single Molecules  

SciTech Connect

A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.

Kieron Burke

2012-04-30

74

Towards single molecule detection using photoacoustic microscopy  

NASA Astrophysics Data System (ADS)

Recently, a number of optical imaging modalities have achieved single molecule sensitivity, including photothermal imaging, stimulated emission microscopy, ground state depletion microscopy, and transmission microscopy. These optical techniques are based on optical absorption contrast, extending single-molecule detection to non-fluorescent chromophores. Photoacoustics is a hybrid technique that utilizes optical excitation and ultrasonic detection, allowing it to scale both the optical and acoustic regimes with 100% sensitivity to optical absorption. However, the sensitivity of photoacoustics is limited by thermal noise, inherent in the medium itself in the form of acoustic black body radiation. In this paper, we investigate the molecular sensitivity of photoacoustics in the context of the thermal noise limit. We show that single molecule sensitivity is achievable theoretically at room temperature for molecules with sufficiently fast relaxation times. Hurdles to achieve single molecule sensitivity in practice include development of detection schemes that work at short working distance, <100 microns, high frequency, <100 MHz, and low loss, <10 dB.

Winkler, Amy M.; Maslov, Konstantin; Wang, Lihong V.

2013-03-01

75

Thermodynamics for single-molecule stretching experiments  

E-print Network

Thermodynamics for single-molecule stretching experiments J.M. Rubi,a D. Bedeauxb and S. Kjelstrupb, Trondheim, 7491-Norway May 3, 2006 Abstract We show how to construct non-equilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a non

Kjelstrup, Signe

76

Multiplexed single-molecule assay for  

E-print Network

-molecule measurements reduces the number of experiments required to accrue enough data to draw statistically sound NA 0.45 BS L4L3 M1 L2 L1 CCD Iris Diffuser L6 L5 M2 Microscope a b c Figure 1 | Single-molecule assay

Xie, Xiaoliang Sunney

77

Incoherent x-ray scattering in single molecule imaging  

NASA Astrophysics Data System (ADS)

Imaging of the structure of single proteins or other biomolecules with atomic resolution would be enormously beneficial to structural biology. X-ray free-electron lasers generate highly intense and ultrashort x-ray pulses, providing a route towards imaging of single molecules with atomic resolution. The information on molecular structure is encoded in the coherent x-ray scattering signal. In contrast to crystallography there are no Bragg reflections in single molecule imaging, which means the coherent scattering is not enhanced. Consequently, a background signal from incoherent scattering deteriorates the quality of the coherent scattering signal. This background signal cannot be easily eliminated because the spectrum of incoherently scattered photons cannot be resolved by usual scattering detectors. We present an ab initio study of incoherent x-ray scattering from individual carbon atoms, including the electronic radiation damage caused by a highly intense x-ray pulse. We find that the coherent scattering pattern suffers from a significant incoherent background signal at high resolution. For high x-ray fluence the background signal becomes even dominating. Finally, based on the atomic scattering patterns, we present an estimation for the average photon count in single molecule imaging at high resolution. By varying the photon energy from 3.5 keV to 15 keV, we find that imaging at higher photon energies may improve the coherent scattering signal quality.

Slowik, J. M.; Son, S.-K.; Dixit, G.; Jurek, Z.; Santra, R.

2014-07-01

78

Single molecule transcription profiling with AFM*  

PubMed Central

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations. PMID:20721301

Reed, Jason; Mishra, Bud; Pittenger, Bede; Magonov, Sergei; Troke, Joshua; Teitell, Michael A; Gimzewski, James K

2009-01-01

79

Automated imaging system for single molecules  

DOEpatents

There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

2012-09-18

80

Single-Molecule Analysis of Biomembranes  

NASA Astrophysics Data System (ADS)

Biomembranes are more than just a cell's envelope - as the interface to the surrounding of a cell they carry key signalling functions. Consequentially, membranes are highly complex organelles: they host about thousand different types of lipids and about half of the proteome, whose interaction has to be orchestrated appropriately for the various signalling purposes. In particular, knowledge on the nanoscopic organization of the plasma membrane appears critical for understanding the regulation of interactions between membrane proteins. The high localization precision of ˜20 nm combined with a high time resolution of ˜1 ms made single molecule tracking an excellent technology to obtain insights into membrane nanostructures, even in a live cell context. In this chapter, we will highlight concepts to achieve superresolution by single molecule imaging, summarize tools for data analysis, and review applications on artificial and live cell membranes.

Schmidt, Thomas; Schütz, Gerhard J.

81

Electrochemical scanning tunneling microscopy and spectroscopy for single-molecule investigation.  

PubMed

The technique of electrochemical scanning tunneling microscopy (ECSTM) and spectroscopy (ECSTS) for studying electron transport through single redox molecules is here described. Redox molecules of both biological and organic nature have been studied by this technique with the aim of understanding the transport mechanisms ruling the flow of electrons via a single molecule placed in a nanometer-sized gap between two electrodes while elucidating the role of the redox density of states brought about by the molecule. The obtained results provide unique clues to single-molecule transport behavior and support the concept of single-molecule electrochemical gating. PMID:23546676

Alessandrini, Andrea; Facci, Paolo

2013-01-01

82

Single-Molecule Investigations of RNA Dissociation  

Microsoft Academic Search

Given the essential cellular roles for ribonucleic acids (RNAs) it is important to understand the stability of three-dimensional structures formed by these molecules. This study aims to investigate the dissociation energy landscape for simple RNA structures via atomic-force-microscopy-based single-molecule force-spectroscopy measurements. This approach provides details on the locations and relative heights of the energy barriers to dissociation, and thus information

Nicola H. Green; Philip M. Williams; Omar Wahab; Martyn C. Davies; Clive J. Roberts; Saul J. B. Tendler; Stephanie Allen

2004-01-01

83

Single-molecule nanometry for biological physics.  

PubMed

Precision measurement is a hallmark of physics but the small length scale (?nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ?0.3 nm precision at ?1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics. PMID:23249673

Kim, Hajin; Ha, Taekjip

2013-01-01

84

Biomedical applications of single molecule detection  

NASA Astrophysics Data System (ADS)

The search for increased sensitivity of bio-analytical techniques has recently shifted from signal generation to detection. While enzyme amplifiers and chemiluminescent reporters developed by chemists over the last two decades gradually moved detection limits to the attomol level, it has taken engineers only a few years to reach single- molecule sensitivity with the development of new instrumentation. A number of different approaches have successfully achieved single-molecule fluorescence detection including confocal and near-field scanning optical microscopy, photon-counting cameras, fluorescence- correlation and time-gated spectroscopy. They detect labels immobilized on substrates, diffusing in solution and flowing in electro-osmotic and hydrodynamically focused streams. Biotechnology has created numerous application s for single- molecule detection. In research labs, it can dramatically increase the rate of DNA sequencing, screen libraries for products of directed evolution, and characterize compounds in drug discovery programs. In medical diagnostics, ultra- sensitive detection technologies can be used for genetic screening, detection of infectious diseases, or multi- analyte profiles. It can be applied to immunoassays as well as DNA or RNA hybridization assays.

Kelso, D. M.

1997-05-01

85

Graphical models for inferring single molecule dynamics  

PubMed Central

Background The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how graphical modeling may be used to learn from biophysical time series data using the variational Bayesian expectation maximization algorithm (VBEM). The discussion is illustrated by the example of single-molecule fluorescence resonance energy transfer (smFRET) versus time data, where the smFRET time series is modeled as a hidden Markov model (HMM) with Gaussian observables. A detailed description of smFRET is provided as well. Results The VBEM algorithm returns the model’s evidence and an approximating posterior parameter distribution given the data. The former provides a metric for model selection via maximum evidence (ME), and the latter a description of the model’s parameters learned from the data. ME/VBEM provide several advantages over the more commonly used approach of maximum likelihood (ML) optimized by the expectation maximization (EM) algorithm, the most important being a natural form of model selection and a well-posed (non-divergent) optimization problem. Conclusions The results demonstrate the utility of graphical modeling for inference of dynamic processes in single molecule biophysics. PMID:21034427

2010-01-01

86

Single-molecule sensing electrode embedded in-plane nanopore  

NASA Astrophysics Data System (ADS)

Electrode-embedded nanopore is considered as a promising device structure for label-free single-molecule sequencing, the principle of which is based on nucleotide identification via transverse electron tunnelling current flowing through a DNA translocating through the pore. Yet, fabrication of a molecular-scale electrode-nanopore detector has been a formidable task that requires atomic-level alignment of a few nanometer sized pore and an electrode gap. Here, we report single-molecule detection using a nucleotide-sized sensing electrode embedded in-plane nanopore. We developed a self-alignment technique to form a nanopore-nanoelectrode solid-state device consisting of a sub-nanometer scale electrode gap in a 15 nm-sized SiO2 pore. We demonstrate single-molecule counting of nucleotide-sized metal-encapsulated fullerenes in a liquid using the electrode-integrated nanopore sensor. We also performed electrical identification of nucleobases in a DNA oligomer, thereby suggesting the potential use of this synthetic electrode-in-nanopore as a platform for electrical DNA sequencing.

Tsutsui, Makusu; Rahong, Sakon; Iizumi, Yoko; Okazaki, Toshiya; Taniguchi, Masateru; Kawai, Tomoji

2011-07-01

87

Application of Recognition Tunneling in Single Molecule Identification  

NASA Astrophysics Data System (ADS)

Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.

Zhao, Yanan

88

Silicon nanowire based single-molecule SERS sensor  

NASA Astrophysics Data System (ADS)

One-dimensional nanowire (NW) optical sensors have attracted great attention as promising nanoscale tools for applications such as probing inside living cells. However, achieving single molecule detection on NW sensors remains an interesting and unsolved problem. In the present paper, we investigate single-molecule detection (SMD) on a single SiNW based surface-enhanced Raman scattering (SERS) sensor, fabricated by controllably depositing silver nanoparticles on a SiNW (AgNP-SiNW). Both Raman spectral blinking and bi-analyte approaches are performed in aqueous solution to investigate SMD on individual SiNW SERS sensors. The results extend the functions of the SiNW sensor to SMD and provide insight into the molecule level illustration on the sensing mechanism of the nanowire sensor.One-dimensional nanowire (NW) optical sensors have attracted great attention as promising nanoscale tools for applications such as probing inside living cells. However, achieving single molecule detection on NW sensors remains an interesting and unsolved problem. In the present paper, we investigate single-molecule detection (SMD) on a single SiNW based surface-enhanced Raman scattering (SERS) sensor, fabricated by controllably depositing silver nanoparticles on a SiNW (AgNP-SiNW). Both Raman spectral blinking and bi-analyte approaches are performed in aqueous solution to investigate SMD on individual SiNW SERS sensors. The results extend the functions of the SiNW sensor to SMD and provide insight into the molecule level illustration on the sensing mechanism of the nanowire sensor. Electronic supplementary information (ESI) available: Additional information on the experimental details, quantitative evaluation of the enhancement factor, and stability of the sensor. See DOI: 10.1039/c3nr01879b

Wang, Hui; Han, Xuemei; Ou, Xuemei; Lee, Chun-Sing; Zhang, Xiaohong; Lee, Shuit-Tong

2013-08-01

89

PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics  

NASA Astrophysics Data System (ADS)

This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar lengths but different energy barrier profiles in order to elucidate electron transport in the molecular junctions. Kiguchi and Murakoshi study metallic atomic wires under electrochemical potential control. Asai reports on a theoretical study of rectification in substituted atomic wires. Finally, Weiss et al report on a new method to pattern and functionalize oxide-free germanium surfaces with self-assembled organic monolayers, which provides interfaces between inorganic semiconductors and organic molecules. Nanoelectronics, sensors and single molecule biophysics contents Biochemistry and semiconductor electronics—the next big hit for silicon?Stuart Lindsay Electrical detection of single pollen allergen particles using electrode-embedded microchannelsChihiro Kawaguchi, Tetsuya Noda, Makusu Tsutsui, Masateru Taniguchi, Satoyuki Kawano and Tomoji Kawai Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structuresAvigail Stern, Dvir Rotem, Inna Popov and Danny Porath Effects of cytosine methylation on DNA charge transportJoshua Hihath, Shaoyin Guo, Peiming Zhang and Nongjian Tao Effect of electrostatics on aggregation of prion protein Sup35 peptideAlexander M Portillo, Alexey V Krasnoslobodtsev and Yuri L Lyubchenko Mapping the intracellular distribution of carbon nanotubes after targeted delivery to carcinoma cells using confocal Raman imaging as a label-free techniqueC Lamprecht, N Gierlinger, E Heister, B Unterauer, B Plochberger, M Brameshuber, P Hinterdorfer, S Hild and A Ebner Caveolae-mediated endocytosis of biocompatible gold nanoparticles in living Hela cellsXian Hao, Jiazhen Wu, Yuping Shan, Mingjun Cai, Xin Shang, Junguang Jiang and Hongda Wang Stability of an aqueous quadrupole micro-trapJae Hyun Park and Predrag S Krsti? Electron transport properties of single molecular junctions under mechanical modulationsJianfeng Zhou, Cunlan Guo and Bingqian Xu An approach to measure electromechanical properties of atomic and molecular junctionsIlya V Pobelov, Gábor Mészáros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski S

Tao, Nongjian

2012-04-01

90

Single-molecule electrophoresis. Final report  

SciTech Connect

A novel method for the detection and identification of single molecules in solution has been devised, computer-simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required by individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed beforehand in order to estimate the experimental feasibility of the method, and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented.

Castro, A.; Shera, E.B.

1996-05-22

91

Promising anchoring groups for single-molecule conductance measurements.  

PubMed

The understanding of the charge transport through single molecule junctions is a prerequisite for the design and building of electronic circuits based on single molecule junctions. However, reliable and robust formation of such junctions is a challenging task to achieve. In this topical review, we present a systematic investigation of the anchoring group effect on single molecule junction conductance by employing two complementary techniques, namely scanning tunneling microscopy break junction (STM-BJ) and mechanically controllable break junction (MCBJ) techniques, based on the studies published in the literature and important results from our own work. We compared conductance studies for conventional anchoring groups described earlier with the molecular junctions formed through ?-interactions with the electrode surface (Au, Pt, Ag) and we also summarized recent developments in the formation of highly conducting covalent Au-C ?-bonds using oligophenyleneethynylene (OPE) and an alkane molecular backbone. Specifically, we focus on the electron transport properties of diaryloligoyne, oligophenyleneethynylene (OPE) and/or alkane molecular junctions composed of several traditional anchoring groups, (dihydrobenzo[b]thiophene (BT), 5-benzothienyl analogue (BTh), thiol (SH), pyridyl (PY), amine (NH2), cyano (CN), methyl sulphide (SMe), nitro (NO2)) and other anchoring groups at the solid/liquid interface. The qualitative and quantitative comparison of the results obtained with different anchoring groups reveals structural and mechanistic details of the different types of single molecular junctions. The results reported in this prospective may serve as a guideline for the design and synthesis of molecular systems to be used in molecule-based electronic devices. PMID:25285778

Kaliginedi, Veerabhadrarao; V Rudnev, Alexander; Moreno-García, Pavel; Baghernejad, Masoud; Huang, Cancan; Hong, Wenjing; Wandlowski, Thomas

2014-11-21

92

Hafnium metallocene compounds used as cathode interfacial layers for enhanced electron transfer in organic solar cells.  

PubMed

We have used hafnium metallocene compounds as cathode interfacial layers for organic solar cells [OSCs]. A metallocene compound consists of a transition metal and two cyclopentadienyl ligands coordinated in a sandwich structure. For the fabrication of the OSCs, poly[3,4-ethylenedioxythiophene]:poly(styrene sulfonate), poly(3-hexylthiophene-2,5-diyl) + 66-phenyl C61 butyric acid methyl ester, bis-(ethylcyclopentadienyl)hafnium(IV) dichloride, and aluminum were deposited as a hole transport layer, an active layer, a cathode interfacial layer, and a cathode, respectively. The hafnium metallocene compound cathode interfacial layer improved the performance of OSCs compared to that of OSCs without the interfacial layer. The current density-voltage characteristics of OSCs with an interfacial layer thickness of 0.7 nm and of those without an interfacial layer showed power conversion efficiency [PCE] values of 2.96% and 2.34%, respectively, under an illumination condition of 100 mW/cm2 (AM 1.5). It is thought that a cathode interfacial layer of an appropriate thickness enhances the electron transfer between the active layer and the cathode, and thus increases the PCE of the OSCs. PMID:22230259

Park, Keunhee; Oh, Seungsik; Jung, Donggeun; Chae, Heeyeop; Kim, Hyoungsub; Boo, Jin-Hyo

2012-01-01

93

Hafnium metallocene compounds used as cathode interfacial layers for enhanced electron transfer in organic solar cells  

NASA Astrophysics Data System (ADS)

We have used hafnium metallocene compounds as cathode interfacial layers for organic solar cells [OSCs]. A metallocene compound consists of a transition metal and two cyclopentadienyl ligands coordinated in a sandwich structure. For the fabrication of the OSCs, poly[3,4-ethylenedioxythiophene]:poly(styrene sulfonate), poly(3-hexylthiophene-2,5-diyl) + [6, 6]-phenyl C61 butyric acid methyl ester, bis-(ethylcyclopentadienyl)hafnium(IV) dichloride, and aluminum were deposited as a hole transport layer, an active layer, a cathode interfacial layer, and a cathode, respectively. The hafnium metallocene compound cathode interfacial layer improved the performance of OSCs compared to that of OSCs without the interfacial layer. The current density-voltage characteristics of OSCs with an interfacial layer thickness of 0.7 nm and of those without an interfacial layer showed power conversion efficiency [PCE] values of 2.96% and 2.34%, respectively, under an illumination condition of 100 mW/cm2 (AM 1.5). It is thought that a cathode interfacial layer of an appropriate thickness enhances the electron transfer between the active layer and the cathode, and thus increases the PCE of the OSCs.

Park, Keunhee; Oh, Seungsik; Jung, Donggeun; Chae, Heeyeop; Kim, Hyoungsub; Boo, Jin-Hyo

2012-01-01

94

Deciphering the scaling of single-molecule interactions using Jarzynski's equality.  

PubMed

Unravelling the complexity of the macroscopic world relies on understanding the scaling of single-molecule interactions towards integral macroscopic interactions. Here, we demonstrate the scaling of single acid-amine interactions through a synergistic experimental approach combining macroscopic surface forces apparatus experiments and single-molecule force spectroscopy. This experimental framework is ideal for testing the well-renowned Jarzynski's equality, which relates work performed under non-equilibrium conditions with equilibrium free energy. Macroscopic equilibrium measurements scale linearly with the number density of interfacial bonds, providing acid-amine interaction energies of 10.9±0.2?kT. Irrespective of how far from equilibrium single-molecule experiments are performed, the Jarzynski's free energy converges to 11±1?kT. Our results validate the applicability of Jarzynski's equality to unravel the scaling of non-equilibrium single-molecule experiments to scenarios where large numbers of molecules interacts simultaneously in equilibrium. The developed scaling strategy predicts large-scale properties such as adhesion or cell-cell interactions on the basis of single-molecule measurements. PMID:25412574

Raman, Sangeetha; Utzig, Thomas; Baimpos, Theodoros; Ratna Shrestha, Buddha; Valtiner, Markus

2014-01-01

95

Theoretical investigation on single-molecule chiroptical spectroscopy  

SciTech Connect

Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

Wakabayashi, M. [Tokyo Institute of Technology, School and Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa (Japan); Yokojima, S. [Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachiouji-shi, Tokyo (Japan); Fukaminato, T. [Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020 (Japan); Ogata, K.; Nakamura, S. [Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2013-12-10

96

Photochromism of diarylethene single molecules and single crystals.  

PubMed

Photochromism is characterized as a reversible colour change of a chemical species upon photoirradiation. Although vast numbers of photochromic molecules have been so far synthesized, molecules which exhibit thermally irreversible photochromic reactivity are limited within a few families of compounds. Among the thermally irreversible photochromic molecules, diarylethene derivatives are the most promising candidates for applications to opto-electronic devices because of their fatigue resistance, high sensitivity and rapid response. In this review, characteristic photochromic performances of the derivatives, detection and analysis of the photochromic reactions at a single-molecule level and application of the single-crystalline photochromism to molecular machinery will be described. PMID:20959925

Irie, Masahiro

2010-12-01

97

Single Molecule Studies of Nucleocytoplasmic Transport  

PubMed Central

Molecular traffic between the cytoplasm and the nucleoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs). Hundreds, if not thousands, of molecules interact with and transit through each NPC every second. The pore is blocked by a permeability barrier, which consists of a network of intrinsically unfolded polypeptides containing thousands of phenylalanine-glycine (FG) repeat motifs. This FG-network rejects larger molecules and admits smaller molecules or cargos bound to nuclear transport receptors (NTRs). For a cargo transport complex, minimally consisting of a cargo molecule plus an NTR, access to the permeability barrier is provided by interactions between the NTR and the FG repeat motifs. Numerous models have been postulated to explain the controlled accessibility and the transport characteristics of the FG-network, but the amorphous, flexible nature of this structure has hindered characterization. A relatively recent development is the ability to monitor the real-time movement of single molecules through individual NPCs via single molecule fluorescence (SMF) microscopy. A major advantage of this approach is that it can be used to continuously monitor a series of specific molecular interactions in an active pore with millisecond time resolution, which therefore allows one to distinguish between kinetic and thermodynamic control. Novel insights and prospects for the future are outlined in this review. PMID:21167872

Tu, Li-Chun; Musser, Siegfried M.

2011-01-01

98

Large negative differential conductance in single-molecule break junctions  

NASA Astrophysics Data System (ADS)

Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks. To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport is mainly determined by the alignment of the molecular orbital levels with respect to the Fermi energies of the electrodes and the electronic coupling with those electrodes. Particularly appealing exceptions include molecules in which two moieties are twisted with respect to each other and molecules in which quantum interference effects are possible. Here, we report the experimental observation of pronounced negative differential conductance in the current–voltage characteristics of a single molecule in break junctions. The molecule of interest consists of two conjugated arms, connected by a non-conjugated segment, resulting in two coupled sites. A voltage applied across the molecule pulls the energy of the sites apart, suppressing resonant transport through the molecule and causing the current to decrease. A generic theoretical model based on a two-site molecular orbital structure captures the experimental findings well, as confirmed by density functional theory with non-equilibrium Green's functions calculations that include the effect of the bias. Our results point towards a conductance mechanism mediated by the intrinsic molecular orbitals alignment of the molecule.

Perrin, Mickael L.; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S.; Gil, Jose A. Celis; Valkenier, Hennie; Hummelen, Jan C.; Renaud, Nicolas; Grozema, Ferdinand C.; Thijssen, Joseph M.; Duli?, Diana; van der Zant, Herre S. J.

2014-10-01

99

Large negative differential conductance in single-molecule break junctions.  

PubMed

Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks. To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport is mainly determined by the alignment of the molecular orbital levels with respect to the Fermi energies of the electrodes and the electronic coupling with those electrodes. Particularly appealing exceptions include molecules in which two moieties are twisted with respect to each other and molecules in which quantum interference effects are possible. Here, we report the experimental observation of pronounced negative differential conductance in the current-voltage characteristics of a single molecule in break junctions. The molecule of interest consists of two conjugated arms, connected by a non-conjugated segment, resulting in two coupled sites. A voltage applied across the molecule pulls the energy of the sites apart, suppressing resonant transport through the molecule and causing the current to decrease. A generic theoretical model based on a two-site molecular orbital structure captures the experimental findings well, as confirmed by density functional theory with non-equilibrium Green's functions calculations that include the effect of the bias. Our results point towards a conductance mechanism mediated by the intrinsic molecular orbitals alignment of the molecule. PMID:25173832

Perrin, Mickael L; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S; Gil, Jose A Celis; Valkenier, Hennie; Hummelen, Jan C; Renaud, Nicolas; Grozema, Ferdinand C; Thijssen, Joseph M; Duli?, Diana; van der Zant, Herre S J

2014-10-01

100

Single-molecule studies of RNAPII elongation.  

PubMed

Elongation, the transcriptional phase in which RNA polymerase (RNAP) moves processively along a DNA template, occurs via a fundamental enzymatic mechanism that is thought to be universally conserved among multi-subunit polymerases in all kingdoms of life. Beyond this basic mechanism, a multitude of processes are integrated into transcript elongation, among them fidelity control, gene regulatory interactions involving elongation factors, RNA splicing or processing factors, and regulatory mechanisms associated with chromatin structure. Many kinetic and molecular details of the mechanism of the nucleotide addition cycle and its regulation, however, remain elusive and generate continued interest and even controversy. Recently, single-molecule approaches have emerged as powerful tools for the study of transcription in eukaryotic organisms. Here, we review recent progress and discuss some of the unresolved questions and ongoing debates, while anticipating future developments in the field. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation. PMID:22982192

Zhou, Jing; Schweikhard, Volker; Block, Steven M

2013-01-01

101

Single-molecule studies of RNAPII elongation  

PubMed Central

Elongation, the transcriptional phase in which RNA polymerase (RNAP) moves processively along a DNA template, occurs via a fundamental enzymatic mechanism that is thought to be universally conserved among multi-subunit polymerases in all kingdoms of life. Beyond this basic mechanism, a multitude of processes are integrated into transcript elongation, among them fidelity control, gene regulatory interactions involving elongation factors, RNA splicing or processing factors, and regulatory mechanisms associated with chromatin structure. Many kinetic and molecular details of the mechanism of the nucleotide addition cycle and its regulation, however, remain elusive and generate continued interest and even controversy. Recently, single-molecule approaches have emerged as powerful tools for the study of transcription in eukaryotic organisms. Here, we review recent progress and discuss some of the unresolved questions and ongoing debates, while anticipating future developments in the field. PMID:22982192

Zhou, Jing; Schweikhard, Volker; Block, Steven M.

2012-01-01

102

Current-induced nonequilibrium vibrations in single-molecule devices Jens Koch, Matthias Semmelhack, and Felix von Oppen  

E-print Network

of molecules. Experiments with single-molecule devices have demonstrated effects of electron-phonon cou- plingCurrent-induced nonequilibrium vibrations in single-molecule devices Jens Koch, Matthias Semmelhack vibra- tions phonons . By a mapping to a Fokker-Planck equation, we obtain analytical scaling forms

von Oppen, Felix

103

Franck-Condon Blockade and Giant Fano Factors in Transport through Single Molecules Jens Koch and Felix von Oppen  

E-print Network

Franck-Condon Blockade and Giant Fano Factors in Transport through Single Molecules Jens Koch single molecules with strong coupling between electronic and vibrational degrees of freedom. Transport-Poissonian noise has been discovered in systems with instabilities [2­4] and, very recently, with dynamical spin

von Oppen, Felix

104

Single-Molecule Investigations of RNA Dissociation  

PubMed Central

Given the essential cellular roles for ribonucleic acids (RNAs) it is important to understand the stability of three-dimensional structures formed by these molecules. This study aims to investigate the dissociation energy landscape for simple RNA structures via atomic-force-microscopy-based single-molecule force-spectroscopy measurements. This approach provides details on the locations and relative heights of the energy barriers to dissociation, and thus information upon the relative kinetic stabilities of the formed complexes. Our results indicate that a simple dodecamer RNA helix undergoes a forced dissociation process similar to that previously observed for DNA oligonucleotides. Incorporating a UCU bulge motif is found to introduce an additional energy barrier closer to the bound state, and also to destabilize the duplex. In the absence of magnesium ions a duplex containing this UCU bulge is destabilized and a single, shorter duplex is formed. These results reveal that a bulge motif impacts upon the forced dissociation of RNA and produces an energy landscape sensitive to the presence of magnesium ions. Interestingly, the obtained data compare well with previously reported ensemble measurements, illustrating the potential of this approach to improve our understanding of RNA stability and dissociation kinetics. PMID:15189877

Green, Nicola H.; Williams, Philip M.; Wahab, Omar; Davies, Martyn C.; Roberts, Clive J.; Tendler, Saul J. B.; Allen, Stephanie

2004-01-01

105

'Single molecule': theory and experiments, an introduction  

PubMed Central

At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

2013-01-01

106

Organization of Single Molecule Magnets on Surfaces  

NASA Astrophysics Data System (ADS)

The field of magnetic molecular clusters showing slow relaxation of the magnetization has attracted a great interest for the spectacular quantum effects in the dynamics of the magnetization that range from resonant quantum tunneling to topological interferences. Recently these systems, known as Single Molecule Magnets (SMMs), have also been proposed as model systems for the investigation of flame propagation in flammable substances. A renewed interest in SMMs also comes from the possibility to exploit their rich and complex magnetic behavior in nano-spintronics. However, at the crystalline state these molecular materials are substantially insulating. They can however exhibit significant transport properties if the conduction occurs through one molecule connected to two metal electrodes, or through a tunneling mechanism when the SMM is grafted on a conducting surface, as occurs in scanning tunnel microscopy experiments. Molecular compounds can be organized on surfaces thanks to the self assembly technique that exploits the strong affinity of some groups for the surface, e.g. thiols for gold surfaces. However the deposition of large molecules mainly comprising relatively weak coordinative bonds is far from trivial. Several different approaches have started to be investigated. We will briefly review here the strategies developed in a collaboration between the Universities of Florence and Modena. Well isolated molecules on Au(111) surfaces have been obtained with sub-monolayer coverage and different spacers. Organization on a large scale of micrometric structures has been obtained thanks to micro-contact printing. The magnetic properties of the grafted molecules have been investigated through magneto-optical techniques and the results show a significant change in the magnetization dynamics whose origin is still object of investigations.

Sessoli, Roberta

2006-03-01

107

Microarray analysis at single molecule resolution  

PubMed Central

Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

Muresan, Leila; Jacak, Jaroslaw; Klement, Erich Peter; Hesse, Jan; Schutz, Gerhard J.

2010-01-01

108

From single molecule to single tubules  

NASA Astrophysics Data System (ADS)

Biological systems often make decisions upon conformational changes and assembly of single molecules. In vivo, epithelial cells (such as the mammary gland cells) can respond to extracellular matrix (ECM) molecules, type I collagen (COL), and switch their morphology from a lobular lumen (100-200 micron) to a tubular lumen (1mm-1cm). However, how cells make such a morphogenetic decision through interactions with each other and with COL is unclear. Using a temporal control of cell-ECM interaction, we find that epithelial cells, in response to a fine-tuned percentage of type I collagen (COL) in ECM, develop various linear patterns. Remarkably, these patterns allow cells to self-assemble into a tubule of length ˜ 1cm and diameter ˜ 400 micron in the liquid phase (i.e., scaffold-free conditions). In contrast with conventional thought, the linear patterns arise through bi-directional transmission of traction force, but not through diffusible biochemical factors secreted by cells. In turn, the transmission of force evokes a long-range (˜ 600 micron) intercellular mechanical interaction. A feedback effect is encountered when the mechanical interaction modifies cell positioning and COL alignment. Micro-patterning experiments further reveal that such a feedback is a novel cell-number-dependent, rich-get-richer process, which allows cells to integrate mechanical interactions into long-range (> 1mm) linear coordination. Our results suggest a mechanism cells can use to form and coordinate long-range tubular patterns, independent of those controlled by diffusible biochemical factors, and provide a new strategy to engineer/regenerate epithelial organs using scaffold-free self-assembly methods.

Guo, Chin-Lin

2012-02-01

109

Quantum phase transition in a single-molecule quantum dot.  

PubMed

Quantum criticality is the intriguing possibility offered by the laws of quantum mechanics when the wave function of a many-particle physical system is forced to evolve continuously between two distinct, competing ground states. This phenomenon, often related to a zero-temperature magnetic phase transition, is believed to govern many of the fascinating properties of strongly correlated systems such as heavy-fermion compounds or high-temperature superconductors. In contrast to bulk materials with very complex electronic structures, artificial nanoscale devices could offer a new and simpler means of understanding quantum phase transitions. Here we demonstrate this possibility in a single-molecule quantum dot, where a gate voltage induces a crossing of two different types of electron spin state (singlet and triplet) at zero magnetic field. The quantum dot is operated in the Kondo regime, where the electron spin on the quantum dot is partially screened by metallic electrodes. This strong electronic coupling between the quantum dot and the metallic contacts provides the strong electron correlations necessary to observe quantum critical behaviour. The quantum magnetic phase transition between two different Kondo regimes is achieved by tuning gate voltages and is fundamentally different from previously observed Kondo transitions in semiconductor and nanotube quantum dots. Our work may offer new directions in terms of control and tunability for molecular spintronics. PMID:18509439

Roch, Nicolas; Florens, Serge; Bouchiat, Vincent; Wernsdorfer, Wolfgang; Balestro, Franck

2008-05-29

110

Interfacial Electron Transfer and Transient Photoconductivity Studied with Terahertz Spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz spectroscopy is distinguished from other far infrared and millimeter wave spectroscopies by its inherent phase sensitivity and sub-picosecond time resolution making it a versatile technique to study a wide range of physical phenomena. As THz spectroscopy is still a relatively new field, many aspects of THz generation mechanisms have not been fully examined. Using terahertz emission spectroscopy (TES), THz emission from ZnTe(110) was analyzed and found to be limited by two-photon absorption and free-carrier generation at high excitation fluences. Due to concerns about the continued use of fossil fuels, solar energy has been widely investigated as a promising source of renewable energy. Dye-sensitized solar cells (DSSCs) have been developed as a low-cost alternative to conventional photovoltaic solar cells. To solve the issues of the intermittency and inefficient transport associated with solar energy, researchers are attempting to adapt DSSCs for water oxidation and chemical fuel production. Both device designs incorporate sensitizer molecules covalently bound to metal oxide nanoparticles. The sensitizer, which is comprised of a chromophore and anchoring group, absorbs light and transfers an electron from its excited state to the conduction band of the metal oxide, producing an electric current. Using time-resolved THz spectroscopy (TRTS), an optical pump/THz probe technique, the efficiency and dynamics of electron injection from sensitizers to metal oxides was evaluated as a function of the chromophore, its anchoring group, and the metal oxide identity. Experiments for studying fully functioning DSSCs and water oxidation devices are also described. Bio-inspired pentafluorophenyl porphyrin chromophores have been designed and synthesized for use in photoelectrochemical water oxidation cells. Influences on the efficiency and dynamics of electron injection from the chromophores into TiO2 and SnO2 nanoparticles due to changes in both the central substituent to the porphyrin ring and degree of fluorination of ring substituents were analyzed. Due to the high reduction potentials of these sensitizers, injection into TiO2 was generally not observed. Injection timescales from the porphyrins into SnO2 depended strongly on the identity of the central substituent and were affected by competition with excited-state deactivation processes. The carboxylate anchoring group is commonly used to bind DSSC sensitizers to metal oxide surfaces but is typically not stable under the aqueous and oxidative conditions required for water oxidation. Electron injection efficiency and water stability of several alternative anchoring groups, including phosphonic acid, hydroxamic acid, acerylacetone, and boronic acid, were evaluated. While all of the anchoring groups exhibited water stability superior to carboxylate, the hydroxamate anchor had the best combination of ease of handling and electron injection efficiency. The effects on photoconductivity due to metal oxide morphology and the addition of dopants were also analyzed. Mixtures of anatase and rutile TiO 2 nanoparticles are known to exhibit cooperative effects which increase the efficiency of DSSCs and photocatalysis relative to the pure-phase materials. Through analysis of TRTS measurements, the mechanism of this synergistic effect was found to involve electron transfer from the lower-mobility, higher surface area rutile nanoparticles to anatase particles, resulting in a higher charge collection efficiency. In addition to morphology, doping has been investigated as a means of expanding the spectral range of visible absorption of photocatalysts. Doping ZnO nanowires with manganese(II) was found to significantly decrease the electron mobility, and doping with cobalt(II) increased the timescale for electron trapping. These differences can be understood by considering the changes to the band structure of ZnO effected by the dopants. Preliminary analyses of the solvent and electrolyte dependence on the electron injection rate and efficiency suggest that electron injection can be affected by

Milot, Rebecca Lee

111

Simultaneous widefield single molecule orientation and FRET microscopy in cells.  

PubMed

We combine single molecule fluorescence orientation imaging with single-pair fluorescence resonance energy transfer microscopy, using a total internal reflection microscope. We show how angles and FRET efficiencies can be determined for membrane proteins at the single molecule level and provide data from the epidermal growth factor receptor system in cells. PMID:19065164

Webb, S E D; Rolfe, D J; Needham, S R; Roberts, S K; Clarke, D T; McLachlan, C I; Hobson, M P; Martin-Fernandez, M L

2008-12-01

112

TOPICAL REVIEW: Single-molecule fluorescence spectroscopy of biomolecular folding  

Microsoft Academic Search

Single-molecule fluorescence spectroscopy is emerging as an important tool for studying biomolecular folding dynamics. Its usefulness stems from its ability to directly map heterogeneities in folding pathways and to provide information about the energy landscape of proteins and ribonucleic acid (RNA) molecules. Single-molecule fluorescence techniques relevant for folding studies, including methods for trapping and immobilizing molecules, are described and compared

Gilad Haran

2003-01-01

113

Single molecule magnets: a new class of magnetic materials  

Microsoft Academic Search

Recently it has been discovered that some molecules comprising a large number of coupled metal ions show slow relaxation of the magnetization at low temperature. This gives rise to magnetic hysteresis effects of molecular origin which in principle allow the storage of information in a single molecule (Single molecule magnets). A short overview of the current status of research in

Dante Gatteschi

2001-01-01

114

Supplementary Material Free energy recovery in single molecule experiments  

E-print Network

Supplementary Material Free energy recovery in single molecule experiments Single molecule force measurements (experimental setup shown in Fig. S1) can be used to determine free-energy differences between the unfolding process and using the thermodynamic relation revWG = , we can estimate the RNA folding free energy

Ritort, Felix

115

Enzymology and Life at the Single Molecule Level  

E-print Network

on biological discovery, as well as prospects for medicine. 22.1 Introduction Advances in life sciences-field microscope, together with the then emerging single-molecule manip- ulation techniques [11­13], opened of physics, chemistry and biology. The application of single-molecule imaging, spectroscopy and manipulation

Xie, Xiaoliang Sunney

116

Structure and mechanics of proteins from single molecules to cells  

NASA Astrophysics Data System (ADS)

Physical factors drive evolution and play important roles in motility and attachment as well as in differentiation. As animal cells adhere to survive, they generate force and "feel" various mechanical features of their surroundings and respond to externally applied forces. This mechanosensitivity requires a substrate for cells to adhere to and a mechanism for cells to apply force, followed by a cellular response to the mechanical properties of the substrate. We have taken an outside-in approach to characterize several aspects of cellular mechanosensitivity. First, we used single molecule force spectroscopy to measure how fibrinogen, an extracellular matrix protein that forms the scaffold of blood clots, responds to applied force and found that it rapidly unfolds in 23 nm steps at forces around 100 pN. Second, we used tensile testing to measure the force-extension behavior of fibrin gels and found that they behave almost linearly to strains of over 100%, have extensibilities of 170 +/- 15%, and undergo a large volume decrease that corresponds to a large and negative peak in compressibility at low strain, which indicates a structural transition. Using electron microscopy and X-ray scattering we concluded that these properties are likely due to coiled-coil unfolding, as observed at the single molecule level in fibrinogen. Moving inside cells, we used total internal reflection fluorescence and atomic force microscopy to image self-assembled myosin filaments. These filaments of motor proteins that are responsible for cell and muscle contractility were found to be asymmetric, with an average of 32% more force generating heads on one half than the other. This could imply a force imbalance, so that rather than being simply contractile, myosin filaments may also be motile in cells.

Brown, Andre E.

117

Evidence for interfacial space-charge regions in electron-beam-evaporated SiO  

Microsoft Academic Search

We report here I-V and capacitance data and SEM observations made on thin-film SiO metal-insulator-metal structures. Devices were fabricated using electron-beam-evaporated SiO and several different metals for the electrodes. I-V observations alone could be interpreted as bulk-limited conduction; however, the dispersion of the capacitance in frequency is bias dependent and suggests interfacial space-charge regions. SEM observations support this interpretation and

Jean-Alain Roger; C. H. S. Dupuy; Stephen J. Fonash

1975-01-01

118

Interfacial electronic charge transfer and density of states in short period Cu/Cr multilayers  

SciTech Connect

Nanometer period metallic multilayers are ideal structures to investigate electronic phenomena at interfaces between metal films since interfacial atoms comprise a large atomic fraction of the samples. The multilayers studied were fabricated by magnetron sputtering and consist of bilayers from 1.9 mn to 3.3 mn. X-ray diffraction, cross-section TEM and plan-view TEM show the Cu layers to have a BCC structure Cu in contrast to its equilibrium FCC structure. The electronic structure of the Cu and the Cr layers in several samples of thin Cu/Cr multilayers were studied using x-ray absorption spectroscopy (XAS). Total electron yield was measured and used to study the white lines at the Cu L{sub 2} and L{sub 3} absorption edges. The white lines at the Cu absorption edges are strongly related to the unoccupied d-orbitals and are used to calculate the amount of charge transfer between the Cr and Cu atoms in interfaces. Analysis of the Cu white lines show a charge transfer of 0.026 electrons/interfacial Cu atom to the interfacial Cr atoms. In the Cu XAS spectra we also observe a van Hove singularity between the L{sub 2} and L{sub 3} absorption edges as expected from the structural analysis. The absorption spectra are compared to partial density of states obtained from a full-potential linear muffin-tin orbital calculation. The calculations confirm the presence of charge transfer and indicate that it is localized to the first two interfacial layers in both Cu and Cr.

Bello, A.F.; Van Buuren, T.; Kepesis, J.E.; Barbee, T.W., Jr.

1998-04-01

119

Effect of interactions and degeneracy on transmission through a single molecule  

NASA Astrophysics Data System (ADS)

Electron transmission through a single-molecule junction in the Coulomb blockade regime is analyzed in the isolated resonance approximation for molecules with degenerate HOMO and/or LUMO orbitals. Electron-electron interactions are included in a capacitive charging model derived from pi-electron effective field theory. For the case of a buckyball junction with Pt electrodes, we find that the number of transmission channels is limited by the five-fold degenerate HOMO resonance.

Stefferson, Michael; Hudson, Jarred; Stafford, Charles

2011-10-01

120

Organic-Oxide Interfacial Layer on the Studies of Organic Electronics (Light-Emitting Diodes and Solar Cells).  

National Technical Information Service (NTIS)

This project investigated a novel approach to apply an organic-oxide interfacial layer to improve the performance of organic electronic devices, including organic light emitting diodes and organic solar cells.

T. Guo

2008-01-01

121

Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering  

PubMed Central

Single molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, non-fluorescent single molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems. PMID:23323846

Choi, Yongki; Olsen, Tivoli J.; Sims, Patrick C.; Moody, Issa S.; Corso, Brad L.; Dang, Mytrang N.; Weiss, Gregory A.; Collins, Philip G.

2013-01-01

122

Measurement and understanding of single-molecule break junction rectification caused by asymmetric contacts.  

PubMed

The contact effects of single-molecule break junctions on rectification behaviors were experimentally explored by a systematic control of anchoring groups of 1,4-disubstituted benzene molecular junctions. Single-molecule conductance and I-V characteristic measurements reveal a strong correlation between rectifying effects and the asymmetry in contacts. Analysis using energy band models and I-V calculations suggested that the rectification behavior is mainly caused by asymmetric coupling strengths at the two contact interfaces. Fitting of the rectification ratio by a modified Simmons model we developed suggests asymmetry in potential drop across the asymmetric anchoring groups as the mechanism of rectifying I-V behavior. This study provides direct experimental evidence and sheds light on the mechanisms of rectification behavior induced simply by contact asymmetry, which serves as an aid to interpret future single-molecule electronic behavior involved with asymmetric contact conformation. PMID:25106605

Wang, Kun; Zhou, Jianfeng; Hamill, Joseph M; Xu, Bingqian

2014-08-01

123

Breaking the concentration limit of optical single-molecule detection.  

PubMed

Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach. PMID:24019005

Holzmeister, Phil; Acuna, Guillermo P; Grohmann, Dina; Tinnefeld, Philip

2014-02-21

124

Real-time single-molecule imaging of quantum interference  

E-print Network

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and it differs from classical wave-physics in that it can even be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here we show how a combination of nanofabrication and nanoimaging methods allows us to record the full two-dimensional build-up of quantum diffraction patterns in real-time for phthalocyanine molecules PcH2 and their tailored derivatives F24PcH2 with a mass of 1298 amu. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence and the gratings were machined in 10 nm thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy was used to detect the position of each molecule with an accuracy of 10 nm and to reveal the build-up of a deterministic ensemble interference pattern from stochastically arriving and internally hot single molecules.

Thomas Juffmann; Adriana Milic; Michael Müllneritsch; Peter Asenbaum; Alexander Tsukernik; Jens Tüxen; Marcel Mayor; Ori Cheshnovsky; Markus Arndt

2014-02-08

125

Single molecule fluorescence analysis in solution  

Microsoft Academic Search

Over the past decade, the sensitivity of laser-based fluorescence detection has developed to the point where it is now possible to detect and identify single fluorescent molecules in fluid solution. As a single fluorescent molecule passes through a focused laser beam, it is continuously cycled between its ground and first excited electronic states and emits a burst of photons. If

Richard A. Keller; W. Patrick Ambrose; Peter M. Goodwin; James H. Jett; John C. Martin; Ming Wu

1996-01-01

126

Understanding Enzyme Activity Using Single Molecule Tracking (Poster)  

SciTech Connect

This poster describes single-molecule tracking and total internal reflection fluorescence microscopy. It discusses whether the carbohydrate-binding module (CBM) moves on cellulose, how the CBM binds to cellulose, and the mechanism of cellulosome assembly.

Liu, Y.-S.; Zeng, Y.; Luo, Y.; Xu, Q.; Himmel, M.; Smith S.; Wei, H.; Ding, S.-Y.

2009-06-01

127

Exploring the mechanome with optical tweezers and single molecule fluorescence  

E-print Network

The combination of optical tweezers and single molecule fluorescence into an instrument capable of making combined, coincident measurements adds an observable dimension that allows for the examination of the localized ...

Brau, Ricardo R. (Ricardo Rafael), 1979-

2008-01-01

128

Modeling and analysis of single-molecule experiments  

E-print Network

Single molecule experiments offer a unique window into the molecular world. This window allows us to distinguish the behaviors of individual molecules from the behavior of bulk by observing rare events and heterogeneity ...

Witkoskie, James B

2005-01-01

129

Single-molecule emulsion PCR in microfluidic droplets.  

PubMed

The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis. PMID:22451171

Zhu, Zhi; Jenkins, Gareth; Zhang, Wenhua; Zhang, Mingxia; Guan, Zhichao; Yang, Chaoyong James

2012-06-01

130

A practical guide to single-molecule FRET  

Microsoft Academic Search

Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of

Rahul Roy; Sungchul Hohng; Taekjip Ha

2008-01-01

131

Single-molecule probes in organic field-effect transistors  

Microsoft Academic Search

The goal of this thesis is to study charge transport phenomena in organic materials. This is done optically by means of single-molecule\\u000aspectroscopy in a field-effect transistor based on a molecular crystal.\\u000a\\u000aWe present (in Chapter 2) a fundamental requirement for single-molecule\\u000aspectroscopy concerning the energy levels of the guest molecule with\\u000arespect to the ones of the host molecule.

Aurélien Armel Louis Nicolet

2007-01-01

132

Interfacial electron transfer dynamics of ru(II)-polypy6ridine sensitized TiO2  

SciTech Connect

Quantum dynamics simulations combined with density functional theory calculations are applied to study interfacial electron transfer (IET) from pyridine-4-phosphonic acid, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} and [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} into the (101) surface of anatase TiO{sub 2}. IET rate from pyridine-4-phosphonic acid attached to the nanoparticle in bidentate mode ({tau} {approx} 100 fs) is an order of magnitude faster than the IET rate of the adsorbate attached in the monodentate mode ({tau} {approx} 1 ps). Upon excitation with visible light, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} attached to TiO{sub 2} in bidentate binding mode will undergo IET with the rate of {approx} 1-10 ps, which is competitive with the excited state decay into the ground state. The probability of electron injection from [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} is rather low, as the excitation with visible light localizes the excited electron in the tpy-tpy bridge, which does not have favorable coupling with the TiO{sub 2} nanoparticle. The results are relevant to better understanding of the adsorbate features important for promoting efficient interfacial electron transfer into the semiconductor.

Jakubikova, Elena [Los Alamos National Laboratory; Martin, Richard L [Los Alamos National Laboratory; Batista, Enrique R [Los Alamos National Laboratory; Snoeberger, Robert C [YALE UNIV.; Batista, Victor S [YALE UNIV.

2009-01-01

133

Interplay of local and global interfacial electronic structure of a strongly coupled dipolar organic semiconductor  

NASA Astrophysics Data System (ADS)

We investigate the consequences of strong electronic coupling at the organic semiconductor/metal interface in both the ground and excited state manifold for the case of chloro-boron subphthalocyanine on Cu(111). Using a combination of low-temperature scanning tunneling microscopy and ultraviolet photoelectron spectroscopy and angle-resolved two-photon photoemission, we are able to connect local electronic interactions at the interface with thin film structure despite complex growth in the submonolayer regime. We show that strong coupling leads to charge transfer from the surface to the molecule, and we are able to correlate this observation with the specific molecular adsorption geometry. Strong coupling further results in molecular excited state anion resonances and is responsible for autoionization of highly excited image potential states, relating to the heterogeneous electronic environment in these thin films. This study provides a step towards disentangling interfacial electronic interactions at complex organic/metal interfaces.

Ilyas, Nahid; Monti, Oliver L. A.

2014-09-01

134

Nanoscale Methods for Single-Molecule Electrochemistry  

NASA Astrophysics Data System (ADS)

The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.

Mathwig, Klaus; Aartsma, Thijs J.; Canters, Gerard W.; Lemay, Serge G.

2014-06-01

135

Developing DNA nanotechnology using single-molecule fluorescence.  

PubMed

CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and Holliday junctions and of the interactions of DNA strands with DNA origami and origami-related devices such as a DNA bipedal motor are provided. These examples demonstrate how SMF can be utilized for measurement of distances and conformational distributions and equilibrium and nonequilibrium kinetics, to monitor structural integrity and operation of DNA devices, and for isolation and investigation of minor subpopulations including malfunctioning and nonreactive devices. Utilization of a flow-cell to achieve measurements of dynamics with increased time resolution and for convenient and efficient operation of DNA devices is discussed briefly. We conclude by summarizing the various benefits provided by SMF for the development of DNA nanotechnology and suggest that the method can significantly assist in the design and manufacture and evaluation of operation of DNA devices. PMID:24828396

Tsukanov, Roman; Tomov, Toma E; Liber, Miran; Berger, Yaron; Nir, Eyal

2014-06-17

136

Fluorinated copper phthalocyanine nanowires for enhancing interfacial electron transport in organic solar cells.  

PubMed

Zinc oxide is a promising candidate as an interfacial layer (IFL) in inverted organic photovoltaic (OPV) cells due to the n-type semiconducting properties as well as chemical and environmental stability. Such ZnO layers collect electrons at the transparent electrode, typically indium tin oxide (ITO). However, the significant resistivity of ZnO IFLs and an energetic mismatch between the ZnO and the ITO layers hinder optimum charge collection. Here we report that inserting nanoscopic copper hexadecafluorophthalocyanine (F(16)CuPc) layers, as thin films or nanowires, between the ITO anode and the ZnO IFL increases OPV performance by enhancing interfacial electron transport. In inverted P3HT:PC(61)BM cells, insertion of F(16)CuPc nanowires increases the short circuit current density (J(sc)) versus cells with only ZnO layers, yielding an enhanced power conversion efficiency (PCE) of ?3.6% vs ?3.0% for a control without the nanowire layer. Similar effects are observed for inverted PTB7:PC(71)BM cells where the PCE is increased from 8.1% to 8.6%. X-ray scattering, optical, and electrical measurements indicate that the performance enhancement is ascribable to both favorable alignment of the nanowire ?-? stacking axes parallel to the photocurrent flow and to the increased interfacial layer-active layer contact area. These findings identify a promising strategy to enhance inverted OPV performance by inserting anisotropic nanostructures with ?-? stacking aligned in the photocurrent flow direction. PMID:23181741

Yoon, Seok Min; Lou, Sylvia J; Loser, Stephen; Smith, Jeremy; Chen, Lin X; Facchetti, Antonio; Marks, Tobin J; Marks, Tobin

2012-12-12

137

Massively Parallel Single-Molecule Manipulation Using Centrifugal Force  

NASA Astrophysics Data System (ADS)

Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force [1]. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.[4pt] [1] K. Halvorsen, W.P. Wong, Biophysical Journal - Letters 98 (11), (2010).

Wong, Wesley; Halvorsen, Ken

2011-03-01

138

Single-Molecule Protein Conformational Dynamics in Cell Signaling  

SciTech Connect

We have demonstrated the application of single-molecule imaging and ultrafast spectroscopy to probe protein conformational dynamics in solution and in lipid bilayers. Dynamic protein-protein interactions involve significant conformational motions that initiate chain reactions leading to specific cellular responses. We have carried out a single molecule study of dynamic protein-protein interactions in a GTPase intracellular signaling protein Cdc42 in complex with a downstream effector protein, WASP. We were able to probe hydrophobic interactions significant to Cdc42/WASP recognition. Single molecule fluorescence intensity and polarization measurements have revealed the dynamic and inhomogeneous nature of protein-protein interactions within the Cdc42/WASP complex that is characterized by structured distributions of conformational fluctuation rates. Conducting a single-molecule fluorescence anisotropy study of calmodulin (CaM), a regulatory protein for calcium-dependent cell signaling, we were able to probe CaM conformational dynamics at a wide time scale. In this study, CaM contains a site-specifically inserted tetra-cysteine motif that reacted with FlAsH, a biarsenic fluorescein derivative that can be rotationally locked to the host protein. The study provided direct characterization of the nanosecond motions of CaM tethered to a biologically compatible surface under physiological buffer solution. The unique technical approaches are applicable of studying single-molecule dynamics of protein conformational motions and protein-protein interactions at a wide time range without the signal convolution of probe-dye molecule motions

Lu, H PETER.

2004-08-22

139

Towards physiological complexity with in vitro single-molecule biophysics  

PubMed Central

Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein–nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance. PMID:23267187

Duzdevich, Daniel; Greene, Eric C.

2013-01-01

140

Observing single molecule chemical reactions on metal nanoparticles.  

SciTech Connect

We report the study of the photodecomposition of single Rhodamine 6G (R6G) dye molecules adsorbed on silver nanoparticles. The nanoparticles were immobilized and spatially isolated on polylysine-derivatized glass coverslips, and confocal laser microspectroscopy was used to obtain surface-enhanced Raman scattering (SERS) spectra from individual R6G molecules. The photodecomposition of these molecules was observed with 150-ms temporal resolution. The photoproduct was identified as graphitic carbon based on the appearance of broad SERS vibrational bands at 1592 cm{sup -1} and 1340 cm{sup -1} observed in both bulk and averaged single-molecule photoproduct spectra. In contrast, when observed at the single-molecule level, the photoproduct yielded sharp SERS spectra. The inhomogeneous broadening of the bulk SERS spectra is due to a variety of photoproducts in different surface orientations and is a characteristic of ensemble-averaged measurements of disordered systems. These single-molecule studies indicate a photodecomposition pathway by which the R6G molecule desorbs from the metal surface, an excited-state photoreaction occurs, and the R6G photoproduct(s) readsorbs to the surface. A SERS spectrum is obtained when either the intact R6G or the R6G photoproduct(s) are adsorbed on a SERS-active site. This work further illustrates the power of single-molecule spectroscopy (SMS) to reveal unique behaviors of single molecules that are not discernable with bulk measurements.

Emory, S. R. (Steven R.); Ambrose, W. Patrick; Goodwin, P. M. (Peter M); Keller, Richard A.

2001-01-01

141

Blinking photoluminescence properties of single TiO2 nanodiscs: interfacial electron transfer dynamics.  

PubMed

Blinking photoluminescence was observed in single TiO2 nanodiscs (NDs) by using a laser scanning confocal microscope (LSCM)-coupled steady-state and ps-time-resolved photoluminescence (PL) spectroscopic system, while it was not significantly observed for TiO2 quantum dots (QDs). Analysis of the PL blinking time trajectories revealed single-exponential kinetics with the average lifetimes of on-state (approximately 286 ms) and off-state (approximately 58 ms), implying the existence of inherent surface-trap sites which can be filled by photogenerated electron or hole. The PL spectra of single TiO2 NDs exhibited broad surface emissions with four decay times, which may be due to diffusion of the energies of electron or hole trap states related to surface structural changes by modification of TiO2 QDs. These results and the surface structural analysis (IR and XPS) suggests a simple model for the PL blinking of single TiO2 NDs that is based on repetitive interfacial electron transfer to the inherent surface trap sites (4Ti4+-OH) with Auger-assisted hole trapping in the multiple surface states as modified by the diffusive coordinate model and the surface-trap-filling model. Based on this blinking mechanism and kinetics, the rates of the interfacial electron transfer and the back electron transfer in TiO2 NDs were determined to be 18 ns and 58 ms, respectively, which are slow enough to keep the polarization of e-h pairs at the surface for efficient photocatalysis and photovoltaic activities. The present methodology and results may be applicable to obtain surface exciton dynamics of various photoelectronic semiconductor nanostructures. PMID:19283271

Jeon, Ki-Seok; Oh, Seung-Do; Suh, Yung Doug; Yoshikawa, Hiroyuki; Masuhara, Hiroshi; Yoon, Minjoong

2009-01-21

142

Single-Molecule Dynamics and Mechanisms of Metalloregulators and Metallochaperones  

PubMed Central

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interfaces of chemistry and biology. This Current Topics article reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein–DNA and protein–protein interactions offer efficient pathways for MerR-family metalloregulators and copper chaperones to fulfill their functions. The article also summarizes other related single-molecule studies of bioinorganic systems, and gives an outlook toward single-molecule imaging of metalloprotein functions in living cells. PMID:24053279

Chen, Peng; Keller, Aaron M.; Joshi, Chandra P.; Martell, Danya J.; Andoy, Nesha May; Benítez, Jaime J.; Chen, Tai-Yen; Santiago, Ace George; Yang, Feng

2013-01-01

143

Single molecule views of Nature's nano-machines  

NASA Astrophysics Data System (ADS)

We are interested in the perturbational analysis of biological molecules to better understand their mechanisms. Our readout is the fluorescence signal from individual biomolecules, mainly in the form of single molecule fluorescence resonance energy transfer (FRET). We are pioneering approaches to perturb and control biomolecular conformations using external force (combination of single molecule FRET and optical trap) or other biological motifs (DNA hybridization, G-quadruplex, aptamers,.). In this talk, I will present our latest results on mapping the conformational energy landscape of the Holliday junction through simultaneous fluorescence and force measurements. In addition, a new nanomechanical device called single molecule nano-metronome will be discussed with an outlook toward controlling protein conformations using nucleic acids motifs.

Ha, Taekjip

2006-03-01

144

Single-molecule fluorescence characterization in native environment  

PubMed Central

Single-molecule detection (SMD) with fluorescence is a widely used microscopic technique for biomolecule structure and function characterization. The modern light microscope with high numerical aperture objective and sensitive CCD camera can image the brightly emitting organic and fluorescent protein tags with reasonable time resolution. Single-molecule imaging gives an unambiguous bottom-up biomolecule characterization that avoids the “missing information” problem characteristic of ensemble measurements. It has circumvented the diffraction limit by facilitating single-particle localization to ~1 nm. Probes developed specifically for SMD applications extend the advantages of single-molecule imaging to high probe density regions of cells and tissues. These applications perform under conditions resembling the native biomolecule environment and have been used to detect both probe position and orientation. Native, high density SMD may have added significance if molecular crowding impacts native biomolecule behavior as expected inside the cell. PMID:21179385

Ajtai, Katalin

2010-01-01

145

Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones.  

PubMed

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells. PMID:24053279

Chen, Peng; Keller, Aaron M; Joshi, Chandra P; Martell, Danya J; Andoy, Nesha May; Benítez, Jaime J; Chen, Tai-Yen; Santiago, Ace George; Yang, Feng

2013-10-15

146

Probing the Conformations of Single Molecule via Photon Counting Statistics  

E-print Network

We suggest an approach to detect the conformation of single molecule by using the photon counting statistics. The generalized Smoluchoswki equation is employed to describe the dynamical process of conformational change of single molecule. The resonant trajectories of the emission photon numbers $$ and the Mandel's $Q$ parameter, in the space of conformational coordinates $\\bm{\\mathcal{X}}$ and frequency $\\omega_L$ of external field ($\\bm{\\mathcal{X}}-\\omega_L$ space), can be used to rebuild the conformation of the single molecule. As an example, we consider Thioflavin T molecule. It demonstrates that the results of conformations extracted by employing the photon counting statistics is excellent agreement with the results of {\\it ab initio} computation.

Peng, Yonggang; Yang, Chuanlu; Zheng, Yujun

2014-01-01

147

Single-molecule fluorescence inside solid-state nanochannels  

NASA Astrophysics Data System (ADS)

One major limitation of single-molecule fluorescence spectroscopy is the finite residence time of diffusing molecules in the confocal detection volume. The time ranges in the order of milliseconds. This has typical size of femtoliter. Here, we present a concept of extending the residence time using nanochannels of ca. 60 nm x 60 nm cross-section to restrict the molecular motion. We use solid-state nanochannels of silicon and silicon dioxide. This work is aimed to use for dual-focus fluorescence detection combining Anti-Brownian ELectrophoretic or ABEL trap to actively trap single molecule.

Ghosh, Siddharth; Kumbhakar, Manoj; Platen, Mitja; Gregor, Ingo; Enderlein, Jörg

2014-03-01

148

Magnetic trapping of single molecules: principles, developments, and applications  

NASA Astrophysics Data System (ADS)

Over the last decade, magnetic trapping has emerged as a tool which can complement the optical trap in certain key biophysical assays. Through its low cost, ease of use, stability and scalability, magnetic trapping is an attractive tool for micro-rheological analysis, generation of sorting structures for microfluidics, and also single-molecule experimentation. Here we will compare and contrast optical and magnetic trapping as they pertain to singlemolecule experimentation, and in particular to the study of interactions between single molecules such as proteins and nucleic acids.

Grange, W.; Strick, T. R.

2013-09-01

149

Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging  

PubMed Central

We apply the astronomical data-analysis technique, Lucky imaging, to improve resolution in single molecule fluorescence microscopy. We show that by selectively discarding data points from individual single-molecule trajectories, imaging resolution can be improved by a factor of 1.6 for individual fluorophores and up to 5.6 for more complex images. The method is illustrated using images of fluorescent dye molecules and quantum dots, and the in vivo imaging of fluorescently labeled linker for activation of T cells. PMID:19348772

Cronin, Brid; de Wet, Ben; Wallace, Mark I.

2009-01-01

150

An improved surface passivation method for single-molecule studies.  

PubMed

We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution. PMID:25306544

Hua, Boyang; Han, Kyu Young; Zhou, Ruobo; Kim, Hajin; Shi, Xinghua; Abeysirigunawardena, Sanjaya C; Jain, Ankur; Singh, Digvijay; Aggarwal, Vasudha; Woodson, Sarah A; Ha, Taekjip

2014-12-01

151

Radio Frequency Scanning Tunneling Spectroscopy for Single-Molecule Spin Resonance  

NASA Astrophysics Data System (ADS)

We probe nuclear and electron spins in a single molecule even beyond the electromagnetic dipole selection rules, at readily accessible magnetic fields (few mT) and temperatures (5 K) by resonant radio-frequency current from a scanning tunneling microscope. We achieve subnanometer spatial resolution combined with single-spin sensitivity, representing a 10 orders of magnitude improvement compared to existing magnetic resonance techniques. We demonstrate the successful resonant spectroscopy of the complete manifold of nuclear and electronic magnetic transitions of up to ?Iz=±3 and ?Jz=±12 of single quantum spins in a single molecule. Our method of resonant radio-frequency scanning tunneling spectroscopy offers, atom-by-atom, unprecedented analytical power and spin control with an impact on diverse fields of nanoscience and nanotechnology.

Müllegger, Stefan; Tebi, Stefano; Das, Amal K.; Schöfberger, Wolfgang; Faschinger, Felix; Koch, Reinhold

2014-09-01

152

Radio frequency scanning tunneling spectroscopy for single-molecule spin resonance.  

PubMed

We probe nuclear and electron spins in a single molecule even beyond the electromagnetic dipole selection rules, at readily accessible magnetic fields (few mT) and temperatures (5 K) by resonant radio-frequency current from a scanning tunneling microscope. We achieve subnanometer spatial resolution combined with single-spin sensitivity, representing a 10 orders of magnitude improvement compared to existing magnetic resonance techniques. We demonstrate the successful resonant spectroscopy of the complete manifold of nuclear and electronic magnetic transitions of up to ?I_{z}=±3 and ?J_{z}=±12 of single quantum spins in a single molecule. Our method of resonant radio-frequency scanning tunneling spectroscopy offers, atom-by-atom, unprecedented analytical power and spin control with an impact on diverse fields of nanoscience and nanotechnology. PMID:25302884

Müllegger, Stefan; Tebi, Stefano; Das, Amal K; Schöfberger, Wolfgang; Faschinger, Felix; Koch, Reinhold

2014-09-26

153

Single-molecule magnet Mn12 on graphene  

NASA Astrophysics Data System (ADS)

We study energetics, electronic and magnetic structures, and magnetic anisotropy barriers of a monolayer of single-molecule magnets (SMMs), [Mn12O12(COOR)16](H2O)4 (abbreviated as Mn12, with R=H, CH3, C6H5, and CHCl2), on a graphene surface using spin-polarized density-functional theory with generalized gradient corrections and the inclusion of van der Waals interactions. We find that Mn12 molecules with ligands -H, -CH3, and -C6H5 are physically adsorbed on graphene through weak van der Waals interactions, and a much stronger ionic interaction occurs using a -CHCl2 ligand. The strength of bonding is closely related to the charge transfer between the molecule and the graphene sheet and can be manipulated by strain in the graphene; specifically, tension enhances n doping of graphene, and compression encourages p doping. The magnetic anisotropy barrier is computed by including the spin-orbit interaction within density-functional theory. The barriers for the Mn12 molecules with ligands -H, -CH3 and -C6H5 on graphene surfaces remain unchanged (within 1K) from those of isolated molecules because of their weak interaction, and a much larger reduction (10K) is observed when using the -CHCl2 ligand on graphene due to a substantial structural deformation as a consequence of the much stronger interaction. Neither strain in graphene nor charge transfer affects the magnetic anisotropy barrier significantly. Finally, we discuss the effect of strong correlation in the high-spin state of a Mn12 SMM and the consequence of SMM-surface adsorption.

Li, Xiang-Guo; Fry, James N.; Cheng, Hai-Ping

2014-09-01

154

A gate controlled conjugated single molecule diode: Its rectification could be reversed  

NASA Astrophysics Data System (ADS)

A gate controlled Au/diphenyldipyrimidinyl/Au single molecule diode is simulated by a tight-binding Hamiltonian combined with Green's Function and transport methods. After calculating a number of electronic transport characteristics under various gate voltages, a clear modulation by gate is got and when the positive voltage is high enough, the rectification could be reversed. This is advisable for the designing and building future molecular logic devices and integrated circuits.

Zhang, Qun

2014-10-01

155

Single molecule techniques in DNA repair: a primer.  

PubMed

A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair. PMID:24819596

Hughes, Craig D; Simons, Michelle; Mackenzie, Cassidy E; Van Houten, Bennett; Kad, Neil M

2014-08-01

156

Statistics and Related Topics in Single-Molecule Biophysics  

PubMed Central

Since the universal acceptance of atoms and molecules as the fundamental constituents of matter in the early twentieth century, molecular physics, chemistry and molecular biology have all experienced major theoretical breakthroughs. To be able to actually “see” biological macromolecules, one at a time in action, one has to wait until the 1970s. Since then the field of single-molecule biophysics has witnessed extensive growth both in experiments and theory. A distinct feature of single-molecule biophysics is that the motions and interactions of molecules and the transformation of molecular species are necessarily described in the language of stochastic processes, whether one investigates equilibrium or nonequilibrium living behavior. For laboratory measurements following a biological process, if it is sampled over time on individual participating molecules, then the analysis of experimental data naturally calls for the inference of stochastic processes. The theoretical and experimental developments of single-molecule biophysics thus present interesting questions and unique opportunity for applied statisticians and probabilists. In this article, we review some important statistical developments in connection to single-molecule biophysics, emphasizing the application of stochastic-process theory and the statistical questions arising from modeling and analyzing experimental data. PMID:25009825

Qian, Hong; Kou, S. C.

2014-01-01

157

Single-molecule magnets: Uranyl steps in the ring  

NASA Astrophysics Data System (ADS)

Uranium and manganese cations have been combined in a wheel-shaped supramolecular assembly that retains its magnetic spin state after the external field is removed, with a high barrier to its relaxation. This cluster supports recent predictions of the usefulness of the actinides in single-molecule magnetic devices.

Arnold, Polly L.

2012-12-01

158

Optical collection efficiency function in single-molecule detection experiments  

E-print Network

Optical collection efficiency function in single-molecule detection experiments Jo¨ rg Enderlein and W. Patrick Ambrose The optical collection efficiency function for an optical system on a geometrical optics approx- imation are presented. Comparison is made with exact wave optics calculations

Enderlein, Jörg

159

The dynamics of single-molecule DNA in flow  

Microsoft Academic Search

Within the last decade, fluorescence microscopy of single molecules of DNA in a plethora of flow fields has allowed an unprecedented examination of the dynamics of polymers in flow. As a result, new principles (e.g. “molecular individualism”) have been developed regarding these dynamics and old debates (e.g. conformational hysteresis of polymers in extensional flow) have received a fresh airing. The

Eric S. G. Shaqfeh

2005-01-01

160

SINGLE-MOLECULE DETECTION AND DNA SEQUENCING-BY-SYNTHESIS  

E-print Network

has established itself as one of the main techniques of interrogation of biological systems. Extending those techniques to decrease the sample size to single molecules provides an absolute standard for bulk allowed sequencing-by-synthesis to be conducted in the microfluidic environment using optical techniques

Quake, Stephen R.

161

Free energy reconstruction from nonequilibrium single-molecule pulling experiments  

E-print Network

Free energy reconstruction from nonequilibrium single-molecule pulling experiments Gerhard Hummer also drives the system away from equilibrium. Nevertheless, we show how equilibrium free energy of an extension of Jarzynski's remarkable identity between free energies and the irreversible work. Recent

Weeks, Eric R.

162

Strong extinction of a laser beam by a single molecule  

E-print Network

We present an experiment where a single molecule strongly affects the amplitude and phase of a laser field emerging from a subwavelength aperture. We achieve a visibility of -6% in direct and +10% in cross-polarized detection schemes. Our analysis shows that a close to full extinction should be possible using near-field excitation.

I. Gerhardt; G. Wrigge; P. Bushev; G. Zumofen; R. Pfab; V. Sandoghdar

2006-04-24

163

Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose  

SciTech Connect

This report seeks to elucidate the role of cellobiohydrolase-I (CBH I) in the hydrolysis of crystalline cellulose. A single-molecule approach uses various imaging techniques to investigate the surface structure of crystalline cellulose and changes made in the structure by CBH I.

Liu, Y.-S.; Luo, Y.; Baker, J. O.; Zeng, Y.; Himmel, M. E.; Smith, S.; Ding, S.-Y.

2009-12-01

164

FISHER INFORMATION FOR EMCCD IMAGING WITH APPLICATION TO SINGLE MOLECULE MICROSCOPY  

PubMed Central

Owing to its high quantum efficiency, the charge-coupled device (CCD) is an important imaging tool employed in biological applications such as single molecule microscopy. Under extremely low light conditions, however, a CCD is generally unsuitable because its readout noise can easily overwhelm the weak signal. Instead, an electron-multiplying charge-coupled device (EMCCD), which stochastically amplifies the acquired signal to drown out the readout noise, can be used. We have previously proposed a framework for calculating the Fisher information, and hence the Cramer-Rao lower bound, for estimating parameters (e.g., single molecule location) from the images produced by an optical microscope. Here, we develop the theory that is needed for deriving, within this framework, performance measures pertaining to the estimation of parameters from an EMCCD image. Our results allow the comparison of a CCD and an EMCCD in terms of the best accuracy with which parameters can be estimated from their acquired images. PMID:22735093

Chao, Jerry; Ward, E. Sally; Ober, Raimund J.

2012-01-01

165

Coherent manipulation and decoherence of s=10 single-molecule magnets.  

PubMed

We report coherent manipulation of S=10 Fe8 single-molecule magnets. The temperature dependence of the spin decoherence time T2 measured by high-frequency pulsed electron paramagnetic resonance indicates that strong spin decoherence is dominated by Fe8 spin bath fluctuations. By polarizing the spin bath in Fe8 single-molecule magnets at magnetic field B=4.6 T and temperature T=1.3 K, spin decoherence is significantly suppressed and extends the spin decoherence time T2 to as long as 712 ns. A second decoherence source is likely due to fluctuations of the nuclear spin bath. This hints that the spin decoherence time can be further extended via isotopic substitution to smaller nuclear magnetic moments. PMID:19257788

Takahashi, Susumu; van Tol, Johan; Beedle, Christopher C; Hendrickson, David N; Brunel, Louis-Claude; Sherwin, Mark S

2009-02-27

166

In situ Formation of Highly Conducting Covalent Au-C Contacts for Single-Molecule Junctions  

SciTech Connect

Charge transport across metal-molecule interfaces has an important role in organic electronics. Typically, chemical link groups such as thiols or amines are used to bind organic molecules to metal electrodes in single-molecule circuits, with these groups controlling both the physical structure and the electronic coupling at the interface. Direct metal-carbon coupling has been shown through C60, benzene and {pi}-stacked benzene but ideally the carbon backbone of the molecule should be covalently bonded to the electrode without intervening link groups. Here, we demonstrate a method to create junctions with such contacts. Trimethyl tin (SnMe{sub 3})-terminated polymethylene chains are used to form single-molecule junctions with a break-junction technique. Gold atoms at the electrode displace the SnMe{sub 3} linkers, leading to the formation of direct Au-C bonded single-molecule junctions with a conductance that is {approx}100 times larger than analogous alkanes with most other terminations. The conductance of these Au-C bonded alkanes decreases exponentially with molecular length, with a decay constant of 0.97 per methylene, consistent with a non-resonant transport mechanism. Control experiments and ab initio calculations show that high conductances are achieved because a covalent Au-C sigma ({sigma}) bond is formed. This offers a new method for making reproducible and highly conducting metal-organic contacts.

Cheng, Z.L.; Hybertsen, M.; Skouta, R.; Vazquez, H.; Widawsky, J.R.; Schneebeli, S.; Chen, W.; Breslow, R.; Venkataraman, L.

2011-06-01

167

Single molecule approaches for studying spliceosome assembly and catalysis.  

PubMed

Single molecule assays of splicing and spliceosome assembly can provide unique insights into pre-mRNA processing that complement other technologies. Key to these experiments is the fabrication of fluorescent molecules (pre-mRNAs and spliceosome components) and passivated glass slides for each experiment. Here we describe how to produce fluorescent RNAs by splinted RNA ligation and fluorescent spliceosome subunits by SNAP-tagging proteins in cell lysate. We then depict how to passivate glass slides with polyethylene glycol for use on an inverted microscope with objective-based total internal reflection fluorescence (TIRF) optics. Finally, we describe how to tether the pre-mRNA onto the passivated slide surface and introduce the SNAP-tagged cell lysate for analysis of spliceosome assembly by single molecule fluorescence. PMID:24549668

Anderson, Eric G; Hoskins, Aaron A

2014-01-01

168

Single-Molecule Observation of Prokaryotic DNA Replication  

PubMed Central

Recent advances in optical imaging and molecular manipulation techniques have made it possible to observe the activity of individual enzymes and study the dynamic properties of processes that are challenging to elucidate using ensemble-averaging techniques. The use of single-molecule approaches has proven to be particularly successful in the study of the dynamic interactions between the components at the replication fork. In this section, we describe the methods necessary for in vitro single-molecule studies of prokaryotic replication systems. Through these experiments, accurate information can be obtained on the rates and processivities of DNA unwinding and polymerization. The ability to monitor in real time the progress of a single replication fork allows for the detection of short-lived, intermediate states that would be difficult to visualize in bulk-phase assays. PMID:19563119

Tanner, Nathan A.; van Oijen, Antoine M.

2010-01-01

169

Single Molecule Junctions: Probing Contact Chemistry and Fundamental Circuit Laws  

SciTech Connect

By exploiting selective link chemistry, formation of single molecule junctions with reproducible conductance has become established. Systematic studies reveal the structure-conductance relationships for diverse molecules. I will draw on experiments from my collaborators at Columbia University, atomic-scale calculations and theory to describe progress in two areas. First, I will describe a novel route to form single molecule junctions, based on SnMe3 terminated molecules, in which gold directly bonds to carbon in the molecule backbone resulting in near ideal contact resistance [1]. Second, comparison of the conductance of junctions formed with molecular species containing either one backbone or two backbones in parallel allows demonstration of the role of quantum interference in the conductance superposition law at the molecular scale [2].

Hybertsen M. S.

2013-04-11

170

Single-Molecule Studies of DNA Replisome Function  

PubMed Central

Fast and accurate replication of DNA is accomplished by the interactions of multiple proteins in the dynamic DNA replisome. The DNA replisome effectively coordinates the leading and lagging strand synthesis of DNA. These complex, yet elegantly organized, molecular machines have been studied extensively by kinetic and structural methods to provide an in-depth understanding of the mechanism of DNA replication. Owing to averaging of observables, unique dynamic information of the biochemical pathways and reactions are concealed in conventional ensemble methods. However, recent advances in the rapidly expanding field of single-molecule analyses to study single biomolecules offer opportunities to probe and understand the dynamic processes involved in large biomolecular complexes such as replisomes. This review will focus on the recent developments in the biochemistry and biophysics of DNA replication employing single-molecule techniques and the insights provided by these methods towards a better understanding of the intricate mechanisms of DNA replication. PMID:19665592

Perumal, Senthil K.; Yue, Hongjun; Hu, Zhenxin; Spiering, Michelle M.; Benkovic, Stephen J.

2010-01-01

171

Visualization and thermodynamic encoding of single-molecule partition functions  

E-print Network

Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and enthalpy at finite-temperatures are challenging to determine with ensemble-averaging alone. Here, we provide a method to access single-molecule thermodynamics, by confining an individual molecule to a nanoscopic pore of a two-dimensional metal-organic nanomesh, where we directly record finite-temperature time-averaged statistical weights using temperature-controlled scanning tunneling microscopy. The obtained patterns represent a real space equilibrium probability distribution. We associate this distribution with a partition function projection to assess spatially resolved thermodynamic quantities, by means of computational modeling. The presented molecular dynamics based Boltzmann weighting model is able to reproduce experimentally observed molecular states with high accur...

Palma, Carlos-Andres; Klappenberger, Florian; Arras, Emmanuel; Kühne, Dirk; Stafström, Sven; Barth, Johannes V

2014-01-01

172

STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis  

NASA Astrophysics Data System (ADS)

The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

Hla, Saw-Wai; Rieder, Karl-Heinz

2003-10-01

173

High-throughput single-molecule optofluidic analysis  

PubMed Central

We describe a high-throughput, automated single-molecule measurement system, equipped with microfluidics. the microfluidic mixing device has integrated valves and pumps to accurately accomplish titration of biomolecules with picoliter resolution. We demonstrate that the approach enabled rapid sampling of biomolecule conformational landscape and of enzymatic activity, in the form of transcription by Escherichia coli RNA polymerase, as a function of the chemical environment. PMID:21297618

Kim, Soohong; Streets, Aaron M; Lin, Ron R; Quake, Stephen R; Weiss, Shimon; Majumdar, Devdoot S

2011-01-01

174

Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS)  

Microsoft Academic Search

By exploiting the extremely large effective cross sections ( 10-17-10-16 cm2\\/molecule) available from surface-enhanced Raman scattering (SERS), we achieved the first observation of single molecule Raman scattering. Measured spectra of a single crystal violet molecule in aqueous colloidal silver solution using one second collection time and about 2×105 W\\/cm2 nonresonant near-infrared excitation show a clear ``fingerprint'' of its Raman features

Katrin Kneipp; Yang Wang; Harald Kneipp; Lev T. Perelman; Irving Itzkan; Ramachandra R. Dasari; Michael S. Feld

1997-01-01

175

Single-Molecule Nanosecond Anisotropy Dynamics of Tethered Protein Motions  

SciTech Connect

Confined and hindered protein motions are generally found in living cells, with tethered rotational motions of proteins or protein domains particularly associated with and relevant to the early events of molecular interactions in cell signaling at extra- and intracellular membrane surfaces. Ensemble-averaged time-resolved fluorescence anisotropy has been extensively applied to study the protein rotational and conformational motion dynamics under physiologically relevant conditions. However, the spatial and temporal inhomogeneities of the non-synchronizable stochastic protein rotational and conformational motions are extremely difficult for such ensemble-averaged measurements to characterize. Here, we report on a demonstration of the single-molecule nanosecond anisotropy and its application to studying the tethered protein motion of a T4 lysozyme on a biologically comparable surface under water. The rotational motions of the tethered proteins are confined in a half-sphere volume primarily defined by the linker and the surface. We have observed dynamic inhomogeneity of the rotational diffusion dynamics, i.e., diffusion rate fluctuation, due to interactions between the proteins and the surface. However, we also found that the long-time averages of the dynamically inhomogeneous diffusion rates of single molecules are essentially homogeneous amongst the single molecules examined.

Hu, Dehong; Lu, H Peter

2003-01-16

176

Single-molecule imaging studies of protein dynamics  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence imaging is a powerful method for studying biological events. The work of this thesis primarily focuses on single molecule studies of the dynamics of Green Fluorescent Protein (GFP) and other fluorescent-labeled proteins by utilizing Total Internal Reflection Fluorescence (TIRF) microscopy and imaging. The single molecule experiments of this thesis covered three broad topics. First, the adsorption mechanisms of proteins onto hydrophobic and hydrophilic fused silica surfaces were imaged and reversible and irreversible adsorption mechanisms were observed. The second topic covered a new technique for measuring the diffusion coefficient of Brownian diffusing proteins, in particular GFP, in solution via a single image. The corresponding experiments showed a relationship between the intensity profile width and the diffusion coefficient of the diffusing molecules. The third topic covered an in vivo experiment involving imaging and quantifying prokaryotic cell metabolism protein dynamics inside the Bacillus subtilis bacteria, in which a helical diffusion pattern for the protein was observed. These topics are presented in the chronological order of the experiments conducted.

Zareh, Shannon Kian G.

177

Trapping single molecules with a solid state nanopore  

NASA Astrophysics Data System (ADS)

I describe a system for measuring and manipulating single molecules using a solid state nanopore, a small hole in an insulating film fashioned using solid-state Silicon processing techniques. In this work, pores less than 10 nanometers in diameter in 20-30 nm thick Silicon Nitride membranes are used to join two reservoirs of salt water. DNA molecules added to one reservoir are forced through the nanopore by an applied voltage bias. Single molecules of DNA are detected passing through the pore by a blockage of the ionic current between the reservoirs. The depth and duration of the current blockages reveal information about the molecule's geometry while the shape of the blockage depends on the molecule's conformation. If the driving voltage is reversed soon after a molecule has passed through the nanopore, the same molecule can be "recaptured," induced to pass through the pore a second time. This process reveals information about the dynamics of the molecule outside of and its interaction with the nanopore. The recapture process can be repeated multiple times to form a single molecule trap.

Gershow, Marc Herman

178

Single-molecule imaging of hyaluronan in human synovial fluid  

NASA Astrophysics Data System (ADS)

Human synovial fluid contains a high concentration of hyaluronan, a high molecular weight glycosaminoglycan that provides viscoelasticity and contributes to joint lubrication. In osteoarthritis synovial fluid, the concentration and molecular weight of hyaluronan decrease, thus impairing shock absorption and lubrication. Consistently, substitution of hyaluronan (viscosupplementation) is a widely used treatment for osteoarthritis. So far, the organization and dynamics of hyaluronan in native human synovial fluid and its action mechanism in viscosupplementation are poorly characterized at the molecular level. Here, we introduce highly sensitive single molecule microscopy to analyze the conformation and interactions of fluorescently labeled hyaluronan molecules in native human synovial fluid. Our findings are consistent with a random coil conformation of hyaluronan in human synovial fluid, and point to specific interactions of hyaluronan molecules with the synovial fluid matrix. Furthermore, single molecule microscopy is capable of detecting the breakdown of the synovial fluid matrix in osteoarthritis. Thus, single molecule microscopy is a useful new method to probe the structure of human synovial fluid and its changes in disease states like osteoarthritis.

Kappler, Joachim; Kaminski, Tim P.; Gieselmann, Volkmar; Kubitscheck, Ulrich; Jerosch, Jörg

2010-11-01

179

Improved Dye Stability in Single-Molecule Fluorescence Experiments  

NASA Astrophysics Data System (ADS)

Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

180

Single-molecule fluorescence spectroscopy in (bio)catalysis  

PubMed Central

The ever-improving time and space resolution and molecular detection sensitivity of fluorescence microscopy offer unique opportunities to deepen our insights into the function of chemical and biological catalysts. Because single-molecule microscopy allows for counting the turnover events one by one, one can map the distribution of the catalytic activities of different sites in solid heterogeneous catalysts, or one can study time-dependent activity fluctuations of individual sites in enzymes or chemical catalysts. By experimentally monitoring individuals rather than populations, the origin of complex behavior, e.g., in kinetics or in deactivation processes, can be successfully elucidated. Recent progress of temporal and spatial resolution in single-molecule fluorescence microscopy is discussed in light of its impact on catalytic assays. Key concepts are illustrated regarding the use of fluorescent reporters in catalytic reactions. Future challenges comprising the integration of other techniques, such as diffraction, scanning probe, or vibrational methods in single-molecule fluorescence spectroscopy are suggested. PMID:17664433

Roeffaers, Maarten B. J.; De Cremer, Gert; Uji-i, Hiroshi; Muls, Beniot; Sels, Bert F.; Jacobs, Pierre A.; De Schryver, Frans C.; De Vos, Dirk E.; Hofkens, Johan

2007-01-01

181

Viruses and tetraspanins: lessons from single molecule approaches.  

PubMed

Tetraspanins are four-span membrane proteins that are widely distributed in multi-cellular organisms and involved in several infectious diseases. They have the unique property to form a network of protein-protein interaction within the plasma membrane, due to the lateral associations with one another and with other membrane proteins. Tracking tetraspanins at the single molecule level using fluorescence microscopy has revealed the membrane behavior of the tetraspanins CD9 and CD81 in epithelial cell lines, providing a first dynamic view of this network. Single molecule tracking highlighted that these 2 proteins can freely diffuse within the plasma membrane but can also be trapped, permanently or transiently, in tetraspanin-enriched areas. More recently, a similar strategy has been used to investigate tetraspanin membrane behavior in the context of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection. In this review we summarize the main results emphasizing the relationship in terms of membrane partitioning between tetraspanins, some of their partners such as Claudin-1 and EWI-2, and viral proteins during infection. These results will be analyzed in the context of other membrane microdomains, stressing the difference between raft and tetraspanin-enriched microdomains, but also in comparison with virus diffusion at the cell surface. New advanced single molecule techniques that could help to further explore tetraspanin assemblies will be also discussed. PMID:24800676

Dahmane, Selma; Rubinstein, Eric; Milhiet, Pierre-Emmanuel

2014-05-01

182

Single-Molecule Studies of Actin Assembly and Disassembly Factors  

PubMed Central

The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of single-filament and single-molecule fluorescence imaging methods has provided a powerful new approach to discovering actin-regulatory activities and obtaining direct, quantitative insights into the pathways of molecular interactions that regulate actin network architecture and dynamics. Here we describe techniques for acquisition and analysis of single-molecule data, applied to the novel challenges of studying the filament assembly and disassembly activities of actin-associated proteins in vitro. We discuss the advantages of single-molecule analysis in directly visualizing the order of molecular events, measuring the kinetic rates of filament binding and dissociation, and studying the coordination among multiple factors. The methods described here complement traditional biochemical approaches in elucidating actin-regulatory mechanisms in reconstituted filamentous networks. PMID:24630103

Smith, Benjamin A.; Gelles, Jeff; Goode, Bruce L.

2014-01-01

183

Single Molecule Sensing by Nanopores and Nanopore Devices  

PubMed Central

Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore. PMID:20174694

Gu, Li-Qun; Shim, Ji Wook

2010-01-01

184

Toward single-molecule optical mapping of the epigenome.  

PubMed

The past decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity at the population level. The complex composition of the genome has made it an ideal system to study at the single-molecule level, and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical-based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nanoscale and enhanced optical resolving power for analysis of genomic information. During the past few years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation. PMID:24328256

Levy-Sakin, Michal; Grunwald, Assaf; Kim, Soohong; Gassman, Natalie R; Gottfried, Anna; Antelman, Josh; Kim, Younggyu; Ho, Sam O; Samuel, Robin; Michalet, Xavier; Lin, Ron R; Dertinger, Thomas; Kim, Andrew S; Chung, Sangyoon; Colyer, Ryan A; Weinhold, Elmar; Weiss, Shimon; Ebenstein, Yuval

2014-01-28

185

Development of new photon-counting detectors for single-molecule fluorescence microscopy.  

PubMed

Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level. PMID:23267185

Michalet, X; Colyer, R A; Scalia, G; Ingargiola, A; Lin, R; Millaud, J E; Weiss, S; Siegmund, Oswald H W; Tremsin, Anton S; Vallerga, John V; Cheng, A; Levi, M; Aharoni, D; Arisaka, K; Villa, F; Guerrieri, F; Panzeri, F; Rech, I; Gulinatti, A; Zappa, F; Ghioni, M; Cova, S

2013-02-01

186

Passive water-lipid peptide translocators with conformational switches: From single-molecule probe to cellular assay  

PubMed Central

Peptide design for unassisted passive water/lipid translocation remains a challenge, notwithstanding its importance for drug delivery. We introduce a design paradigm based on conformational switches operating as passive translocation vehicles. The interfacial behavior of the molecular prototype, probed in single-molecule AFM experiments, reveals a near-barrierless translocation. The associated free-energy agrees with mesoscopic measurements, and the in vitro behavior is quantitatively reproduced in cellular assays. The prototypes herald the advent of novel nano-biomaterials for passive translocation. PMID:18044863

Fernandez, Ariel; Crespo, Alejandro; Blau, Axel

2008-01-01

187

"Sticky electrons" transport and interfacial transfer of electrons in the dye-sensitized solar cell.  

PubMed

Dye-sensitized solar cells (DSCs, also known as Gratzel cells) mimic the photosynthetic process by using a sensitizer dye to harvest light energy to generate electrical power. Several functional features of these photochemical devices are unusual, and DSC research offers a rewarding arena in which to test new ideas, new materials, and new methodologies. Indeed, one of the most attractive chemical features of the DSC is that the basic concept can be used to construct a range of devices, replacing individual components with alternative materials. Despite two decades of increasing research activity, however, many aspects of the behavior of electrons in the DSC remain puzzling. In this Account, we highlight current understanding of the processes involved in the functioning of the DSC, with particular emphasis on what happens to the electrons in the mesoporous film following the injection step. The collection of photoinjected electrons appears to involve a random walk process in which electrons move through the network of interconnected titanium dioxide nanoparticles while undergoing frequent trapping and detrapping. During their passage to the cell contact, electrons may be lost by transfer to tri-iodide species in the redox electrolyte that permeates the mesoporous film. Competition between electron collection and back electron transfer determines the performance of a DSC: ideally, all injected electrons should be collected without loss. This Account then goes on to survey recent experimental and theoretical progress in the field, placing particular emphasis on issues that need to be resolved before we can gain a clear picture of how the DSC works. Several important questions about the behavior of "sticky" electrons, those that undergo multiple trapping and detrapping, in the DSC remain unanswered. The most fundamental of these concerns is the nature of the electron traps that appear to dominate the time-dependent photocurrent and photovoltage response of DSCs. The origin of the nonideality factor in the relationship between the intensity and the DSC photovoltage is also unclear, as is the discrepancy in electron diffusion length values determined by steady-state and non-steady-state methods. With these unanswered questions, DSC research is likely to remain an active and fruitful area for some years to come. PMID:19637905

Peter, Laurence

2009-11-17

188

Single-molecule studies on individual metal complexes  

NASA Astrophysics Data System (ADS)

Some fluorescent dyes, like Atto635 or Cy5, exhibit alterations in fluorescence emission in the presence of various metal ions and metal ion complexes. We used this effect to design dye-ligand conjugates that can be immobilized on glass surfaces and allow studying metal-ion binding using time-resolved single-molecule fluorescence spectroscopy (SMFS). Double-stranded DNA served as a rigid scaffold carrying 2,2'-bipyridene-4,4'-dicarboxylic acid as chelating ligand and a fluorescent dye as reporter, placed in close vicinity to the ligand. In the absence of metal ions, the probes showed high fluorescence quantum yield, whereas strong fluorescence quenching upon binding of Cu 2+-ions was observed. Time-resolved single-molecule measurements revealed stochastic switching between a highly fluorescent ("on") and a low fluorescent ("off") state. The coordination of the metal ion to the ligand is thus indicated by intramolecular fluorescence quenching of the dye. We screened various fluorescent dyes for their sensitivity to Cu 2+-coordination, and found that both Atto620 and MR121 are well-suited for this application. Ensemble studies of the fluorescence lifetimes of metalsensors with Atto620 showed only small dependence on the metal-ion concentration, while single-molecule studies reported strong changes in the fluorescence lifetimes which were correlated with the observed on- and off-states. Our results further indicate that the fluorescence of Atto620 is not completely quenched upon association of the metal-ion complex; either because a less fluorescent complex is formed or because of intramolecular collisional quenching due to conformational changes of the C6-linker used for covalent coupling of the fluorescent dye.

Kiel, Alexander; Järve, Anne; Kovacs, Janos; Mokhir, Andriy; Krämer, Roland; Herten, Dirk-Peter

2007-02-01

189

The statistics of single molecule detection: An overview  

SciTech Connect

An overview of our recent results in modeling single molecule detection in fluid flow is presented. Our mathematical approach is based on a path integral representation. The model accounts for all experimental details, such as light collection, laser excitation, hydrodynamics and diffusion, and molecular photophysics. Special attention is paid to multiple molecule crossings through the detection volume. Numerical realization of the theory is discussed. Measurements of burst size distributions in single B-phycoerythrin molecule detection experiments are presented and compared with theoretical predictions.

Enderlein, J.; Robbins, D.L.; Ambrose, W.P. [and others

1995-12-31

190

Multiphoton cascade absorption in single molecule fluorescence saturation spectroscopy.  

PubMed

Saturation spectroscopy is a relevant method to investigate photophysical parameters of single fluorescent molecules. Nevertheless, the impact of a gradual increase, over a broad range, of the laser excitation on the intramolecular dynamics is not completely understood, particularly concerning their fluorescence emission (the so-called brightness). Thus, we propose a comprehensive theoretical and experimental study to interpret the unexpected evolution of the brightness with the laser power taking into account the cascade absorption of two and three photons. Furthermore, we highlight the key role played by the confocal observation volume in fluorescence saturation spectroscopy of single molecules in solution. PMID:23521543

Winckler, Pascale; Jaffiol, Rodolphe

2013-05-01

191

Tunneling anisotropic magnetoresistance in single-molecule magnet junctions  

NASA Astrophysics Data System (ADS)

We theoretically investigate quantum transport through single-molecule magnet (SMM) junctions with ferromagnetic and normal-metal leads in the sequential regime. The current obtained by means of the rate-equation gives rise to the tunneling anisotropic magnetoresistance (TAMR), which varies with the angle between the magnetization direction of ferromagnetic lead and the easy axis of SMM. The angular dependence of TAMR can serve as a probe to determine experimentally the easy axis of SMM. Moreover, it is demonstrated that both the magnitude and the sign of TAMR are tunable by the bias voltage, suggesting a new spin-valve device with only one magnetic electrode in molecular spintronics.

Xie, Haiqing; Wang, Qiang; Jiao, Hujun; Liang, J.-Q.

2012-08-01

192

Single Molecule as a Local Acoustic Detector for Mechanical Oscillators  

NASA Astrophysics Data System (ADS)

A single molecule can serve as a nanometer-sized detector of acoustic strain. Such a nanomicrophone has the great advantage that it can be placed very close to acoustic signal sources and high sensitivities can be achieved. We demonstrate this scheme by monitoring the fluorescence intensity of a single dibenzoterrylene molecule in an anthracene crystal attached to an oscillating tuning fork. The characterization of the vibration amplitude and of the detection sensitivity is a first step towards detection and control of nanomechanical oscillators through optical detection and feedback.

Tian, Yuxi; Navarro, Pedro; Orrit, Michel

2014-09-01

193

Single molecule as a local acoustic detector for mechanical oscillators.  

PubMed

A single molecule can serve as a nanometer-sized detector of acoustic strain. Such a nanomicrophone has the great advantage that it can be placed very close to acoustic signal sources and high sensitivities can be achieved. We demonstrate this scheme by monitoring the fluorescence intensity of a single dibenzoterrylene molecule in an anthracene crystal attached to an oscillating tuning fork. The characterization of the vibration amplitude and of the detection sensitivity is a first step towards detection and control of nanomechanical oscillators through optical detection and feedback. PMID:25302904

Tian, Yuxi; Navarro, Pedro; Orrit, Michel

2014-09-26

194

Fluorescence correlation spectroscopy of single molecules on an optofluidic chip  

NASA Astrophysics Data System (ADS)

We review our recent progress in bringing fluorescent correlation spectroscopy (FCS) of single molecules on a silicon optofluidic platform. Starting from basic concepts and applications of FCS we move to a description of our integrated optofluidic device, briefly outlining the physics behind its function and relevant geometrical characteristics. We then derive an FCS theoretical model for our sensor geometry, which we subsequently apply to the examination of molecular properties of single fluorophores and bioparticles. The model allows us to extract the diffusion coefficient, translational velocity and local concentration of particles in question. We conclude with future directions of this research.

Rudenko, M. I.; Kühn, S.; Lunt, E. J.; Phillips, B. S.; Deamer, D. W.; Hawkins, A. R.; Schmidt, H.

2008-02-01

195

Single Molecule Studies on Dynamics in Liquid Crystals  

PubMed Central

Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

Tauber, Daniela; von Borczyskowski, Christian

2013-01-01

196

Detection at the single molecule level using an optical fiber  

NASA Astrophysics Data System (ADS)

We are developing a method for detecting single Ba+ ions in solid xenon on a fiber probe for the EXO double beta decay experiment. As a demonstration of potential capability, we have explored detection of Rhodamine 6G molecules and quantum dots in solution using the same optical setup. We report results on detection of ˜1 dye molecule on the average in the probe volume and attempts to do the same with quantum dots. Steps to fix single dye molecules or quantum dots in position and observe blinking from single molecules or dots will follow.

Topel, Thomas; Mong, Brian; Chen, Wei-Ting; Fairbank, William

2009-10-01

197

Single-molecule chemistry of metal phthalocyanine on noble metal surfaces.  

PubMed

To develop new functional materials and nanoscale electronics, researchers would like to accurately describe and precisely control the quantum state of a single molecule on a surface. Scanning tunneling microscopy (STM), combined with first-principles simulations, provides a powerful technique for acquiring this level of understanding. Traditionally, metal phthalocyanine (MPc) molecules, composed of a metal atom surrounded by a ligand ring, have been used as dyes and pigments. Recently, MPc molecules have shown great promise as components of light-emitting diodes, field-effect transistors, photovoltaic cells, and single-molecule devices. In this Account, we describe recent research on the characterization and control of adsorption and electronic states of a single MPc molecule on noble metal surfaces. In general, the electronic and magnetic properties of a MPc molecule largely depend on the type of metal ion within the phthalocyanine ligand and the type of surface on which the molecule is adsorbed. However, with the STM technique, we can use on-site molecular "surgery" to manipulate the structure and the properties of the molecule. For example, STM can induce a dehydrogenation reaction of the MPc, which allows us to control the Kondo effect, which describes the spin polarization of the molecule and its interaction with the complex environment. A specially designed STM tip can allow researchers to detect certain molecule-surface hybrid states that are not accessible by other techniques. By matching the local orbital symmetry of the STM tip and the molecule, we can generate the negative differential resistance effect in the formed molecular junction. This orbital symmetry based mechanism is extremely robust and does not critically depend on the geometry of the STM tip. In summary, this simple model system, a MPc molecule absorbed on a noble metal surface, demonstrates the power of STM for quantum characterization and manipulation of single molecules, highlighting the potential of this technique in a variety of applications. PMID:20359193

Li, Zhenyu; Li, Bin; Yang, Jinlong; Hou, Jian Guo

2010-07-20

198

Electric field induced fluorescence hysteresis of single molecules in poly(methyl methacrylate)  

NASA Astrophysics Data System (ADS)

Single molecule (SM) chips could serve as the fundamental devices in quantum information processing. In this context, a chip with the non-polar SMs of squaraine-derived rotaxanes embedded in a polar poly(methyl methacrylate) matrix was realized and the SM fluorescence hysteresis induced by the electric field was observed at room temperature. Here, we presented a model considering both of the electron transfer and space charge relaxation processes to explain the fluorescence hysteresis effect, and the model-based simulations agreed reasonably well with the experimental results.

Zhou, Haitao; Qin, Chengbing; Chen, Ruiyun; Zhang, Guofeng; Xiao, Liantuan; Jia, Suotang

2014-10-01

199

Watching Individual Proteins Acting on Single Molecules of DNA  

PubMed Central

In traditional biochemical experiments, the behavior of individual proteins is obscured by ensemble averaging. To better understand the behavior of proteins that bind to and/or translocate on DNA, we have developed instrumentation that uses optical trapping, microfluidic solution delivery, and fluorescent microscopy to visualize either individual proteins or assemblies of proteins acting on single molecules of DNA. The general experimental design involves attaching a single DNA molecule to a polystyrene microsphere that is then used as a microscopic handle to manipulate individual DNA molecules with a laser trap. Visualization is achieved by fluorescently labeling either the DNA or the protein of interest, followed by direct imaging using high-sensitivity fluorescence microscopy. We describe the sample preparation and instrumentation used to visualize the interaction of individual proteins with single molecules of DNA. As examples, we describe the application of these methods to the study of proteins involved in recombination-mediated DNA repair, a process essential for the maintenance of genomic integrity. PMID:20580968

Amitani, Ichiro; Liu, Bian; Dombrowski, Christopher C.; Baskin, Ronald J.; Kowalczykowski, Stephen C.

2011-01-01

200

Single molecule enzymology a la Michaelis-Menten  

E-print Network

In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that allow the measurement of enzyme- catalysed and other biopolymer-mediated reactions inside single cells at the single molecule level. Time course data obtained by these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single cell data requires stochastic methods, rather than deterministic rate equations. Here we concisely review both experimental and theoretical techniques which enable single molecule analysis with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-twentieth century to its modern day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment and how estimation of rate constants from single cell data is possible using recently developed stochastic approaches.

Ramon Grima; Nils Walter; Santiago Schnell

2013-11-28

201

Surface passivation for single-molecule protein studies.  

PubMed

Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation. PMID:24797261

Chandradoss, Stanley D; Haagsma, Anna C; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

2014-01-01

202

Modeling single molecule detection probabilities in microdroplets. Final report  

SciTech Connect

Optimization of molecular detection efficiencies is important for analytical applications of single molecule detection methods. In microdroplets some experimental limitations can be reduced, primarily because the molecule cannot diffuse away from the excitation and collection volume. Digital molecular detection using a stream of microdroplets has been proposed as a method of reducing concentration detection limits by several orders of magnitude relative to conventional measurements. However, the bending and reflection of light at the microdroplet`s liquid-air interface cause the illumination intensity and fluorescence intensity collected to be strongly dependent on the position of the molecule within the droplet. The goal is to model the detection of single molecules in microdroplets so that one can better understand and optimize detection efficiencies. In the first year of this modeling effort the authors studied the collection of fluorescence from unit-amplitude dipoles inside of spheres. In this second year they modified their analysis to accurately model the effects of excitation inhomogeneities, including effects of molecular saturation, motion of the droplet, and phase variations between the two counter-propagating waves that illuminate the droplet. They showed that counter-propagating plane wave illumination can decrease the variations in the intensity which excites the molecules. Also in this second year they simulated (using a Monte Carlo method) the detection of fluorescence from many droplets, each of which may contain zero, or one (or at higher concentrations, a few) fluorescent molecules.

Hill, S.C.

1997-05-22

203

Probing the Kinetics of Single Molecule Protein Folding  

PubMed Central

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments (for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier. The ratio between first-passage-time moments is proposed to be a good variable to quantitatively probe these kinetic changes. The temperature-dependent kinetics is consistent with the strange kinetics found in folding dynamics experiments. The potential applications of the current results to single-molecule protein folding are discussed. PMID:15465871

Leite, Vitor B. P.; Onuchic, Jose N.; Stell, George; Wang, Jin

2004-01-01

204

Surface Passivation for Single-molecule Protein Studies  

PubMed Central

Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation. PMID:24797261

Chandradoss, Stanley D.; Haagsma, Anna C.; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

2014-01-01

205

Fast single-molecule FRET spectroscopy: theory and experiment.  

PubMed

Single-molecule spectroscopy is widely used to study macromolecular dynamics. Although this technique provides unique information that cannot be obtained at the ensemble level, the possibility of studying fast molecular dynamics is limited by the number of photons detected per unit time (photon count rate), which is proportional to the illumination intensity. However, simply increasing the illumination intensity often does not help because of various photophysical and photochemical problems. In this Perspective, we show how to improve the dynamic range of single-molecule fluorescence spectroscopy at a given photon count rate by considering each and every photon and using a maximum likelihood method. For a photon trajectory with recorded photon colors and inter-photon times, the parameters of a model describing molecular dynamics are obtained by maximizing the appropriate likelihood function. We discuss various likelihood functions, their applicability, and the accuracy of the extracted parameters. The maximum likelihood method has been applied to analyze the experiments on fast two-state protein folding and to measure transition path times. Utilizing other information such as fluorescence lifetimes is discussed in the framework of two-dimensional FRET efficiency-lifetime histograms. PMID:25088495

Chung, Hoi Sung; Gopich, Irina V

2014-09-21

206

Single-Molecule Electrical Random Resequencing of DNA and RNA  

NASA Astrophysics Data System (ADS)

Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

2012-07-01

207

Insights into Human -Cardiac Myosin Function from Single Molecule and Single Cell Studies  

E-print Network

using single molecule and single cell approaches. Keywords Hypertrophic Cardiomyopathy. Single Molecule Analysis . Cardiac Myosin Introduction Hypertrophic cardiomyopathy (HCM) is the most common inherited contractile proteins [4]. Despite our understanding of the genetic underpinnings of cardiomyopathy

Spudich, James A.

208

Single-molecule light emission at room temperature on a wide-band-gap semiconductor  

NASA Astrophysics Data System (ADS)

Room-temperature light emission from single chemisorbed perylene based molecules adsorbed on silicon carbide (SiC) is probed by scanning tunneling microscopy (STM). A new approach to STM-induced luminescence of a single molecule is explored using a wide-band-gap semiconductor to decouple electronically the molecule from the surface. After molecular adsorption, the lowest unoccupied molecular orbital and the highest occupied molecular orbital (HOMO) both lie within the bulk band gap and below the Fermi level of the substrate. The maximum photon energy of the light emission from the molecule shows a fixed shift of 1.5 eV relative to the maximum energy of the tunnel electrons. This is consistent with the photons being generated by inelastic electron tunneling between the HOMO and the unoccupied electronic states of the STM tip.

Yang, H.; Mayne, A. J.; Comtet, G.; Dujardin, G.; Kuk, Y.; Nagarajan, S.; Gourdon, A.

2014-09-01

209

Effect of ligand substitution on the exchange interactions in {Mn(12)}-type single-molecule magnets.  

PubMed

We investigate how ligand substitution affects the intramolecular spin exchange interactions, studying a prototypical family of single-molecule magnets comprising dodecanuclear cluster molecules [Mn(III)(8)Mn(IV)(4)O(12)(COOR)(16)]. We identify a simple scheme based on accumulated Pauling electronegativity numbers (AEN) of the carboxylate ligand groups (R). The redistribution of the electron density, controlled by the AEN of a ligand, changes the degree of hybridization between 3d electrons of manganese and 2p electrons of oxygen atoms, thus changing the exchange interactions. This scheme, despite its conceptual simplicity, provides a strong correlation with the exchange energies associated with carboxylate bridges and is confirmed by the electronic structure calculations taking into account the Coulomb correlations in magnetic molecules. PMID:21043473

Boukhvalov, Danil W; Dobrovitski, Viatcheslav V; Kögerler, Paul; Al-Saqer, Mohammad; Katsnelson, Mikhail I; Lichtenstein, Alexander I; Harmon, Bruce N

2010-12-01

210

Identifying transport behavior of single-molecule trajectories.  

PubMed

Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We use a renormalization group operator to identify the anomalous (non-Fickian) diffusion behavior from a short trajectory of a single molecule. The method provides quantitative information about the underlying stochastic process, including its anomalous scaling exponent. The classification algorithm is first validated on simulated trajectories of known scaling. Then it is applied to experimental trajectories of microspheres diffusing in cytoplasm, revealing heterogeneous diffusive dynamics. The simplicity and robustness of this classification algorithm makes it an effective tool for analysis of rare stochastic events that occur in complex biological systems. PMID:25418303

Regner, Benjamin M; Tartakovsky, Daniel M; Sejnowski, Terrence J

2014-11-18

211

Processive cytoskeletal motors studied with single-molecule fluorescence techniques.  

PubMed

Processive cytoskeletal motors from the myosin, kinesin, and dynein families walk on actin filaments and microtubules to drive cellular transport and organization in eukaryotic cells. These remarkable molecular machines are able to take hundreds of successive steps at speeds of up to several microns per second, allowing them to effectively move vesicles and organelles throughout the cytoplasm. Here, we focus on single-molecule fluorescence techniques and discuss their wide-ranging applications to the field of cytoskeletal motor research. We cover both traditional fluorescence and sub-diffraction imaging of motors, providing examples of how fluorescence data can be used to measure biophysical parameters of motors such as coordination, stepping mechanism, gating, and processivity. We also outline some remaining challenges in the field and suggest future directions. PMID:24882363

Belyy, Vladislav; Yildiz, Ahmet

2014-10-01

212

Three dimensional single molecule localization using a phase retrieved pupilfunction  

PubMed Central

Localization-based superresolution imaging is dependent on finding the positions of individualfluorophores in a sample by fitting the observed single-molecule intensity pattern to the microscopepoint spread function (PSF). For three-dimensional imaging, system-specific aberrations of theoptical system can lead to inaccurate localizations when the PSF model does not account for theseaberrations. Here we describe the use of phase-retrieved pupil functions to generate a more accuratePSF and therefore more accurate 3D localizations. The complex-valued pupil function containsinformation about the system-specific aberrations and can thus be used to generate the PSF forarbitrary defocus. Further, it can be modified to include depth dependent aberrations. We describethe phase retrieval process, the method for including depth dependent aberrations, and a fastfitting algorithm using graphics processing units. The superior localization accuracy of the pupilfunction generated PSF is demonstrated with dual focal plane 3D superresolution imaging ofbiological structures. PMID:24514501

Liu, Sheng; Kromann, Emil B.; Krueger, Wesley D.; Bewersdorf, Joerg; Lidke, Keith A.

2013-01-01

213

Enhancing single molecule imaging in optofluidics and microfluidics.  

PubMed

Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking. PMID:21954349

Vasdekis, Andreas E; Laporte, Gregoire P J

2011-01-01

214

Eukaryotic transcriptional dynamics: from single molecules to cell populations  

PubMed Central

Transcriptional regulation is achieved through combinatorial interactions between regulatory elements in the human genome and a vast range of factors that modulate the recruitment and activity of RNA polymerase. Experimental approaches for studying transcription in vivo now extend from single-molecule techniques to genome-wide measurements. Parallel to these developments is the need for testable quantitative and predictive models for understanding gene regulation. These conceptual models must also provide insight into the dynamics of transcription and the variability that is observed at the single-cell level. In this Review, we discuss recent results on transcriptional regulation and also the models those results engender. We show how a non-equilibrium description informs our view of transcription by explicitly considering time-and energy-dependence at the molecular level. PMID:23835438

Coulon, Antoine; Chow, Carson C.; Singer, Robert H.; Larson, Daniel R.

2013-01-01

215

Reconstructing folding energy landscapes by single-molecule force spectroscopy.  

PubMed

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Woodside, Michael T; Block, Steven M

2014-01-01

216

Plasmon-enhanced colorimetric ELISA with single molecule sensitivity.  

PubMed

Robust but ultrasensitive biosensors with a capability of detecting low abundance biomarkers could revolutionize clinical diagnostics and enable early detection of cancer, neurological diseases, and infections. We utilized a combination of localized surface plasmon resonance (LSPR) refractive index sensing and the well-known enzyme-linked immunosorbent assay to develop a simple colorimetric biosensing methodology with single molecule sensitivity. The technique is based on spectral imaging of a large number of isolated gold nanoparticles. Each particle binds a variable number of horseradish peroxidase (HRP) enzyme molecules that catalyze a localized precipitation reaction at the particle surface. The enzymatic reaction dramatically amplifies the shift of the LSPR scattering maximum, ?(max), and makes it possible to detect the presence of only one or a few HRP molecules per particle. PMID:21428275

Chen, Si; Svedendahl, Mikael; Duyne, Richard P Van; Käll, Mikael

2011-04-13

217

Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS)  

SciTech Connect

By exploiting the extremely large effective cross sections (10{sup -17}{endash}10{sup -16}cm{sup 2}/molecule) available from surface-enhanced Raman scattering (SERS), we achieved the first observation of single molecule Raman scattering. Measured spectra of a single crystal violet molecule in aqueous colloidal silver solution using one second collection time and about 2{times}10{sup 5}W/cm{sup 2} nonresonant near-infrared excitation show a clear {open_quotes}fingerprint{close_quotes} of its Raman features between 700 and 1700cm{sup -1}. Spectra observed in a time sequence for an average of 0.6 dye molecule in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1, 2, or 3 molecules. {copyright} {ital 1997} {ital The American Physical Society}

Kneipp, K.; Wang, Y.; Kneipp, H.; Perelman, L.T.; Itzkan, I.; Dasari, R.R.; Feld, M.S. [George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); [Department of Physics, Technical University of Berlin, D 10623 Berlin (Germany)

1997-03-01

218

Nanopore single-molecule detection of circulating microRNAs.  

PubMed

MicroRNAs (miRNAs) are a class of tiny noncoding RNAs that play an important role in regulating every aspect of cellular activities. Dysfunctional expression of miRNAs disrupts normal biological processes, leading to the development of various diseases including cancer. Circulating miRNAs are being investigated as biomarkers with a potential for noninvasive disease detection. This demands the development of new technologies to accurately detect miRNAs with short assay time and affordable cost. We have proposed a nanopore single-molecule method for accurate, label-free detection of circulating miRNAs without amplification of the target miRNA. This concise protocol describes how to device a protein nanopore to quantify target miRNAs in RNA extraction, and discusses at the end the advantages, challenges, and broad impact of the nanopore approach for miRNA detection. PMID:23719958

Gu, Li-Qun; Wang, Yong

2013-01-01

219

Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis  

SciTech Connect

This is the final report of a one-year laboratory-directed research and development project at Los Alamos National Laboratory. There has been considerable interest in the development of very sensitive clinical diagnostic techniques over the last few years. Many pathogenic agents are often present in extremely small concentrations in clinical samples, especially at the initial stages of infection, making their detection very difficult. This project sought to develop a new technique for the detection and accurate quantification of specific bacterial and viral nucleic acid sequences in clinical samples. The scheme involved the use of novel hybridization probes for the detection of nucleic acids combined with our recently developed technique of single-molecule electrophoresis. This project is directly relevant to the DOE`s Defense Programs strategic directions in the area of biological warfare counter-proliferation.

Castro, A; Shera, E.B.

1996-09-01

220

Super-Resolution Fluorescence Imaging with Single Molecules  

PubMed Central

The ability to detect, image and localize single molecules optically with high spatial precision by their fluorescence enables an emergent class of super-resolution microscopy methods which have overcome the longstanding diffraction barrier for far-field light-focusing optics. Achieving spatial resolutions of 20–40 nm or better in both fixed and living cells, these methods are currently being established as powerful tools for minimally-invasive spatiotemporal analysis of structural details in cellular processes which benefit from enhanced resolution. Briefly covering the basic principles, this short review then summarizes key recent developments and application examples of two- and three-dimensional (3D) multi-color techniques and faster time-lapse schemes. The prospects for quantitative imaging – in terms of its ability to correct for dipole-emission-induced systematic localization errors and to provide accurate counts of molecular copy numbers within nanoscale cellular domains – are discussed. PMID:23932284

Sahl, Steffen J.; Moerner, W. E.

2013-01-01

221

Single-molecule controlled emission in planar plasmonic cavities  

NASA Astrophysics Data System (ADS)

We study the fluorescence emission from single dye molecules in coplanar plasmonic cavities composed of a thin gold film surrounded by two in-plane surface plasmon Bragg mirrors. We first discuss the effect of the presence of Bragg mirrors on the radiation diagram of surface plasmon coupled emission. Then, we investigate the role of the planar cavity size by single-molecule fluorescence lifetime imaging. Experimental data are compared to numerical simulations of the decay rates calculated as a function of the molecule orientation and position within the cavity. The creation of new decay channels by coupling to the cavity modes is also discussed. We measure a plasmonic Purcell factor up to five, attributed to the enhancement of the radiative rate.

Derom, S.; Bouhelier, A.; Kumar, A.; Leray, A.; Weeber, J.-C.; Buil, S.; Quélin, X.; Hermier, J. P.; Francs, G. Colas des

2014-01-01

222

Progress towards DNA sequencing at the single molecule level  

SciTech Connect

We describe progress towards sequencing DNA at the single molecule level. Our technique involves incorporation of fluorescently tagged nucleotides into a targeted sequence, anchoring the labeled DNA strand in a flowing stream, sequential exonuclease digestion of the DNA strand, and efficient detection and identification of single tagged nucleotides. Experiments demonstrating strand specific exonuclease digestion of fluorescently labeled DNA anchored in flow as well as the detection of single cleaved fluorescently tagged nucleotides from a small number of anchored DNA fragments axe described. We find that the turnover rate of Esherichia coli exonuclease III on fluorescently labeled DNA in flow at 36{degree}C is {approximately}7 nucleotides per DNA strand per second, which is approximately the same as that measured for this enzyme on native DNA under static, saturated (excess enzyme) conditions. Experiments demonstrating the efficient detection of single fluorescent molecules delivered electrokinetically to a {approximately}3 pL probe volume are also described.

Goodwin, P.M.; Affleck, R.L.; Ambrose, W.P. [and others

1995-12-01

223

Alternating-laser excitation: single-molecule FRET and beyond.  

PubMed

The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems. PMID:24037326

Hohlbein, Johannes; Craggs, Timothy D; Cordes, Thorben

2014-02-21

224

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes  

PubMed Central

A journey back in time is possible at the molecular level by reconstructing proteins from extinct organisms. Here we report the reconstruction, based on sequence predicted by phylogenetic analysis, of seven Precambrian thioredoxin enzymes (Trx), dating back between ~1.4 and ~4 billion years (Gyr). The reconstructed enzymes are up to 32° C more stable than modern enzymes and the oldest show significantly higher activity than extant ones at pH 5. We probed their mechanisms of reduction using single-molecule force spectroscopy. From the force-dependency of the rate of reduction of an engineered substrate, we conclude that ancient Trxs utilize chemical mechanisms of reduction similar to those of modern enzymes. While Trx enzymes have maintained their reductase chemistry unchanged, they have adapted over a 4 Gyr time span to the changes in temperature and ocean acidity that characterize the evolution of the global environment from ancient to modern Earth. PMID:21460845

Perez-Jimenez, Raul; Ingles-Prieto, Alvaro; Zhao, Zi-Ming; Sanchez-Romero, Inmaculada; Alegre-Cebollada, Jorge; Kosuri, Pallav; Garcia-Manyes, Sergi; Kappock, T. Joseph; Tanokura, Masaru; Holmgren, Arne; Sanchez-Ruiz, Jose M.; Gaucher, Eric A.; Fernandez, Julio M.

2011-01-01

225

Single-molecule analysis of Pseudomonas fluorescens footprints.  

PubMed

Understanding the molecular mechanisms of bacterial adhesion and biofilm formation is an important topic in current microbiology and a key in nanomedicine for developing new antibacterial strategies. There is growing evidence that the production of extracellular polymeric substances at the cell-substrate interface plays a key role in strengthening bacterial adhesion. Yet, because these adhesive polymers are available in small amounts and are localized at interfaces, they are difficult to study using traditional techniques. Here, we use single-molecule atomic force microscopy (AFM) to functionally analyze the biophysical properties (distribution, adhesion, and extension) of bacterial footprints, that is, adhesive macromolecules left on substrate surfaces after removal of the attached cells. We focus on the large adhesin protein LapA from Pseudomonas fluorescens, which mediates cell attachment to a wide diversity of surfaces. Using AFM tips functionalized with specific antibodies, we demonstrate that adhesion of bacteria to hydrophobic substrates leads to the active accumulation of the LapA protein at the cell-substrate interface. We show that single LapA proteins left on the substrate after cell detachment localize into microscale domains corresponding to the bacterial size and exhibit multiple adhesion peaks reflecting the adhesion and extension of adsorbed LapA proteins. The mechanical behavior of LapA-based footprints makes them ideally suited to function as multipurpose bridging polymers, enabling P. fluorescens to attach to various surfaces. Our experiments show that single-molecule AFM offers promising prospects for characterizing the biophysics and dynamics of the cell-substrate interface in the context of bacterial adhesion, on a scale that was not accessible before. PMID:24456070

El-Kirat-Chatel, Sofiane; Boyd, Chelsea D; O'Toole, George A; Dufrêne, Yves F

2014-02-25

226

Exploring single-molecule dynamics with fluorescence nanoscopy  

NASA Astrophysics Data System (ADS)

The study of molecular dynamics at the single-molecule level with fluorescence correlation spectroscopy (FCS) and far-field optics has contributed greatly to the functional understanding of complex systems. Unfortunately, such studies are restricted to length scales of >200 nm because diffraction does not allow further reduction of the measurement volume. This sets an upper limit on the applicable concentration of fluorescently labeled molecules and even more importantly, averages out details of nanoscale dynamics. By combining FCS and fluorescence intensity distribution analysis (FIDA) with sub-diffraction-resolution stimulated emission depletion (STED) nanoscopy, we remove this restriction and obtain open measurement volumes of nanoscale dimensions which are tunable in size. As a consequence, single-molecule studies can now be extended to nanoscale dynamics and may be applied to much larger, often endogenous concentrations. In solution, low-brightness signal from axial out-of-focus volume shells was taken into account by using both FCS and FIDA in conjunction to analyze the data. In two-dimensional systems, such as lipid membranes, the background is greatly reduced and measurements feature excellent signal-to-noise ratios. Measurement foci of down to 30 nm in diameter directly reveal anomalous diffusion of lipids in the plasma membrane of living cells and allow for the determination of on/off rates of the binding of lipids to other membrane constituents. Such important insight into the prominent biological question of lipid membrane organization or 'lipid rafts' shows that combining fluctuation analysis with STED-engineered ultra-small measurement volumes is a viable and powerful new approach to probing molecular dynamics on the nanoscale.

Ringemann, Christian; Harke, Ben; von Middendorff, Claas; Medda, Rebecca; Honigmann, Alf; Wagner, Richard; Leutenegger, Marcel; Schönle, Andreas; Hell, Stefan W.; Eggeling, Christian

2009-10-01

227

Nanoscale characterization of interfacial electronic properties and degradation mechanisms of organic thin films for electroluminescence displays  

NASA Astrophysics Data System (ADS)

For the first time, the promising organic light-emitting diode (OLED), indium tin oxide (ITO)/copper phthalocyanine (CuPc)/N,N '-di(naphthalene-l-yl)-N,N'-diphthalbenzidine (NPB)/tris(8-quinolinolatoline) aluminum (Alq3) (ITO/CuPc/NPB/Alq 3), has been selected for investigating its interfacial properties, and morphological degradation mechanisms induced by moisture and temperature through the systematic visualization by the state-of-the-art scanning probe microscopy (SPM). The motivation of this thesis lies in the importance of the OLED interfaces associated with the OLED's quantum efficiency, and morphological alteration in respect to device lifetime and luminance. Variable-temperature ultrahigh vacuum scanning tunnelling microscopy and spectroscopy (VT-UHV/STM and STS) are used to investigate the interfacial electronic properties at the Au(111)/CuPc interface. The energy band gap of CuPc ultrathin films on Au(111) measured by the charge injection from the STM tip into the highest occupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbitals (LUMO) levels of CuPc is ˜1.9--2.1 eV, which is comparable to the optical band gap (˜1.7 eV). This result indicates that a dipole layer and/or image forces is present right at the Au(111)/CuPc interface, and confirms that the common vacuum level alignment at the interface is invalid. Also, it is found that the morphological features probably affect the tunnelling current. To scrutinize the degradation associated with morphological variations of the Alga-based OLED structures, a variable-temperature tapping mode atomic force microscope (VT-AFM) and other complementary techniques such as thickness-shear mode (TSM) acoustic wave mass sensor and micro-Raman spectroscopy have been employed to sift the degradation mechanisms induced by ambient atmosphere and Joule heating. A volatile species released from the Alq3 thin films under exposure to moisture has been traced by the TSM acoustic wave mass sensor. This volatile species is most likely to be the freed 8-quinolinolatoline (8-Hq), a product of the reaction by Alq3 with water. As a result, the degradation mechanisms associated with morphological change of Alq 3 thin film by moisture are the crystallization of Alq3, the hydration of Alq3, and the reaction by Alq3 complex with moisture. Moreover, it has been visualized that the hydrated Alq 3 can be transformed into crystalline Alq3 structures and dark holes by the captioned reactions. Similarly, the ambient-induced morphological changes of ITO/CuPc, ITO/CuPc/NPB and ITO/CuPc/NPB/Alq3 structures have also been investigated. It is found that indium diffusion from the ITO substrate into organic layers possibly exists. After stored in an ambient atmosphere, crystallization of NPB thin films takes place. Photoluminescence (PL) investigation and local current map of the various degrading/degraded thin films suggest that the morphological changes, e.g., the formation of dark holes and Alq3 crystalline structures, essentially affect the PL and electrical characteristics. (Abstract shortened by UMI.)

Xu, Mingsheng

228

Studying the mechanism of CD47-SIRP? interactions on red blood cells by single molecule force spectroscopy  

NASA Astrophysics Data System (ADS)

The interaction forces and binding kinetics between SIRP? and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRP? and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level.The interaction forces and binding kinetics between SIRP? and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRP? and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level. Electronic supplementary information (ESI) available: Experimental section. See DOI: 10.1039/c4nr02889a

Pan, Yangang; Wang, Feng; Liu, Yanhou; Jiang, Junguang; Yang, Yong-Guang; Wang, Hongda

2014-08-01

229

Placing Single-Molecule T4 Lysozyme Enzymes on a Bacterial Cell Surface: Toward Probing Single-Molecule Enzymatic Reaction in Living Cells  

SciTech Connect

TheT4 lysozyme enzymatic hydrolyzation reaction of bacterial cell walls is an important biological process, and single-molecule enzymatic reaction dynamics had been studied under physiological condition using purified E. Coli cell walls as substrates. Here, we report progress toward characterizing the T4 lysozyme enzymatic reaction on a living bacterial cell wall using a combined single-molecule placement and spectroscopy. Placing a dye-labeled single T4 lysozyme molecule on a targeted cell wall by using a hydrodynamic micro-injection approach, we monitored single-molecule rotational motions during binding, attachment to, and dissociation from the cell wall by tracing single-molecule fluorescence intensity time trajectories and polarization. The single-molecule attachment duration of the T4 lysozyme to the cell wall during enzymatic reactions was typically shorter than photobleaching time under physiological conditions.

Hu, Dehong; Lu, H PETER.

2004-07-01

230

Modification and characterization of fluorescent conjugated polymer nanoparticles for single molecule detection  

NASA Astrophysics Data System (ADS)

Single molecule tracking using fluorescent dye or nanoparticle labels has emerged as a useful technique for probing biomolecular processes. Considerable interest arises in the development of nanoparticle labels with brighter fluorescence in order to improve the spatial and temporal resolution of single molecule detection and to facilitate the application of single molecule detection methods to a wider range of intracellular processes. The McNeill laboratory recently reported that conjugated polymer nanoparticles exhibit fluorescence cross-sections roughly 10--100 times higher than other luminescent nanoparticles of similar size, excellent photostability (2.2x108 photons emitted per nanoparticle prior to photobleaching), and saturated emission rates roughly 100 times higher than that of the molecular dyes and more than 1000 times higher than that of colloidal semiconductor quantum dots. One purpose of this graduate research is the development of highly fluorescent, bioconjugated nanoparticle labels based on conjugated polymers for demanding fluorescence applications such as single molecule tracking in live cells. Three surface modification methods (conjugated polymer nanoparticles encapsulated with lipid silica agents, conjugated polymer nanoparticles encapsulated with tetraethyl orthosilicate(TEOS) and hybrid nanoparticles with thiol pendant groups by the Stober Method (3-mercaptopropyl trimethoxysilane (MPS))) have been developed to protect the conjugated polymer, passivate the nanoparticle surface, and provide a chemical handle for bioconjugation such as nanoparticle encapsulation with alkoxysilanes and Stober method. After encapsulation, the fluorescence quantum yield of silica-encapsulated nanoparticles is improved by 20% as compared to bare conjugated polymer nanoparticles, while the photostability is improved by a factor of 2, indicating that some protection of the polymer is provided by the encapsulating layer. Another purpose of my research is the manipulation of the photophysics and photochemistry of conjugated polymer nanoparticles based on developing a more complete understanding of the various processes that control or limit nanoparticle brightness and photostability. The results indicate that a combination of photophysical processes including electron transfer to molecular oxygen, energy transfer, and exciton diffusion result in saturation and photobleaching phenomena that currently limit brightness. This study provides the potential methods and strategies aimed at manipulating such processes or limiting their effect on fluorescence brightness. Finally, efficient intra-particle energy transfer has been demonstrated in dye-doped CP nanoparticles, which provides a new strategy for improving nanoparticle fluorescence brightness and photostability, obtaining nanoparticles with red emission to avoid autofluorescence in mammalian tissue, and for designing novel sensitive biosensors based on energy transfer to sensor dyes.

Zheng, Yueli

231

Single Molecule Detection in Living Biological Cells using Carbon Nanotube Optical Probes  

NASA Astrophysics Data System (ADS)

Nanoscale sensing elements offer promise for single molecule analyte detection in physically or biologically constrained environments. Molecular adsorption can be amplified via modulation of sharp singularities in the electronic density of states that arise from 1D quantum confinement [1]. Single-walled carbon nanotubes (SWNT), as single molecule optical sensors [2-3], offer unique advantages such as photostable near-infrared (n-IR) emission for prolonged detection through biological media, single-molecule sensitivity and, nearly orthogonal optical modes for signal transduction that can be used to identify distinct classes of analytes. Selective binding to the SWNT surface is difficult to engineer [4]. In this lecture, we will briefly review the immerging field of fluorescent diagnostics using band gap emission from SWNT. In recent work, we demonstrate that even a single pair of SWNT provides at least four optical modes that can be modulated to uniquely fingerprint chemical agents by the degree to which they alter either the emission band intensity or wavelength. We validate this identification method in vitro by demonstrating detection and identification of six genotoxic analytes, including chemotherapeutic drugs and reactive oxygen species (ROS), which are spectroscopically differentiated into four distinct classes. We also demonstrate single-molecule sensitivity in detecting hydrogen peroxide, one of the most common genotoxins and an important cellular signal. Finally, we employ our sensing and fingerprinting method of these analytes in real time within live 3T3 cells, demonstrating the first multiplexed optical detection from a nanoscale biosensor and the first label-free tool to optically discriminate between genotoxins. We will also discuss our recent efforts to fabricate biomedical sensors for real time detection of glucose and other important physiologically relevant analytes in-vivo. The response of embedded SWNT in a swellable hydrogel construct to osmotic pressure gradients will be discussed, as well as its potential as a unique transduction mechanism for a new class of implantable sensors. [4pt] [1] Saito, R., Dresselhaus, G. & Dresselhaus, M. S. Physical Properties of Carbon Nanotubes (Imperial College Press, London, 1998). [0pt] [2] Barone, P. W., Baik, S., Heller, D. A. & Strano, M. S. Near-Infrared Optical Sensors Based on Single-Walled Carbon Nanotubes. Nature Materials 4, 86-92 (2005). [0pt] [3] Jeng, E. S., Moll, A. E., Roy, A. C., Gastala, J. B. & Strano, M. S. Detection of DNA hybridization using the near infrared band-gap fluorescence of single-walled carbon nanotubes. Nano Letters 6, 371-375 (2006). [0pt] [4] Heller, D. A. et al. Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes. Science 311, 508-511 (2006).

Strano, Michael

2009-03-01

232

An approach for an advanced anode interfacial layer with electron-blocking ability to achieve high-efficiency organic photovoltaics.  

PubMed

The interfacial properties of PEDOT:PSS, pristine r-GO, and r-GO with sulfonic acid (SR-GO) in organic photovoltaic are investigated to elucidate electron-blocking property of PEDOT:PSS anode interfacial layer (AIL), and to explore the possibility of r-GO as electron-blocking layers. The SR-GO results in an optimized power conversion efficiency of 7.54% for PTB7-th:PC71BM and 5.64% for P3HT:IC61BA systems. By combining analyses of capacitance-voltage and photovoltaic-parameters dependence on light intensity, it is found that recombination process at SR-GO/active film is minimized. In contrast, the devices using r-GO without sulfonic acid show trap-assisted recombination. The enhanced electron-blocking properties in PEDOT:PSS and SR-GO AILs can be attributed to surface dipoles at AIL/acceptor. Thus, for electron-blocking, the AIL/acceptor interface should be importantly considered in OPVs. Also, by simply introducing sulfonic acid unit on r-GO, excellent contact selectivity can be realized in OPVs. PMID:25343490

Yeo, Jun-Seok; Yun, Jin-Mun; Kang, Minji; Khim, Dongyoon; Lee, Seung-Hoon; Kim, Seok-Soon; Na, Seok-In; Kim, Dong-Yu

2014-11-26

233

Single Molecule Screening of Disease DNA Without Amplification  

SciTech Connect

The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA was probed with fluorescently-labeled probe molecules and imaged. When only the probes were stained and hybridized in a vial, it had 6 orders of magnitude dynamic range with a detection limit of {approx}0.7 copy/cell. A second dye was added to lower the false positive levels. Although there was a sacrifice of two orders of magnitude in detection limit, the number of false positives was reduced to zero. HPV-16 DNA was also hybridized and detected on surface-tethered probes. When the entire human genomic DNA and HPV was labeled and hybridized, the detection limit was similar to that of one-color assay detected in capillary. However, non-specific adsorption was high, and the dynamic range was narrow because of saturation of the surface and electrostatic repulsion between hybridized targets on the surface. The second probe was introduced to lower non-specific adsorption, and the strategy succeeded in 4 orders of magnitude linear dynamic range in a log-log plot, along with 2.4 copies/cell detection limit. DNA extracts of cell lines that contained a known copy number of HPV-16 DNA were tested with the four strategies described above. The calculated numbers from observed molecule counts matched the known values. Results from the Pap test sample with added HPV DNA were similar to those of purified DNA, suggesting our method is compatible with the conventional Pap test sample collection method. Further optimization will be needed before this single molecule level detection and identification can actually be used in a real clinical lab, but it has good potential and applicability. Improvement such as automated imaging and scanning, more accurate data processing software as well as sensitive camera, should help increase the efficiency and throughput.

Ji-Young Lee

2006-12-12

234

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport  

PubMed Central

The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics. PMID:22850865

Muren, Natalie B.; Olmon, Eric D.; Barton, Jacqueline K.

2012-01-01

235

Compact quantum dots for single-molecule imaging.  

PubMed

Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology (1-4). To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study. Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation (5). Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large (4,6,7). Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past (8,9). The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an insulating CdyZn1-yS shell, further coated with a multidentate polymer ligand modified with short polyethylene glycol (PEG) chains (Figure 1). Compared with conventional CdSe nanocrystals, HgxCd1-xSe alloys offer greater quantum yields of fluorescence, fluorescence at red and near-infrared wavelengths for enhanced signal-to-noise in cells, and excitation at non-cytotoxic visible wavelengths. Multidentate polymer coatings bind to the nanocrystal surface in a closed and flat conformation to minimize hydrodynamic size, and PEG neutralizes the surface charge to minimize nonspecific binding to cells and biomolecules. The end result is a brightly fluorescent nanocrystal with emission between 550-800 nm and a total hydrodynamic size near 12 nm. This is in the same size range as many soluble globular proteins in cells, and substantially smaller than conventional PEGylated QDs (25-35 nm). PMID:23093375

Smith, Andrew M; Nie, Shuming

2012-01-01

236

Single-molecule photochemical reactions of Auger-ionized quantum dots  

PubMed Central

Photoinduced electron transfer in donor-acceptor systems composed of quantum dots (QDs) and electron donors or acceptors is a subject of considerable recent research interest due to the potential applications of such systems in both solar energy harvesting and degradation of organic pollutants. Herein, we employed single-molecule imaging and spectroscopy techniques for the detection of photochemical reactions between 1,4-diaminobutane (DAB) and CdSe/ZnS single QDs. We investigated the reactions by analyzing photoluminescence (PL) intensity and lifetime of QDs at ensemble and single-molecule levels. While DAB was applied to single QDs tethered on a cover slip or QDs dispersed in a solution, PL intensity of QD continuously decreased with a concomitant increase in the PL lifetime. Interestingly, these changes in the PL properties of QD were predominant under high-intensity photoactivation. We hypothesize that the above changes in the PL properties surface due to the transfer of an electron from DAB to Auger-ionized QD followed by elimination of a proton from DAB and the formation of a QD-DAB adduct. Thus, a continuous decrease in the PL intensity of QDs under high-intensity photoactivation is attributed to continuous photochemical reactions of DAB with single QDs and the formation of QD-(DAB)n adducts. We believe that detection and analysis of such photochemical reactions of single QDs with amines will be of considerable broad interest due to the significant impact of photoinduced electron transfer reactions in energy management and environmental remediation. PMID:22132300

Hamada, Morihiko; Shibu, Edakkattuparambil Sidharth; Itoh, Tamitake; Kiran, Manikantan Syamala; Nakanishi, Shunsuke; Ishikawa, Mitsuru; Biju, Vasudevanpillai

2011-01-01

237

Controlled interfacial electron dynamics in highly efficient Zn2 SnO4 -based dye-sensitized solar cells.  

PubMed

Among ternary oxides, Zn2 SnO4 (ZSO) is considered for dye-sensitized solar cells (DSSCs) because of its wide bandgap, high optical transmittance, and high electrical conductivity. However, ZSO-based DSSCs have a poor performance record owing largely to the absence of systematic efforts to enhance their performance. Herein, general strategies are proposed to improve the performance of ZSO-based DSSCs involving interfacial engineering/modification of the photoanode. A conformal ZSO thin film (blocking layer) deposited at the fluorine-doped tin oxide-electrolyte interface by pulsed laser deposition suppressed the back-electron transfer effectively while maintaining a high optical transmittance, which resulted in a 22 % improvement in the short-circuit photocurrent density. Surface modification of ZSO nanoparticles (NPs) resulted in an ultrathin ZnO shell layer, a 9 % improvement in the open-circuit voltage, and a 4 % improvement in the fill factor because of the reduced electron recombination at the ZSO NPs-electrolyte interface. The ZSO-based DSSCs exhibited a faster charge injection and electron transport than their TiO2 -based counterparts, and their superior properties were not inhibited by the ZnO shell layer, which indicates their feasibility for highly efficient DSSCs. Each interfacial engineering strategy could be applied to the ZSO-based DSSC independently to lead to an improved conversion efficiency of 6 %, a very high conversion efficiency for a non-TiO2 based DSSC. PMID:24347268

Shin, Seong Sik; Kim, Dong Wook; Hwang, Daesub; Suk, Jae Ho; Oh, Lee Seul; Han, Byung Suh; Kim, Dong Hoe; Kim, Ju Seong; Kim, Dongho; Kim, Jin Young; Hong, Kug Sun

2014-02-01

238

Single-Molecule Fluorescence Spectroscopy using Phospholipid Bilayer Nanodiscs  

PubMed Central

Nanodiscs are a new class of model membranes that are being used to solubilize and study a range of integral membrane proteins and membrane-associated proteins. Unlike other model membranes, the Nanodisc bilayer is bounded by a scaffold protein coat that confers enhanced stability and a narrow particle size distribution. The bilayer diameter can be precisely controlled by changing the diameter of the protein coat. All these properties make Nanodiscs excellent model membranes for single molecule fluorescence applications. In this chapter, we describe our work using Nanodiscs to apply total internal reflection fluorescence microscopy (TIRFM), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) to study the integral membrane protein cytochrome P450 3A4 and the membrane-binding proteins islet amyloid popypeptide (IAPP) and ?-synuclein, respectively. The monodisperse size distribution of Nanodiscs enhances control over the oligomeric state of the membrane protein of interest, and also facilitates accurate solution-based measurements. Nanodiscs also comprise an excellent system to stably immobilize integral membrane proteins in a bilayer without covalent modification, enabling a range of surface-based experiments where accurate localization of the protein of interest is required. PMID:20580961

Nath, Abhinav; Trexler, Adam J.; Koo, Peter; Miranker, Andrew D.; Atkins, William M.; Rhoades, Elizabeth

2012-01-01

239

A single molecule study of cellulase hydrolysis of crystalline cellulose  

NASA Astrophysics Data System (ADS)

Cellobiohydrolase-I (CBH I), a processive exoglucanase secreted by Trichoderma reesei, is one of the key enzyme components in a commercial cellulase mixture currently used for processing biomass to biofuels. CBH I contains a family 7 glycoside hydrolase catalytic module, a family 1 carbohydrate-binding module (CBM), and a highlyglycosylated linker peptide. It has been proposed that the CBH I cellulase initiates the hydrolysis from the reducing end of one cellulose chain and successively cleaves alternate ?-1,4-glycosidic bonds to release cellobiose as its principal end product. The role each module of CBH I plays in the processive hydrolysis of crystalline cellulose has yet to be convincingly elucidated. In this report, we use a single-molecule approach that combines optical (Total Internal Reflection Fluorescence microscopy, or TIRF-M) and non-optical (Atomic Force Microscopy, or AFM) imaging techniques to analyze the molecular motion of CBM tagged with green fluorescence protein (GFP), and to investigate the surface structure of crystalline cellulose and changes made in the structure by CBM and CBH I. The preliminary results have revealed a confined nanometer-scale movement of the TrCBM1-GFP bound to cellulose, and decreases in cellulose crystal size as well as increases in surface roughness during CBH I hydrolysis of crystalline cellulose.

Liu, Yu-San; Luo, Yonghua; Baker, John O.; Zeng, Yining; Himmel, Michael E.; Smith, Steve; Ding, Shi-You

2010-02-01

240

Optical Microcavity: Sensing down to Single Molecules and Atoms  

PubMed Central

This review article discusses fundamentals of dielectric, low-loss, optical micro-resonator sensing, including figures of merit and a variety of microcavity designs, and future perspectives in microcavity-based optical sensing. Resonance frequency and quality (Q) factor are altered as a means of detecting a small system perturbation, resulting in realization of optical sensing of a small amount of sample materials, down to even single molecules. Sensitivity, Q factor, minimum detectable index change, noises (in sensor system components and microcavity system including environments), microcavity size, and mode volume are essential parameters to be considered for optical sensing applications. Whispering gallery mode, photonic crystal, and slot-type microcavities typically provide compact, high-quality optical resonance modes for optical sensing applications. Surface Bloch modes induced on photonic crystals are shown to be a promising candidate thanks to large field overlap with a sample and ultra-high-Q resonances. Quantum optics effects based on microcavity quantum electrodynamics (QED) would provide novel single-photo-level detection of even single atoms and molecules via detection of doublet vacuum Rabi splitting peaks in strong coupling. PMID:22319393

Yoshie, Tomoyuki; Tang, Lingling; Su, Shu-Yu

2011-01-01

241

Interpretation of stochastic events in single molecule conductance measurements.  

PubMed

The electrical conductance of a series of thiol-terminated alkanes, (1,6-hexanedithiol (HDT), 1,8-octanedithiol (ODT), and 1,10-decanedithol (DDT)) was measured using a modified scanning tunneling microscope break junction technique. The interpretation of data obtained in this technique is complicated due to multiple effects such as microscopic details of the metal-molecule junctions, superposition of tunneling currents, and conformational changes in the molecules. A new method called the last-step analysis (LSA) is introduced here to clarify the contribution of these effects. In direct contrast to previous work, LSA does not require any data preselection, making the results less subjective and more reproducible. Finally, LSA was used to obtain the conductance of single molecules (HDT, (3.6 x 10(-4))G(o); ODT, (4.4 x 10(-5))G(o); DDT, (5.7 x 10(-6))G(o)). The tunneling decay parameter (beta) was calculated, and it was found to be approximately 1.0 per carbon atom. PMID:17034112

Jang, Sung-Yeon; Reddy, Pramod; Majumdar, Arun; Segalman, Rachel A

2006-10-01

242

High-Resolution Optical Tweezers for Single-Molecule Manipulation  

PubMed Central

Forces hold everything together and determine its structure and dynamics. In particular, tiny forces of 1-100 piconewtons govern the structures and dynamics of biomacromolecules. These forces enable folding, assembly, conformational fluctuations, or directional movements of biomacromolecules over sub-nanometer to micron distances. Optical tweezers have become a revolutionary tool to probe the forces, structures, and dynamics associated with biomacromolecules at a single-molecule level with unprecedented resolution. In this review, we introduce the basic principles of optical tweezers and their latest applications in studies of protein folding and molecular motors. We describe the folding dynamics of two strong coiled coil proteins, the GCN4-derived protein pIL and the SNARE complex. Both complexes show multiple folding intermediates and pathways. ATP-dependent chromatin remodeling complexes translocate DNA to remodel chromatin structures. The detailed DNA translocation properties of such molecular motors have recently been characterized by optical tweezers, which are reviewed here. Finally, several future developments and applications of optical tweezers are discussed. These past and future applications demonstrate the unique advantages of high-resolution optical tweezers in quantitatively characterizing complex multi-scale dynamics of biomacromolecules. PMID:24058311

Zhang, Xinming; Ma, Lu; Zhang, Yongli

2013-01-01

243

Single-Molecule Localization Microscopy using mCherry.  

PubMed

We demonstrate the potential of the commonly used red fluorescent protein mCherry for single-molecule super-resolution imaging. mCherry can be driven into a light-induced dark state in the presence of a thiol from which it can recover spontaneously or by irradiation with near UV light. We show imaging of subcellular protein structures such as microtubules and the nuclear pore complex with a resolution below 40 nm. We were able to image the C-terminus of the nuclear pore protein POM121, which is on the inside of the pore and not readily accessible for external labeling. The photon yield for mCherry is comparable to that of the latest optical highlighter fluorescent proteins. Our findings show that the widely used mCherry red fluorescent protein and the vast number of existing mCherry fusion proteins are readily amenable to super-resolution imaging. This obviates the need for generating novel protein fusions that may compromise function or the need for external fluorescent labeling. PMID:25111075

Winterflood, Christian M; Ewers, Helge

2014-11-10

244

Classification of dynamical diffusion states in single molecule tracking microscopy.  

PubMed

Single molecule tracking of membrane proteins by fluorescence microscopy is a promising method to investigate dynamic processes in live cells. Translating the trajectories of proteins to biological implications, such as protein interactions, requires the classification of protein motion within the trajectories. Spatial information of protein motion may reveal where the protein interacts with cellular structures, because binding of proteins to such structures often alters their diffusion speed. For dynamic diffusion systems, we provide an analytical framework to determine in which diffusion state a molecule is residing during the course of its trajectory. We compare different methods for the quantification of motion to utilize this framework for the classification of two diffusion states (two populations with different diffusion speed). We found that a gyration quantification method and a Bayesian statistics-based method are the most accurate in diffusion-state classification for realistic experimentally obtained datasets, of which the gyration method is much less computationally demanding. After classification of the diffusion, the lifetime of the states can be determined, and images of the diffusion states can be reconstructed at high resolution. Simulations validate these applications. We apply the classification and its applications to experimental data to demonstrate the potential of this approach to obtain further insights into the dynamics of cell membrane proteins. PMID:25099798

Bosch, Peter J; Kanger, Johannes S; Subramaniam, Vinod

2014-08-01

245

Mechanical Properties of ?-Catenin Revealed by Single-Molecule Experiments  

PubMed Central

?-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of ?-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the ?-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous ?-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region. PMID:23083718

Valbuena, Alejandro; Vera, Andres Manuel; Oroz, Javier; Menendez, Margarita; Carrion-Vazquez, Mariano

2012-01-01

246

Single Molecule Analysis of Serotonin Transporter Regulation Using Quantum Dots  

NASA Astrophysics Data System (ADS)

For the first time, we implement a novel, single molecule approach to define the localization and mobility of the brain's major target of widely prescribed antidepressant medications, the serotonin transporter (SERT). SERT labeled with single quantum dot (Qdot) revealed unsuspected features of transporter mobility with cholesterol-enriched membrane microdomains (often referred to as "lipid rafts") and cytoskeleton network linked to transporter activation. We document two pools of surface SERT proteins defined by their lateral mobility, one that exhibits relatively free diffusion in the plasma membrane and a second that displays significantly restricted mobility and localizes to cholesterol-enriched microdomains. Diffusion model prediction and instantaneous velocity analysis indicated that stimuli that act through p38 MAPK-dependent signaling pathways to activate SERT trigger rapid SERT movements within membrane microdomains. Cytoskeleton disruption showed that SERT lateral mobility behaves a membrane raft-constrained, cytoskeleton-associated manner. Our results identify an unsuspected aspect of neurotransmitter transporter regulation that we propose reflects the dissociation of inhibitory, SERT-associated cytoskeletal anchors.

Chang, Jerry; Tomlinson, Ian; Warnement, Michael; Ustione, Alessandro; Carneiro, Ana; Piston, David; Blakely, Randy; Rosenthal, Sandra

2011-03-01

247

DNA y structure: a versatile, multidimensional single molecule assay.  

PubMed

Optical trapping is a powerful single molecule technique used to study dynamic biomolecular events, especially those involving DNA and DNA-binding proteins. Current implementations usually involve only one of stretching, unzipping, or twisting DNA along one dimension. To expand the capabilities of optical trapping for more complex measurements would require a multidimensional technique that combines all of these manipulations in a single experiment. Here, we report the development and utilization of such a novel optical trapping assay based on a three-branch DNA construct, termed a "Y structure". This multidimensional assay allows precise, real-time tracking of multiple configurational changes. When the Y structure template is unzipped under both force and torque, the force and extension of all three branches can be determined simultaneously. Moreover, the assay is readily compatible with fluorescence, as demonstrated by unzipping through a fluorescently labeled, paused transcription complex. This novel assay thus allows for the visualization and precision mapping of complex interactions of biomechanical events. PMID:25291441

Inman, James T; Smith, Benjamin Y; Hall, Michael A; Forties, Robert A; Jin, Jing; Sethna, James P; Wang, Michelle D

2014-11-12

248

Quantum interference in off-resonant transport through single molecules  

NASA Astrophysics Data System (ADS)

We provide a simple set of rules for predicting interference effects in off-resonant transport through single molecule junctions. These effects fall into two classes, showing, respectively, an odd or an even number of nodes in the linear conductance within a given molecular charge state, and we demonstrate how to decide the interference class directly from the contacting geometry. For neutral alternant hydrocarbons, we employ the Coulson-Rushbrooke-McLachlan pairing theorem to show that the interference class is decided simply by tunneling on and off the molecule from same or different sublattices. More generally, we investigate a range of smaller molecules by means of exact diagonalization combined with a perturbative treatment of the molecule-lead tunnel coupling. While these results generally agree well with GW calculations, they are shown to be at odds with simpler mean-field treatments. For molecules with spin-degenerate ground states, we show that for most junctions interference causes no transmission nodes, but we argue that it may lead to a nonstandard gate dependence of the zero-bias Kondo resonance.

Pedersen, Kim G. L.; Strange, Mikkel; Leijnse, Martin; Hedegârd, Per; Solomon, Gemma C.; Paaske, Jens

2014-09-01

249

Dependence of the direct electron transfer activity and adsorption kinetics of cytochrome c on interfacial charge properties.  

PubMed

With the advantages of in situ analysis and high surface sensitivity, surface-enhanced infrared absorption spectroscopy in attenuated total reflection mode (ATR-SEIRAS) combined with electrochemical methods has been employed to examine the interfacial direct electron transfer activity and adsorption kinetics of cytochrome c (cyt c). This work presents data on cyt c adsorption onto negatively charged mercaptohexanoic acid (MHA) and positively charged 6-amino-1-hexanethiol (MHN) self-assembled monolayers (SAMs) on gold nanofilm surfaces. The adsorbed cyt c displays a higher apparent electron transfer rate constant (33.5 ± 2.4 s(-1)) and apparent binding rate constant (73.1 ± 5.2 M(-1) s(-1)) at the MHA SAMs surface than those on the MHN SAMs surface. The results demonstrate that the surface charge density determines the protein adsorption kinetics, while the surface charge character determines the conformation and orientation of proteins assembled which in turn affects the direct electron transfer activity. PMID:23912152

Wang, Gui-Xia; Wang, Min; Wu, Zeng-Qiang; Bao, Wen-Jing; Zhou, Yue; Xia, Xing-Hua

2013-10-01

250

Interfacial electron and phonon scattering processes in high-powered nanoscale applications.  

SciTech Connect

The overarching goal of this Truman LDRD project was to explore mechanisms of thermal transport at interfaces of nanomaterials, specifically linking the thermal conductivity and thermal boundary conductance to the structures and geometries of interfaces and boundaries. Deposition, fabrication, and post possessing procedures of nanocomposites and devices can give rise to interatomic mixing around interfaces of materials leading to stresses and imperfections that could affect heat transfer. An understanding of the physics of energy carrier scattering processes and their response to interfacial disorder will elucidate the potentials of applying these novel materials to next-generation high powered nanodevices and energy conversion applications. An additional goal of this project was to use the knowledge gained from linking interfacial structure to thermal transport in order to develop avenues to control, or 'tune' the thermal transport in nanosystems.

Hopkins, Patrick E.

2011-10-01

251

Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images  

NASA Astrophysics Data System (ADS)

We developed a Bayesian method to extract macromolecular structure information from sparse single-molecule x-ray free-electron laser diffraction images. The method addresses two possible scenarios. First, using a "seed" structural model, the molecular orientation is determined for each of the provided diffraction images, which are then averaged in three-dimensional reciprocal space. Subsequently, the real space electron density is determined using a relaxed averaged alternating reflections algorithm. In the second approach, the probability that the "seed" model fits to the given set of diffraction images as a whole is determined and used to distinguish between proposed structures. We show that for a given x-ray intensity, unexpectedly, the achievable resolution increases with molecular mass such that structure determination should be more challenging for small molecules than for larger ones. For a sufficiently large number of recorded photons (>200) per diffraction image an M1/6 scaling is seen. Using synthetic diffraction data for a small glutathione molecule as a challenging test case, successful determination of electron density was demonstrated for 20000 diffraction patterns with random orientations and an average of 82 elastically scattered and recorded photons per image, also in the presence of up to 50% background noise. The second scenario is exemplified and assessed for three biomolecules of different sizes. In all cases, determining the probability of a structure given set of diffraction patterns allowed successful discrimination between different conformations of the test molecules. A structure model of the glutathione tripeptide was refined in a Monte Carlo simulation from a random starting conformation. Further, effective distinguishing between three differently arranged immunoglobulin domains of a titin molecule and also different states of a ribosome in a tRNA translocation process was demonstrated. These results show that the proposed method is robust and enables structure determination from sparse and noisy x-ray diffraction images of single molecules spanning a wide range of molecular masses.

Walczak, Micha?; Grubmüller, Helmut

2014-08-01

252

Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images.  

PubMed

We developed a Bayesian method to extract macromolecular structure information from sparse single-molecule x-ray free-electron laser diffraction images. The method addresses two possible scenarios. First, using a "seed" structural model, the molecular orientation is determined for each of the provided diffraction images, which are then averaged in three-dimensional reciprocal space. Subsequently, the real space electron density is determined using a relaxed averaged alternating reflections algorithm. In the second approach, the probability that the "seed" model fits to the given set of diffraction images as a whole is determined and used to distinguish between proposed structures. We show that for a given x-ray intensity, unexpectedly, the achievable resolution increases with molecular mass such that structure determination should be more challenging for small molecules than for larger ones. For a sufficiently large number of recorded photons (>200) per diffraction image an M^{1/6} scaling is seen. Using synthetic diffraction data for a small glutathione molecule as a challenging test case, successful determination of electron density was demonstrated for 20000 diffraction patterns with random orientations and an average of 82 elastically scattered and recorded photons per image, also in the presence of up to 50% background noise. The second scenario is exemplified and assessed for three biomolecules of different sizes. In all cases, determining the probability of a structure given set of diffraction patterns allowed successful discrimination between different conformations of the test molecules. A structure model of the glutathione tripeptide was refined in a Monte Carlo simulation from a random starting conformation. Further, effective distinguishing between three differently arranged immunoglobulin domains of a titin molecule and also different states of a ribosome in a tRNA translocation process was demonstrated. These results show that the proposed method is robust and enables structure determination from sparse and noisy x-ray diffraction images of single molecules spanning a wide range of molecular masses. PMID:25215765

Walczak, Micha?; Grubmüller, Helmut

2014-08-01

253

Single molecule fluorescence probes dynamics of barrier crossing  

PubMed Central

Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium1,2. At the viscosity of water, the kinetics of unimolecular reactions are described by diffusion of a Brownian particle over a free-energy barrier separating reactants and products. For reactions in solution this famous theory extended Eyring's transition state theory, and is widely applied in physics, chemistry, and biology, including reactions as complex as protein folding3,4. Because the diffusion coefficient of Kramers theory is determined by the dynamics in the sparsely-populated region of the barrier top, its properties have not been directly measured for any molecular system. Here we show that the Kramers diffusion coefficient and free energy barrier can be characterized by measuring the temperature- and viscosity-dependence of the transition path time for protein folding. The transition path is the small fraction of an equilibrium trajectory for a single molecule when the free-energy barrier separating two states is actually crossed (Fig. 1a). Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions5. Our finding of a long transition path time with an unusually small solvent viscosity-dependence suggests that internal friction as well as solvent friction determine the Kramers diffusion coefficient for ?-helical proteins, as opposed to a breakdown of his theory that occurs for many small-molecule reactions2. It is noteworthy that the new and fundamental information concerning Kramers theory and the dynamics of barrier crossings obtained here come from experiments on a protein rather than a much simpler chemical or physical system. PMID:24153185

Chung, Hoi Sung; Eaton, William A.

2013-01-01

254

A CMOS enhanced solid-state nanopore based single molecule detection platform.  

PubMed

Solid-state nanopores have emerged as a single molecule label-free electronic detection platform. Existing transimpedance stages used to measure ionic current nanopores suffer from dynamic range limitations resulting from steady-state baseline currents. We propose a digitally-assisted baseline cancellation CMOS platform that circumvents this issue. Since baseline cancellation is a form of auto-zeroing, the 1/f noise of the system is also reduced. Our proposed design can tolerate a steady state baseline current of 10µA and has a usable bandwidth of 750kHz. Quantitative DNA translocation experiments on 5kbp DNA was performed using a 5nm silicon nitride pore using both the CMOS platform and a commercial system. Comparison of event-count histograms show that the CMOS platform clearly outperforms the commercial system, allowing for unambiguous interpretation of the data. PMID:24109650

Chen, Chinhsuan; Yemenicioglu, Sukru; Uddin, Ashfaque; Corgliano, Ellie; Theogarajan, Luke

2013-01-01

255

Single-molecule surface-enhanced Raman spectroscopy with nanowatt excitation.  

PubMed

We demonstrate the possibility of single molecule (SM) detection via surface-enhanced Raman spectroscopy (SERS) in two seemingly challenging and unexpected cases: first with ultra-low excitation powers of the order of nanowatts and second in as-synthesized and not deliberately-aggregated silver colloid solution. The experiments are carried out using the bi-analyte method on a methylated form of Rhodamine 6G and one of its isotopologues excited at 514 nm close to the electronic resonance. This study spectacularly highlights the fact that SM-SERS detection is much more common and easier to achieve than typically thought, in particular in the case of resonance Raman excitation. As a result, SM-SERS detection in such cases should not be viewed as an indication of good SERS substrate performance as sometimes implicitly assumed. PMID:25277821

Darby, Brendan L; Etchegoin, Pablo G; Le Ru, Eric C

2014-11-21

256

Debye screening in single-molecule carbon nanotube field-effect sensors.  

PubMed

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough gate potentials, the target DNA is completely repelled and RTN is suppressed. PMID:21806018

Sorgenfrei, Sebastian; Chiu, Chien-Yang; Johnston, Matthew; Nuckolls, Colin; Shepard, Kenneth L

2011-09-14

257

Photophysical Properties of Acene DCDHF Fluorophores: Long-Wavelength Single-Molecule Emitters Designed for Cellular Imaging  

PubMed Central

We report the solvatochromic, viscosity-sensitive, and single-molecule photophysics of the fluorophores DCDHF-N-6 and DCDHF-A-6. These molecules are members of the dicyanomethylenedihydrofuran (DCDHF) class of single-molecule emitters that contain an amine electron donor and a DCDHF acceptor linked by a conjugated unit; DCDHF-N-6 and DCDHF-A-6 have naphthalene- and anthracene-conjugated linkers, respectively. These molecules maintain the beneficial photophysics of the phenylene-linked DCDHF (i.e., photostability, emission wavelength dependence on solvent polarity, and quantum yield sensitivity to solvent viscosity), yet offer absorption and emission at longer wavelengths that are more appropriate for cellular imaging. We demonstrate that these new fluorophores are less photolabile in an aqueous environment than several other commonly used dyes (rhodamine 6G, Texas Red, and fluorescein). Finally, we image single copies of the acene DCDHFs diffusing in the plasma membrane of living cells. PMID:17718454

Lord, Samuel J.; Lu, Zhikuan; Wang, Hui; Willets, Katherine A.; Schuck, P. James; Lee, Hsiao-lu D.; Nishimura, Stefanie Y.; Twieg, Robert J.; Moerner, W. E.

2009-01-01

258

Ultrafast interfacial electron transfer in dye-sensitized ZnO nanocrystalline films: comparison with other metal oxides (Invited Paper)  

NASA Astrophysics Data System (ADS)

Dye sensitized nanocrystalline semiconductor films are used as a photoactive part in dye-sensitized solar cells, which are recently attracting much interest both in basic and applied studies. Electron transfer reaction from a photoexcited dye molecule, which is chemically adsorbed on the surface of semiconductor, into the semiconductor conduction band is the primary step to generate photocurrent. Ultrafast pump-probe spectroscopy with a <100 fs time resolution and in a visible-to-IR wavelength range was used to elucidate the interfacial electron transfer mechanism in dye-sensitized nanocrystalline metal oxide films of ZnO, TiO2, and others. We found two types of reaction paths; one is direct electron transfer from the excited molecule to the conduction band and the other is stepwise transfer through an intermediate, which was assigned to a charge transfer complex formed by the excited molecule and a surface state on the semiconductor. The order of the observed electron transfer rates for different semiconductors was qualitatively explained by the idea of the density of electron acceptor states; that is, the larger the density of states near the energy level of the excited molecules was, the faster the electron transfer took place.

Furube, Akihiro; Katoh, Ryuzi; Hara, Kohjiro; Tachiya, Masanori

2005-04-01

259

Single Molecule Study of DNA Organization and Recombination  

NASA Astrophysics Data System (ADS)

We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force, which depends on salt concentration. We also report experiments with the recombinase Hin mutant H107Y. The synapse formation is demonstrated with single DNA containing two hix sites. We further show preliminary data for cleavage and subunit rotation from a braiding assay. These direct observations elucidate the recombination mechanism.

Xiao, Botao

260

Single-molecule studies of DNA dynamics and intermolecular forces  

NASA Astrophysics Data System (ADS)

DNA molecules were used as a model system to investigate fundamental problems in polymer physics; namely, how molecular length, topology and concentration influence the dynamical properties of polymers. A set of DNA molecules suitable for polymer studies was prepared using molecular biology techniques. Video fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules. Optical tweezers were used to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with molecular length was in agreement with the Zimm model for dilute solutions of linear and circular DNA, indicating that excluded volume effects are appreciable for both topologies. Scaling of diffusion with concentration was also determined for the four possible topological combinations of linear and circular molecules: linear DNA diffusing in a solution of linear DNA, linear DNA in circular DNA, circular in circular, and circular in linear. For lower concentrations molecular topology had little effect and scaling was in agreement with that of the Rouse model. As concentration was increased topology played a much larger role and scaling crossed over to that of the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion observed for a circular molecule diffusing in an entangled linear solution, suggesting the importance of constraint release. Using a new experimental approach with optical tweezers, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius of the entangled solution was also determined, close to the classically predicted value. The dependence of the above findings on molecular topology and concentration was also investigated. In particular, for an entangled solution of circular DNA of the same length and concentration, the confining tube radius was 25% smaller and the longest relaxation time was ˜3 times shorter than with linear DNA. For large displacements the confining force for circular DNA was also substantially lower and shorter range than that measured with linear DNA.

Robertson, Rae Marie

261

Theory of vibrational absorption sidebands in the Coulomb-blockade regime of single-molecule transistors  

E-print Network

-molecule transistors Matthias C. Lüffe,1 Jens Koch,2 and Felix von Oppen1 1Institut für Theoretische Physik, Freie-driven vibrational nonequilibrium induces vibrational sidebands in single-molecule transistors which arise from.125306 PACS number s : 73.23.Hk, 73.63. b, 85.65. h I. INTRODUCTION Single-molecule junctions and transistors

von Oppen, Felix

262

On detailed balance and reversibility of semi-Markov processes and single-molecule enzyme kinetics  

E-print Network

On detailed balance and reversibility of semi-Markov processes and single- molecule enzyme kinetics://jmp.aip.org/about/rights_and_permissions #12;On detailed balance and reversibility of semi-Markov processes and single-molecule enzyme kinetics-Markov processes have found increasing applications in modeling the kinet- ics of single enzyme molecules. Detailed

Miekisz, Jacek

263

Entropy and Heat Capacity of DNA Melting from Temperature Dependence of Single Molecule Stretching  

Microsoft Academic Search

When a single molecule of double-stranded DNA is stretched beyond its B-form contour length, the measured force shows a highly cooperative overstretching transition. We have measured the force at which this transition occurs as a function of temperature. To do this, single molecules of DNA were captured between two polystyrene beads in an optical tweezers apparatus. As the temperature of

Mark C. Williams; Jay R. Wenner; Ioulia Rouzina; Victor A. Bloomfield

2001-01-01

264

Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments  

E-print Network

Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments process. We use simulations and single-molecule force spectroscopy to map the complex energy landscape experiments. By using the combined approach, we show that forced unfolding of GFP involves a bifurcation

Dietz, Hendrik

265

Image Analysis of Defocused Single-Molecule Images for Three-Dimensional Molecule Orientation Studies  

E-print Network

Image Analysis of Defocused Single-Molecule Images for Three-Dimensional Molecule Orientation-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three- dimensional molecule orientations in defocused single-molecule images

Enderlein, Jörg

266

Single-molecule chemical reactions: Reexamination of the Kramers approach G. Margolin1  

E-print Network

on chemical conformational changes, and simple chemical processes in condensed phase environments, for exampleSingle-molecule chemical reactions: Reexamination of the Kramers approach G. Margolin1 and E; published 2 August 2005 Single-molecule chemical reactions yield insight into fluctuation phenomena

Barkai, Eli

267

In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair.  

PubMed

In vivo single-molecule experiments offer new perspectives on the behaviour of DNA binding proteins, from the molecular level to the length scale of whole bacterial cells. With technological advances in instrumentation and data analysis, fluorescence microscopy can detect single molecules in live cells, opening the doors to directly follow individual proteins binding to DNA in real time. In this review, we describe key technical considerations for implementing in vivo single-molecule fluorescence microscopy. We discuss how single-molecule tracking and quantitative super-resolution microscopy can be adapted to extract DNA binding kinetics, spatial distributions, and copy numbers of proteins, as well as stoichiometries of protein complexes. We highlight experiments which have exploited these techniques to answer important questions in the field of bacterial gene regulation and transcription, as well as chromosome replication, organisation and repair. Together, these studies demonstrate how single-molecule imaging is transforming our understanding of DNA-binding proteins in cells. PMID:24859634

Stracy, Mathew; Uphoff, Stephan; Garza de Leon, Federico; Kapanidis, Achillefs N

2014-10-01

268

Integration of biological ion channels onto optically addressable micro-fluidic electrode arrays for single molecule characterization.  

SciTech Connect

The challenge of modeling the organization and function of biological membranes on a solid support has received considerable attention in recent years, primarily driven by potential applications in biosensor design. Affinity-based biosensors show great promise for extremely sensitive detection of BW agents and toxins. Receptor molecules have been successfully incorporated into phospholipid bilayers supported on sensing platforms. However, a collective body of data detailing a mechanistic understanding of membrane processes involved in receptor-substrate interactions and the competition between localized perturbations and delocalized responses resulting in reorganization of transmembrane protein structure, has yet to be produced. This report describes a systematic procedure to develop detailed correlation between (recognition-induced) protein restructuring and function of a ligand gated ion channel by combining single molecule fluorescence spectroscopy and single channel current recordings. This document is divided into three sections: (1) reported are the thermodynamics and diffusion properties of gramicidin using single molecule fluorescence imaging and (2) preliminary work on the 5HT{sub 3} serotonin receptor. Thirdly, we describe the design and fabrication of a miniaturized platform using the concepts of these two technologies (spectroscopic and single channel electrochemical techniques) for single molecule analysis, with a longer term goal of using the physical and electronic changes caused by a specific molecular recognition event as a transduction pathway in affinity based biosensors for biotoxin detection.

Brozik, Susan Marie; Frink, Laura J. Douglas; Bachand, George David; Keller, David J. (University of New Mexico, Albuquerque, NM); Patrick, Elizabeth L.; Marshall, Jason A. (University of New Mexico, Albuquerque, NM); Ortiz, Theodore P. (University of New Mexico, Albuquerque, NM); Meyer, Lauren A. (University of New Mexico, Albuquerque, NM); Davis, Ryan W. (University of New Mexico, Albuquerque, NM); Brozik, James A. (University of New Mexico, Albuquerque, NM); Flemming, Jeb Hunter

2004-12-01

269

Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface  

NASA Astrophysics Data System (ADS)

Evaluating the built-in functionality of nanomaterials under practical conditions is central for their proposed integration as active components in next-generation electronics. Low-dimensional materials from single atoms to molecules have been consistently resolved and manipulated under ultrahigh vacuum at low temperatures. At room temperature, atomic-scale imaging has also been performed by probing materials at the solid/liquid interface. We exploit this electrical interface to develop a robust electronic decoupling platform that provides precise information on molecular energy levels recorded using in situ scanning tunnelling microscopy/spectroscopy with high spatial and energy resolution in a high-density liquid environment. Our experimental findings, supported by ab initio electronic structure calculations and atomic-scale molecular dynamics simulations, reveal direct mapping of single-molecule structure and resonance states at the solid/liquid interface. We further extend this approach to resolve the electronic structure of graphene monolayers at atomic length scales under standard room-temperature operating conditions.

Nirmalraj, Peter; Thompson, Damien; Molina-Ontoria, Agustín; Sousa, Marilyne; Martín, Nazario; Gotsmann, Bernd; Riel, Heike

2014-10-01

270

Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry  

NASA Astrophysics Data System (ADS)

Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the dz2 and the degenerate d? orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe2+ ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe dz2 and NO 5? and 2?* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe2+ ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly.

Tsukahara, Noriyuki; Minamitani, Emi; Kim, Yousoo; Kawai, Maki; Takagi, Noriaki

2014-08-01

271

Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface.  

PubMed

Evaluating the built-in functionality of nanomaterials under practical conditions is central for their proposed integration as active components in next-generation electronics. Low-dimensional materials from single atoms to molecules have been consistently resolved and manipulated under ultrahigh vacuum at low temperatures. At room temperature, atomic-scale imaging has also been performed by probing materials at the solid/liquid interface. We exploit this electrical interface to develop a robust electronic decoupling platform that provides precise information on molecular energy levels recorded using in situ scanning tunnelling microscopy/spectroscopy with high spatial and energy resolution in a high-density liquid environment. Our experimental findings, supported by ab initio electronic structure calculations and atomic-scale molecular dynamics simulations, reveal direct mapping of single-molecule structure and resonance states at the solid/liquid interface. We further extend this approach to resolve the electronic structure of graphene monolayers at atomic length scales under standard room-temperature operating conditions. PMID:25129620

Nirmalraj, Peter; Thompson, Damien; Molina-Ontoria, Agustín; Sousa, Marilyne; Martín, Nazario; Gotsmann, Bernd; Riel, Heike

2014-10-01

272

Interfacial electronic properties of the heterojunctions C{sub 60}/rubrene/Au and rubrene/C{sub 60}/Au  

SciTech Connect

Using synchrotron-radiation photoemission, we have studied the electronic structures of rubrene:C{sub 60} heterojunctions on Au substrates. The photoelectron spectra show that the interfacial properties at the C{sub 60}/rubrene/Au and rubrene/C{sub 60}/Au interfaces are asymmetric and do not follow the commutation rule. In the C{sub 60}/rubrene case, a gap state appearing in the initial deposition stage results from negative charges transferred from rubrene to C{sub 60}, while in the inverse deposition process, no strong chemical reaction could be found. A significant shift of the vacuum level induced by alignment of the charge neutrality levels of the two materials was observed in both cases. Furthermore, the charge transfer strongly enhances the dipole potential of the C{sub 60}/rubrene interface. The energy level diagrams show that the C{sub 60}-on-rubrene process has a superior number of advantages in the photovoltaic applications.

Cheng, Chiu-Ping; Chan, Yi-Wei; Hsueh, Chih-Feng [Department of Electrophysics, National Chiayi University, 300 University Road, Chiayi 60004, Taiwan (China); Pi, Tun-Wen [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China)

2012-07-15

273

Effect of interfacial bond type on the electronic and structural properties of GaSb/InAs superlattices  

SciTech Connect

We have investigated the effects of interfacial bond configuration on the electronic and structural properties of thin (001)GaSb/InAs superlattices by using state-of-the-art ab initio molecular dynamics techniques to calculate the electronic and structural properties of two twelve-atom model GaSb/InAs superlattices which have been constructed to contain only In-Sb (model 1) or Ga-As (model 2) interface bonds, respectively. We find the strain at the interface to be different in the two cases. In model 1, the In and Sb atoms at the interface move away from each other toward the InAs and GaSb layers, respectively, increasing the interfacial separation (4.3% greater than in bulk InSb) and compressing the back bonds to the atoms in the layer below the interface. In model 2 the Ga and As atoms move toward each other, decreasing the interplanar separation at the interface (3.2% smaller than in bulk GaAs) and stretching the back bonds to the neighboring Sb and In atoms, respectively. We calculate the valence band offset for the Ga-As bonded structure to be 0.15 eV smaller than that for the model containing only In-Sb bonds. This smaller band offset leads to more mixing of As p character into the highest lying valence band of the superlattice and results in a 0.015 eV smaller spin-orbit splitting at the valence band edge of the Ga-As bonded structure. This result is consistent with the 0.05 eV larger band gap observed for Ga-As bonded structures in recent photoconductivity measurements made on both Ga-As and In-Sb bonded samples grown by molecular-beam epitaxy. 16 refs., 1 fig.

Hemstreet, L.A. [Naval Research Lab., Washington, DC (United States)] [Naval Research Lab., Washington, DC (United States); Fong, C.Y. [Univ. of California, Davis, CA (United States)] [Univ. of California, Davis, CA (United States); Nelson, J.S. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States)

1993-07-01

274

"Butterfly Effect" in CuO/Graphene Composite Nanosheets: A Small Interfacial Adjustment Triggers Big Changes in Electronic Structure and Li-Ion Storage Performance.  

PubMed

Generally speaking, excellent electrochemical performance of metal oxide/graphene nanosheets (GNSs) composite is attributed to the interfacial interaction (or "synergistic effect") between constituents. However, there are no any direct observations on how the electronic structure is changed and how the properties of Li-ion storage are affected by adjusting the interfacial interaction, despite of limited investigations on the possible nature of binding between GNSs and metal oxide. In this paper, CuO nanosheets/GNSs composites with a little Cu2O (ca. 4 wt %) were utilized as an interesting model to illustrate directly the changes of interfacial nature as well as its deep influence on the electronic structure and Li-ion storage performance of composite. The interfacial adjustment was successfully fulfilled by removal of Cu2O in the composite by NH3·H2O. Formation of Cu-O-C bonds on interfaces both between CuO and GNSs, and Cu2O and GNSs in the original CuO/GNSs composites was detected. The small interfacial alteration by removal of the little Cu2O results in the obvious changes in electronic structure, such as weakening of covalent Cu-O-C interfacial interaction and recovery of ? bonds in graphene, and simultaneously leads to variations in electrochemical performance of composites, including a 21% increase of reversible capacity, degradation of cyclic stability and rate-performance, and obvious increase of charge-transfer resistance, which can be called a "butterfly effect" in graphene-based metal oxide composites. These interesting phenomena could be helpful to design not only the high-performance graphene/metal oxide anode materials but also various advanced graphene-based composites used in the other fields such as sensors, catalysis, fuel cells, solar cells, etc. PMID:25226227

Zhang, Xiaoting; Zhou, Jisheng; Song, Huaihe; Chen, Xiaohong; Fedoseeva, Yu V; Okotrub, A V; Bulusheva, L G

2014-10-01

275

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling.  

PubMed

The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic 'fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore. PMID:24705512

Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, JongOne; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

2014-06-01

276

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling  

NASA Astrophysics Data System (ADS)

The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

2014-06-01

277

Single-molecule photon stamping FRET spectroscopy study of enzymatic conformational dynamics  

PubMed Central

The fluorescence resonant energy transfer (FRET) from a donor to an acceptor via transition dipole–dipole interactions decreases the donor's fluorescent lifetime. The donor's fluorescent lifetime decreases as the FRET efficiency increases, following the equation: EFRET = 1 ? ?DA/?D, where ?D and ?DA are the donor fluorescence lifetime without FRET and with FRET. Accordingly, the FRET time trajectories associated with single-molecule conformational dynamics can be recorded by measuring the donor's lifetime fluctuations. In this article, we report our work on the use of a Cy3/Cy5-labeled enzyme, HPPK to demonstrate probing single-molecule conformational dynamics in an enzymatic reaction by measuring single-molecule FRET donor lifetime time trajectories. Compared with single-molecule fluorescence intensity-based FRET measurements, single-molecule lifetime-based FRET measurements are independent of fluorescence intensity. The latter has an advantage in terms of eliminating the analysis background noise from the acceptor fluorescence detection leak through noise, excitation light intensity noise, or light scattering noise due to local environmental factors, for example, in a AFM-tip correlated single-molecule FRET measurements. Furthermore, lifetime-based FRET also supports simultaneous single-molecule fluorescence anisotropy. PMID:23085845

He, Yufan; Lu, Maolin

2013-01-01

278

Self-Doping, O2-Stable, n-Type Interfacial Layer for Organic Electronics  

SciTech Connect

Solid films of a water-soluble dicationic perylene diimide salt, perylene bis(2-ethyltrimethylammonium hydroxide imide), Petma{sup +}OH{sup -}, are strongly doped n-type by dehydration and reversibly de-doped by hydration. The hydrated films consist almost entirely of the neutral perylene diimide, PDI, while the dehydrated films contain {approx}50% PDI anions. The conductivity increases by five orders of magnitude upon dehydration, probably limited by film roughness, while the work function decreases by 0.74 V, consistent with an n-type doping density increase of {approx}12 orders of magnitude. Remarkably, the PDI anions are stable in dry air up to 120 C. The work function of the doped film, {phi} (3.96 V vs. vacuum), is unusually negative for an O{sub 2}-stable contact. Petma{sup +} OH{sup -} is also characterized as an interfacial layer, IFL, in two different types of organic photovoltaic cells. Results are comparable to state of the art cesium carbonate IFLs, but may improve if film morphology can be better controlled. The films are stable and reversible over many months in air and light. The mechanism of this unusual self-doping process may involve the change in relative potentials of the ions in the film caused by their deshielding and compaction as water is removed, leading to charge transfer when dry.

Reilly, T. H. III; Hains, A. W.; Chen, H. Y.; Gregg, B. A.

2012-04-01

279

Do-it-yourself guide: How to use the modern single molecule toolkit  

PubMed Central

Single molecule microscopy has evolved into the ultimate-sensitivity toolkit to study systems from small molecules to living cells, with the prospect of revolutionizing the modern biosciences. Here we survey the current state-of-the-art in single molecule tools including fluorescence spectroscopy, tethered particle microscopy, optical and magnetic tweezers, and atomic force microscopy. Our review seeks to guide the biological scientist in choosing the right approach from the available single molecule toolkit for applications ranging as far as structural biology, enzymology, nanotechnology, and systems biology. PMID:18511916

Walter, Nils G.; Huang, Cheng-Yen; Manzo, Anthony J.; Sobhy, Mohamed A.

2008-01-01

280

Fast recognition of single molecules based on single event photon statistics  

E-print Network

Mandel Q-parameter, which is determined from single event photon statistics, provides an alternative to differentiate single-molecule with fluorescence detection. In this work, by using the Q-parameter of the sample fluorescence compared to that of an ideal double-molecule system with the same average photon number, we present a novel and fast approach for identifying single molecules based on single event photon statistics analyses, compared with commonly used two-time correlation measurements. The error estimates for critical values of photon statistics are also presented for single-molecule determination.

Shuangli Dong; Tao Huang; Yuan Liu; Jun Wang; Guofeng Zhang; Liantuan Xiao+; Suotang Jia

2007-08-02

281

Versatile electron-collecting interfacial layer by in situ growth of silver nanoparticles in nonconjugated polyelectrolyte aqueous solution for polymer solar cells.  

PubMed

Novel PEIE-Ag composites by in situ growth of silver nanoparticles in poly(ethylenimine)-ethoxylated (PEIE) aqueous solution are explored as an efficient interfacial layer for improving inverted polymer solar cells (PSCs) performance. The hybrid PEIE-Ag interfacial material is simple to fabricate only via ultraviolet irradiation with good water-solubility and unique film formation. The generated Ag nanoparticles can anchor in the PEIE polymer chains to form a conductive continuous interpenetrating network structure. Combining of the advantages of PEIE and Ag nanoparticles, the PEIE-Ag shows enhanced charge transport, electron selective and collection, and improved light-harvesting, mainly due to the surface plasmon resonance effect, better energy alignment induced by the formation of ideal dipole layer, as well as the improved conductivity. These distinguished interfacial properties result in the power conversion efficiency of inverted PSCs based on poly[4,8-bis(2-ethyl-hexyl-thiophene-5-yl)-benzo[1,2-b:4,5-b]dithiophene-2,6-diyl]-alt-[2-(2-ethyl-hexanoyl)-thieno[3,4-b]thiophen-4,6-diyl] (PBDTTT-C-T) and [6,6]-phenyl C71-butyric acid methyl ester (PC71BM) photoactive layer substantially improved up to 7.66% from 6.11%. Moreover, the device performance is insensitively dependent on the thickness of the PEIE-Ag interfacial layer, broadening the thicknesses selection window for interfacial materials. These results demonstrate that PEIE-Ag is a potential interfacial material compatible with roll-to-roll techniques and suitable for printed electronic devices. PMID:25207753

Yuan, Kai; Chen, Lie; Chen, Yiwang

2014-10-01

282

Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing.  

PubMed

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls. PMID:20564484

Wei, Ruoshan; Pedone, Daniel; Zürner, Andreas; Döblinger, Markus; Rant, Ulrich

2010-07-01

283

Mechanically controlled molecular orbital alignment in single molecule junctions.  

PubMed

Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude. PMID:22138861

Bruot, Christopher; Hihath, Joshua; Tao, Nongjian

2012-01-01

284

Aromaticity Decreases Single-Molecule Junction Conductance. Wenbo Chen,  

E-print Network

; the nonaromatic cyclopentadiene derivative has the highest conductance, while the most aromatic of this series of aromatic compounds. Conjugated organic oligomer wires have formed the building blocks of organic conductance through a thiophene, furan, and cyclopentadiene species. Cyclopentadiene has 4 electrons

Venkataraman, Latha

285

Single-Molecule Spectroscopic Tools for Measuring Microsecond to Millisecond Dynamics of Calmodulin  

E-print Network

-channel, confocal microscope system used for fluorescence correlation spectroscopy (FCS) and scanning single-molecule measurements. Secondly, the newly built system was tested by performing two-channel FCS measurements using a FRET-pair labeled synthetic polyproline...

Price, E. Shane

2009-09-01

286

On single-molecule DNA sequencing with atomic force microscopy using functionalized carbon nanotube probes  

E-print Network

A novel DNA sequencing method is proposed based on the specific binding nature of nucleotides and measured by an atomic force microscope (AFM). A single molecule of DNA is denatured and immobilized on an atomically fiat ...

Burns, Daniel James

2004-01-01

287

Theoretical study of single-molecule spectroscopy and vibrational spectroscopy in condensed phases  

E-print Network

In this thesis, theoretical models and computer simulations are employed to study several problems of single-molecule spectroscopy and vibrational spectroscopy in condensed phases. The first part of the thesis concentrates ...

Yang, Shilong, 1975-

2005-01-01

288

Thermodynamics for Single-Molecule Stretching Experiments J. M. Rubi,*, D. Bedeaux, and S. Kjelstrup  

E-print Network

Thermodynamics for Single-Molecule Stretching Experiments J. M. Rubi,*, D. Bedeaux, and S to construct nonequilibrium thermodynamics for systems too small to be considered thermodynamically be viewed as a large thermodynamic system, we discuss the validity of nonequilibrium thermodynamics

Kjelstrup, Signe

289

A label-free untethered approach to single-molecule protein binding kinetics.  

PubMed

Single molecule approaches provide rich real-time dynamics of molecular interactions that are not accessible to ensemble measurements. Previous single molecule studies have relied on labeling and tethering, which alters the natural state of the protein. Here we use the double-nanohole (DNH) optical tweezer approach to measure protein binding kinetics at the single molecule level in a label-free, free-solution (untethered) way. The binding kinetics of human serum albumin (HSA) to tolbutamide and to phenytoin are in quantitative agreement with previous measurements, and our single-molecule approach reveals a biexponential behavior characteristic of a multistep process. The DNH optical tweezer is an inexpensive platform for studying the real-time binding kinetics of protein-small molecule interactions in a label-free, free-solution environment, which will be of interest to future studies including drug discovery. PMID:25211555

Al Balushi, Ahmed A; Gordon, Reuven

2014-10-01

290

Single-molecule detection using continuous wave excitation of two-photon fluorescence  

NASA Astrophysics Data System (ADS)

Two-photon fluorescence (TPF) is one of the most important discoveries for biological imaging. Although a cw laser is known to excite TPF, its application in TPF imaging has been very limited due to the perceived low efficiency of excitation. Here we directly excited fluorophores with an IR cw laser used for optical trapping and achieved single-molecule fluorescence sensitivity: discrete stepwise photobleaching of enhanced green fluorescent proteins was observed. The single-molecule fluorescence intensity analysis and on-time distribution strongly indicate that a cw laser can generate TPF detectable at the single-molecule level, and thus opens the door to single-molecule TPF imaging using cw lasers.

Hou, Ximiao; Cheng, Wei

2011-08-01

291

Coherent anti-Stokes Raman scattering with single-molecule sensitivity using a plasmonic Fano resonance  

NASA Astrophysics Data System (ADS)

Plasmonic nanostructures are of particular interest as substrates for the spectroscopic detection and identification of individual molecules. Single-molecule sensitivity Raman detection has been achieved by combining resonant molecular excitation with large electromagnetic field enhancements experienced by a molecule associated with an interparticle junction. Detection of molecules with extremely small Raman cross-sections (~10-30?cm2 sr-1), however, has remained elusive. Here we show that coherent anti-Stokes Raman spectroscopy (CARS), a nonlinear spectroscopy of great utility and potential for molecular sensing, can be used to obtain single-molecule detection sensitivity, by exploiting the unique light harvesting properties of plasmonic Fano resonances. The CARS signal is enhanced by ~11 orders of magnitude relative to spontaneous Raman scattering, enabling the detection of single molecules, which is verified using a statistically rigorous bi-analyte method. This approach combines unprecedented single-molecule spectral sensitivity with plasmonic substrates that can be fabricated using top-down lithographic strategies.

Zhang, Yu; Zhen, Yu-Rong; Neumann, Oara; Day, Jared K.; Nordlander, Peter; Halas, Naomi J.

2014-07-01

292

Single-molecule imaging of EGFR signalling on the surface of living cells  

Microsoft Academic Search

The early events in signal transduction from the epidermal growth factor (EGF) receptor (EGFR) are dimerization and autophosphorylation of the receptor, induced by binding of EGF. Here we observe these events in living cells by visualizing single molecules of fluorescent-dye-labelled EGF in the plasma membrane of A431 carcinoma cells. Single-molecule tracking reveals that the predominant mechanism of dimerization involves the

Yasushi Sako; Shigeru Minoghchi; Toshio Yanagida

2000-01-01

293

Peptide Nucleic Acids as Tools for Single-Molecule Sequence Detection and Manipulation  

NASA Astrophysics Data System (ADS)

The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to individual double-stranded (ds) DNA molecules is critical to a variety of single-molecule experiments. We propose using modified peptide nucleic acids (PNAs) for this purpose and implement them in two model single-molecule experiments where individual DNA molecules are manipulated via microfluidic flow and optical tweezers, respectively. We demonstrate that PNAs are versatile and robust sequence-specific tethers.

Zohar, Hagar; Hetherington, Craig; Bustamante, Carlos; Muller, Susan

2011-03-01

294

Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics  

Microsoft Academic Search

Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and

M. A. Sobhy; M. M. Elshenawy; M. Takahashi; B. H. Whitman; N. G. Walter; S. M. Hamdan

2011-01-01

295

Single-molecule Detection of Reactive Oxygen Species: Application to Photocatalytic Reactions  

Microsoft Academic Search

In this review, we have focused on the oxidation reactions of single dye molecules by reactive oxygen species (ROS). The methodologies\\u000a for the single-molecule detection of ROS, such as hydroxyl radical (HO•), singlet oxygen (O2(a1?g)), and hydrogen peroxide (H2O2), have been introduced together with examples. In particular, a successful application using the single-molecule fluorescence\\u000a technique for the investigation of the

Takashi Tachikawa; Tetsuro Majima

2007-01-01

296

Statistics of Single-Molecule Detection Jo1rg Enderlein,* David L. Robbins, W. Patrick Ambrose, Peter M. Goodwin, and  

E-print Network

Statistics of Single-Molecule Detection Jo1rg Enderlein,* David L. Robbins, W. Patrick Ambrose for the calculation of the photon detection statistics in single-molecule detection experiments is presented detection statistics in single- molecule detection experiments in a fluid flow. Using a path integral

Enderlein, Jörg

297

The Kondo Effect in Transition Metal Ion Based Single-Molecule Transistor  

NASA Astrophysics Data System (ADS)

We have used an electromigration technique to fabricate single-molecule transistors (SMTs). The molecule used is C32H16XN10S4, where X is a single transition metal ion (e.g. Co, Ni, Cu, Zn), coordinated by conjugated ligands. Upon assembly on gold in tetrahydrofuran (THF), the molecule undergoes loss of the (CN) moieties, and the remaining molecule is covalently bonded to surface Au atoms on the electrodes of the transistors. In several devices we observed conductance features characteristic of the Kondo effect, a coherent many-body state comprising an unpaired spin on the molecule coupled by exchange to the conduction electrons of the leads. We will discuss the temperature dependence of the peak conductance and the low temperature width of the Kondo resonance of the various transition metal ion based SMTs. We have also observed asymmetric Fano-like resonances in some SMTs, which we believe result from interference between a resonant and a nonresonant conduction path through the SMTs. We will report the temperature and gate voltage dependences of the lineshape of these Fano-like resonances, and discuss possible origins of the nonresonant conduction path.

Yu, Lam; Ciszek, Jacob; Natelson, Douglas

2005-03-01

298

A redox responsive, fluorescent supramolecular metallohydrogel consists of nanofibers with single-molecule width.  

PubMed

The integration of a tripeptide derivative, which is a versatile self-assembly motif, with a ruthenium(II)tris(bipyridine) complex affords the first supramolecular metallo-hydrogelator that not only self assembles in water to form a hydrogel but also exhibits gel-sol transition upon oxidation of the metal center. Surprisingly, the incorporation of the metal complex in the hydrogelator results in the nanofibers, formed by the self-assembly of the hydrogelator in water, to have the width of a single molecule of the hydrogelator. These results illustrate that metal complexes, besides being able to impart rich optical, electronic, redox, or magnetic properties to supramolecular hydrogels, also offer a unique geometrical control to prearrange the self-assembly motif prior to self-assembling. The use of metal complexes to modulate the dimensionality of intermolecular interactions may also help elucidate the interactions of the molecular nanofibers with other molecules, thus facilitating the development of supramolecular hydrogel materials for a wide range of applications. PMID:23521132

Zhang, Ye; Zhang, Bei; Kuang, Yi; Gao, Yuan; Shi, Junfeng; Zhang, Xi Xiang; Xu, Bing

2013-04-01

299

Interfacial electronic structure of SrTiO3\\/SrRuO3 heterojuctions studied by in situ photoemission spectroscopy  

Microsoft Academic Search

In situ photoemission spectroscopy (PES) has been performed on SrTiO3 (STO)\\/SrRuO3 (SRO) bilayers to study the interfacial electronic structure of a SRO layer buried in STO. Using the interface (surface) sensitivity of PES measurements, the interface spectra of Ru 4d derived states near the Fermi level (EF) were extracted from the spectra of STO\\/SRO bilayers, as well as the surface

H. Kumigashira; M. Minohara; M. Takizawa; A. Fujimori; D. Toyota; I. Ohkubo; M. Oshima; M. Lippmaa; M. Kawasaki

2008-01-01

300

Impact of the interfacial nanostructures on the electronic processes in organic solar cells  

NASA Astrophysics Data System (ADS)

After a brief description of the optical and electronic processes that take place in a solid-state organic solar cell [1], we turn our attention to recent theoretical advances regarding the determination of the energetics and dynamics at the organic-organic, donor-acceptor interfaces [2]. We underline the complexity of the processes taking place at the nanoscale [3] and highlight the balance that needs to be found for the optimization of materials parameters in terms of photovoltaic performance. [4pt] [1] J.L. Bredas, J. Norton, J. Cornil, and V. Coropceanu, Acc. Chem. Res. 42, 1691 (2009).[0pt] [2] Y.Yi, V. Coropceanu, and J.L. Bredas, J. Amer. Chem. Soc. 131, 5131 (2009); ibid., J. Mater. Chem. (2010).[0pt] [3] M. Linares et al., J. Phys. Chem. C 114, 3215 (2010).

Bredas, Jean-Luc

2011-03-01

301

Dielectric dependence of single-molecule photoluminescence intermittency: nile red in poly(vinylidene fluoride).  

PubMed

The dependence of single-molecule photoluminescence intermittency (PI) or "blinking" on the local dielectric constant (?) is examined for nile red (NR) in thin films of poly(vinylidene fluoride) (PVDF). In previous studies, variation of the local dielectric constant was accomplished by studying luminophores in chemically and structurally different hosts. In contrast, the NR/PVDF guest-host pair allows for the investigation of PI as a function of ? while keeping the chemical composition of both the luminophore and host unchanged. The solvatochromic properties of NR are used to measure the local ?, while fluctuations in NR emission intensity over time provide a measure of the PI. PVDF is an ideal host for this study because it provides submicron-sized dielectric domains that vary from nonpolar (? ? 2) to very polar (? ? 70). The results presented here demonstrate that the local dielectric environment can have a pronounced effect on PI. We find that the NR emissive events increase 5-fold with an increase in ? from 2.2 to 74. A complex dependence on ? is also observed for NR nonemissive event durations, initially increasing as ? increases from 2.2 to 3.4 but decreasing in duration with further increase in ?. The variation in emissive event durations with ? is reproduced using a photoinduced electron-transfer model involving electron transfer from NR to PVDF. In addition, an increase in NR photostability with an increase in ? is observed, suggesting that the dielectric environment plays an important role in defining the photostability of NR in PVDF. PMID:24995904

Hess, Chelsea M; Riley, Erin A; Reid, Philip J

2014-07-24

302

Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy.  

PubMed

Optical trapping and single-molecule fluorescence are two major single-molecule approaches. Their combination has begun to show greater capability to study more complex systems than either method alone, but met many fundamental and technical challenges. We built an instrument that combines base-pair resolution dual-trap optical tweezers with single-molecule fluorescence microscopy. The instrument has complementary design and functionalities compared with similar microscopes previously described. The optical tweezers can be operated in constant force mode for easy data interpretation or in variable force mode for maximum spatiotemporal resolution. The single-molecule fluorescence detection can be implemented in either wide-field or confocal imaging configuration. To demonstrate the capabilities of the new instrument, we imaged a single stretched ? DNA molecule and investigated the dynamics of a DNA hairpin molecule in the presence of fluorophore-labeled complementary oligonucleotide. We simultaneously observed changes in the fluorescence signal and pauses in fast extension hopping of the hairpin due to association and dissociation of individual oligonucleotides. The combined versatile microscopy allows for greater flexibility to study molecular machines or assemblies at a single-molecule level. PMID:23020384

Sirinakis, George; Ren, Yuxuan; Gao, Ying; Xi, Zhiqun; Zhang, Yongli

2012-09-01

303

Blinking effect and the use of quantum dots in single molecule spectroscopy  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer It is possible to eliminate the blinking effect of a water-soluble QD. Black-Right-Pointing-Pointer We provide a direct method to study protein function and dynamics at the single level. Black-Right-Pointing-Pointer QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the 'on'/'off' states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein-protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany)] [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Domingo, M.P. [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain)] [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Pardo, Julian [Grupo Apoptosis, Inmunidad y Cancer, Departamento Bioquimica y Biologia Molecular y Celular, Fac. Ciencias, Universidad de Zaragoza, Zaragoza (Spain) [Grupo Apoptosis, Inmunidad y Cancer, Departamento Bioquimica y Biologia Molecular y Celular, Fac. Ciencias, Universidad de Zaragoza, Zaragoza (Spain); Fundacion Aragon I-D (ARAID), Gobierno de Aragon, Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain); Graeber, P. [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany)] [Albert-Ludwigs-Universitaet Freiburg, Institut fuer Physikalische Chemie, Albertstrasse 23a, 79104 Freiburg (Germany); Galvez, E.M., E-mail: eva@icb.csic.es [Instituto de Carboquimica (CSIC), Miguel Luesma 4, 50018 Zaragoza (Spain); Immune Effector Cells Group, Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA) Fundacion Aragon I-D - ARAID, Gobierno de Aragon, Zaragoza (Spain)

2013-01-04

304

DNA origami as biocompatible surface to match single-molecule and ensemble experiments  

PubMed Central

Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

2012-01-01

305

Electron Transfer as a Probe of the Interfacial Quantum Dot-Organic Molecule Interaction  

NASA Astrophysics Data System (ADS)

This dissertation describes a set of experimental and theoretical studies of the interaction between small organic molecules and the surfaces of semiconductor nanoparticles, also called quantum dots (QDs). Chapter 1 reviews the literature on the influence of ligands on exciton relaxation dynamics following photoexcitation of semiconductor QDs, and describes how ligands promote or inhibit processes such as emission, nonradiative relaxation, and charge transfer to redox active adsorbates. Chapter 2 investigates the specific interaction of alkylcarboxylated viologen derivatives with CdS QDs, and shows how a combination of steady-state photoluminescence (PL) and transient absorption (TA) experiments can be used to reveal the specific binding geometry of redox active organic molecules on QD surfaces. Chapter 3 expands on Chapter 2 by using PL and TA to provide information about the mechanisms through which methyl viologen (MV 2+) associates with CdS QDs to form a stable QD/MV2+ complex, suggesting two chemically distinct reactions. We use our understanding of the QD/molecule interaction to design a drug delivery system in Chapter 4, which employs PL and TA experiments to show that conformational changes in a redox active adsorbate may follow electron transfer, "activating" a biologically inert Schiff base to a protein inhibitor form. The protein inhibitor limits cell motility and may be used to prevent tumor metastasis in cancer patients. Chapter 5 discusses future applications of QD/molecule redox couples with an emphasis on efficient multiple charge-transfer reactions -- a process facilitated by the high degeneracy of band-edge states in QDs. These multiple charge-transfer reactions may potentially increase the thermodynamic efficiency of solar cells, and may also facilitate the splitting of water into fuel. Multiple exciton generation procedures, multi-electron transfer experiments, and future directions are discussed.

Peterson, Mark D.

306

The Use of Ultrashort Picosecond Laser Pulses to Generate Quantum Optical Properties of Single Molecules in Biophysics  

NASA Astrophysics Data System (ADS)

Generation of quantum optical states from ultrashort laser-molecule interactions have led to fascinating discoveries in physics and chemistry. In recent years, these interactions have been extended to probe phenomena in single molecule biophysics. Photons emitted from a single fluorescent molecule contains important properties about how the molecule behave and function in that particular environment. Analysis of the second order coherence function through fluorescence correlation spectroscopy plays a pivotal role in quantum optics. At very short nanosecond timescales, the coherence function predicts photon antibunching, a purely quantum optical phenomena which states that a single molecule can only emit one photon at a time. Photon antibunching is the only direct proof of single molecule emission. From the nanosecond to microsecond timescale, the coherence function gives information about rotational diffusion coefficients, and at longer millisecond timescales, gives information regarding the translational diffusion coefficients. In addition, energy transfer between molecules from dipole-dipole interaction results in FRET, a highly sensitive method to probe conformational dynamics at nanometer distances. Here I apply the quantum optical techniques of photon antibunching, fluorescence correlation spectroscopy and FRET to probe how lipid nanodiscs form and function at the single molecule level. Lipid nanodiscs are particles that contain two apolipoprotein (apo) A-I circumventing a lipid bilayer in a belt conformation. From a technological point of view, nanodiscs mimics a patch of cell membrane that have recently been used to reconstitute a variety of membrane proteins including cytochrome P450 and bacteriorhodopsin. They are also potential drug transport vehicles due to its small and stable 10nm diameter size. Biologically, nanodiscs resemble to high degree, high density lipoproteins (HDL) in our body and provides a model platform to study lipid-protein interactions and their dynamic formation to lipoprotein particles without having to extract from human blood plasma. Although HDL has been studied extensively within the last thirty years, many questions still remain regarding the structure of apoA-I, the protein associated exclusively with it. Despite our ability to detect and image these nanodiscs by blotting, atomic force microscopy (AFM), or electron microscopy (EM), many basic properties such as their specific hydrated shape in solution, or the precise conformation of the apolipoproteins surrounding the particles are still unknown. The dynamic interactions of apoA-I with lipids are also rather poorly understood on a fundamental level, and are only characterized in bulk (biochemical blotting) or stationary methods (AFM, EM), making it impossible to study individual steps with high spatial or temporal resolution.

Ly, Sonny

307

Correlation of interfacial electronic structures and transport properties in organic light emitting diodes  

NASA Astrophysics Data System (ADS)

Turn on voltage in the current density-voltage characteristics is one of the important factors to evaluate the performance of organic light emitting diodes (OLEDs). In this paper, we report investigation of the origins of turn-on voltage, defined at where log J (current density) has a sharp rise and starts to increase dramatically. In OLEDs with NPB as the hole transport layer (HTL) and Alq3 as the electron transport layer (ETL), we find that the turn on voltage is always at 2V, regardless the cathode structures, such as Ca, Al, LiF/Al, and Cs2CO3/Al, being used. The turn on voltage is also independent on the thickness of organic layers. Beside NPB and Alq3, we also study the J-V characteristics on OLEDs with various combinations of HTLs and ETLs. In all the devices investigated, the turn on voltage just equals to the difference between the LUMO of ETL and the HOMO of HTL, taking into consideration of vacuum level shift at organic interfaces measured from the ultraviolet photoemission spectroscopy (UPS). Combined with J-V characteristics of OLEDs and UPS measurement, we propose that the turn on voltage of organic light emitting devices is determined by the difference between LUMO of ETL and HOMO of HTL and is independent of the cathode and thickness of organic layers. We also found that the charge transfers at the interface of ETL/HTL play an important role to the turn on voltage of OLEDs.

Wu, I.-Wen; Chen, Yu-Hung; Wang, Chao-Kung; Wu, Chih-I.

2009-08-01

308

Zero-mode waveguides: sub-wavelength nanostructures for single molecule studies at high concentrations.  

PubMed

The study of single fluorescent molecules allows individual measurements which can reveal characteristics typically obscured by ensemble averages. Yet, single molecule spectroscopy through traditional optical techniques is hindered by the diffraction limit of light. This restricts the accessible concentrations for single molecule experiments to the nano- to picomolar range. Zero-mode waveguides (ZMWs), optical nanostructures fabricated in a thin aluminum film, confine the observation volume to the range of atto- to zeptoliters. Thus, they extend the accessible concentrations for single molecule spectroscopy to the micro- to millimolar regime. Through the combination of ZMWs and fluorescence correlation spectroscopy, a number of biologically relevant systems have been studied at physiological concentrations. In this review, the concept and implementation of ZMWs is outlined, along with their application to the study of freely diffusing, and membrane-bound fluorescent biomolecules. PMID:18586103

Moran-Mirabal, Jose M; Craighead, Harold G

2008-09-01

309

Single-Molecule Spectroscopy Selectively Probes Donor and Acceptor Chromophores in the Phycobiliprotein Allophycocyanin  

PubMed Central

We report on single-molecule fluorescence measurements performed on the phycobiliprotein allophycocyanin (APC). Our data support the presence of a unidirectional Förster-type energy transfer process involving spectrally different chromophores, ?84 (donor) and ?84 (acceptor), as well as of energy hopping amongst ?84 chromophores. Single-molecule fluorescence spectra recorded from individual immobilized APC proteins indicate the presence of a red-emitting chromophore with emission peaking at 660 nm, which we connect with ?84, and a species with the emission peak blue shifted at 630 nm, which we attribute to ?84. Polarization data from single APC trimers point to the presence of three consecutive red emitters, suggesting energy hopping amongst ?84 chromophores. Based on the single-molecule fluorescence spectra and assuming that emission at the ensemble level in solution comes mainly from the acceptor chromophore, we were able to resolve the individual absorption and emission spectra of the ?84 and ?84 chromophores in APC. PMID:15454454

Loos, Davey; Cotlet, Mircea; De Schryver, Frans; Habuchi, Satoshi; Hofkens, Johan

2004-01-01

310

Bifunctional nanoarrays for probing the immune response at the single-molecule level  

PubMed Central

Bifunctional nanoarrays were created to simulate the immunological synapse and probe the T-cell immune response at the single-molecule level. Sub-5?nm AuPd nanodot arrays were fabricated using both e-beam and nanoimprint lithography. The nanoarrays were then functionalized by two costimulatory molecules: antibody UCHT1 Fab, which binds to the T-cell receptor (TCR) and activates the immune response, bound to metallic nanodots; and intercellular adhesion molecule-1, which enhances cell adhesion, on the surrounding area. Initial T-cell experiments show successful attachment and activation on the bifunctional nanoarrays. This nanoscale platform for single-molecule control of TCR in living T-cells provides a new approach to explore how its geometric arrangement affects T-cell activation and behavior, with potential applications in immunotherapy. This platform also serves as a general model for single-molecule nanoarrays where more than one molecular species is required. PMID:24353927

Cai, Haogang; Depoil, David; Palma, Matteo; Sheetz, Michael P.; Dustin, Michael L.; Wind, Shalom J.

2013-01-01

311

A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence techniques have emerged as a powerful approach to understanding complex biological systems. However, a challenge researchers still face is the limited photostability of nearly all organic fluorophores, including the cyanine and Alexa dyes. We report a new, monovalent probe that emits in the far-red region of the visible spectrum with properties desirable for single-molecule optical imaging. This probe is based on a ring-fused boron-dipyrromethene (BODIPY) core that is conjugated to a polyglycerol dendrimer (PGD). The dendrimer makes the hydrophobic fluorophore water-soluble. This probe exhibits excellent brightness, with an emission maximum of 705 nm. We have observed strikingly long and stable emission from individual PGD-BODIPY probes, even in the absence of anti-fading agents such as Trolox, a combined oxidizing-reducing agent often used in single-molecule studies for improving the photostability of common imaging probes. These interesting properties greatly simplify use of the fluorophore.

Yang, Si Kyung; Shi, Xinghua; Park, Seongjin; Ha, Taekjip; Zimmerman, Steven C.

2013-08-01

312

Interfacial electron-transfer kinetics of ferrocene through oligophenyleneethynylene bridges attached to gold electrodes as constituents of self-assembled monolayers: observation of a nonmonotonic distance dependence.  

PubMed

The standard heterogeneous electron-transfer rate constants (k(n)0) between substrate gold electrodes and the ferrocene redox couple attached to the electrode surface by variable lengths of substituted or unsubstituted oligophenyleneethynylene (OPE) bridges as constituents of mixed self-assembled monolayers were measured as a function of temperature. The distance dependences of the unsubstituted OPE standard rate constants and of the preexponential factors (An) obtained from an Arrhenius analysis of the unsubstituted OPE k(n)0 versus temperature data are not monotonic. This surprising result, together with the distance dependence of the substituted OPE preexponential factors, may be assessed in terms of the likely conformational variability of the OPE bridges (as a result of the low intrinsic barrier to rotation of the phenylene rings in these bridges) and the associated sensitivity of the rate of electron transfer (and, hence, the single-molecule conductance which may be estimated using An) through these bridges to the conformation of the bridge. Additionally, the measured standard rate constants were independent of the identity of the diluent component of the mixed monolayer, and using an unsaturated OPE diluent has no effect on the rate of electron transfer through a long-chain alkanethiol bridge. These observations indicate that the diluent does not participate in the electron-transfer event. PMID:15521782

Smalley, John F; Sachs, Sandra B; Chidsey, Christopher E D; Dudek, Stephen P; Sikes, Hadley D; Creager, Stephen E; Yu, C J; Feldberg, Stephen W; Newton, Marshall D

2004-11-10

313

Single-molecule imaging in vivo: the dancing building blocks of the cell.  

PubMed

A cell can be viewed as a dynamic puzzle, where single pieces shuffle in space, change their conformation to fit different partners, and new pieces are generated while old ones are destroyed. Microscopy has become capable of directly observing the pieces of the puzzle, which are single molecules. Single-molecule microscopy in vivo provides new insights into the molecular processes underlying the physiology of a cell, allowing not only for visualizing how molecules distribute with nanometer resolution in the cellular environment, but also for characterizing their movement with high temporal precision. This approach reveals molecular behaviors normally invisible in ensemble measurements. Depending on the molecule, the process, and the cellular region studied, single molecules can be followed by conventional epifluorescence microscopy, or by illuminating only a thin region of the cell, as in Total Internal Reflection Fluorescence (TIRF) and Selective Plane Illumination Microscopy (SPIM), and by limiting the amount of detectable molecules, as in Fluorescence Speckle Microscopy (FSM) and Photo-Activation (PA). High spatial resolution can be obtained by imaging only a fraction of the molecules at a time, as in Photo-Activated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM), or by de-exciting molecules in the periphery of the detection region as in Stimulated Emission-Depletion (STED) microscopy. Single-molecule techniques in vivo are becoming widespread; however, it is important to choose the most suited technique for each biological question or sample. Here we review single-molecule microscopy techniques, describe their basic principles, advantages for in vivo application, and discuss the lessons that can be learned from live single-molecule imaging. PMID:23525260

Coelho, Miguel; Maghelli, Nicola; Toli?-Nørrelykke, Iva M

2013-05-01

314

Mechanisms of interfacial electron-transfer within high-surface-area metal-oxide thin films  

NASA Astrophysics Data System (ADS)

The direct conversion of solar photon energy into electrical power is achieved with photovoltaic technology, yet existing technology is too inefficient or expensive to implement on a global scale. Dye sensitized solar cells (DSSCs) based on earth abundant low cost materials could overcome the barriers for world-wide implantation of photovoltaic technology. Historically the most efficient regenerative DSSCs utilize iodide based redox mediators in nitrile solvents. Despite the dominance of iodide redox mediator in DSSCs, the chemical attribute(s) that make iodide based electrolytes superior to other electrolyte is yet unproven. Discovering the chemical cause of iodide's superiority as a redox mediator was and important aspect of this thesis research. In Chapter 2 the photoinitated formation and cleavage of I-I bonds is demonstrated at an un-sensitized potentiostatically controlled mesoporous nanocrystalline (anatase) TiO2 thin film. After pulsed laser excitation of a TiO2 thin film, I2·- was observed that disproportionated to yield I3- and I-, but did not react with TiO2. In contrast evidence for a quasi-Fermi level dependent reaction between TiO2(e -) and I3- was observed. In agreement with the findings at un-sensitized TiO2 in Chapter 2, the results presented in Chapter 3 demonstrate that after pulsed laser excitation of an operational DSSC: I2·- is observed, I2·-does not react with TiO 2, and that charge recombination between I3- and TiO2(e-) is operative. In addition to absorption changes attributed to iodide redox chemistry, evidence for a transient electric field induced Stark effect was observed in the operational DSSC. Absorption changes reporting on the electric field at the TiO2 surface were simultaneously quantified at specific power conditions fo the operational DSSC. Chapter 4 explores alternative redox mediators to the iodide/triiodide couple. The photophysical studies presented herein provide key mechanistic details on kinetic processes pertinent to operational DSSCs. Specifically, electron transfer to and from iodide species found in an operational DSSC were quantified. Taken together this research advances the body of knowledge quantifying the chemical properties that make iodide based electrolytes a superior redox mediator in dye sensitized solar cells.

Rowley, John G.

315

Intensity and wavelength control of a single molecule reaction: simulation of photodissociation of cold-trapped MgH+.  

PubMed

Photodissociation of cold magnesium hydride ions MgH(+) leading to either Mg(+)+H or Mg+H(+) is simulated from first principles. The purpose is to study the possibility of single molecule control of the products in the presence of two laser fields. The system evolves on four electronic potential-energy curves, X(1) Sigma, A(1) Sigma, B(1) Pi, and C(1) Sigma. These potential-energy curves are calculated from first principles using multireference self-consistent field theory. The accuracy of the electronic potential curves has been checked by calculating the energies of the rovibrational eigenstates and comparing them to experimental findings. The photodissociation dynamics has furthermore been simulated by solving the time-dependent Schrodinger equation. It is shown that the branching ratio of the two dissociation channels, Mg(+)+H or Mg+H(+), can be controlled by changing the intensity and wavelength of the two driving laser fields. PMID:16164340

Jørgensen, Solvejg; Drewsen, Michael; Kosloff, Ronnie

2005-09-01

316

Intensity and wavelength control of a single molecule reaction: Simulation of photodissociation of cold-trapped MgH+  

NASA Astrophysics Data System (ADS)

Photodissociation of cold magnesium hydride ions MgH+ leading to either Mg++H or Mg +H+ is simulated from first principles. The purpose is to study the possibility of single molecule control of the products in the presence of two laser fields. The system evolves on four electronic potential-energy curves, X1?, A1?, B1?, and C1?. These potential-energy curves are calculated from first principles using multireference self-consistent field theory. The accuracy of the electronic potential curves has been checked by calculating the energies of the rovibrational eigenstates and comparing them to experimental findings. The photodissociation dynamics has furthermore been simulated by solving the time-dependent Schrödinger equation. It is shown that the branching ratio of the two dissociation channels, Mg++H or Mg +H+, can be controlled by changing the intensity and wavelength of the two driving laser fields.

Jørgensen, Solvejg; Drewsen, Michael; Kosloff, Ronnie

2005-09-01

317

Towards sorting of biolibraries using single-molecule fluorescence detection techniques.  

PubMed

The selection of specific binding molecules like peptides and proteins from biolibraries using, for instance, phage display methods can be quite time-consuming. It is therefore desirable to develop a strategy that is much faster in selection and sorting of potential binders out of a biolibrary. In this contribution we separately discuss the current achievements in generation of biolibraries, single-molecule detection techniques and microfluidic devices. A high-throughput microfluidic platform is then proposed that combines the propulsion of liquid containing fluorescent components of the biolibrary through microchannels, single-molecule fluorescence photon burst detection and real-time sorting of positive hits. PMID:15078151

Visser, Antonie J W G; Kunst, Beno H; Keller, Hans; Schots, Arjen

2004-04-01

318

Information Theoretical Approach to Single-Molecule Experimental Design and Interpretation  

PubMed Central

We use Shannon’s definition of information to develop a theory to predict a photon-counting-based single-molecule experiment’s ability to measure the desired property. We treat three phenomena that are commonly measured on single molecules: spectral fluctuations of a solvatochromic dye; assignment of the azimuthal dipole angle; determination of a distance by fluorescence resonant energy transfer using Forster’s theory. We consider the effect of background and other “imperfections” on the measurement through the decrease in information. PMID:16884207

Talaga, David S.

2007-01-01

319

Sub-diffraction limit differentiation of single fluorophores using Single Molecule Image Deconvolution (SMID)  

NASA Astrophysics Data System (ADS)

In order to better understand biological systems, researchers demand new techniques and improvements in single molecule differentiation. We present a unique approach utilizing an analysis of the standard deviation of the Gaussian point spread function of single immobile fluorescent molecules. This technique, Single Molecule Image Deconvolution (SMID), is applicable to standard TIRF instrumentation and standard fluorophores. We demonstrate the method by measuring the separation of two Cy3 molecules attached to the ends of short double-stranded DNA immobilized on a surface without photobleaching. Preliminary results and further applications will be presented.

Decenzo, Shawn H.; Desantis, Michael C.; Wang, Y. M.

2009-03-01

320

Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction  

NASA Astrophysics Data System (ADS)

Motor proteins such as myosin and kinesin hydrolyze ATP into ADP and Pi to convert chemical energy into mechanical work. This resultsin various motile processes like muscle contraction, vesicle transport and cell division. Recent single molecule experiments have revealed that external load applied to these motor proteins perturb not only the mechanical motion, but the ATP hydrolysis cycle as well, making these molecules mechano-enzymes. Here, we describe our single molecule detection techniques to reveal the mechano-enzymatic properties of myosin and introduce recent progress from both experimental and theoretical approaches at the single- and multiple-molecule level.

Iwaki, Mitsuhiro; Marcucci, Lorenzo; Togashi, Yuichi; Yanagida, Toshio

2013-12-01

321

Understanding the physics of DNA using nanoscale single-molecule manipulation  

NASA Astrophysics Data System (ADS)

Processes for decoding the genetic information in cells, including transcription, replication, recombination and repair, involve the deformation of DNA from its equilibrium structures such as bending, stretching, twisting, and unzipping of the double helix. Single-molecule manipulation techniques have made it possible to control DNA conformation and simultaneously detect the induced changes, revealing a rich variety of mechanically-induced conformational changes and thermodynamic states. These single-molecule techniques helped us to reveal the physics of DNA and the processes involved in the passing on of the genetic code.

Frey, Eric W.; Gooding, Ashton A.; Wijeratne, Sitara; Kiang, Ching-Hwa

2012-10-01

322

Analysis of `blinking' or `hopping' single molecule signals with a limited number of transitions  

NASA Astrophysics Data System (ADS)

Most single molecule fluorescence signals exhibit two characteristic features: sudden intensity changes ('blinking', 'hopping') and a limited length ('bleaching'). I show that the correlation functions of such 'truncated telegraph signals' for Poisson processes contain linear segments and oscillatory features, deviating strongly from the expected exponential decay. I find that the slope of the initial linear section of the normalized signal autocorrelation is a robust and reliable statistical estimate for the rate of sudden intensity changes in single molecule fluorescence signals with 4 to 100 transitions per trace, significantly outperforming an exponential fit.

Bingemann, Dieter

2006-12-01

323

Four-color single molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes  

PubMed Central

To allow studies of conformational changes within multi-molecular complexes, we present a simultaneous, 4-color single molecule fluorescence methodology implemented with total internal reflection illumination and camera based, wide-field detection. We further demonstrate labeling histidine-tagged proteins non-covalently with tris-Nitrilotriacetic acid (tris-NTA) conjugated dyes to achieve single molecule detection. We combine these methods to co-localize the mismatch repair protein MutS? on DNA while monitoring MutS?-induced DNA bending using Förster resonance energy transfer (FRET) and to monitor assembly of membrane-tethered SNARE protein complexes. PMID:21091445

DeRocco, Vanessa C.; Anderson, Trevor; Piehler, Jacob; Erie, Dorothy A.; Weninger, Keith

2010-01-01

324

Coherent Interaction of Light and Single Molecules in a Dielectric Nanoguide  

E-print Network

We present a new scheme for performing optical spectroscopy on single molecules. A glass capillary with a diameter of 600 nm filled with an organic crystal tightly guides the excitation light and provides a maximum spontaneous emission coupling factor ($\\beta$) of 18% for the dye molecules doped in the organic crystal. Combination of extinction, fluorescence excitation and resonance fluorescence spectroscopy with microscopy provides high-resolution spatio-spectral access to a very large number of single molecules in a linear geometry. We discuss strategies for exploring a range of quantum optical phenomena, including coherent cooperative interactions in a mesoscopic ensemble of molecules mediated by a single mode of propagating photons.

Sanli Faez; Pierre Türschmann; Harald R. Haakh; Stephan Götzinger; Vahid Sandoghdar

2014-07-10

325

Single molecule experiments challenge the strict wave-particle dualism of light.  

PubMed

Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the "single photon limit" of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. "Single photon detectors" do not meet their promise-only "photon number resolving single photon detectors" do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified. PMID:20162017

Greulich, Karl Otto

2010-01-01

326

Highly anisotropic rhenium(IV) complexes: new examples of mononuclear single-molecule magnets.  

PubMed

The rhenium(IV) complex (NBu4)2[ReBr4(ox)] (1) (ox = oxalate and NBu4(+) = tetra-n-butylammonium cation) has been prepared and its crystal structure determined by X-ray diffraction. The structure is made up of discrete [ReBr4(ox)](2-) anions and bulky NBu4(+) cations. Each [ReBr4(ox)](2-) anion is surrounded by six NBu4(+) cations, which preclude any significant intermolecular contact between the anionic entities, the shortest rhenium···rhenium distance being 9.373(1) Å. Variable temperature dc and ac magnetic susceptibility measurements and field-dependent magnetization experiments on polycrystalline samples of 1 reveal the occurrence of highly anisotropic magnetically isolated Re(IV) centers (S(Re) = 3/2), which exhibit slow relaxation of the magnetization at very low temperatures in a dc field. Ac measurements conducted on a polycrystalline sample of the complex (NBu4)2[ReCl4(ox)] (2) [compound isostructural to 1 whose structure and dc magnetic susceptibility study were previously reported in Tomkiewicz, A.; Bartczak, T. J.; Kruszy?ski, R.; Mrozi?ski, J. J. Mol. Struct. 2001, 595, 225] show a similar behavior, both complexes thus constituting new examples of mononuclear single-molecule magnets. High-frequency and -field electron paramagnetic resonance on polycrystalline samples of 1 and 2 and on single crystals of 2 allowed for the determination for the first time of the negative sign and confirmed a significant magnitude and rhombicity (E/D) of the zero-field splitting tensor of the [ReCl4(ox)](2-) and [ReBr4(ox)](2-) centers, originating from a combination of spin-orbit coupling and low molecular symmetry. D and E values of 1 and 2 were estimated through magnetization measurements and theoretically calculated through complete active space and density functional theory methodologies. PMID:23957361

Martínez-Lillo, José; Mastropietro, Teresa F; Lhotel, Elsa; Paulsen, Carley; Cano, Joan; De Munno, Giovanni; Faus, Juan; Lloret, Francesc; Julve, Miguel; Nellutla, Saritha; Krzystek, J

2013-09-18

327

Plasmon Mapping in Metallic Nanostructures and its Application to Single Molecule Surface Enhanced Raman Scattering: Imaging Electromagnetic Hot-Spots and Analyte Location  

SciTech Connect

A major component of this proposal is to elucidate the connection between optical and electron excitation of plasmon modes in metallic nanostructures. These accomplishments are reported: developed a routine protocol for obtaining spatially resolved, low energy EELS spectra, and resonance Rayleigh scattering spectra from the same nanostructures.; correlated optical scattering spectra and plasmon maps obtained using STEM/EELS.; and imaged electromagnetic hot spots responsible for single-molecule surface-enhanced Raman scattering (SMSERS).

Camden, Jon P

2013-07-16

328

Kinetics of complexin binding to the SNARE complex: correcting single molecule FRET measurements for hidden events.  

PubMed

Virtually all measurements of biochemical kinetics have been derived from macroscopic measurements. Single-molecule methods can reveal the kinetic behavior of individual molecular complexes and thus have the potential to determine heterogeneous behaviors. Here we have used single-molecule fluorescence resonance energy transfer to determine the kinetics of binding of SNARE (soluble N-ethyl maleimide-sensitive fusion protein attachment protein receptor) complexes to complexin and to a peptide derived from the central SNARE binding region of complexin. A Markov model was developed to account for the presence of unlabeled competitor in such measurements. We find that complexin associates rapidly with SNARE complexes anchored in lipid bilayers with a rate constant of 7.0 x 10(6) M(-1) s(-1) and dissociates slowly with a rate constant of 0.3 s(-1). The complexin peptide associates with SNARE complexes at a rate slower than that of full-length complexin (1.2 x 10(6) M(-1) s(-1)), and dissociates much more rapidly (rate constant >67 s(-1)). Comparison of single-molecule fluorescence resonance energy transfer measurements made using several dye attachment sites illustrates that dye labeling of complexin can modify its rate of unbinding from SNAREs. These rate constants provide a quantitative framework for modeling of the cascade of reactions underlying exocytosis. In addition, our theoretical correction establishes a general approach for improving single-molecule measurements of intermolecular binding kinetics. PMID:17513363

Li, Yulong; Augustine, George J; Weninger, Keith

2007-09-15

329

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems  

E-print Network

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems. 1 Biomolecules, molecular demons and statistical physics. Biophysics is a relatively young reasons behind this general upsurge of interest, a very attractive aspect of biophysics is its strong

Ritort, Felix

330

Precise quantification of transcription factors in a surface-based single-molecule assay.  

PubMed

Biosensors have recognized a rapid development the last years in both industry and science. Recently, a single-molecule assay based on alternating laser excitation has been established for the quantitative detection of transcription factors. These proteins specifically recognize and bind DNA and play an important role in controlling gene expression. We implemented this assay format on a total internal reflection fluorescence microscope to detect transcription factors with immobilized single-molecule DNA biosensors. We quantify transcription factors via colocalization of the two halves of their binding site with immobilized single molecules of a two-color DNA biosensor. We could detect a model transcription factor, the bacterial lactose repressor, at different concentrations down to 150pM. We found that robust modeling of stoichiometry derived TIRF data is achieved with Student's t-distributions and nonlinear least-squares estimation with weights equal to the inverse of the expected number of bin entries. This significantly improved transcription factor concentration estimates with respect to distribution modeling with Gaussians without adding notable computational effort. The proposed model may enhance the precision of other single-molecule assays quantifying molecular distributions. Our measurements reliably confirm that the immobilized biosensor format is more sensitive than a previously published solution based approach. PMID:24012911

Grußmayer, Kristin S; Ehrhard, Tanja; Lymperopoulos, Konstantinos; Herten, Dirk-Peter

2013-12-31

331

Visualizing and quantifying protein polySUMOylation at the single-molecule level.  

PubMed

Protein polySUMOylation, the attachment of small ubiquitin-like modifier (SUMO) chains to the target protein, is associated with a variety of physiological processes. However, the analysis of protein polySUMOylation is often complicated by the heterogeneity of SUMO-target conjugates. Here, we develop a new strategy to visualize and quantify polySUMOylation at the single-molecule level by integrating the tetracysteine (TC) tag labeling technology and total internal reflection fluorescence (TIRF)-based single-molecule imaging. As a proof-of-concept, we employ the human SUMO-2 as the model. The addition of TC tag to SUMO-2 can specifically translate the SUMO-mediated modification into visible fluorescence signal without disturbing the function of SUMO-2. The SUMO monomers display homogeneous fluorescence spots at the single-molecule level, whereas the mixed SUMO chains exhibit nonuniform fluorescence spots with a wide range of intensities. Analysis of the number and the brightness of fluorescence spots enable quantitative measurement of the polySUMOylation degree inside the cells under different physiological conditions. Due to the frequent occurrence of posttranslational modification by polymeric chains in cells, this single-molecule strategy has the potential to be broadly applied for studying protein posttranslational modification in normal cellular physiology and disease etiology. PMID:24383460

Yang, Yong; Zhang, Chun-yang

2014-01-21

332

Enhanced Single Molecule Fluorescence and Reduced Observation Volumes on Nanoporous Gold (NPG) Films  

PubMed Central

We report single molecule fluorescence studies on nanoporous gold films. We observed dramatically enhanced intensities from individual immobilized fluorophores and reduced effective observation volumes in the nanopores. The overlaid mapping image derived from surface reflectance and fluorescence emission visualizes the enhanced localized plasmon field existing in the “nanovoid” regions. PMID:24129372

Zhang, Jian; Nowaczyk, Kazimierz; Lakowicz, Joseph R.

2014-01-01

333

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman  

SciTech Connect

Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Wieman, Carl

2008-08-30

334

Branching out of single-molecule fluorescence spectroscopy: challenges for chemistry and influence on biology.  

PubMed

In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells. PMID:15849689

Tinnefeld, Philip; Sauer, Markus

2005-04-29

335

Directional Raman Scattering from Single Molecules in the Feed Gaps of Optical Antennas  

E-print Network

using the enhanced fields around nanostructures in the method known as surface-enhanced Raman scattering by a silver ring, all on a SiO2 spacer layer on a silver mirror. The silver particles are separated by a gap. KEYWORDS: Optical antenna, optical antenna chip, SERS enhancement, single molecule SERS, directional Raman

336

Recent developments in single-molecule DNA mechanics Zev Bryant1,2  

E-print Network

synergistic relationship between single-molecule manipulation and structural DNA nanotechnology. Addresses 1, Stanford University School of Medicine, Stanford, CA 94305, USA 3 Department of Applied Physics, Stanford is emerging between single-mol- ecule mechanics and structural DNA nanotechnology: mechanical properties

Bryant, Zev

337

Supplementary Information for: Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models  

E-print Network

parame- ters are found by the HMM algorithm. The conver- gence of the HMM algorithm and the validity emission process, which gives rise to the ob- served photon-by-photon trace in a single-molecule FRET is the number of observed donor photons, ka and kd represent the emission rates of acceptor and donor photons

338

Single-molecule mechanics of mussel adhesion Haeshin Lee*, Norbert F. Scherer  

E-print Network

for stability within the tidal marine environment. The remarkable features of mussel adhesion in- cludeSingle-molecule mechanics of mussel adhesion Haeshin Lee*, Norbert F. Scherer , and Phillip B proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces

Scherer, Norbert F.

339

Amine-linked single-molecule circuits: systematic trends across molecular families  

Microsoft Academic Search

A comprehensive review is presented of single-molecule junction conductance measurements across families of molecules measured while breaking a gold point contact in a solution of molecules with amine end groups. A theoretical framework unifies the picture for the amine–gold link bonding and the tunnel coupling through the junction using density functional theory based calculations. The reproducible electrical characteristics and utility

Mark S. Hybertsen; Latha Venkataraman; Jennifer E. Klare; Adam C. Whalley; Michael L. Steigerwald; Colin Nuckolls

2008-01-01

340

Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own “personalities” regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.

Ha, Taekjip; Tinnefeld, Philip

2012-05-01

341

Author's personal copy 9.21 Single Molecule Fluorescence Methods in Enzymology  

E-print Network

The rapid advances in single-molecule methods have enabled many innovative studies in the life sciences categories: optical (e.g., fluorescence and nonlinear optical microscopy), mechanical (e.g., optical tweezers because of their straightforward instrumentation and easy operation.4,29­32 One can monitor

Chen, Peng

342

Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics  

E-print Network

(2004) Improvement of detected intensity in confocal microscopy by using reflecting optical system Rev OF SCIENTIFIC INSTRUMENTS 82, 113702 (2011) Versatile single-molecule multi-color excitation and detection of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal

Walter, Nils G.

343

Origins of concentration dependence of waiting times for single-molecule fluorescence binding  

NASA Astrophysics Data System (ADS)

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here, we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. [Proc. Natl. Acad. Sci. U.S.A. 104, 18013 (2007)].

Yang, Jin; Pearson, John E.

2012-06-01

344

Reduction of photobleaching and photodamage in single molecule detection: observing single actin monomer in skeletal myofibrils.  

PubMed

Recent advances in detector technology make it possible to achieve single molecule detection (SMD) in a cell. SMD avoids complications associated with averaging signals from large assemblies and with diluting and disorganizing proteins. However, it requires that cells be illuminated with an intense laser beam, which causes photobleaching and cell damage. To reduce these effects, we study cells on coverslips coated with silver nanoparticle monolayers (NML). Muscle is used as an example. Actin is labeled with a low concentration of fluorescent phalloidin to assure that less than a single molecule in a sarcomere is fluorescent. On a glass substrate, the fluorescence of actin decays in a step-wise fashion, establishing a single molecule detection regime. Single molecules of actin in living muscle are visualized for the first time. NML coating decreases the fluorescence lifetime 17 times and enhances intensity ten times. As a result, fluorescence of muscle bleaches four to five times slower than on glass. Monolayers decrease photobleaching because they shorten the fluorescence lifetime, thus decreasing the time that a fluorophore spends in the excited state when it is vulnerable to oxygen attack. They decrease damage to cells because they enhance the electric field near the fluorophore, making it possible to illuminate samples with weaker light. PMID:18601566

Borejdo, Julian; Muthu, Priya; Talent, John; Gryczynski, Zygmunt; Calander, Nils; Akopova, Irina; Shtoyko, Tanya; Gryczynski, Ignacy

2008-01-01

345

Rapid analysis of specific DNA sequences by Fluorescent single-molecule detection  

SciTech Connect

We have developed a technique for the detection of specific nucleic acid sequences at the single molecule level of sensitivity. This method is based on the synthesis of a highly fluorescent reporter molecule using the target nucleic acid as a template.

Castro, A. (Alonso)

2002-01-01

346

A plasmonic `antenna-in-box' platform for enhanced single-molecule analysis at micromolar concentrations  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence techniques are key for a number of applications, including DNA sequencing, molecular and cell biology and early diagnosis. Unfortunately, observation of single molecules by diffraction-limited optics is restricted to detection volumes in the femtolitre range and requires pico- or nanomolar concentrations, far below the micromolar range where most biological reactions occur. This limitation can be overcome using plasmonic nanostructures, which enable the confinement of light down to nanoscale volumes. Although these nanoantennas enhance fluorescence brightness, large background signals and/or unspecific binding to the metallic surface have hampered the detection of individual fluorescent molecules in solution at high concentrations. Here we introduce a novel `antenna-in-box' platform that is based on a gap-antenna inside a nanoaperture. This design combines fluorescent signal enhancement and background screening, offering high single-molecule sensitivity (fluorescence enhancement up to 1,100-fold and microsecond transit times) at micromolar sample concentrations and zeptolitre-range detection volumes. The antenna-in-box device can be optimized for single-molecule fluorescence studies at physiologically relevant concentrations, as we demonstrate using various biomolecules.

Punj, Deep; Mivelle, Mathieu; Moparthi, Satish Babu; van Zanten, Thomas S.; Rigneault, Hervé; van Hulst, Niek F.; García-Parajó, María F.; Wenger, Jérôme

2013-07-01

347

Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions  

E-print Network

CONCEPTS Optical Detection and Manipulation of Single Molecules in Room-Temperature Solutions. Keywords: single-moleculedetection - single-moleculema- nipulation - laser-induced fluorescence * optical, frcquency-modulated optical ab- sorption and fluorescence excitation have been used to investi- gate

Zare, Richard N.

348

Statistical approaches for probing single-molecule dynamics photon-by-photon  

E-print Network

Statistical approaches for probing single-molecule dynamics photon-by-photon Haw Yang1 , X. Sunney 02138, USA Received 19 December 2001 Abstract The recently developed photon-by-photon approach [H. Yang, each photon represents a data point, thereby affording better statistics. Here, we utilize

Xie, Xiaoliang Sunney

349

Single-Molecule Magnets [(Tp)8(H2O)6CuII  

E-print Network

Single-Molecule Magnets [(Tp)8(H2O)6CuII 6FeIII 8(CN)24]4+ : A Cyanide- Bridged Face that can yield clusters with a large spin and/or anisotropy. Metal­cyanide cluster systems offer in the resulting cluster is readily predicted.[9] One approach to synthesizing high-nuclearity metal­cyanide

350

Single-molecule mechanical unfolding of amyloidogenic beta2-microglobulin: the force-spectroscopy approach.  

PubMed

The recombinant production of a novel chimeric polyprotein is described. The new protein contains either wild-type beta(2)-microglobulin (beta(2)m) or its truncated variant (DeltaN6 beta(2)m) (see picture). Structural characterization is achieved by means of single-molecule force spectroscopy studies of specific beta(2)m regions which could be involved in amyloidogenesis. PMID:19496082

Sorce, B; Sabella, S; Sandal, M; Samorì, B; Santino, A; Cingolani, R; Rinaldi, R; Pompa, P P

2009-07-13

351

INVITED REVIEW Analysis of DNA interactions using single-molecule force  

E-print Network

to investigate DNA intercalation, complexes involving DNA aptamers and peptide­ and protein­DNA interactionsINVITED REVIEW Analysis of DNA interactions using single-molecule force spectroscopy Markus February 2013 / Published online: 7 March 2013 � Springer-Verlag Wien 2013 Abstract Protein­DNA

Bielefeld, Universität

352

Photochemistry and Photobiology, 2003, 78(6): 576581 Single-molecule Fluorescence Spectroscopy of TOTO on  

E-print Network

- pected from previous study, the excited state lifetime of TOTO intercalated in DNA is dependent of equilibrium binding distributions in DNA using single-molecule methods. INTRODUCTION Homodimeric bis-intercalating for the study and identification of DNA (1). As is the case for other intercalating dyes, the quantum yield

Enderlein, Jörg

353

Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching  

E-print Network

Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching Ioana D molecule stretching to investigate DNA intercalation by ethidium and three ruthenium complexes not intercalate under experimentally accessible solution conditions. As ligand concentration increased, the DNA

Cai, Long

354

Recovery of Free Energy Branches in Single Molecule Experiments Ivan Junier,1  

E-print Network

Recovery of Free Energy Branches in Single Molecule Experiments Ivan Junier,1 Alessandro Mossa,2 19 February 2009) We present a method for determining the free energy of coexisting states from use optical tweezers to determine the free energy branches of the native and unfolded states of a two

Ritort, Felix

355

Autofluorescent Proteins in Single-Molecule Research: Applications to Live Cell Imaging Microscopy  

Microsoft Academic Search

The spectral and photophysical characteristics of the autofluorescent proteins were analyzed and compared to flavinoids to test their applicability for single-molecule microscopy in live cells. We compare 1) the number of photons emitted by individual autofluorescent proteins in artificial and in vivo situations, 2) the saturation intensities of the various autofluorescent proteins, and 3) the maximal emitted photons from individual

Gregory S. Harms; Laurent Cognet; Piet H. M. Lommerse; Gerhard A. Blab; Thomas Schmidt

2001-01-01

356

Single-molecule insights into retention at a reversed-phase chromatographic interface.  

PubMed

The efficiency of chromatographic separations decreases markedly when peaks exhibit asymmetry (e.g., "peak tailing"). Theoretically, these effects can arise from heterogeneous adsorption kinetics. To investigate the nature and consequences of such heterogeneity, we used a combination of single-molecule imaging and reversed-phase liquid chromatography (RPLC). In both single-molecule and macroscopic RPLC experiments, the stationary phase was hydrophobic end-capped (trimethylsilyl-functionalized) silica, which we exposed to different methanol/water solutions (50%-62% methanol), containing a fluorescent fatty acid analyte. Super-resolution maps based on single-molecule observations revealed rare, strong adsorption sites with activity that varied significantly with methanol concentration. The adsorption and desorption kinetics on the strong sites were heterogeneous and positively correlated, suggesting a broad underlying distribution of site binding energies. Adsorption equilibrium on the strong sites was more sensitive to solution conditions than overall retention measured in RPLC experiments, suggesting that the effect of strong sites on the overall adsorption kinetics should change with solution conditions. Interestingly, in RPLC experiments, peak tailing had a nonmonotonic dependence on methanol concentration within the range studied. Using the stochastic model of chromatography, we showed quantitatively that our single-molecule kinetic results were consistent with this macroscopic trend. This approach to identifying and quantifying adsorption sites should be useful for designing better chromatographic separations and for identifying the role of heterogeneous surface chemistry in molecular dynamics. PMID:25188676

Mabry, Joshua N; Skaug, Michael J; Schwartz, Daniel K

2014-10-01

357

Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.  

PubMed

Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy. PMID:25212907

Widom, Julia R; Dhakal, Soma; Heinicke, Laurie A; Walter, Nils G

2014-11-01

358

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy  

PubMed Central

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

Neuman, Keir C.; Nagy, Attila

2012-01-01

359

Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering  

E-print Network

into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional recording of conformational variability of the same molecule. As a complementary new technique, SWNT FETs limitations. This resolution may help expand single-molecule research by, for example, revealing transient

Weiss, Gregory A.

360

Single-Molecule Force Spectroscopy Measurements of Bond Elongation during a Bimolecular Reaction  

E-print Network

to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (SN2) reaction. We use calculations of the role of solvent molecules in the reduction TS of an SN2 reaction. These results demonstrateSingle-Molecule Force Spectroscopy Measurements of Bond Elongation during a Bimolecular Reaction

Koti, Ainavarapu Sri Rama

361

Levy Statistics for Random Single-Molecule Line Shapes in a Glass E. Barkai,1  

E-print Network

on the dynamics and statics of the host glass. SM experiments have been performed both in low- temperature glasses [2­6] and recently close to the glass transition temperature [7]. For low-temperature glassesLe´vy Statistics for Random Single-Molecule Line Shapes in a Glass E. Barkai,1 A.V. Naumov,2 Yu. G

Barkai, Eli

362

Single molecule fluorescence burst detection of DNA fragments separated by capillary electrophoresis.  

PubMed

A method has been developed for detecting DNA separated by capillary gel electrophoresis (CGE) using single molecule photon burst counting. A confocal fluorescence microscope was used to observe the fluorescence bursts from single molecules of DNA multiply labeled with the thiazole orange derivative T06 as they passed through the approximately 2 micrometer diameter focused laser beam. Amplified photoelectron pulses from the photomultiplier are grouped into bins of 360-450 micros in duration, and the resulting histogram is stored in a computer for analysis. Solutions of M13 DNA were first flowed through the capillary at various concentrations, and the resulting data were used to optimize the parameters for digital filtering using a low-pass Fourier filter, selecting a discriminator level for peak detection, and applying a peak-calling algorithm. Statistical analyses showed that (i) the number of M13 molecules counted versus concentration was linear with slope = 1, (ii) the average burst duration was consistent with the expected transit time of a single molecule through the laser beam, and (iii) the number of detected molecules was consistent with single molecule detection. The optimized single molecule counting method was then applied to an electrophoretic separation of M13 DNA and to a separation of pBR 322 DNA from pRL 277 DNA. Clusters of discreet fluorescence bursts were observed at the expected appearance time of each DNA band. The autocorrelation function of these data indicated transit times that were consistent with the observed electrophoretic velocity. These separations were easily detected when only 50-100 molecules of DNA per band traveled through the detection region. This new detection technology should lead to the routine analysis of DNA in capillary columns with an on-column sensitivity of approximately 100 DNA molecules/band or better. PMID:11407410

Haab, B B; Mathies, R A

1995-09-15

363

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging  

NASA Astrophysics Data System (ADS)

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5 nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50 °C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Kennard, Raymond; Desisto, William J.; Giririjan, Thanu Praba; Mason, Michael D.

2008-04-01

364

Coherent Anti-Stokes Raman Scattering Spectroscopy of Single Molecules in Solution  

SciTech Connect

During this funding period, we have developed two breakthrough techniques. The first is stimulated Raman scattering microscopy, providing label-free chemical contrast for chemical and biomedical imaging based on vibrational spectroscopy. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. We developed a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We demonstrated a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis. This technology offers exciting prospect for medical imaging. The second technology we developed is stimulated emission microscopy. Many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. We use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, as a new contrast mechanism for optical microscopy. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distribu- tions without histological sectioning, and label-free microvascular imaging based on endogenous contrast of haemoglobin. For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging. Although we did not accomplish the original goal of detecting single-molecule by CARS, our quest for high sensitivity of nonlinear optical microscopy paid off in providing the two brand new enabling technologies. Both techniques were greatly benefited from the use of high frequency modulation for microscopy, which led to orders of magnitude increase in sensitivity. Extensive efforts have been made on optics and electronics to accomplish these breakthroughs.

Sunney Xie, Wei Min, Chris Freudiger, Sijia Lu

2012-01-18

365

Single molecule confocal fluorescence lifetime correlation spectroscopy for accurate nanoparticle size determination.  

PubMed

We report on an experimental procedure in confocal single molecule fluorescence lifetime correlation spectroscopy (FLCS) to determine the range of excitation power and molecular or particulate concentration in solution under which the application of an unmodified model autocorrelation function is justified. This procedure enables fitting of the autocorrelation to an accurate model to measure diffusion length (r) and diffusion time (?D) of single molecules in solution. We also report on the pinhole size dependency of r and ?D in a confocal FLCS platform. This procedure determines a set of experimental parameters with which the Stokes-Einstein (S-E) equation accurately measures the hydrodynamic radii of spherical nanoparticles, enabling the determination of the particle size range for which the hydrodynamic radius by the S-E equation measures the real particle radius. PMID:24879354

Chon, Bonghwan; Briggman, Kimberly; Hwang, Jeeseong

2014-07-14

366

Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging.  

PubMed

Single-molecule imaging and manipulation of biochemical reactions continues to reveal numerous biological insights. To facilitate these studies, we have developed and implemented a high-throughput approach to organize and image hundreds of individual DNA molecules at aligned diffusion barriers. Nonetheless, obtaining statistically relevant data sets under a variety of reaction conditions remains challenging. Here, we present a method for integrating high-throughput single-molecule "DNA curtain" imaging with poly(dimethylsiloxane) (PDMS)-based microfluidics. Our benchtop fabrication method can be accomplished in minutes with common tools found in all molecular biology laboratories. We demonstrate the utility of this approach by simultaneous imaging of two independent biochemical reaction conditions in a laminar flow device. In addition, five different reaction conditions can be observed concurrently in a passive linear gradient generator. Combining rapid microfluidic fabrication with high-throughput DNA curtains greatly expands our capability to interrogate complex biological reactions. PMID:24734940

Robison, Aaron D; Finkelstein, Ilya J

2014-05-01

367

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations  

NASA Astrophysics Data System (ADS)

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-10-01

368

Largely enhanced single-molecule fluorescence in plasmonic nanogaps formed by hybrid silver nanostructures.  

PubMed

It has been suggested that narrow gaps between metallic nanostructures can be practical for producing large field enhancement. We design a hybrid silver nanostructure geometry in which fluorescent emitters are sandwiched between silver nanoparticles and silver island film (SIF). A desired number of polyelectrolyte layers are deposited on the SIF surface before the self-assembly of a second silver nanoparticle layer. Layer-by-layer configuration provides a well-defined dye position. It allows us to study the photophyical behaviors of fluorophores in the resulting gap at the single molecule level. The enhancement factor of a fluorophore located in the gap is much higher than those on silver surfaces alone and on glass. These effects may be used for increased detectability of single molecules bound to surfaces which contain metallic structures for either biophysical studies or high sensitivity assays. PMID:23373787

Fu, Yi; Zhang, Jian; Lakowicz, Joseph R

2013-02-26

369

Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments.  

PubMed

We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (P(fold)=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that P(fold) is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles. PMID:21517423

Morrison, Greg; Hyeon, Changbong; Hinczewski, Michael; Thirumalai, D

2011-04-01

370

Three-dimensional super-resolution and localization of dense clusters of single molecules  

PubMed Central

When a single molecule is detected in a wide-field microscope, the image approximates the point spread function of the system. However, as the distribution of molecules becomes denser and their images begin to overlap, existing solutions to determine the number of molecules present and their precise three-dimensional locations can tolerate little to no overlap. We propose a localization scheme that can identify several overlapping molecule images while maintaining high localization precision. A solution to this problem involving matched optical and digital techniques, as here proposed, can substantially increase the allowable labeling density and accelerate the data collection time of single-molecule localization microscopy by more than one order of magnitude. PMID:24953078

Barsic, Anthony; Grover, Ginni; Piestun, Rafael

2014-01-01

371

Evidence of disorder in biological molecules from single molecule pulling experiments  

E-print Network

Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due...

Hyeon, Changbong; Thirumalai, D

2014-01-01

372

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations.  

PubMed

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876

Serag, Maged F; Abadi, Maram; Habuchi, Satoshi

2014-01-01

373

Single-molecule fluorescence microscopy on nucleotide excision repair complexes using GFP fusion proteins  

NASA Astrophysics Data System (ADS)

Scanning Confocal Fluorescence Microscopy is used for single molecule studies on DNA-protein complexes that occur in Nucleotide Excision Repair (NER). During DNA-damage elimination by the NER-pathway, complex protein structures assemble over DNA. It is our aim to resolve the architecture of these DNA-protein complexes and to study dynamic changes that occur in these structures. For this purpose NER- complexes are partly reconstituted onto DNA-substrates using NER-proteins fused to different Green Fluorescent Protein mutants. Here we describe the recombinant production of NER- GFP fusion proteins. Characterization of GFP fluorescence is shown together with results of GFP single molecule imaging. First results with NER-GFP fusion proteins are presented as well.

Segers-Nolten, Ine; Rademakers, Suzanne; Vermeulen, Wim; Lenferink, Aufried; Otto, Cees; Hoeijmakers, Jan; Greve, Jan

2000-12-01

374

A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell  

NASA Astrophysics Data System (ADS)

By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.

Xie, Sunney; Choi, Paul; Cai, Long

2009-03-01

375

Aptamer-based single-molecule imaging of insulin receptors in living cells  

NASA Astrophysics Data System (ADS)

We present a single-molecule imaging platform that quantitatively explores the spatiotemporal dynamics of individual insulin receptors in living cells. Modified DNA aptamers that specifically recognize insulin receptors (IRs) with a high affinity were selected through the SELEX process. Using quantum dot-labeled aptamers, we successfully imaged and analyzed the diffusive motions of individual IRs in the plasma membranes of a variety of cell lines (HIR, HEK293, HepG2). We further explored the cholesterol-dependent movement of IRs to address whether cholesterol depletion interferes with IRs and found that cholesterol depletion of the plasma membrane by methyl-?-cyclodextrin reduces the mobility of IRs. The aptamer-based single-molecule imaging of IRs will provide better understanding of insulin signal transduction through the dynamics study of IRs in the plasma membrane.

Chang, Minhyeok; Kwon, Mijin; Kim, Sooran; Yunn, Na-Oh; Kim, Daehyung; Ryu, Sung Ho; Lee, Jong-Bong

2014-05-01

376

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations  

PubMed Central

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

377

Theoretical underpinning of the single-molecule-dilution (SMD) method of direct haplotype resolution.  

PubMed Central

In a recent paper we have shown that DNA haplotypes of multiply heterozygous individuals can be resolved directly by polymerase-chain-reaction (PCR) amplification of a single molecule of genomic template. Our method (the single-molecule-dilution [SMD] method) relies on the stochastic separation of maternal and paternal alleles at high dilution. The stochasticity of separation and the potential for DNA shearing (which could separate the loci of interest) are two factors that can compromise the results of the experiment. This paper explores the consequences of these two factors and shows that the SMD method can be expected to work very reliably even in the presence of a moderate amount of DNA shearing. PMID:2339707

Stephens, J C; Rogers, J; Ruano, G

1990-01-01

378

Extending microscopic resolution with single-molecule imaging and active control.  

PubMed

Superresolution imaging of biological structures provides information beyond the optical diffraction limit. One class of superresolution techniques uses the power of single fluorescent molecules as nanoscale emitters of light combined with emission control, variously described by the acronyms PALM/FPALM/STORM and many others. Even though the acronyms differ and refer mainly to different active-control mechanisms, the underlying fundamental principles behind these "pointillist" superresolution imaging techniques are the same. Circumventing the diffraction limit requires two key steps. The first step (superlocalization) is the detection and localization of spatially separated single molecules. The second step actively controls the emitting molecules to ensure a very low concentration of single emitters such that they do not overlap in any one imaging frame. The final image is reconstructed from time-sequential imaging and superlocalization of the single emitting labels decorating the structure of interest. The statistical, imaging, and active-control strategies for achieving superresolution imaging with single molecules are reviewed. PMID:22577822

Thompson, Michael A; Lew, Matthew D; Moerner, W E

2012-01-01

379

Nonlinear optical measurement of membrane potential around single molecules at selected cellular sites  

PubMed Central

Membrane potential around single molecules has been measured by using the nonlinear optical phenomenon of second harmonic generation. This advance results from the interaction between a highly dipolar molecule with a selectively directed highly polarizable 1-nm gold particle. With this approach, a second harmonic signal, which is enhanced by the nanoparticle, is detected from a volume of nanometric dimensions. This present work clearly shows that functional cellular imaging around single molecules is possible by selectively directing an antibody with a 1-nm gold label to a specific membrane protein. The results of this work open the way for three-dimensional, high resolution functional imaging of membrane electrophysiology in cells and cellular networks. PMID:10359775

Peleg, Gadi; Lewis, Aaron; Linial, Michal; Loew, Leslie M.

1999-01-01

380

Three-dimensional super-resolution and localization of dense clusters of single molecules  

NASA Astrophysics Data System (ADS)

When a single molecule is detected in a wide-field microscope, the image approximates the point spread function of the system. However, as the distribution of molecules becomes denser and their images begin to overlap, existing solutions to determine the number of molecules present and their precise three-dimensional locations can tolerate little to no overlap. We propose a localization scheme that can identify several overlapping molecule images while maintaining high localization precision. A solution to this problem involving matched optical and digital techniques, as here proposed, can substantially increase the allowable labeling density and accelerate the data collection time of single-molecule localization microscopy by more than one order of magnitude.

Barsic, Anthony; Grover, Ginni; Piestun, Rafael

2014-06-01

381

Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories  

NASA Astrophysics Data System (ADS)

Folding and unfolding rates for the ultrafast folding villin subdomain were determined from a photon-by-photon analysis of fluorescence trajectories in single molecule FRET experiments. One of the obstacles to measuring fast kinetics in single molecule fluorescence experiments is blinking of the fluorophores on a timescale that is not well separated from the process of interest. By incorporating acceptor blinking into a two-state kinetics model, we show that it is possible to extract accurate rate coefficients on the microsecond time scale for folding and unfolding using the maximum likelihood method of Gopich and Szabo. This method yields the most likely parameters of a given model that can reproduce the observed photon trajectories. The extracted parameters agree with both the decay rate of the donor-acceptor cross correlation function and the results of ensemble equilibrium and kinetic experiments using nanosecond laser temperature jump.

Chung, Hoi Sung; Cellmer, Troy; Louis, John M.; Eaton, William A.

2013-08-01

382

Revealing -1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods  

PubMed Central

Programmed ribosomal frameshifting (PRF) serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate ?1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of ?1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous ?1 PRF mechanism among viruses. PMID:22545064

Chang, Kai-Chun

2012-01-01

383

Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy  

PubMed Central

DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170?nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

2011-01-01

384

Copper nanoparticle heterogeneous catalytic ‘click’ cycloaddition confirmed by single-molecule spectroscopy  

NASA Astrophysics Data System (ADS)

Colloidal or heterogeneous nanocatalysts can improve the range and diversity of Cu(I)-catalysed click reactions and facilitate catalyst separation and reuse. Catalysis by metal nanoparticles raises the question as to whether heterogeneous catalysts may cause homogeneous catalysis through metal ion leaching, since the catalytic process could be mediated by the particle, or by metal ions released from it. The question is critical as unwanted homogeneous processes could offset the benefits of heterogeneous catalysis. Here, we combine standard bench scale techniques with single-molecule spectroscopy to monitor single catalytic events in real time and demonstrate that click catalysis occurs directly at the surface of copper nanoparticles; this general approach could be implemented in other systems. We use ‘from the mole to the molecule’ to describe this emerging idea in which mole scale reactions can be optimized through an intimate understanding of the catalytic process at the single-molecule—single catalytic nanoparticle level.

Decan, Matthew R.; Impellizzeri, Stefania; Marin, M. Luisa; Scaiano, Juan C.

2014-08-01

385

Radio-frequency excitation of single molecules by scanning tunnelling microscopy  

NASA Astrophysics Data System (ADS)

We have upgraded a low-temperature scanning tunnelling microscope (STM) with a radio-frequency (RF) modulation system to extend STM spectroscopy to the range of low energy excitations (<1 meV). We studied single molecules of a stable hydrocarbon π-radical weakly physisorbed on Au(111). At 5 K thermal excitation of the adsorbed molecules is inhibited due to the lack of short-wavelength phonons of the substrate. We demonstrate resonant excitation of mechanical modes of single molecules by RF tunnelling at 115 MHz, which induces structural changes in the molecule ranging from controlled diffusion and modification of bond angles to bond breaking as the ultimate climax (resonance catastrophe). Our results pave the way towards RF-STM-based spectroscopy and controlled manipulation of molecular nanostructures on a surface.

Müllegger, Stefan; Das, Amal K.; Mayr, Karlheinz; Koch, Reinhold

2014-04-01

386

Radio-frequency excitation of single molecules by scanning tunnelling microscopy.  

PubMed

We have upgraded a low-temperature scanning tunnelling microscope (STM) with a radio-frequency (RF) modulation system to extend STM spectroscopy to the range of low energy excitations (<1 meV). We studied single molecules of a stable hydrocarbon ?-radical weakly physisorbed on Au(111). At 5 K thermal excitation of the adsorbed molecules is inhibited due to the lack of short-wavelength phonons of the substrate. We demonstrate resonant excitation of mechanical modes of single molecules by RF tunnelling at 115 MHz, which induces structural changes in the molecule ranging from controlled diffusion and modification of bond angles to bond breaking as the ultimate climax (resonance catastrophe). Our results pave the way towards RF-STM-based spectroscopy and controlled manipulation of molecular nanostructures on a surface. PMID:24594655

Müllegger, Stefan; Das, Amal K; Mayr, Karlheinz; Koch, Reinhold

2014-04-01

387

Study of Large Multimeric Biomolecules by Single-Molecule Manipulation and Imaging  

NASA Astrophysics Data System (ADS)

Single-molecule manipulation enables us to study the properties of long chain, multimeric biomolecules. Perlecan, a giant secreted heparin sulfate proteoglycan, is a major component of basement membrane, bone stroma and blood vessels. It is involved in processes such as cell adhesion, migration and modulation of apoptosis. The changes in its synthesis and function are closely associated with many diseases, including cancer. Von Willebrand factor is a large multimeric protein circulating in blood, and is crucial for initiation of blood coagulation. We use atomic force microscope to obtain force curves and images of these proteins. We characterized the mechanical property of perlecan as well as the domain conformational changes of von Willebrand factor. The results demonstrate that single-molecule manipulation can probe directly the dynamics of large biomolecules that are usually not accessible with other methods.

Lou, Kai; Wijeratne, Sitara S.; Martinez, Jerahme; Yeh, Hui-Chun; Moake, Joel; Dong, Jing-Fei; Farach-Carson, Mary C.; Kiang, Ching-Hwa

2012-02-01

388

Single-molecule analysis of chirality in a multicomponent reaction network.  

PubMed

Single-molecule approaches to chemical reaction analysis can provide information that is not accessible by studying ensemble systems. Changes in the molecular structures of compounds tethered to the inner wall of a protein pore are known to affect the current carried through the pore by aqueous ions under a fixed applied potential. Here, we use this approach to study the substitution reactions of arsenic(III) compounds with thiols, stretching the limits of the protein pore technology to track the interconversion of seven reaction components in a network that comprises interconnected Walden cycles. Single-molecule pathway analysis of 'allowed' and 'forbidden' reactions reveals that sulfur-sulfur substitution occurs with stereochemical inversion at the arsenic centre. Hence, we demonstrate that the nanoreactor approach can be a valuable technique for the analysis of dynamic reaction systems of relevance to biology. PMID:24950330

Steffensen, Mackay B; Rotem, Dvir; Bayley, Hagan

2014-07-01

389

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution  

PubMed Central

Forty years of classical biochemical analysis have identified the molecular players involved in initiation of transcription by eukaryotic RNA polymerase II (Pol II) and largely assigned their functions. However, a dynamic picture of Pol II transcription initiation and an understanding of the mechanisms of its regulation have remained elusive due in part to inherent limitations of conventional ensemble biochemistry. Here we have begun to dissect promoter-specific transcription initiation directed by a reconstituted human Pol II system at single-molecule resolution using fluorescence video-microscopy. We detected several stochastic rounds of human Pol II transcription from individual DNA templates, observed attenuation of transcription by promoter mutations, observed enhancement of transcription by activator Sp1, and correlated the transcription signals with real-time interactions of holo-TFIID molecules at individual DNA templates. This integrated single-molecule methodology should be applicable to studying other complex biological processes. PMID:22810624

Revyakin, Andrey; Zhang, Zhengjian; Coleman, Robert A.; Li, Yan; Inouye, Carla; Lucas, Julian K.; Park, Sang-Ryul; Chu, Steven; Tjian, Robert

2012-01-01

390

High-throughput scanning confocal microscope for single molecule Chandran R. Sabanayagam, John S. Eid, and Amit Mellera)  

E-print Network

High-throughput scanning confocal microscope for single molecule analysis Chandran R. Sabanayagam and programmable confocal microscope that can acquire upwards of 103 single-molecule fluorescence resonance energy transfer FRET time traces is presented. The microscope augments the capabilities of current instruments

Meller, Amit

391

Single-Molecule Orientations in Dyed Salt Crystals Kristin L. Wustholz, Bart Kahr,* and Philip J. Reid*  

E-print Network

Single-Molecule Orientations in Dyed Salt Crystals Kristin L. Wustholz, Bart Kahr,* and Philip J-1700 ReceiVed: June 7, 2005; In Final Form: July 8, 2005 We present single-molecule confocal microscopy) crystals. The incorporation of dye molecules that bear no size or shape similarity to the host ions

Reid, Philip J.

392

Single-Molecule Trapping Dynamics of Sugar-Uptake Channels in Marine Bacteria  

NASA Astrophysics Data System (ADS)

Stochastic fluctuations of ion current through one chitoporin (ChiP) channel within a bilayer lipid membrane in sugar solution are analyzed. These reflect single-molecule dynamics, which indicate that ChiP has multiple binding sites for sugar and exploits interactions between bound molecules to direct sugar passage. Since ChiP is used by marine bacteria, this is likely an adaptive strategy to enhance sugar translocation from rough water.

Suginta, Wipa; Smith, M. F.

2013-06-01

393

Single-molecule trapping dynamics of sugar-uptake channels in marine bacteria.  

PubMed

Stochastic fluctuations of ion current through one chitoporin (ChiP) channel within a bilayer lipid membrane in sugar solution are analyzed. These reflect single-molecule dynamics, which indicate that ChiP has multiple binding sites for sugar and exploits interactions between bound molecules to direct sugar passage. Since ChiP is used by marine bacteria, this is likely an adaptive strategy to enhance sugar translocation from rough water. PMID:25167532

Suginta, Wipa; Smith, M F

2013-06-01

394

Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics  

NASA Astrophysics Data System (ADS)

Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy transfer (FRET) and a technically challenging four-color FRET experiments on doubly labeled duplex DNA and quadruple-labeled Holliday junction, respectively.

Sobhy, M. A.; Elshenawy, M. M.; Takahashi, M.; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

2011-11-01

395

Platinum plasmonic nanostructure arrays for massively parallel single-molecule detection based on enhanced fluorescence measurements  

Microsoft Academic Search

We fabricated platinum bowtie nanostructure arrays producing fluorescence enhancement and evaluated their performance using two-photon photoluminescence and single-molecule fluorescence measurements. A comprehensive selection of suitable materials was explored by electromagnetic simulation and Pt was chosen as the plasmonic material for visible light excitation near 500 nm, which is preferable for multicolor dye-labeling applications like DNA sequencing. The observation of bright

Toshiro Saito; Satoshi Takahashi; Takayuki Obara; Naoshi Itabashi; Kazumichi Imai

2011-01-01

396

Development of High-Resolution Magnetic Tweezers for Single-Molecule Measurements  

Microsoft Academic Search

Magnetic tweezers can sense single-molecule DNA-protein interactions through optical tracking of the motion of a colloidal particle. This is typically done by relating changes in the colloid's diffraction pattern to its position. While diffraction-tracking is relatively simple to implement, it is intrinsically limited in its resolution. To improve this, we have developed a tracking technique based on Reflection Interference Contrast

Kipom Kim; Omar A. Saleh

2007-01-01

397

Electrochemical single-molecule detection in aqueous solution using self-aligned nanogap transducers.  

PubMed

Electrochemical detection of individual molecular tags in nanochannels may enable cost-effective, massively parallel analysis and diagnostics platforms. Here we demonstrate single-molecule detection of prototypical analytes in aqueous solution based on redox cycling in 40 nm nanogap transducers. These nanofluidic devices are fabricated using standard microfabrication techniques combined with a self-aligned approach that minimizes gap size and dead volume. We demonstrate the detection of three common redox mediators at physiological salt concentrations. PMID:24279688

Kang, Shuo; Nieuwenhuis, Ab F; Mathwig, Klaus; Mampallil, Dileep; Lemay, Serge G

2013-12-23

398

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.  

PubMed

The effects of "molecular crowding" on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop-receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high-molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ??G° ? -2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple "hard-sphere" treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ??G° ? -5 kcal/mol free-energy stabilization at excluded volume fractions of 30%. PMID:24850865

Dupuis, Nicholas F; Holmstrom, Erik D; Nesbitt, David J

2014-06-10

399

Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes  

PubMed Central

Next-generation sequencing has become the most widely used sequencing technology in genomics research, but it has inherent drawbacks when dealing with high-GC content genomes. Recently, single-molecule real-time sequencing technology (SMRT) was introduced as a third-generation sequencing strategy to compensate for this drawback. Here, we report that the unbiased and longer read length of SMRT sequencing markedly improved genome assembly with high GC content via gap filling and repeat resolution. PMID:23894349

Shin, Seung Chul; Ahn, Do Hwan; Kim, Su Jin; Lee, Hyoungseok; Oh, Tae-Jin; Lee, Jong Eun; Park, Hyun

2013-01-01

400

Using a Nanopore for Single Molecule Detection and Single Cell Transfection†  

PubMed Central

We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity. PMID:22645737

Nelson, Edward M.; Kurz, Volker; Shim, Jiwook; Timp, Winston; Timp, Gregory

2012-01-01

401

Single-molecule studies reveal the function of a third polymerase in the replisome  

PubMed Central

The Escherichia coli replisome contains three polymerases, one more than necessary to duplicate the two parental strands. Using single-molecule studies, we reveal two advantages conferred by the third polymerase. First, dipolymerase replisomes are inefficient at synthesizing lagging strands, leaving single-strand gaps, whereas tripolymerase replisomes fill strands almost to completion. Second, tripolymerase replisomes are much more processive than dipolymerase replisomes. These features account for the unexpected three-polymerase-structure of bacterial replisomes. PMID:22157955

Georgescu, Roxana E; Kurth, Isabel; O'Donnell, Mike E

2013-01-01

402

A comparative EPR study of high- and low-spin Mn 6 single-molecule magnets  

Microsoft Academic Search

We report detailed numerical and spectroscopic studies of two complexes from a family of recently discovered Mn6III single-molecule magnets (SMMs) with large barriers to magnetization reversal. These complexes consist of a pair of Mn3III triangles with a ferromagnetic interaction between the triangles. Recent studies have shown that the exchange interactions within the triangular Mn3III units can be switched from antiferromagnetic

Saiti Datta; Erica Bolin; Ross Inglis; Constantinos J. Milios; Euan K. Brechin; Stephen Hill

2009-01-01

403

Visualizing Protein-DNA Interactions at the Single-Molecule Level  

PubMed Central

Summary Recent advancements in single-molecule methods have allowed researchers to directly observe proteins acting on their DNA targets in real-time. Single-molecule imaging of protein-DNA interactions permits detection of the dynamic behavior of individual complexes that otherwise would be obscured in ensemble experiments. The kinetics of these processes can be monitored directly, permitting identification of unique sub-populations or novel reaction intermediates. Innovative techniques have been developed to isolate and manipulate individual DNA or protein molecules, and to visualize their interactions. The actions of proteins that have been visualized include: duplex DNA unwinding, DNA degradation, DNA packaging, translocation on DNA, sliding, superhelical twisting, and DNA bending, extension, and condensation. These single-molecule studies have provided new insights into nearly all aspects of DNA metabolism. Here we focus primarily on recent advances in fluorescence imaging and mechanical detection of individual protein-DNA complexes, with emphasis on selected proteins involved in DNA recombination: DNA helicases, DNA translocases, and DNA strand exchange proteins. PMID:19945909

Hilario, Jovencio; Kowalczykowski, Stephen C.

2009-01-01

404

Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence  

PubMed Central

The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule Fluorescence Resonance Energy Transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single molecule intensity-time trajectories of enzyme 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. PMID:21823644

He, Yufan; Li, Yue; Mukherjee, Saptarshi; Wu, Yan; Yan, Honggao; Lu, H. Peter

2011-01-01

405

Massively Parallel Haplotyping on Microscopic Beads for the High-Throughput Phase Analysis of Single Molecules  

PubMed Central

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1?10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases. PMID:22558329

Tiemann-Boege, Irene

2012-01-01

406

Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy  

NASA Astrophysics Data System (ADS)

The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostructures (``metasurfaces'') can achieve near-total power absorption at visible and near-infrared wavelengths. Thus far, however, both aims (i.e. single molecule Raman and total power absorption) have only been achieved using metal nanostructures produced by techniques (high resolution lithography or colloidal synthesis) that are complex and/or difficult to implement over large areas. Here, we demonstrate a metasurface that achieves the near-perfect absorption of visible-wavelength light and enables the Raman spectroscopy of single molecules. Our metasurface is fabricated using thin film depositions, and is of unprecedented (wafer-scale) extent.

Wang, Dongxing; Zhu, Wenqi; Best, Michael D.; Camden, Jon P.; Crozier, Kenneth B.

2013-10-01

407

Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy  

PubMed Central

The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostructures (“metasurfaces”) can achieve near-total power absorption at visible and near-infrared wavelengths. Thus far, however, both aims (i.e. single molecule Raman and total power absorption) have only been achieved using metal nanostructures produced by techniques (high resolution lithography or colloidal synthesis) that are complex and/or difficult to implement over large areas. Here, we demonstrate a metasurface that achieves the near-perfect absorption of visible-wavelength light and enables the Raman spectroscopy of single molecules. Our metasurface is fabricated using thin film depositions, and is of unprecedented (wafer-scale) extent. PMID:24091825

Wang, Dongxing; Zhu, Wenqi; Best, Michael D.; Camden, Jon P.; Crozier, Kenneth B.

2013-01-01

408

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level  

PubMed Central

Rho termination factor is an essential hexameric helicase responsible for terminating 20–50% of all mRNA synthesis in E. coli. We used single- molecule force spectroscopy to investigate Rho-RNA binding interactions at the Rho- utilization (rut) site of the ? tR1 terminator. Our results are consistent with Rho complexes adopting two states, one that binds 57 ±2 nucleotides of RNA across all six of the Rho primary binding sites, and another that binds 85 ±2 nucleotides at the six primary sites plus a single secondary site situated at the center of the hexamer. The single-molecule data serve to establish that Rho translocates 5?-to-3? towards RNA polymerase (RNAP) by a tethered-tracking mechanism, looping out the intervening RNA between the rut site and RNAP. These findings lead to a general model for Rho binding and translocation, and establish a novel experimental approach that should facilitate additional single- molecule studies of RNA-binding proteins. PMID:22885804

Koslover, Daniel J.; Fazal, Furqan M.; Mooney, Rachel A.; Landick, Robert; Block, Steven M.

2012-01-01

409

Reducing assembly complexity of microbial genomes with single-molecule sequencing  

PubMed Central

Background The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. Results To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Conclusions Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization. PMID:24034426

2013-01-01

410

Precursor configurations and post-rupture evolution of Ag-CO-Ag single-molecule junctions.  

PubMed

Experimental correlation analysis and first-principles theory are used to probe the structure and evolution of Ag-CO-Ag single-molecule junctions both before the formation and after the rupture of the junctions. Two dimensional correlation histograms and conditional histograms demonstrate that prior to the single-molecule bridge configuration the CO molecule is already bound parallel to the Ag single-atom contact. This molecular precursor configuration is accompanied by the opening of additional conductance channels compared to the single-channel transport in pure Ag monoatomic junctions. To investigate the post-rupture evolution of the junction we introduce a cross-correlation analysis between the opening and the subsequent closing conductance traces. This analysis implies that the molecule is bound rigidly to the apex of one electrode, and so the same single-molecule configuration is re-established as the junction is closed. The experimental results are confirmed by ab initio simulations of the evolution of contact geometries, transmission eigenvalues and scattering wavefunctions. PMID:25358380

Balogh, Zoltán; Visontai, Dávid; Makk, Péter; Gillemot, Katalin; Oroszlány, László; Pósa, László; Lambert, Colin; Halbritter, András

2014-12-21

411

Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.  

PubMed

Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps. PMID:24963600

Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

2014-01-01

412

Nanoengineering a single-molecule mechanical switch using DNA self-assembly  

NASA Astrophysics Data System (ADS)

The ability to manipulate and observe single biological molecules has led to both fundamental scientific discoveries and new methods in nanoscale engineering. A common challenge in many single-molecule experiments is reliably linking molecules to surfaces, and identifying their interactions. We have met this challenge by nanoengineering a novel DNA-based linker that behaves as a force-activated switch, providing a molecular signature that can eliminate errant data arising from non-specific and multiple interactions. By integrating a receptor and ligand into a single piece of DNA using DNA self-assembly, a single tether can be positively identified by force-extension behavior, and receptor-ligand unbinding easily identified by a sudden increase in tether length. Additionally, under proper conditions the exact same pair of molecules can be repeatedly bound and unbound. Our approach is simple, versatile and modular, and can be easily implemented using standard commercial reagents and laboratory equipment. In addition to improving the reliability and accuracy of force measurements, this single-molecule mechanical switch