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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

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking  

PubMed Central

The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2012-01-01

3

Single Molecule Spectroscopy of Electron Transfer  

SciTech Connect

The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

Michael Holman; Ling Zang; Ruchuan Liu; David M. Adams

2009-10-20

4

Methods and applications in single molecule electronics  

NASA Astrophysics Data System (ADS)

In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a single molecule, to extract information about changes in the configuration of a single molecule junction during an experiment, and to correlate these changes with changes in the conductance of the molecule.

Hihath, Joshua

5

Single Molecule Electron Transfer Process of Ruthenium Complexes.  

SciTech Connect

Transition metal complexes such as ruthenium complexes, having metal-to-ligand charge transfer states, are extensively used in solar energy conversion and electron transfer in biological systems and at interfaces. The dynamics of metal-to-ligand charge transfer and subsequent intermolecular, intramolecular, and interfacial electron transfer processes can be highly complex and inhomogeneous, especially when molecules are involved in interactions and perturbations from heterogeneous local environments and gated by conformation fluctuations. We have employed the single-molecule spectroscopy, a powerful approach for inhomogeneous systems to study the electron transfer dynamics of ruthenium complexes. We have applied a range of statistical analysis methods to reveal nonclassical photon emission behavior of the single ruthenium complex, i.e., photon antibunching, and photophysical ground-state recovering dynamics on a microsecond time scale. The use of photon antibunching to measure phosphorescence lifetimes and single-molecule electron transfer dynamics at room temperature is demonstrated.

Hu, Dehong; Lu, H PETER.

2006-03-01

6

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

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

Contact and Length Dependent Effects in Single-Molecule Electronics  

NASA Astrophysics Data System (ADS)

Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.

Hines, Thomas

10

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.

11

Single-molecule resolution of interfacial fibrinogen behavior: Effects of oligomer populations and surface chemistry  

PubMed Central

Using single-molecule total internal reflection fluorescence microscopy, the dynamic behavior of fibrinogen was observed at the interface between aqueous solution and various solid surfaces. Multiple populations of objects were observed, as characterized by surface residence times, interfacial diffusion, and fluorescence intensity. On all surfaces, populations exhibited direct links between surface residence time, rate of diffusion and fluorescence intensity. In particular longer-lived populations diffused more slowly and exhibited greater fluorescence intensity, leading to the conclusion that the objects represented fibrinogen monomers and discrete oligomer populations (dimers, trimers, etc.), and that these oligomer populations play an important role in the protein-surface interaction because of their long surface residence times. Two or three diffusive modes were observed for most populations, indicating that protein aggregates have multiple mechanisms for interaction with solid substrates. In addition, the fastest diffusive mode is believed to represent a hopping mode that often precedes desorption events. Surprisingly, a monolayer of PEG(5000) increased surface residence time and slowed diffusion of fibrinogen relative to bare fused silica or hydrophobically-modified fused silica, suggesting that the mechanism of PEG resistance to protein adhesion is more sophisticated than the simple repulsion of individual proteins. PMID:21391676

Kastantin, Mark; Langdon, Blake B.; Chang, Erin L.; Schwartz, Daniel K.

2011-01-01

12

Basic concepts of quantum interference and electron transport in single-molecule electronics.  

PubMed

This tutorial outlines the basic theoretical concepts and tools which underpin the fundamentals of phase-coherent electron transport through single molecules. The key quantity of interest is the transmission coefficient T(E), which yields the electrical conductance, current-voltage relations, the thermopower S and the thermoelectric figure of merit ZT of single-molecule devices. Since T(E) is strongly affected by quantum interference (QI), three manifestations of QI in single-molecules are discussed, namely Mach-Zehnder interferometry, Breit-Wigner resonances and Fano resonances. A simple MATLAB code is provided, which allows the novice reader to explore QI in multi-branched structures described by a tight-binding (Hückel) Hamiltonian. More generally, the strengths and limitations of materials-specific transport modelling based on density functional theory are discussed. PMID:25255961

Lambert, C J

2014-09-26

13

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer  

Microsoft Academic Search

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over

Haw Yang; Guobin Luo; Pallop Karnchanaphanurach; Tai-Man Louie; Ivan Rech; Sergio Cova; Luying Xun; X. Sunney Xie

2003-01-01

14

Single-molecule mapping of long-range electron transport for a cytochrome b(562) variant.  

PubMed

Cytochrome b(562) was engineered to introduce a cysteine residue at a surface-exposed position to facilitate direct self-assembly on a Au(111) surface. The confined protein exhibited reversible and fast electron exchange with a gold substrate over a distance of 20 Å between the heme redox center and the gold surface, a clear indication that a long-range electron-transfer pathway is established. Electrochemical scanning tunneling microscopy was used to map electron transport features of the protein at the single-molecule level. Tunneling resonance was directly imaged and apparent molecular conductance was measured, which both show strong redox-gated effects. This study has addressed the first case of heme proteins and offered new perspectives in single-molecule bioelectronics. PMID:21105644

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

2011-01-12

15

Single-molecule imaging with x-ray free-electron lasers: dream or reality?  

PubMed

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. PMID:21469805

Fratalocchi, A; Ruocco, G

2011-03-11

16

Intramolecular Distances and Dynamics from the Combined Photon Statistics of Single-Molecule FRET and Photoinduced Electron  

E-print Network

Intramolecular Distances and Dynamics from the Combined Photon Statistics of Single-Molecule FRET resonance energy transfer (FRET) and photo- induced electron transfer (PET) have developed into versatile are frequently used as a donor and acceptor for single-molecule FRET, are also suitable as PET probes

Schuler, Ben

17

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

18

Single-Molecule Measurements of T4 Lysozyme using Carbon Nanotube Electronic Circuits  

NASA Astrophysics Data System (ADS)

Because of their unique electronic and chemical properties, single-walled carbon nanotubes (SWNTs) are attractive candidates for label-free, single-molecule sensing and detection applications. In this work, a field-effect transistor (FET) architecture comprised of an individual SWNT is used to transduce the conformational motion of a single T4 lysozyme protein, conjugated to the SWNT side wall, into a corresponding electrical current signal. The SWNTs are grown using chemical vapor deposition, and metal electrical contacts are formed using electron beam evaporation. Using N-(1-Pyrene)maleimide, the protein is conjugated to the SWNT side wall. After conjugation, the sensing area of the device is submerged in an electrolyte solution, and the source-drain current is measured while applying an electrolyte-gate. Analysis of the signal provided single-molecule resolution of the dynamical activity of lysozyme as it hydrolyzes macromolecular peptidoglycan, a component of bacterial cell walls. This analysis revealed seven different independent time scales that govern the activity of lysozyme, the pH dependence of these time scales, and a lower limit on the number rate-limiting steps in lysozyme's hinge opening and closing motions. Furthermore, the signals elucidated differences in how lysozyme traverses and catalyzes structurally varying peptidoglycan constructs.

Sims, Patrick Craig

19

In situ superexchange electron transfer through a single molecule: A rectifying effect  

PubMed Central

An increasingly comprehensive body of literature is being devoted to single-molecule bridge-mediated electronic nanojunctions, prompted by their prospective applications in molecular electronics and single-molecule analysis. These junctions may operate in gas phase or electrolyte solution (in situ). For biomolecules, the latter is much closer to their native environment. Convenient target molecules are aromatic molecules, peptides, oligonucleotides, transition metal complexes, and, broadly, molecules with repetitive units, for which the conducting orbitals are energetically well below electronic levels of the solvent. A key feature for these junctions is rectification in the current–voltage relation. A common view is that asymmetric molecules or asymmetric links to the electrodes are needed to acquire rectification. However, as we show here, this requirement could be different in situ, where a structurally symmetric system can provide rectification because of the Debye screening of the electric field in the nanogap if the screening length is smaller than the bridge length. The Galvani potentials of each electrode can be varied independently and lead to a transistor effect. We explore this behavior for the superexchange mechanism of electron transport, appropriate for a wide class of molecules. We also include the effect of conformational fluctuations on the lowest unoccupied molecular orbital (LUMO) energy levels; that gives rise to non-Arrhenius temperature dependence of the conductance, affected by the molecule length. Our study offers an analytical formula for the current–voltage characteristics that demonstrates all these features. A detailed physical interpretation of the results is given with a discussion of reported experimental data. PMID:16641101

Kornyshev, Alexei A.; Kuznetsov, Alexander M.; Ulstrup, Jens

2006-01-01

20

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

21

Measurement and control of detailed electronic properties in a single molecule break junction.  

PubMed

The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction, providing us insightful clues towards the next step for in-depth study. PMID:25485840

Wang, Kun; Hamill, Joseph; Zhou, Jianfeng; Guo, Cunlan; Xu, Bingqian

2014-01-01

22

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

SciTech Connect

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., E-mail: c.lambert@lancaster.ac.uk [Department of Physics, Lancaster University, Lancaster LA1 4YB (United Kingdom); Bryce, Martin R. [Department of Chemistry, Durham University, Durham DH1 3LE (United Kingdom)] [Department of Chemistry, Durham University, Durham DH1 3LE (United Kingdom); Frampton, Harry; Chappell, David [BP Exploration Operating Company Limited, Chertsey Road, Sunbury on Thames, Middlesex TW16 7BP (United Kingdom)] [BP Exploration Operating Company Limited, Chertsey Road, Sunbury on Thames, Middlesex TW16 7BP (United Kingdom)

2014-02-07

23

Effects of electron-vibration coupling in transport through single molecules.  

PubMed

Using scanning tunneling spectroscopy, we study the transport of electrons through C(60) molecules on different metal surfaces. When electrons tunnel through a molecule, they may excite molecular vibrations. A fingerprint of these processes is a characteristic sub-structure in the differential conductance spectra of the molecular junction reflecting the onset of vibrational excitation. Although the intensity of these processes is generally weak, they become more important as the resonant character of the transport mechanism increases. The detection of single vibrational levels crucially depends on the energy level alignment and lifetimes of excited states. In the limit of large current densities, resonant electron-vibration coupling leads to an energy accumulation in the molecule, which eventually leads to its decomposition. With our experiments on C(60) we are able to depict a molecular scale picture of how electrons interact with the vibrational degrees of freedom of single molecules in different transport regimes. This understanding helps in the development of stable molecular devices, which may also carry a switchable functionality. PMID:22964796

Franke, Katharina J; Pascual, Jose Ignacio

2012-10-01

24

Electron transport in single molecule magnet transistors and optical transitions in the 15nitrogen-vacancy- center in diamond  

Microsoft Academic Search

This thesis presents theoretical studies dealing with quantum interference effects in electron transport through single molecule magnet transistors and a study on optical Lambda transitions in the 15NV - center in diamond. The thesis starts with a brief general introduction to the physics of quantum transport through single electron transistors. Afterwards, the main body of the thesis is divided into

Gabriel Gonzalez

2009-01-01

25

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

26

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.

27

Electron transport in single molecule magnet transistors and optical transitions in the 15nitrogen-vacancy- center in diamond  

NASA Astrophysics Data System (ADS)

This thesis presents theoretical studies dealing with quantum interference effects in electron transport through single molecule magnet transistors and a study on optical ? transitions in the 15NV - center in diamond. The thesis starts with a brief general introduction to the physics of quantum transport through single electron transistors. Afterwards, the main body of the thesis is divided into three studies: (i) In chapter (2) we describe the properties of single molecule magnets and the Berry phase interference present in these nanomagnets. We then propose a way to detect quantum interference experimentally in the current of a single molecule magnet transistor using polarized leads. We apply our theoretical results to the newly synthesized nanomagnet Ni4. (ii) In chapter (3) we review the Kondo effect and present a microscopic derivation of the Kondo Hamiltonian suitable for full and half-integer spin nanomagnets. We then calculate the conductance of the single molecule magnet transistor in the presence of the Kondo effect for Ni4 and show how the Berry phase interference becomes temperature dependent. (iii) We conclude in chapter (4) with a theoretical study of the single Nitrogen vacancy defect center in diamond. We show that it is possible to have spin non-conserving transitions via the hyperfine interaction and propose a way to write and read quantum information using circularly polarized light by means of optical ? transitions in this solid state system.

Gonzalez, Gabriel

28

Single-molecule electronic detection using nanoscale field-effect devices  

Microsoft Academic Search

Traditionally, biomolecular systems have been studied in ensemble. While much can be determined with ensemble measurements, scientific and technological interest is rapidly moving to single-molecule techniques, which rely primarily on fluorescent markers and advanced microscopy techniques. In this paper, we describe recent work using nanoscale transistors based on carbon nanotubes as charge-sensitive detectors. We show carbon nanotubes can be used

Sebastian Sorgenfrei; Kenneth Shepard

2011-01-01

29

Real-Space First-Principles Electron Transport in Single Molecules Dustin Lagoy, Eric Polizzi  

E-print Network

called NESSIE that is capable of such simulations and modeling for arbitrary devices. We are creating nanoscale potential systems such as single molecules within the NESSIE framework. · Perform simulations barrier calculated in the 3D framework Methods · Within the NESSIE framework the calculations

Mountziaris, T. J.

30

Direct observation of apolipoprotein B refolding at single molecule level by ultra sensitive fluorescence microscopy and solution transmission electron microscopy  

NASA Astrophysics Data System (ADS)

Apolipoprotein (apo) B is the only protein of low-density lipoprotein (LDL). The huge size and extreme hydrophobicity of apoB make examination of its lipidation process an experimental challenge. In this study, we showed that apoB lipidation and its intermediates could be observed at single molecule level by an on-path folding process. When carboxyl-terminal-truncated mutants apoB-29 and apoB-48, representing the amino-terminal 29% and 48%, respectively, of the full-length apoB (apoB-100), were used for comparison, we observed that the refolded apoB-100 resembled both native LDL and VLDL precursors. Thus the process of lipidation recapitulates that of pre-VLDL assembly, in vitro. These results suggest that the assembly of mature VLDL requires involvement of factors in addition to apoB-100 and lipids. Using solution transmission electron microscopy (TEM), we were able to detect incorporation of hydrophobic super-paramagnetic iron oxide nanoparticles into apoB-100 particles at the initial, but not final, stage of refolding. The current study thus demonstrates that VLDL assembly can be monitored at single molecule level, too.

Chang, Chia-Ching; Chu, Hsueh-Liang; Lee, Hsing-Yuan; Cheng, Tsai-Mu; Chen, Gong-Shen; Chen, Fu-Rong

2013-03-01

31

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

32

Structural and electronic dependence of the single-molecule-magnet behavior of dysprosium(III) complexes.  

PubMed

We investigate and compare the magnetic properties of two isostructural Dy(III)-containing complexes. The Dy(III) ions are chelated by hexadentate ligands and possess two apical bidendate nitrate anions. In dysprosium(III) N,N'-bis(imine-2-yl)methylene-1,8-diamino-3,6-dioxaoctane (1), the ligand's donor atoms are two alkoxo, two pyridine, and two imine nitrogen atoms. Dysprosium(III) N,N'-bis(amine-2-yl)methylene-1,8-diamino-3,6-dioxaoctane (2) is identical with 1 except for one modification: the two imine groups have been replaced by amine groups. This change has a minute effect on the structure and a larger effect the magnetic behavior. The two complexes possess slow relaxation of the magnetization in the presence of an applied field of 1000 Oe but with a larger barrier for reorientation of the magnetization for 1 (Ueff/kB = 50 K) than for 2 (Ueff/kB = 34 K). First-principles calculations using the spin-orbit complete active-space self-consistent-field method were performed and allowed to fit the experimental magnetization data. The calculations gave the energy spectrum of the 2J + 1 sublevels issued from the J = 15/2 free-ion ground state. The lowest-lying sublevels were found to have a large contribution of MJ = ±15/2 for 1, while for 2, MJ = ±13/2 was dominant. The observed differences were attributed to a synergistic effect between the electron density of the ligand and the small structural changes provoked by a slight alteration of the coordination environment. It was observed that the stronger ligand field (imine) resulted in complex 1 with a larger energy barrier for reorientation of the magnetization than 2. PMID:24533673

Campbell, Victoria E; Bolvin, Hélène; Rivière, Eric; Guillot, Regis; Wernsdorfer, Wolfgang; Mallah, Talal

2014-03-01

33

Conformational analysis of single perfluoroalkyl chains by single-molecule real-time transmission electron microscopic imaging.  

PubMed

Whereas a statistical average of molecular ensembles has been the conventional source of information on molecular structures, atomic resolution movies of single organic molecules obtained by single-molecule real-time transmission electron microscopy have recently emerged as a new tool to study the time evolution of the structures of individual molecules. The present work describes a proof-of-principle study of the determination of the conformation of each C-C bond in single perfluoroalkyl fullerene molecules encapsulated in a single-walled carbon nanotube (CNT) as well as those attached to the outer surface of a carbon nanohorn (CNH). Analysis of 82 individual molecules in CNTs under a 120 kV electron beam indicated that 6% of the CF2-CF2 bonds and about 20% of the CH2-CH2 bonds in the corresponding hydrocarbon analogue are in the gauche conformation. This comparison qualitatively matches the known conformational data based on time- and molecular-average as determined for ensembles. The transmission electron microscopy images also showed that the molecules entered the CNTs predominantly in one orientation. The molecules attached on a CNH surface moved more freely and exhibited more diverse conformation than those in a CNT, suggesting the potential applicability of this method for the determination of the dynamic shape of flexible molecules and of detailed conformations. We observed little sign of any decomposition of the specimen molecules, at least up to 10(7) e·nm(-2) (electrons/nm(2)) at 120 kV acceleration voltage. Decomposition of CNHs under irradiation with a 300 kV electron beam was suppressed by cooling to 77 K, suggesting that the decomposition is a chemical process. Several lines of evidence suggest that the graphitic substrate and the attached molecules are very cold. PMID:24341551

Harano, Koji; Takenaga, Shinya; Okada, Satoshi; Niimi, Yoshiko; Yoshikai, Naohiko; Isobe, Hiroyuki; Suenaga, Kazu; Kataura, Hiromichi; Koshino, Masanori; Nakamura, Eiichi

2014-01-01

34

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

35

Single molecule laser spectroscopy  

NASA Astrophysics Data System (ADS)

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.

Atta, Diaa; Okasha, Ali

2015-01-01

36

Single-molecule transistors.  

PubMed

The use of a gate electrode allows us to gain deeper insight into the electronic structure of molecular junctions. It is widely used for spectroscopy of the molecular levels and its excited states, for changing the charge state of the molecule and investigating higher order processes such as co-tunneling and the Kondo effect. Gate electrodes have been implemented in several types of nanoscale devices such as electromigration junctions, mechanically controllable break junctions, and devices with carbon-based electrodes. Here we review the state-of-the-art in the field of single-molecule transitors. We discuss the experimental challenges and describe the advances made for the different approaches. PMID:25310767

Perrin, Mickael L; Burzurí, Enrique; van der Zant, Herre S J

2015-02-10

37

Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.  

PubMed

"The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

Nakamura, Eiichi

2013-01-01

38

Tight-binding model of Mn12 single-molecule magnets: Electronic and magnetic structure and transport properties  

NASA Astrophysics Data System (ADS)

We describe and analyze a tight-binding model of single-molecule magnets (SMMs) that captures both the spin and spatial aspects of the SMM electronic structure. The model generalizes extended Hückel theory to include the effects of spin polarization and spin-orbit coupling. For neutral and negatively charged Mn12 SMMs with acetate or benzoate ligands, the model yields the total SMM spin, the spins of the individual Mn ions, the magnetic easy axis orientation, the size of the magnetic anisotropy barrier, and the size of the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gap consistent with experiment. For neutral molecules, the predicted spins and spatial locations of the HOMO are consistent with the results of density functional calculations. For the total spin and location of the LUMO, density functional theory based calculations yield varied results, while the present model yields results consistent with experiments on negatively charged molecules. For Mn12 SMMs with thiolate- and methylsulphide-terminated benzoate ligands (Mn12-Ph-Th), we find the HOMO to be located on the magnetic core of the molecule, but (unlike for the Mn12 SMMs that have previously been studied theoretically) we predict the LUMO and near-LUMO orbitals of Mn12-Ph-Th to be located on ligands. Therefore, we predict that for these Mn12 SMMs, resonant and off-resonant coherent transport via near-LUMO orbitals, not subject to Coulomb blockade, should occur. We propose that this effect can be used to identify specific experimentally realized SMM transistors in which the easy axis and magnetic moment are approximately parallel to the direction of the current flow. We also predict effective spin filtering by these SMMs to occur at low bias whether the transport is mediated by the HOMO that is on the magnetic core of the SMM or by near-LUMO orbitals located on the nominally nonmagnetic ligands.

Rostamzadeh Renani, Fatemeh; Kirczenow, George

2012-06-01

39

Clay Nanoparticle-Supported Single-Molecule Fluorescence Spectroelectrochemistry  

SciTech Connect

We report single-molecule fluorescence spectroelectrochemistry on a clay-modified ITO electrode using cresyl violet as a redox fluorescent probe. Ensemble averaged experiments show that cresyl violet displays well-defined cyclic voltammograms when adsorbed on the clay-modified electrode. By probing the fluorescence intensity of a single cresyl violet molecule absorbed on clay surface, we can trace the redox reaction of individual molecules induced by the cyclic voltammetric potential scanning. Inhomogeneous interfacial electron transfer dynamics of the immobilized single cresyl violet molecules on the clay-modified surface were observed.

Lei, Chenghong; Hu, Dehong; Ackerman, Eric J.

2009-02-11

40

Single-molecule mechanoenzymatics.  

PubMed

The ability of cellular signaling networks to sense, process, and respond to internal and external stimuli relies on their specific detection and transduction based on molecular recognition. The molecular mechanisms by which force is specifically sensed by mechanoenzymatic processes, translated into biochemical signals, and wired to cellular signaling networks recently became accessible with single-molecule force spectroscopy. By stretching such mechanobiochemical converters along their natural reaction coordinate, complex mechanical activation pathways and subsequent biochemical reactions may be measured in a dynamic and highly precise manner. The discovered mechanisms have in common well-tuned force-induced conformational changes that lead to exposure of active recognition sites. Newly developed strategies allow investigators to test different conformational states for activity and to elucidate mechanical architectures leading to highly specific mechanical activation pathways. Here, we discuss the advances in the new field of single-molecule mechanoenzymatics and highlight complementary examples studied in bulk and in vivo. PMID:22577826

Puchner, Elias M; Gaub, Hermann E

2012-01-01

41

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

42

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study  

Microsoft Academic Search

Dynamics of the environments of complex systems such as biomolecules, polar solvents, and glass plays an important role in controlling electron transfer reactions. The kinetics is determined by the nature of a complex multidimensional landscape. By quantifying the mean and high-order statistics of the first-passage time and the associated ratios, the dynamics in electron transfer reactions controlled by the environments

Luciana C. Paula; Jin Wang; Vitor B. P. Leite

2008-01-01

43

Molecular spintronics using single-molecule magnets  

Microsoft Academic Search

A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and

Lapo Bogani; Wolfgang Wernsdorfer

2008-01-01

44

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: a simulation model study.  

PubMed

Dynamics of the environments of complex systems such as biomolecules, polar solvents, and glass plays an important role in controlling electron transfer reactions. The kinetics is determined by the nature of a complex multidimensional landscape. By quantifying the mean and high-order statistics of the first-passage time and the associated ratios, the dynamics in electron transfer reactions controlled by the environments can be revealed. We consider real experimental conditions with finite observation time windows. At high temperatures, exponential kinetics is observed and there are multiple kinetic paths leading to the product state. At and below an intermediate temperature, nonexponential kinetics starts to appear, revealing the nature of the distribution of local traps on the landscape. Discrete kinetic paths emerge. At very low temperatures, nonexponential kinetics continues to be observed. We point out that the size of the observational time window is crucial in revealing the intrinsic nature of the real kinetics. The mean first-passage time is defined as a characteristic time. Only when the observational time window is significantly larger than this characteristic time does one have the opportunity to collect enough statistics to capture rare statistical fluctuations and characterize the kinetics accurately. PMID:19071925

Paula, Luciana C; Wang, Jin; Leite, Vitor B P

2008-12-14

45

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study  

SciTech Connect

Dynamics of the environments of complex systems such as biomolecules, polar solvents, and glass plays an important role in controlling electron transfer reactions. The kinetics is determined by the nature of a complex multidimensional landscape. By quantifying the mean and high-order statistics of the first-passage time and the associated ratios, the dynamics in electron transfer reactions controlled by the environments can be revealed. We consider real experimental conditions with finite observation time windows. At high temperatures, exponential kinetics is observed and there are multiple kinetic paths leading to the product state. At and below an intermediate temperature, nonexponential kinetics starts to appear, revealing the nature of the distribution of local traps on the landscape. Discrete kinetic paths emerge. At very low temperatures, nonexponential kinetics continues to be observed. We point out that the size of the observational time window is crucial in revealing the intrinsic nature of the real kinetics. The mean first-passage time is defined as a characteristic time. Only when the observational time window is significantly larger than this characteristic time does one have the opportunity to collect enough statistics to capture rare statistical fluctuations and characterize the kinetics accurately.

Paula, Luciana C. [Departamento de Fisica, Instituto de Biociencias Letras e Ciencias Exatas, Universidade Estadual Paulista, Sao Jose do Rio Preto, Sao Paulo 15054-000 (Brazil); Departamento de Estudos Basicos e Instrumentais, Universidade Estadual do Sudoeste da Bahia, Itapetinga, Bahia 45700-000 (Brazil); Wang Jin [Department of Chemistry, Physics and Applied Mathematics, State University of New York at Stony Brook, Stony Brook, New York 11794-3800 (United States); State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry of Chinese Academy of Sciences, Changchun 130022 (China); Leite, Vitor B. P. [Departamento de Fisica, Instituto de Biociencias Letras e Ciencias Exatas, Universidade Estadual Paulista, Sao Jose do Rio Preto, Sao Paulo 15054-000 (Brazil)

2008-12-14

46

Measuring single molecule conductance with break junctions.  

PubMed

Single-molecule conductance measurements made under potential control provide a critical link between chemical and molecular electronic data. These measurements are made possible by the STM break-junction method introduced recently, but questions remain about its reliability. Here we report the use of a logarithmic current-to-voltage converter to examine a wide range of currents in an STM break junction study of octanedithiol, clearly showing both the gold-quantum wire regime and the single molecule conductance regime. We find two sets of molecular currents that we tentatively ascribe to different bonding geometries of the molecules in the break junction. PMID:16512369

He, Jin; Sankey, Otto; Lee, Myeong; Tao, Nongjian; Li, Xiulan; Lindsay, Stuart

2006-01-01

47

A quantum chemical study from a molecular transport perspective: ionization and electron attachment energies for species often used to fabricate single-molecule junctions.  

PubMed

The accurate determination of the lowest electron attachment (EA) and ionization (IP) energies for molecules embedded in molecular junctions is important for correctly estimating, for example, the magnitude of the currents (I) or the biases (V) where an I-V curve exhibits significant non-Ohmic behavior. Benchmark calculations for the lowest electron attachment and ionization energies of several typical molecules utilized to fabricate single-molecule junctions characterized by n-type conduction (4,4'-bipyridine, 1,4-dicyanobenzene and 4,4'-dicyano-1,1'-biphenyl) and p-type conduction (benzenedithiol, biphenyldithiol, hexanemonothiol and hexanedithiol) based on the EOM-CCSD (equation-of-motion coupled-cluster singles and doubles) state-of-the-art method of quantum chemistry are presented. They indicate significant differences from the results obtained within current approaches to molecular transport. The present study emphasizes that, in addition to a reliable quantum chemical method, basis sets much better than the ubiquitous double-zeta set employed for transport calculations are needed. The latter is a particularly critical issue for correctly determining EAs, which is impossible without including sufficient diffuse basis functions. The spatial distribution of the dominant molecular orbitals (MOs) is another important issue, on which the present study draws attention, because it sensitively affects the MO energy shifts ? due to image charges formed in electrodes. The present results cannot substantiate the common assumption of a point-like MO midway between electrodes, which substantially affects the actual ?-values. PMID:25270244

Bâldea, Ioan

2014-01-01

48

Ultrafast dynamics of single molecules.  

PubMed

The detection of individual molecules has found widespread application in molecular biology, photochemistry, polymer chemistry, quantum optics and super-resolution microscopy. Tracking of an individual molecule in time has allowed identifying discrete molecular photodynamic steps, action of molecular motors, protein folding, diffusion, etc. down to the picosecond level. However, methods to study the ultrafast electronic and vibrational molecular dynamics at the level of individual molecules have emerged only recently. In this review we present several examples of femtosecond single molecule spectroscopy. Starting with basic pump-probe spectroscopy in a confocal detection scheme, we move towards deterministic coherent control approaches using pulse shapers and ultra-broad band laser systems. We present the detection of both electronic and vibrational femtosecond dynamics of individual fluorophores at room temperature, showing electronic (de)coherence, vibrational wavepacket interference and quantum control. Finally, two colour phase shaping applied to photosynthetic light-harvesting complexes is presented, which allows investigation of the persistent coherence in photosynthetic complexes under physiological conditions at the level of individual complexes. PMID:24473271

Brinks, Daan; Hildner, Richard; van Dijk, Erik M H P; Stefani, Fernando D; Nieder, Jana B; Hernando, Jordi; van Hulst, Niek F

2014-04-21

49

Geometric, electronic and magnetic structures of S = 19/2 and S = 20/2 thiophene-2-carboxylate functionalized Mn12 single molecule magnets.  

PubMed

The geometric and magnetic structures of two structurally related, but magnetically inequivalent, single molecule magnets (SMMs) have been computationally characterized. The first SMM, with formula [Mn12O12(O2CC4H3S)16(H2O)2](-1) (I), has a half-integer spin (S(I) = 19/2) due to ferrimagnetic ordering. The second SMM, with formula Mn12O12(O2CC4H3S)16(H2O)4 (II), has an integer spin (S(II) = 20/2) and its geometric structure has been computationally predicted. Both SMMs include thiophene-2-carboxylate functional groups for potential use in molecular electronics. To determine structural and electronic differences between both SMMs, spin polarized density functional theory was applied to I and II. Hydrogen bonding of two and four Mn-bound water molecules in I and II, respectively, to thiophene-2-carboxylate oxygen atoms and inner cubane oxygen atoms is essential for structural stabilization of both complexes. The one-electron-reduction of I is concomitant with a structural asymmetry within its cubane whereby two ions, of nominal Mn(4+)(Si = 3/2) character, are inequivalent to the other two and acquire an incipient Mn(3+)(Si = 4/2) character. The geometric asymmetry in I provides an extra, albeit small, contribution to its zero field splitting and anisotropy barrier to spin reversal. Thus, despite its lower spin state, the anisotropy barrier of I is only slightly lower than that of II. PMID:25360814

Rodriguez, Jorge H; Ziegler, Christopher J

2015-01-01

50

Fluorescence Microscopy of Single Molecules  

ERIC Educational Resources Information Center

The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

2004-01-01

51

Optofluidic single molecule flow proteometry  

NASA Astrophysics Data System (ADS)

A microfluidic single molecule fluorescence-based detection scheme is developed to identify target protein direct from cell lysate by using polyclonal antibody. Relative concentration of target protein in solution is determined by twodimensional (2D) photon burst analysis. Compared to conventional ensemble measurement assays, this microfluidic single molecule approach combines the advantages of higher sensitivity, fast processing time, small sample consumption and high resolution quantitative analysis.

Jing, Nan; Chou, Chao-Kai; Hung, Mien-Chie; Kameoka, Jun

2009-02-01

52

Rigid adamantane tripod linkage for well-defined conductance of a single-molecule junction.  

PubMed

We present a systematic analysis of molecular level alignments and electron transport characteristics based on the non-equilibrium Green's function (NEGF) approach combined with density functional theory (DFT) for phenyl dithiol (PDT) derivatives with two different linkages, simple thiol (ST) and tripod-shaped adamantane trithiol (ATT). The substantial adamantane-metal bonds afford a rigid contact structure and well-defined conductance of a single-molecule junction irrespective of interfacial phenomena, which accordingly allows us to utilize the intrinsic nature of the molecule for designing molecular devices with prescribed transport characteristics. We suggest a feasible application of the ATT linkage embedded single-molecule junction to a molecular transistor based on the practical feature of the ATT linkage, which is the unsusceptible behavior of transmission under the applied bias voltage. The present result may serve as an important reference point for designing molecular devices with prescribed transport properties. PMID:20694223

Lee, Sang Uck; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2010-10-01

53

Combining single-molecule manipulation and single-molecule detection.  

PubMed

Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. PMID:25255052

Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

2014-10-01

54

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

55

IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure  

PubMed Central

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

56

Single-molecule identification via electric current noise  

PubMed Central

Label-free and real-time single-molecule detection may aid the development of high-throughput biosensing platforms. Molecular fluctuations are a source of noise that often hinders single-molecule identification by obscuring the fine details of molecular identity. In this study, we report molecular identification through direct observation of quantum-fluctuation-induced inelastic noise in single organic molecules. We investigated current fluctuations flowing through a single molecule that is chemically connected to two electrodes. We found increased current oscillations synchronous to electric field excitations of characteristic molecular vibrational modes that contribute to inelastic electron tunnelling. This finding demonstrates a large contribution of charge interaction with nuclear dynamics on noise properties of single-molecule bridges and suggests a potential use of inelastic noise as a valuable molecular signature for single-molecule identification. PMID:21266988

Tsutsui, Makusu; Taniguchi, Masateru; Kawai, Tomoji

2010-01-01

57

Diamond based single molecule magnetic resonance spectroscopy  

E-print Network

The detection of a nuclear spin in an individual molecule represents a key challenge in physics and biology whose solution has been pursued for many years. The small magnetic moment of a single nucleus and the unavoidable environmental noise present the key obstacles for its realization. Here, we demonstrate theoretically that a single nitrogen-vacancy (NV) center in diamond can be used to construct a nano-scale single molecule spectrometer that is capable of detecting the position and spin state of a single nucleus and can determine the distance and alignment of a nuclear or electron spin pair. The proposed device will find applications in single molecule spectroscopy in chemistry and biology, such as in determining protein structure or monitoring macromolecular motions and can thus provide a tool to help unravelling the microscopic mechanisms underlying bio-molecular function.

Jianming Cai; Fedor Jelezko; Martin B. Plenio; Alex Retzker

2012-12-07

58

Correlated Single Quantum Dot Blinking and Interfacial Electron Transfer Dynamics  

PubMed Central

The electron transfer (ET) dynamics from core/multi-shell (CdSe/CdS3MLZnCdS2MLZnS2ML) quantum dots (QDs) to adsorbed Fluorescein (F27) molecules have been studied by single particle spectroscopy to probe the relationship between single QD interfacial electron transfer and blinking dynamics. Electron transfer from the QD to F27 and the subsequent recombination were directly observed by ensemble-averaged transient absorption spectroscopy. Single QD-F27 complexes show correlated fluctuation of fluorescence intensity and lifetime, similar to those observed in free QDs. With increasing ET rate (controlled by F27-to-QD ratio), the lifetime of on states decreases and relative contribution of off states increases. It was shown that ET is active for QDs in on states, the excited state lifetime of which reflects the ET rate, whereas in the off state QD excitons decay by Auger relaxation and ET is not a competitive quenching pathway. Thus, the blinking dynamics of single QDs modulate their interfacial ET activity. Furthermore, interfacial ET provides an additional pathway for generating off states, leading to correlated single QD interfacial ET and blinking dynamics in QD-acceptor complexes. Because blinking is a general phenomenon of single QDs, it appears that the correlated interfacial ET and blinking and the resulting intermittent ET activity are general phenomena for single QDs. PMID:21915369

Jin, Shengye; Hsiang, Jung-Cheng; Zhu, Haiming; Song, Nianhui; Dickson, Robert M.; Lian, Tianquan

2011-01-01

59

Single-molecule optomechanical cycle.  

PubMed

Light-powered molecular machines are conjectured to be essential constituents of future nanoscale devices. As a model for such systems, we have synthesized a polymer of bistable photosensitive azobenzenes. Individual polymers were investigated by single-molecule force spectroscopy in combination with optical excitation in total internal reflection. We were able to optically lengthen and contract individual polymers by switching the azo groups between their trans and cis configurations. The polymer was found to contract against an external force acting along the polymer backbone, thus delivering mechanical work. As a proof of principle, the polymer was operated in a periodic mode, demonstrating for the first time optomechanical energy conversion in a single-molecule device. PMID:12004125

Hugel, Thorsten; Holland, Nolan B; Cattani, Anna; Moroder, Luis; Seitz, Markus; Gaub, Hermann E

2002-05-10

60

Time Resolved Single Molecule Spectroscopy  

NASA Astrophysics Data System (ADS)

A new method based on the calculation of autocorrelation functions for spectra measured at a high acquisition rate is developed to study spectral dynamics of single molecules. The technique allows for spectroscopy with time resolutions down to the luminescence lifetime. The method is used to study spectral diffusion in two-photon excitation spectra of diphenyloctatetraene molecules doped in an n-tetradecane crystal matrix. The diffusion is light induced, and is absent in one-photon excitation spectra. It has a ``steplike'' time behavior, different from gradual diffusion observed in glasses.

Plakhotnik, Taras; Walser, Daniel

1998-05-01

61

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

62

Nanometer Resolution Imaging by SIngle Molecule Switching  

SciTech Connect

The fluorescence intensity of single molecules can change dramatically even under constant laser excitation. The phenomenon is frequently called "blinking" and involves molecules switching between high and low intensity states.[1-3] In additional to spontaneous blinking, the fluorescence of some special fluorophores, such as cyanine dyes and photoactivatable fluorescent proteins, can be switched on and off by choice using a second laser. Recent single-molecule spectroscopy investigations have shed light on mechanisms of single molecule blinking and photoswitching. This ability to controllably switch single molecules led to the invention of a novel fluorescence microscopy with nanometer spatial resolution well beyond the diffraction limit.

Hu, Dehong; Orr, Galya

2010-04-02

63

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

64

Metallic conductance in single-molecule junctions  

NASA Astrophysics Data System (ADS)

Through break junction techniques it has become possible to attach metallic wires to individual molecules. The actual presence of the molecule, its identity, and the numbers of molecules involved in the transport in many cases need to be deduced from measurements of current and voltage only. In parallel, several implementations of non-equilibrium Greens function approaches in combination with density functional theory have been developed in order to compute the properties of molecular junctions. For a sensitive test of the computational models there is a need for more detailed experimental observations on well-characterized model systems. In our experiments we focus on such model systems. They are simple, small molecules which have the advantage that they are relatively easy to handle in computations and they allow for more precise experimental tests at low temperatures. The molecules we have studied include H2, H2O, CO, CO2, C6H6 (benzene), and C60 contacted between Pt leads. The molecular levels hybridize strongly with the Pt metal giving rise to a high conductance. The presence of the molecules can be confirmed by the detection of vibration modes. These modes are visible in the differential conductance, dI/dV, as a function of voltage bias as fine steps at the energies eV=?n corresponding to those of the vibration modes. Further test involve isotope-substituted molecules and stretching of the molecular bridge in order to detect shifts in the energy of the modes. The conductance of a single-molecule bridge cannot be uniquely distinguished from bridges due to several parallel channels. However, by measuring shot noise, i.e. the intrinsic noise in the electron current, it is possible to show that the current is carried by a single molecule. For other molecules the measurement gives evidence that the molecule provides two, or sometimes more channels for conductance. The results are compared with state of the art non-equilibrium DFT calculations.

van Ruitenbeek, Jan

2010-03-01

65

Single-molecule orientational wave packet in ultrafast optical polarization  

NASA Astrophysics Data System (ADS)

The explicit derivation of the ultrafast optical polarization of a single molecule is presented. It is shown that an orientational wave packet carried by the excited molecular electron can provide a sharp definition for the space configuration of the laser-molecule interaction.

Mainos, C.

2006-09-01

66

Auger electron spectroscopy study on interfacial reactions in multilayer thin film systems  

NASA Astrophysics Data System (ADS)

Interfacial reactions at room temperature in multilayer thin film systems have been investigated by the Auger Electron Spectroscopy method. The multilayer thin film structure consists of metal, native oxide, and/or deposited interfacial layers on metal and semiconductor substrates. Various combinations of metals and interfacial layers on different substrates have been investigated. For the multilayer systems Au, Ag, Cu, and Cr were used as metals, GeO2, Bi2O3, SnO2, Sb2O3, Ga2O3, and As2O3 were used as interfacial layers, and GaAs, Si, and Fe were used as substrates. Only 'metal' atoms from the interfacial oxide layers (Ge from GeO2, Sb from Sb2O3, Bi from Bi2O3, Sn from SnO2, and Ga and As from the native oxide mixture of Ga2O3 and As2O3) were detected on the metal surface of Metal-Interfacial layer-Semiconductor and Metal-Interfacial layer-Metal-Semiconductor structures. This indicates that the interfacial reaction takes place only at the metal-interfacial layer interface. 'Drive-out' diffusion is present at all interfacial reactions. The interfacial reactions and the drive-out diffusion processes are thought to play an important role in the degradation of thin film multilayer structures.

Pandelišev, Kiril A.; Wang, Edward Y.

1982-06-01

67

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

68

Indistinguishable Photons from a Single Molecule  

E-print Network

We report the results of coincidence counting experiments at the output of a Michelson interferometer using the zero-phonon-line emission of a single molecule at $1.4 K$. Under continuous wave excitation, we observe the absence of coincidence counts as an indication of two-photon interference. This corresponds to the observation of Hong-Ou-Mandel correlations and proves the suitability of the zero-phonon-line emission of single molecules for applications in linear optics quantum computation.

A. Kiraz; M. Ehrl; Th. Hellerer; O. E. Mustecaplioglu; C. Brauchle; A. Zumbusch

2005-05-05

69

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

E-print Network

irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role at the adhesive substrate interface has led to much speculation regard- ing its role in adhesive bonding. HoweverSingle-molecule mechanics of mussel adhesion Haeshin Lee*, Norbert F. Scherer , and Phillip B

Scherer, Norbert F.

70

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

71

Vibrational Excitation in Single-Molecule Transistors: Deviation from the Simple  

E-print Network

Vibrational Excitation in Single-Molecule Transistors: Deviation from the Simple Franck+) in a single-molecule-transistor geometry. In (Cp)2Fen+ (n ) 0 and 1), almost no vibrations were excited during single-electron transport, whereas in (bpy)3Fen+ (n ) 1, 2, and 3), many distinct vibrations appeared

Heller, Eric

72

Convex lens-induced confinement for imaging single molecules.  

PubMed

Fluorescence imaging is used to study the dynamics of a wide variety of single molecules in solution or attached to a surface. Two key challenges in this pursuit are (1) to image immobilized single molecules in the presence of a high level of fluorescent background and (2) to image freely diffusing single molecules for long times. Strategies that perform well by one measure often perform poorly by the other. Here, we present a simple modification to a wide-field fluorescence microscope that addresses both challenges and dramatically improves single-molecule imaging. The technique of convex lens-induced confinement (CLIC) restricts molecules to a wedge-shaped gap of nanoscale depth, formed between a plano-convex lens and a planar coverslip. The shallow depth of the imaging volume leads to 20-fold greater rejection of background fluorescence than is achieved with total internal reflection fluorescence (TIRF) imaging. Elimination of out-of-plane diffusion leads to an approximately 10,000-fold longer diffusion-limited observation time per molecule than is achieved with confocal fluorescence correlation spectroscopy. The CLIC system also provides a new means to determine molecular size. The CLIC system does not require any nanofabrication, nor any custom optics, electronics, or computer control. PMID:20557026

Leslie, Sabrina R; Fields, Alexander P; Cohen, Adam E

2010-07-15

73

Graphene based single molecule nanojunction  

NASA Astrophysics Data System (ADS)

We introduce the ab-initio framework for zigzag-edged graphene fragment based single-electron transistor (SET) operating in the Coulomb blockade regime. Graphene is modeled using the density-functional theory and the environment is described by a continuum model. The interaction between graphene and the SET environment is treated self-consistently through the Poisson equation. We calculate the charging energy as a function of an external gate potential, and from this we obtain the charge stability diagram. Specifically, the importance of including re-normalization of the charge states due to the polarization of the environment has been demonstrated.

Chowdhury, R.; Adhikari, S.; Rees, P.

2012-03-01

74

Protein folding at single-molecule resolution  

PubMed Central

The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. PMID:21303706

Ferreon, Allan Chris M.; Deniz, Ashok A.

2011-01-01

75

Single molecule nanometry for biological physics  

PubMed Central

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 millisecond time resolution, and how these new tools are providing fundamental insights on 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 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

76

Life at the Single Molecule Level  

SciTech Connect

In a living cell, gene expression—the transcription of DNA to messenger RNA followed by translation to protein—occurs stochastically, as a consequence of the low copy number of DNA and mRNA molecules involved. Can one monitor these processes in a living cell in real time? How do cells with identical genes exhibit different phenotypes? Recent advances in single-molecule imaging in living bacterial cells allow these questions to be answered at the molecular level in a quantitative manner. It was found that rare events of single molecules can have important biological consequences.

Xie, Xiaoliang Sunny (Harvard) [Harvard

2011-03-04

77

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

78

Susanta Kumar Sarkar Single Molecule Biophysics Laboratory  

E-print Network

, NY. Advisor: Dr. Peng Chen EDUCATION 2006 Ph.D. (Physics). Oregon Center for Optics, University.S. (Physical Sciences). Indian Institute of Science, Bangalore, India. 1996 B.Sc. (Physics Honors). UniversitySusanta Kumar Sarkar Single Molecule Biophysics Laboratory Department of Physics 1523 Illinois

79

Investigation of interfacial structures of plasma transferred arc deposited aluminium based composites by transmission electron microscopy  

SciTech Connect

The aim of the present work was to study the interfacial structure and associated microstructural features of three different aluminium based composites. For each composite, the nature of the interfacial structure was examined by transmission electron microscopy (TEM) and correlated to its corrosion and tribological behavior. The nature of the interfacial structures observed by this TEM investigation also help explain the variation in each composite`s tribological behavior. Generally, composites reinforced with TiC or SiC particles exhibited a lower wear rate compared to Al{sub 2}O{sub 3} containing composites. This improvement in wear rate, in part could be attributed to a better interfacial bond whether achieved by a high dislocation density at the interface or by the presence of an interfacial reaction zone. However, other factors such as reinforcement fracture toughness and morphology also play an important role in resistance to wear.

Deuis, R.L.; Subramanian, C. [Univ. of South Australia, South Australia (Australia). Ian Wark Research Inst.] [Univ. of South Australia, South Australia (Australia). Ian Wark Research Inst.; Bee, J.V. [Univ. of Adelaide, South Australia (Australia). Dept. of Mechanical Engineering] [Univ. of Adelaide, South Australia (Australia). Dept. of Mechanical Engineering

1997-09-15

80

Single-molecule sensing electrode embedded in-plane nanopore.  

PubMed

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 SiO(2) 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. PMID:22355565

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

2011-01-01

81

Single-molecule sensing electrode embedded in-plane nanopore  

PubMed Central

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. PMID:22355565

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

2011-01-01

82

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

83

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

84

Lanthanide single molecule magnets: progress and perspective.  

PubMed

The last few years have seen a huge renaissance in the study of single molecule magnets (SMMs) thanks to the extensive applications of lanthanide ions with large inherent anisotropy in molecular magnetism. Particularly, the recent theoretical developments and the experimental expansion into the organometallic avenue have led to an eye-catching boost in this field. Here we highlight the recent progress in this fascinating and challenging field, with emphasis on several combined experimental and theoretical studies. PMID:25641200

Zhang, Peng; Zhang, Li; Tang, Jinkui

2015-02-17

85

Single-Molecule Biomechanics with Optical Methods  

Microsoft Academic Search

duce active movement against load (forexample, "molecular motors" such as myosin,which drives muscle contraction). Anumber of "molecular machines" (for instance,DNA-processing enzymes) are nowaccessible to single-molecule observation andmanipulation. Among other obvious targetswere more passive molecules (such asbiopolymers) that respond to an applied forcein various ways. This field was initially developedby work on DNA, but more recently,it has been extended to structural...

Amit D. Mehta; Matthias Rief; James A. Spudich; David A. Smith; Robert M. Simmons

1999-01-01

86

Single-Molecule Imaging of Cellular Signaling  

NASA Astrophysics Data System (ADS)

Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

87

Trapping and manipulating single molecules of DNA  

NASA Astrophysics Data System (ADS)

This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

Shon, Min Ju

88

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

89

Nonlinear Spectroscopy on a Single Quantum System: Two-Photon Absorption of a Single Molecule  

NASA Astrophysics Data System (ADS)

Two-photon fluorescence excitation spectra of single diphenyloctatetraene molecules trapped in an n-tetradecane matrix were measured at cryogenic temperatures. The purely electronic zero-phonon line (transition at 444 nanometers) of these single molecules with a width of about 60 megahertz was excited by a continuous-wave, single-mode laser at 888 nanometers. Even though the two-photon absorption cross section is extremely small, a high photon count rate and low background allowed nonlinear spectroscopy to be extended to the single-molecule level. This experiment also suggests the possibility of two-photon single-molecule scanning microscopy.

Plakhotnik, Taras; Walser, Daniel; Pirotta, Marco; Renn, Alois; Wild, Urs P.

1996-03-01

90

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

NASA Astrophysics Data System (ADS)

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.

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

2014-11-01

91

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

92

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

93

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

94

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

95

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

96

Hidden Markov Modelling of Single Molecule FRET Trajectories  

E-print Network

Hidden Markov Modelling of Single Molecule FRET Trajectories Life Sciences Interface DTC Short The development of single-molecule fluorescence energy transfer (FRET) microscopy has provided ground-by-eye. In this project, the application of Hidden Markov Modelling (HMM) for the anal- ysis of single-molecule FRET

Goldschmidt, Christina

97

Single molecule immunoassay on plasmonic platforms.  

PubMed

We examined the photophysical properties of the new near infrared (NIR) fluorescent label SeTau-665 on a plasmonic platform of self- assembled colloidal structures (SACS) of silver prepared on a semitransparent silver film. A SeTau-665 immunoassay was performed on this platform and a control glass slide. The fluorescence properties of this label substantially change due to plasmonic interactions. While the average brightness increase of SeTau 665 in ensemble measurements was about 70-fold, fluorescence enhancements up to four-hundred times were observed on certain "hot spots" for single molecule measurements. The intensity increase is strongly correlated with a simultaneous decrease in fluorescence lifetime in these "hot spots". The large increase in brightness allows the reduction of the excitation power resulting in a reduced background and increased photostability. The remarkable fluorescence enhancements observed for SeTau 665 on our plasmonic platform should allow to substantially improve single molecule detection and to reduce the detection limits in sensing devices. PMID:19929821

Luchowski, R; Matveeva, E G; Shtoyko, T; Sarkar, P; Patsenker, L D; Klochko, O P; Terpetschnig, E A; Borejdo, J; Akopova, I; Gryczynski, Z; Gryczynski, I

2010-01-01

98

Mechanoenzymatics and Nanoassembly of Single Molecules  

NASA Astrophysics Data System (ADS)

We investigated the muscle enzyme, titin kinase, by means of single-molecule force spectroscopy. Our results show that the binding of ATP, which is the first step of its signaling cascade controlling the muscle gene expression and protein turnover, is mechanically induced. The detailed determination of barrier positions in the mechanical activation pathway and the corresponding functional states allow structural insight, by comparing the experiment with molecular dynamics simulations. From our results, we conclude that titin kinase acts as a natural force sensor controlling the muscle build-up. To study the interplay of functional units, we developed the single-molecule cut-and-paste technique, which combines the precision of AFM with the selectivity of DNA hybridization. Functional units can be assembled one-by-one in an arbitrarily predefined pattern, with an accuracy that is better than 11 nm. The cyclic assembly process is optically monitored and mechanically recorded by force-extension traces. Using biotin as a functional unit attached to the transported DNA, patterns of binding sites may be created, to which streptavidin-modified nanoobjects like fluorescent nanoparticles can specifically self-assemble in a second step.

Puchner, Elias M.; Gaub, Hermann E.

99

Single-molecule chemical denaturation of riboswitches  

PubMed Central

To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods. PMID:23446276

Dalgarno, Paul A.; Bordello, Jorge; Morris, Rhodri; St-Pierre, Patrick; Dubé, Audrey; Samuel, Ifor D. W.; Lafontaine, Daniel A.; Penedo, J. Carlos

2013-01-01

100

One-by-one single-molecule detection of mutated nucleobases by monitoring tunneling current using a DNA tip.  

PubMed

A DNA molecule was utilized as a probe tip to achieve single-molecule genetic diagnoses. Hybridization of the probe and target DNAs resulted in electron tunneling along the emergent double-stranded DNA. Simple stationary monitoring of the tunneling current leads to single-molecule DNA detection and discovery of base mismatches and methylation. PMID:25503307

Bui, Phuc Tan; Nishino, Tomoaki; Shiigi, Hiroshi; Nagaoka, Tsutomu

2015-01-15

101

Characterization of interfacial reactions in magnetite tunnel junctions with transmission electron microscopy  

E-print Network

Characterization of interfacial reactions in magnetite tunnel junctions with transmission electron of Physics. DOI: 10.1063/1.1688535 I. INTRODUCTION Half metallic magnetite (Fe3O4) has been thought to be one is also discussed. II. EXPERIMENT Thin films were deposited onto Si or oxidized Si wafers by either rf

Laughlin, David E.

102

Proteomics: from single molecules to biological pathways  

PubMed Central

The conventional reductionist approach to cardiovascular research investigates individual candidate factors or linear signalling pathways but ignores more complex interactions in biological systems. The advent of molecular profiling technologies that focus on a global characterization of whole complements allows an exploration of the interconnectivity of pathways during pathophysiologically relevant processes, but has brought about the issue of statistical analysis and data integration. Proteins identified by differential expression as well as those in protein–protein interaction networks identified through experiments and through computational modelling techniques can be used as an initial starting point for functional analyses. In combination with other ‘-omics’ technologies, such as transcriptomics and metabolomics, proteomics explores different aspects of disease, and the different pillars of observations facilitate the data integration in disease-specific networks. Ultimately, a systems biology approach may advance our understanding of cardiovascular disease processes at a ‘biological pathway’ instead of a ‘single molecule’ level and accelerate progress towards disease-modifying interventions. PMID:23180722

Langley, Sarah R.; Dwyer, Joseph; Drozdov, Ignat; Yin, Xiaoke; Mayr, Manuel

2013-01-01

103

Actinide-based single-molecule magnets.  

PubMed

Actinide single-molecule magnetism has experienced steady growth over the last five years since the first discovery of slow magnetic relaxation in the mononuclear complex U(Ph2BPz2)3. Given their large spin-orbit coupling and the radial extension of the 5f orbitals, the actinides are well-suited for the design of both mononuclear and exchange-coupled molecules, and indeed at least one new system has emerged every year. By some measures, the actinides are already demonstrating promise for one day exceeding the performance characteristics of transition metal and lanthanide complexes. However, much further work is needed to understand the nature of the slow relaxation in mononuclear actinide complexes, as well as the influence of magnetic exchange on slow relaxation in multinuclear species. This perspective seeks to summarize the successes in the field and to address some of the many open questions in this up and coming area of research. PMID:25352033

Meihaus, Katie R; Long, Jeffrey R

2015-01-28

104

Nanopore Single-Molecule Analysis of DNA-Doxorubicin Interactions.  

PubMed

Anticancer activity and toxicity of doxorubicin (Dox) are associated with its DNA intercalation. To understand the role in gene regulation and the drug mechanism, it is a challenge to detect the DNA-Dox interaction at the single-molecule level without the use of laborious, time-consuming labeling assays and an error-prone amplification method. Here, we utilized the simplest and cheapest, yet highly sensitive, single-molecule nanopore technology to investigate the DNA-Dox interaction and explore in situ the intercalative reaction kinetics. Distinctive electronic signal patterns between DNA and the DNA-Dox complex allow protein nanopore to readily detect the changes in structure and function of DNA. After Dox insertion, nanopore unzipping time of DNA was elevated 10-fold while the blocking current decreased, demonstrating the higher affinity of the DNA-Dox complex (formation constant Kf = 3.09 × 10(5) M(-1)). Continuous rapid nanopore detection in real time displayed that Dox intercalation in DNA is a two-state dynamic process: fast binding and slow conformational adaption. The nanopore platform provides a powerful tool for studying small molecule-biomacromolecule interactions and paves the way for novel applications aimed at drug screening and functional analysis. PMID:25493921

Yao, Fujun; Duan, Jing; Wang, Ying; Zhang, Yue; Guo, Yanli; Guo, Huilin; Kang, Xiaofeng

2015-01-01

105

Detection of Steps in Single Molecule Data  

PubMed Central

Over the past few decades, single molecule investigations employing optical tweezers, AFM and TIRF microscopy have revealed that molecular behaviors are typically characterized by discrete steps or events that follow changes in protein conformation. These events, that manifest as steps or jumps, are short-lived transitions between otherwise more stable molecular states. A major limiting factor in determining the size and timing of the steps is the noise introduced by the measurement system. To address this impediment to the analysis of single molecule behaviors, step detection algorithms incorporate large records of data and provide objective analysis. However, existing algorithms are mostly based on heuristics that are not reliable and lack objectivity. Most of these step detection methods require the user to supply parameters that inform the search for steps. They work well, only when the signal to noise ratio (SNR) is high and stepping speed is low. In this report, we have developed a novel step detection method that performs an objective analysis on the data without input parameters, and based only on the noise statistics. The noise levels and characteristics can be estimated from the data providing reliable results for much smaller SNR and higher stepping speeds. An iterative learning process drives the optimization of step-size distributions for data that has unimodal step-size distribution, and produces extremely low false positive outcomes and high accuracy in finding true steps. Our novel methodology, also uniquely incorporates compensation for the smoothing affects of probe dynamics. A mechanical measurement probe typically takes a finite time to respond to step changes, and when steps occur faster than the probe response time, the sharp step transitions are smoothed out and can obscure the step events. To address probe dynamics we accept a model for the dynamic behavior of the probe and invert it to reveal the steps. No other existing method addresses the impact of probe dynamics on step detection. Importantly, we have also developed a comprehensive set of tools to evaluate various existing step detection techniques. We quantify the performance and limitations of various step detection methods using novel evaluation scales. We show that under these scales, our method provides much better overall performance. The method is validated on different simulated test cases, as well as experimental data. PMID:23956798

Aggarwal, Tanuj; Materassi, Donatello; Davison, Robert; Hays, Thomas; Salapaka, Murti

2013-01-01

106

Interfacial properties and electronic structure of ?-SiC(111)/?-Ti(0001): A first principle study  

NASA Astrophysics Data System (ADS)

First-principles calculations of ?-SiC(111)/?-Ti(0001) interface have been performed and the adhesion strength, interface energy, interfacial fracture toughness, and electronic structure are obtained. Six C-terminated ?-SiC(111)/?-Ti(0001) interface models are investigated to clarify the influence of stacking sites and Ti atoms tilt direction on the interface bonding and fracture toughness. The hollow-site-stacked interfaces, in which Ti atoms locate on the hollow site of interfacial C atoms (cases III and IV), are more thermodynamically stable with larger work of adhesion, and interfacial fracture toughness. The center-site-stacked (cases I and II) and top-site-stacked (cases V and VI) interfaces have a decreasing interface adhesion as the order. The electronic structure of hollow-site-stacked interface (case IV) gives the evidence that atomic bonding exists between interfacial C, Si, and Ti atoms, and the C-Ti bonds exhibit more covalent features than Si-Ti. The tilt direction of Ti atoms, namely the stacking style of Ti, has a subtle and secondary effect on the interface stability.

Li, Jian; Yang, Yanqing; Li, Lili; Lou, Juhong; Luo, Xian; Huang, Bin

2013-01-01

107

Toward single-molecule nanomechanical mass spectrometry  

PubMed Central

Mass spectrometry (MS) provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule sensitivity will be required. Nanoelectromechanical systems (NEMS) provide unparalleled mass sensitivity, which is now sufficient for the detection of individual molecular species in real time. Here we report the first demonstration of MS based on single-biological-molecule detection with NEMS. In our NEMS-MS system, nanoparticles and protein species are introduced by electrospray injection from fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics. Precipitous frequency shifts, proportional to the mass, are recorded in real time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency NEMS resonator. These first NEMS-MS spectra, obtained with modest mass sensitivity from only several hundred mass adsorption events, presage the future capabilities of this approach. We also outline the substantial improvements that are feasible in the near term, some of which are unique to NEMS-MS. PMID:19581898

Naik, A. K.; Hanay, M. S.; Hiebert, W. K.; Feng, X. L.; Roukes, M. L.

2009-01-01

108

Single molecule fluorescence microscopy of carbon nanotubes  

NASA Astrophysics Data System (ADS)

Single molecule microscopy has been extensively used in the past decade to study individual biomolecules with excellent spatial and temporal resolution. Meanwhile, characterization of nanomaterials and their development towards a variety of biological applications has progressed rapidly. Despite the comparable size of nanoparticles and biomolecules, no microscopy platform and technique currently exists to study the interactions of single biomolecules with nanoparticles. Here, we have successfully developed a set of experimental tools to study the interactions of DNA and proteins on a nanomaterial surface. We observe nucleic acid-encapsulated carbon nanotubes by using fluorophore-labeled complementary DNA to explore the sequence;-specific affinity of DNA to the nano-surface. Our results demonstrate cooperative exfoliation of the oligonucleotides from the nanomaterial surface and sequence-dependent bioavailability of nanotube;-adsorbed DNA for hybridization. The platform is employed in conjunction with a super resolution algorithm to pinpoint sites of DNA hybridization along the length of the nanotube. The ability of a microfluidic channel to easily exchange solution is used to study specific and non;-specific nuclease activity on nanotube;-adsorbed DNA. Protein function is mapped to local DNA topology on the nanomaterial and distance-dependent arrest of protein activity is observed, resulting in a nanotube;-induced arrest of 60% protein activity within 1 nm from the nanoparticle. Accessibility of different points of contact between the DNA and nanotube are assayed for nuclease resistance and range from 5% to 50%.

Jena, Prakrit Vaibhav

109

n and p type character of single molecule diodes.  

PubMed

Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface. PMID:25666850

Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

2015-01-01

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

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

Mure?an, Leila; Jacak, Jaros?aw; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

2010-01-01

112

'Single molecule': theory and experiments, an introduction.  

PubMed

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

Riveline, Daniel

2013-01-01

113

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

114

Organometallic single-molecule electronics: tuning electron transport through X(diphosphine)2FeC4Fe(diphosphine)2X building blocks by varying the Fe-X-Au anchoring scheme from coordinative to covalent.  

PubMed

A series of X(depe)2FeC?C-C?CFe(depe)2X complexes (depe =1,2-bis(diethylphosphino)ethane; X = I 1, NCMe 2, N2 3, C2H 4, C2SnMe3 5, C4SnMe3 6, NCSe 7, NCS 8, CN 9, SH 10, and NO2 11) was designed to study the influence of the anchor group on organometallic molecular transport junctions to achieve high-conductive molecular wires. The FeC4Fe core is electronically functional due to the redox-active Fe centers and sp-bridging ligands allowing a strong electronic delocalization. 1-11 were characterized by elemental analyses, X-ray diffraction, cyclic voltammetry, NMR, IR, and Raman spectroscopy. DFT calculations on model compounds gave the HOMO/LUMO energies. 5-9 were investigated in mechanically controllable break-junctions. For 9, unincisive features at 8.1 × 10(-7) G0 indicate that sterical reasons prevent stable junctions to form or that the coordinative binding motif prohibits electron injection. 7 and 8 with the hitherto unexploited coordinatively binding end groups NCSe and NCS yielded currents of 1.3 × 10(-9) A (7) and 1.8 × 10(-10) A (8) at ±1.0 V. The SnMe3 in 5 and 6 splits off, yielding junctions with covalent C-Au bonds and currents of 6.5 × 10(-7) A (Au-5'-Au) or 2.1 × 10(-7) A (Au-6'-Au). Despite of a length of almost 2 nm, the Au-5'-Au junction reaches 1% of the maximum current assuming one conductance channel in quantum point contacts. Additionally, the current noise in the transport data is considerably reduced for the covalent C-Au coupling compared to the coordinative anchoring of 7-9, endorsing C-Au coupled organometallic complexes as excellent candidates for low-ohmic molecular wires. PMID:25233357

Lissel, Franziska; Schwarz, Florian; Blacque, Olivier; Riel, Heike; Lörtscher, Emanuel; Venkatesan, Koushik; Berke, Heinz

2014-10-15

115

Enzymology and Life at the Single Molecule Level  

E-print Network

facilitated by the development of physical tools, such as X-ray crystallography. We face new challenges [8], the key idea behind single-molecule detection at room temperature was to use a microscope, these developments on room- temperature detection, imaging and spectroscopy of single-molecules with a far

Xie, Xiaoliang Sunney

116

Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases  

E-print Network

Chapter 7 Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases Jan Lipfert, Daniel A properties of type IB topoisomerases can be monitored using this technique. Key words: Single-molecule techniques, magnetic tweezers, topoisomerases, TopIB, spectroscopy. 1. Introduction 1.1. Topoisomerase

Dekker, Nynke

117

Nucleosome disassembly intermediates characterized by single-molecule FRET  

E-print Network

Nucleosome disassembly intermediates characterized by single-molecule FRET Alexander Gansena,1 of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX was induced by increasing NaCl concentration. At least 3 species with different FRET were identi- fied

Langowski, Jörg

118

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

119

Sorting Single Molecules: Application to Diagnostics and Evolutionary Biotechnology  

Microsoft Academic Search

A method is described that provides for detection and identification of single molecules in solution. The method is based on fluoresence correlation spectroscopy, which recoords spatio-temporaal correlation among fluctuating light singles, coupled with devices for trapping single molecules in an electric field. This technique is applied to studies of molecular evolution, where it allows fast screening of large mutant spectra

Manfred Eigen; Rudolf Rigler

1994-01-01

120

Collective effects in Single Molecule Magnets  

NASA Astrophysics Data System (ADS)

Single molecule magnets (SMMs), such as Mn12-acetate, are composed of transition metal ions and consists of identical molecules with large ground-state spin (S = 10) and a strong uniaxial anisotropy (65 K). Below about 3 K, Mn12-acetate exhibits magnetic hysteresis with steps at specific values of longitudinal magnetic field due to resonant quantum tunneling between spin up and down projections along the easy axis. The intermolecular exchange interactions between spins on molecules are quite small and spins are considered to be independent and non-interacting. However, the molecules do interact with each other both through magnetic dipolar interactions and through the lattice (e.g. phonons). I have investigated collective effects in SMMs due to these intermolecular interactions. In the thesis I will present experiments that explored magnetic ordering due to magnetic dipole interactions in Mn12-acetate and Mn12-acetate-MeOH. I will also present exper- iments on the onset of magnetic de agration in Mn12-acetate due to a thermal instability. The magnetic ordering studies involved investigating the effect of transverse fields on the susceptibility of single crystals of Mn12-acetate and Mn12-acetate- MeOH. Transverse fields increase quantum spin uctuations that suppress long- range order. However, the suppression of the Curie temperature by transverse fields in Mn12-acetate is far more rapid than predicted by the Transverse-Field Ising Ferromagnetic Model (TFIFM) and instead agrees with the predictions of the Random-Field Ising Ferromagnet Model. It appears that solvent disorder in Mn12-acetate gives rise to a distribution of random-fields that further suppress long-range order. Subsequent studies on Mn12-acetate-MeOH, with the same spin and similar lattice constants but without solvent disorder as Mn12-acetate, agrees with the TFIFM. The magnetic de agration studies involved studying the instability that leads to the ignition of magnetic deflagration in a thermally driven Mn 12-acetate crystal. When spins prepared in a metastable state reverse, Zeeman energy is released that diffuses away. In some circumstances, the heat released cannot be compensated by thermal diffusion, resulting in an instability that gives rise to a front of rapidly reversing spins traveling through the crystal. We observed a sharp crossover from relaxation driven by heat diffusion to a self-sustained reversal front that propagates at a constant subsonic speed.

Subedi, Pradeep

121

Conductance measurement of pyridyl-based single molecule junctions with Cu and Au contacts  

NASA Astrophysics Data System (ADS)

We studied the conductance of pyridyl-based single molecule junctions with Cu contacts by using an electrochemical jump-to-contact scanning tunneling microscopy break junction (ECSTM-BJ) approach. The single molecule junctions of 4,4?-bipyridine (BPY), 1,2-di(pyridin-4-yl)ethene (BPY-EE) and 1,2-di(pyridin-4-yl)ethane (BPY-EA) bridged with Cu clusters show three sets of conductance values. These values are smaller than the conductance values of single molecule junctions with Au electrodes measured by the traditional scanning tunneling microscopy break junction in acidic or neutral solutions, which can be attributed to the different electronic coupling efficiencies between molecules and electrodes. The consistent conductance of pyridyl-based molecules in acidic and neutral solutions may show that the protonated pyridyl group contacts to the electrode through the deprotonated form.

Zhou, Xiao-Yi; Peng, Zheng-Lian; Sun, Yan-Yan; Wang, Li-Na; Niu, Zhen-Jiang; Zhou, Xiao-Shun

2013-11-01

122

Single-Molecule Surface-Enhanced Raman Scattering: Can STEM/ EELS Image Electromagnetic Hot Spots?  

E-print Network

Single-Molecule Surface-Enhanced Raman Scattering: Can STEM/ EELS Image Electromagnetic Hot Spots-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM) to obtain maps of the localized, the STEM/EELS plasmon maps do not show any direct signature of an electromagnetic hot spot in the gaps

Pennycook, Steve

123

Gap size dependent transition from direct tunneling to field emission in single molecule junctions.  

PubMed

I/V characteristics recorded in mechanically controllable break junctions revealed that field emission transport is enhanced in single molecule junctions as the gap size between two nanoelectrodes is reduced. This observation indicates that Fowler-Nordheim tunneling occurs not only for intermolecular but also for intramolecular electron transport driven by a reduced energy barrier at short tunneling distances. PMID:21409211

Xiang, Dong; Zhang, Yi; Pyatkov, Feliks; Offenhäusser, Andreas; Mayer, Dirk

2011-04-28

124

Single molecule level plasmonic catalysis - a dilution study of p-nitrothiophenol on gold dimers.  

PubMed

Surface plasmons on isolated gold dimers can initiate intermolecular reactions of adsorbed p-nitrothiophenol. At the single molecule level when dimerization is not possible an intramolecular reaction can be observed. Experimental evidence indicates that plasmon-induced hot electrons provide the required activation energy. PMID:25599345

Zhang, Zhenglong; Deckert-Gaudig, Tanja; Singh, Pushkar; Deckert, Volker

2015-02-01

125

Defect-driven interfacial electronic structures at an organic/metal-oxide semiconductor heterojunction.  

PubMed

The electronic structure of the hybrid interface between ZnO and the prototypical organic semiconductor PTCDI is investigated via a combination of ultraviolet and X-ray photoelectron spectroscopy (UPS/XPS) and density functional theory (DFT) calculations. The interfacial electronic interactions lead to a large interface dipole due to substantial charge transfer from ZnO to 3,4,9,10-perylenetetracarboxylicdiimide (PTCDI), which can be properly described only when accounting for surface defects that confer ZnO its n-type properties. PMID:24830796

Winget, Paul; Schirra, Laura K; Cornil, David; Li, Hong; Coropceanu, Veaceslav; Ndione, Paul F; Sigdel, Ajaya K; Ginley, David S; Berry, Joseph J; Shim, Jaewon; Kim, Hyungchui; Kippelen, Bernard; Brédas, Jean-Luc; Monti, Oliver L A

2014-07-16

126

Controlling charge transport in single molecules using electrochemical gate.  

PubMed

We have studied charge transport through single molecules covalently bound to two gold electrodes in electrolytes by applying a voltage between the two electrodes and a reference electrode (gate). This electrochemical gating can effectively control the current through the molecules, depending on the electronic properties of the molecules. For electrochemically inactive molecules, such as 4,4'-bipyridine and 1,4'-benzenedithiol, the gate voltage influences the transport current only slightly (less than 30%). This lack of significant gate effect is attributed to the large LUMO-HOMO gaps of the molecules and the screening of the gate field by the two electrodes. For nitro-oligo(phenylene ethynylene) (OPE-NO2), which undergoes multiple irreversible reductions at negative gate voltages, the current through the molecules can be modulated several folds by the gate. This gate effect is irreversible and associated with the reduction of the NO2 group to different products that have different electron withdrawing capabilities from the conjugate backbone of the molecule. The most interesting molecules are perylene tetracarboxylic diimide compounds (PTCDI), which exhibit fully reversible redox reactions. The current through PTCDI can be reversibly varied and controlled over three orders of magnitude with the gate. Such a large gate effect is related to a redox state-mediated electron transport process. PMID:16512367

Li, Xiulan; Xu, Bingqian; Xiao, Xiaoyin; Yang, Xiaomei; Zang, Ling; Tao, Nongjian

2006-01-01

127

Microscopy beyond the diffraction limit using actively controlled single molecules  

PubMed Central

Summary In this short review, the general principles are described for obtaining microscopic images with resolution beyond the optical diffraction limit with single molecules. Although it has been known for several decades that single-molecule emitters can blink or turn on and off, in recent work the addition of on/off control of molecular emission to maintain concentrations at very low levels in each imaging frame combined with sequential imaging of sparse subsets has enabled the reconstruction of images with resolution far below the optical diffraction limit. Single-molecule active control microscopy provides a powerful window into information about nanoscale structures that was previously unavailable. PMID:22582796

MOERNER, W.E.

2013-01-01

128

Real-time single-molecule imaging of quantum interference.  

PubMed

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, in contrast to classical physics, quantum interference can 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 nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. 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 detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics. PMID:22447163

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

2012-05-01

129

Experimental demonstration of a single-molecule electric motor  

NASA Astrophysics Data System (ADS)

For molecules to be used as components in molecular machines, methods that couple individual molecules to external energy sources and that selectively excite motion in a given direction are required. Significant progress has been made in the construction of molecular motors powered by light and by chemical reactions, but electrically driven motors have not yet been built, despite several theoretical proposals for such motors. Here we report that a butyl methyl sulphide molecule adsorbed on a copper surface can be operated as a single-molecule electric motor. Electrons from a scanning tunnelling microscope are used to drive the directional motion of the molecule in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. The direction and rate of the rotation are related to the chiralities of both the molecule and the tip of the microscope (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices.

Tierney, Heather L.; Murphy, Colin J.; Jewell, April D.; Baber, Ashleigh E.; Iski, Erin V.; Khodaverdian, Harout Y.; McGuire, Allister F.; Klebanov, Nikolai; Sykes, E. Charles H.

2011-10-01

130

Kinetic equations for transport through single-molecule transistors  

NASA Astrophysics Data System (ADS)

We present explicit kinetic equations for quantum transport through a general molecular quantum dot, accounting for all contributions up to fourth order perturbation theory in the tunneling Hamiltonian and the complete molecular density matrix. Such a full treatment describes not only sequential, cotunneling, and pair tunneling, but also contains terms contributing to renormalization of the molecular resonances as well as their broadening. Due to the latter all terms in the perturbation expansion are automatically well defined for any set of system parameters: no divergences occur and no by-hand regularization is required. Additionally we show that, in contrast to second order perturbation theory, in fourth order it is essential to account for quantum coherence between nondegenerate states, entering the theory through the nondiagonal elements of the density matrix. As a first application, we study a single-molecule transistor coupled to a localized vibrational mode (Anderson-Holstein model). We find that cotunneling-assisted sequential tunneling processes involving the vibration give rise to current peaks, i.e., negative differential conductance in the Coulomb-blockade regime. Such peaks occur in the crossover to strong electron-vibration coupling, where inelastic cotunneling competes with Franck-Condon suppressed sequential tunneling, and thereby indicate the strength of the electron-vibration coupling. The peaks depend sensitively on the coupling to a dissipative bath, thus providing also an experimental probe of the Q factor of the vibrational motion.

Leijnse, M.; Wegewijs, M. R.

2008-12-01

131

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

132

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

133

Nano\\/micro technologies for single molecule manipulation and detection  

Microsoft Academic Search

A sensitive, rapid, and efficient single-molecule detection method was developed by combining fluorescence correlation spectroscopy (FCS) and on-chip molecular manipulation techniques. The highly restricted measurement volume in the FCS system significantly reduces the intrinsic background noise and facilitates single-molecule sensitivity. A microchannel integrated with multiple 3-D electrodes was fabricated and used for molecular sensing and manipulation by which individual DNA

Tza-huei Wang; Chih-ming Ho

2003-01-01

134

Single-molecule fluorescence characterization in native environment  

Microsoft Academic Search

Single-molecule detection (SMD) with fluorescence is a widely used microscopic technique for biomolecule structure and function\\u000a characterization. The modern light microscope with high numerical aperture objective and sensitive CCD camera can image the\\u000a brightly emitting organic and fluorescent protein tags with reasonable time resolution. Single-molecule imaging gives an unambiguous\\u000a bottom-up biomolecule characterization that avoids the “missing information” problem characteristic of

Thomas P. Burghardt; Katalin Ajtai

2010-01-01

135

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

136

Optical spectroscopy of the bulk and interfacial hydrated electron from ab initio calculations.  

PubMed

The optical spectrum of the hydrated (aqueous) electron, e(aq)(–), is the primary observable by means of which this species is detected, monitored, and studied. In theoretical calculations, this spectrum has most often been simulated using one-electron models. Here, we present ab initio simulations of that spectrum in both bulk water and, for the first time, at the water/vapor interface, using density functional theory and its time-dependent variant. Our results indicate that this approach provides a reliable description, and quantitative agreement with the experimental spectrum for the bulk species is obtained using a “tuned” long-range corrected functional. The spectrum of the interfacial electron is found to be very similar to the bulk spectrum. PMID:24576141

Uhlig, Frank; Herbert, John M; Coons, Marc P; Jungwirth, Pavel

2014-09-01

137

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

138

Single Molecule Conductance Measurement of Photochromic Molecules and Carotenoids  

NASA Astrophysics Data System (ADS)

We report data for the single molecule conductance of (a) photochromic molecules in the `open' and `closed' forms and (b) carotenoid polyenes. The photochromic molecules we studied switch between an open state (that absorbs in the UV to become closed) and a closed state (that absorbs in the visible to become open) through light-induced isomerization. The molecular resistance is 526±90 M? in the open form and 4±1 M? in the closed form when attached to gold break junction electrodes via thiol linkages. Carotenoid polyenes play an essential role as `molecular wires' in photosynthesis. We measured the electrical conductance of a series of carotenoids with 5, 7, 9 and 11 double-single bond pairs. The electronic decay constant, ?, is determined to be 0.224±0.036å-1 in close agreement with the value obtained from first principles simulations (0.217±0.01 å-1). The absolute values of the molecular conductance are within a factor three of those calculated from first-principles.

He, Jin; Terazono, Yuichi; Lindsay, Stuart

2005-03-01

139

Imaging the charge distribution within a single molecule.  

PubMed

Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules. PMID:22367099

Mohn, Fabian; Gross, Leo; Moll, Nikolaj; Meyer, Gerhard

2012-04-01

140

Detailed single-molecule spectroelectrochemical studies of the oxidation of conjugated polymers.  

PubMed

Single-particle fluorescence spectroelectrochemistry was used to investigate the electrochemical oxidation of isolated, immobilized particles of the conjugated polymers BEH-PPV and MEH-PPV at an indium tin oxide (ITO) electrode immersed in an electrolyte solution. Two types of particles were investigated: (i) polymer single molecules (SM) and (ii) nanoparticle (NP) aggregates of multiple polymer single molecules. For the BEH-PPV polymer, the observation of nearly identical lowest oxidation potentials for different SM in the ensemble is evidence for effective electrostatic screening by the surrounding electrolyte solution. A combination of Monte Carlo simulations and application of Poisson-Boltzmann solvers were used to model the charging of polymer single molecules and nanoparticles in the electrochemical environment. The results indicate that the penetration of electrolyte anions into the polymer nanoparticles is necessary to produce the observed narrow fluorescence quenching vs oxidation potential curves. Finally, fluorescence-lifetime single-molecule spectroelectrochemical (SMS-EC) data revealed that at low potential an excited state reduction process (i.e., electron transfer from ITO to the polymer) is probably the dominant fluorescence quenching process. PMID:19863138

Palacios, Rodrigo E; Chang, Wei-Shun; Grey, John K; Chang, Ya-Lan; Miller, William L; Lu, Chun-Yaung; Henkelman, Graeme; Zepeda, Danny; Ferraris, John; Barbara, Paul F

2009-11-01

141

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

142

Atomic scale control of single molecule charging.  

PubMed

A scanning tunneling microscope was used to study charging of single copper phthalocyanine molecules adsorbed on an ultrathin Al(2)O(3) film grown on a NiAl(110) surface. A double-barrier tunnel junction is formed by a vacuum barrier between the tip and the molecule and an oxide barrier between the molecule and the NiAl. In this geometry the molecule can be charged by the tunneling electrons. This charging was found to be strongly dependent on the position of the tip above the molecule and the applied bias voltage. PMID:16613439

Mikaelian, G; Ogawa, N; Tu, X W; Ho, W

2006-04-01

143

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

144

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

145

Sizing up single-molecule enzymatic conformational dynamics.  

PubMed

Enzymatic reactions and related protein conformational dynamics are complex and inhomogeneous, playing crucial roles in biological functions. The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. It is extremely difficult to characterize and analyze such complex dynamics in an ensemble-averaged measurement, especially when the enzymes are associated with multiple-step, multiple-conformation complex chemical interactions and transformations. Beyond the conventional ensemble-averaged studies, real-time single-molecule approaches have been demonstrated to be powerful in dissecting the complex enzymatic reaction dynamics and related conformational dynamics. Single-molecule enzymology has come a long way since the early demonstrations of the single-molecule spectroscopy studies of enzymatic dynamics about two decades ago. The rapid development of this fundamental protein dynamics field is hand-in-hand with the new development of single-molecule imaging and spectroscopic technology and methodology, theoretical model analyses, and correlations with biological preparation and characterization of the enzyme protein systems. The complex enzymatic reactions can now be studied one molecule at a time under physiological conditions. Most exciting developments include active manipulation of enzymatic conformational changes and energy landscape to regulate and manipulate the enzymatic reactivity and associated conformational dynamics, and the new advancements have established a new stage for studying complex protein dynamics beyond by simply observing but by actively manipulating and observing the enzymatic dynamics at the single-molecule sensitivity temporally and spatially. PMID:24306450

Lu, H Peter

2014-02-21

146

Observing single-molecule chemical reactions on metal nanoparticles  

NASA Astrophysics Data System (ADS)

We report on 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 scatters (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 bread SERS vibrational bands at 1592 cm-1 and 1340 cm-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 measurement 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, Steven R.; Ambrose, W. Patrick; Goodwin, Peter M.; Keller, Richard A.

2001-06-01

147

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

148

Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface  

PubMed Central

Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on the spin transport. Going beyond the investigations focused on physisorbed SMMs, in this work the robust grafting of Terbium(III) bis(phthalocyaninato) complexes to silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here, by exploiting the surface sensitivity of X-ray circular magnetic dichroism we evidence an enhancement of the magnetic bistability of this single-molecule magnet, in contrast to the dramatic reduction of the magnetic hysteresis that characterises monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices. PMID:25109254

Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G.; Dalcanale, Enrico; Sessoli, Roberta

2014-01-01

149

Single-Molecule Fluorescence Imaging in Living Cells  

NASA Astrophysics Data System (ADS)

The transition of single-molecule fluorescence detection and imaging from in vitro to living cells has greatly enriched our knowledge on the behavior of single biomolecules in their native environments and their roles in cellular processes. Here we review recent advances of single-molecule biophysical approaches to live-cell studies based on fluorescence imaging. We start by discussing the practical considerations in designing single-molecule fluorescence imaging in cells, including the choice of fluorescent probes, labeling methods, instrumentation, and imaging techniques. We then describe representative examples in detail to illustrate the physicochemical parameters that can be obtained by imaging individually labeled biomolecules in cells and what can be learned from such characterizations.

Xia, Tie; Li, Nan; Fang, Xiaohong

2013-04-01

150

Evidence of natural isotopic distribution from single-molecule SERS  

E-print Network

We report on the observation of the natural isotopic spread of carbon from single-molecule Surface Enhanced Raman Spectroscopy (SM-SERS). By choosing a dye molecule with a very localized Raman active vibration in a cyano bond (C$\\equiv$N triple bond), we observe (in a SERS colloidal liquid) a small fraction of SM-SERS events where the frequency of the cyano mode is softened and in agreement with the effect of substituting $^{12}$C by the next most abundant $^{13}$C isotope. This example adds another demonstration of single molecule sensitivity in SERS through isotopic editing which is done, in this case, not by artificial isotopic editing but rather by nature itself. It also highlights SERS as a unique spectroscopic tool, capable of detecting an isotopic change in one atom of a single molecule.

P. G. Etchegoin; E. C. Le Ru; M. Meyer

2008-11-03

151

Making connections — strategies for single molecule fluorescence biophysics  

PubMed Central

Fluorescence spectroscopy and fluorescence microscopy carried out on the single molecule level are elegant methods to decipher complex biological systems; it can provide a wealth of information that frequently is obscured in the averaging of ensemble measurements. Fluorescence can be used to localise a molecule, study its binding with interaction partners and ligands, or to follow conformational changes in large multicomponent systems. Efficient labelling of proteins and nucleic acids is very important for any fluorescence method, and equally the development of novel fluorophores has been crucial in making biomolecules amenable to single molecule fluorescence methods. In this paper we review novel coupling strategies that permit site-specific and efficient labelling of proteins. Furthermore, we will discuss progressive single molecule approaches that allow the detection of individual molecules and biomolecular complexes even directly isolated from cellular extracts at much higher and much lower concentrations than has been possible so far. PMID:23769868

Grohmann, Dina; Werner, Finn; Tinnefeld, Philip

2013-01-01

152

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

153

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

154

Single molecule studies of RNA-RNA interactions.  

PubMed

Non-coding RNAs including microRNAs, siRNAs, and snoRNAs interact with their targets directly through RNA-RNA interactions by base-paring (van Himbergen et al., Nucleic Acids Res 21(8):1713-1717, 1993). RNA-RNA interactions play important roles in gene transcription and protein translation, which can be investigated with several experimental techniques including single molecule methods. Here, we describe how single molecule Förster resonance energy transfer (FRET) can be used to study RNA-RNA interactions in vitro by either surface immobilization or vesicle encapsulation. PMID:25352139

Yu, Dongmei; Qin, Peiwu; Cornish, Peter V

2015-01-01

155

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

156

Single-molecule methods for studying gene regulation in vivo.  

PubMed

The recent emergence of new experimental tools employing sensitive fluorescence detection in vivo has made it possible to visualize various aspects of gene regulation at the single-molecule level in the native, intracellular context. In this review, we will first describe general considerations for in vivo, single-molecule fluorescence detection of DNA, mRNA, and protein molecules involved in gene regulation. We will then give an overview of the rapidly evolving suite of molecular tools available for observing gene regulation in vivo and discuss new insights they have brought into gene regulation. PMID:23430319

Hensel, Zach; Xiao, Jie

2013-03-01

157

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, Bríd; de Wet, Ben; Wallace, Mark I.

2009-01-01

158

Single-molecule transition-state analysis of RNA folding  

E-print Network

enzymes and the increasing number of applications of RNA in biotechnology and medicine. A critical step. Our single- molecule experiments in conjunction with site-specific mutations and metal ion titrations in modern biotechnology and medicine (5, 6). For example, recent developments in small interfering RNAs, pro

Walter, Nils G.

159

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

160

A plutonium-based single-molecule magnet.  

PubMed

The magnetic properties of the 5f(5) [tris-(tri-1-pyrazolylborato)-plutonium(III)] complex have been investigated by ac susceptibility measurements, showing it to be the first plutonium single-molecule magnet; its magnetic relaxation slows down with decreasing temperature through a thermally activated mechanism followed by a quantum tunnelling regime below 5 K. PMID:24927255

Magnani, N; Colineau, E; Griveau, J-C; Apostolidis, C; Walter, O; Caciuffo, R

2014-08-01

161

Single-molecule nanocatalysis reveals heterogeneous reaction pathways and  

E-print Network

- state accumulation of redox reactions catalysed by single Au nanocrystals19 . Here, we study the realARTICLES Single-molecule nanocatalysis reveals heterogeneous reaction pathways and catalytic in ensemble measurements. Using a single-nanoparticle single-turnover approach, we study the redox catalysis

Chen, Peng

162

Nanogel surface coatings for improved single-molecule imaging substrates  

E-print Network

Nanogel surface coatings for improved single-molecule imaging substrates Lee A. Tessler1, Casey D counting revealed that nanogel-coated surfaces exhibit lower protein adsorp- tion than covalently coupled-background surface coatings have been developed that reduce protein adsorption to SM levels--levels at which

Mitra, Rob

163

Interlaced Optical Force-Fluorescence Measurements for Single Molecule Biophysics  

PubMed Central

Combining optical tweezers with single molecule fluorescence offers a powerful technique to study the biophysical properties of single proteins and molecules. However, such integration into a combined, coincident arrangement has been severely limited by the dramatic reduction in fluorescence longevity of common dyes under simultaneous exposure to trapping and fluorescence excitation beams. We present a novel approach to overcome this problem by alternately modulating the optical trap and excitation beams to prevent simultaneous exposure of the fluorescent dye. We demonstrate the dramatic reduction of trap-induced photobleaching effects on the common single molecule fluorescence dye Cy3, which is highly susceptible to this destructive pathway. The extension in characteristic fluorophore longevity, a 20-fold improvement when compared to simultaneous exposure to both beams, prolongs the fluorescence emission to several tens of seconds in a combined, coincident arrangement. Furthermore, we show that this scheme, interlaced optical force-fluorescence, does not compromise the trap stiffness or single molecule fluorescence sensitivity at sufficiently high modulation frequencies. Such improvement permits the simultaneous measurement of the mechanical state of a system with optical tweezers and the localization of molecular changes with single molecule fluorescence, as demonstrated by mechanically unzipping a 15-basepair DNA segment labeled with Cy3. PMID:16648165

Brau, Ricardo R.; Tarsa, Peter B.; Ferrer, Jorge M.; Lee, Peter; Lang, Matthew J.

2006-01-01

164

Single-molecule Studies of RNA Polymerase: Motoring Along  

PubMed Central

Single-molecule techniques have advanced our understanding of transcription by RNA polymerase. A new arsenal of approaches, including single-molecule fluorescence, atomic-force microscopy, magnetic tweezers, and optical traps have been employed to probe the many facets of the transcription cycle. These approaches supply fresh insights into the means by which RNA polymerase identifies a promoter; initiates transcription, translocates and pauses along the DNA template, proofreads errors, and ultimately terminates transcription. Results from single-molecule experiments complement knowledge gained from biochemical and genetic assays by facilitating the observation of states that are otherwise obscured by ensemble averaging, such as those resulting from heterogeneity in molecular structure, elongation rate, or pause propensity. Most studies to date have been performed with bacterial RNA polymerase, but work is also being carried out with eukaryotic polymerase (Pol II) and single-subunit polymerases from bacteriophages. We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates. PMID:18410247

Herbert, Kristina M.; Greenleaf, William J.; Block, Steven M.

2010-01-01

165

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

166

Single-molecule photophysics, from cryogenic to ambient conditions.  

PubMed

We review recent progress in characterizing and understanding the photophysics of single molecules in condensed matter, mostly at cryogenic temperatures. We discuss the central role of the triplet state in limiting the number of useful host-guest systems, notably a new channel, intermolecular intersystem crossing. Another important limitation to the use of single molecules is their photo-reactivity, leading to blinking of the fluorescence signal, and eventually to its loss by photo-bleaching. These processes are at the heart of modern super-resolution schemes. We then examine some of the new host-guest systems recently discovered following these general principles, and the mechanisms of spectral diffusion and dephasing that they have revealed. When charges are injected into organic conductors, they get trapped and influence single molecules via the local fields they create in the material, and via their coupling to localized vibrations. Understanding these processes is necessary for better control of spectral diffusion and dephasing of single molecules. We finally conclude by giving some outlook on future directions of this fascinating field. PMID:24190080

Kozankiewicz, Boles?aw; Orrit, Michel

2014-02-21

167

Continuous base identification for single-molecule nanopore DNA sequencing  

Microsoft Academic Search

A single-molecule method for sequencing DNA that does not require fluorescent labelling could reduce costs and increase sequencing speeds. An exonuclease enzyme might be used to cleave individual nucleotide molecules from the DNA, and when coupled to an appropriate detection system, these nucleotides could be identified in the correct order. Here, we show that a protein nanopore with a covalently

Hai-Chen Wu; Lakmal Jayasinghe; Alpesh Patel; Stuart Reid; Hagan Bayley

2009-01-01

168

Single molecule thermodynamics and nanopore-based thermometry  

NASA Astrophysics Data System (ADS)

The nanopore-based resistive pulse method measures the reduction in ionic current caused by the interaction of single molecules with the pore. It has great promise in addressing problems across a range of fields that include biomedicine and genomics. The technique requires the residence time of the molecules in the pore to exceed the inverse bandwidth of the detection system (˜ 10 ?s). Efforts are underway to improve this by molecular modification of the pore wall, but little effort has focused on modifying the solution conditions in and around the pore. We address this issue by precisely controlling the solution temperature around a protein ion channel (alpha hemolysin) via laser-induced heating of gold nanoparticles. In this technique, the nanopore serves dual roles as both a highly local thermometer and single molecule sensor. Preliminary data suggests that the solution temperature can be controlled over a wide range, the nanopore conductance can be used to directly measure rapid changes in temperature, and the temperature change can dramatically alter the interaction kinetics of single molecules with the nanopore. The method will improve the development of biochip sensors and lead to a new platform for single molecule thermodynamic studies.

Reiner, Joseph E.; Robertson, Joseph W. F.; Burden, Lisa K.; Burden, Daniel L.; Kasianowicz, John J.

2012-02-01

169

Masters projects in: Single-molecule tracking of protein  

E-print Network

Masters projects in: Single-molecule tracking of protein synthesis in live E. coli cells Ribosome catalyzed protein synthesis is one of the most fundamental processes in all life forms. From decades catalyzed protein synthesis. However, we have very sparse information about the dynamics of protein

Uppsala Universitet

170

Spectroscopy 18 (2004) 203211 203 Single molecule force spectroscopy studies  

E-print Network

us to measure the stability of DNA under a variety of solution conditions and in the presence of DNASpectroscopy 18 (2004) 203­211 203 IOS Press Single molecule force spectroscopy studies of DNA properties of single macromolecules such as nucleic acids and proteins. In particular, single DNA molecule

Williams, Mark C.

171

A Bayesian method for single molecule, fluorescence burst analysis  

E-print Network

A Bayesian method for single molecule, fluorescence burst analysis P. R. Barber,1,2,* S. M. Ameer of Cancer Research & Randall Division of Cell and Molecular Biophysics, Richard Dimbleby Department of Cancer Research, Guy's Campus, London SE1 1UL, UK *Paul.Barber@rob.ox.ac.uk Abstract: There is currently

Coolen, ACC "Ton"

172

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

173

Single-Molecule Electrochemical Transistor Utilizing a Nickel-Pyridyl Spinterface.  

PubMed

Using a scanning tunnelling microscope break-junction technique, we produce 4,4'-bipyridine (44BP) single-molecule junctions with Ni and Au contacts. Electrochemical control is used to prevent Ni oxidation and to modulate the conductance of the devices via nonredox gating-the first time this has been shown using non-Au contacts. Remarkably the conductance and gain of the resulting Ni-44BP-Ni electrochemical transistors is significantly higher than analogous Au-based devices. Ab-initio calculations reveal that this behavior arises because charge transport is mediated by spin-polarized Ni d-electrons, which hybridize strongly with molecular orbitals to form a "spinterface". Our results highlight the important role of the contact material for single-molecule devices and show that it can be varied to provide control of charge and spin transport. PMID:25456978

Brooke, Richard J; Jin, Chengjun; Szumski, Doug S; Nichols, Richard J; Mao, Bing-Wei; Thygesen, Kristian S; Schwarzacher, Walther

2014-12-01

174

PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis  

PubMed Central

We describe a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that can accurately distinguish four bases by detecting 4 different sized tags released from 5?-phosphate-modified nucleotides. The basic principle is as follows. As each nucleotide is incorporated into the growing DNA strand during the polymerase reaction, its tag is released and enters a nanopore in release order. This produces a unique ionic current blockade signature due to the tag's distinct chemical structure, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof of principle, we attached four different length PEG-coumarin tags to the terminal phosphate of 2?-deoxyguanosine-5?-tetraphosphate. We demonstrate efficient, accurate incorporation of the nucleotide analogs during the polymerase reaction, and excellent discrimination among the four tags based on nanopore ionic currents. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform. PMID:23002425

Kumar, Shiv; Tao, Chuanjuan; Chien, Minchen; Hellner, Brittney; Balijepalli, Arvind; Robertson, Joseph W. F.; Li, Zengmin; Russo, James J.; Reiner, Joseph E.; Kasianowicz, John J.; Ju, Jingyue

2012-01-01

175

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

176

Interfacial electronic structure and ion beam induced effect of anatase TiO 2 surface modified by Pd nanoparticles  

Microsoft Academic Search

Anatase TiO2 surface could be modified by Pd nanoparticles using an electrochemical deposition method. Surface morphology, light absorption and interfacial electronic structures were studied by field emission scanning electron microscopy (FE-SEM), UV–visible reflectance absorption, X-ray diffraction (XRD) crystallography, and depth-profiling X-ray photoelectron spectroscopy (XPS). On the basis of XRD patterns, Pd 3d XPS and valance band spectra, the as-deposited overlayer

Youngku Sohn

2010-01-01

177

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

178

Ensemble and Single-Molecule Studies on Fluorescence Quenching in Transition Metal Bipyridine-Complexes  

PubMed Central

Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer. PMID:23483966

Brox, Dominik; Kiel, Alexander; Wörner, Svenja Johanna; Pernpointner, Markus; Comba, Peter; Martin, Bodo; Herten, Dirk-Peter

2013-01-01

179

Interfacial electronic effects in functional biolayers integrated into organic field-effect transistors  

PubMed Central

Biosystems integration into an organic field-effect transistor (OFET) structure is achieved by spin coating phospholipid or protein layers between the gate dielectric and the organic semiconductor. An architecture directly interfacing supported biological layers to the OFET channel is proposed and, strikingly, both the electronic properties and the biointerlayer functionality are fully retained. The platform bench tests involved OFETs integrating phospholipids and bacteriorhodopsin exposed to 1–5% anesthetic doses that reveal drug-induced changes in the lipid membrane. This result challenges the current anesthetic action model relying on the so far provided evidence that doses much higher than clinically relevant ones (2.4%) do not alter lipid bilayers’ structure significantly. Furthermore, a streptavidin embedding OFET shows label-free biotin electronic detection at 10 parts-per-trillion concentration level, reaching state-of-the-art fluorescent assay performances. These examples show how the proposed bioelectronic platform, besides resulting in extremely performing biosensors, can open insights into biologically relevant phenomena involving membrane weak interfacial modifications. PMID:22493224

Angione, Maria Daniela; Cotrone, Serafina; Magliulo, Maria; Mallardi, Antonia; Altamura, Davide; Giannini, Cinzia; Cioffi, Nicola; Sabbatini, Luigia; Fratini, Emiliano; Baglioni, Piero; Scamarcio, Gaetano; Palazzo, Gerardo; Torsi, Luisa

2012-01-01

180

The 1D and 2D mapping of surface, subsurface and interfacial properties with secondary, backscattered and Auger electrons  

NASA Astrophysics Data System (ADS)

Scanning the small spot size incident electron beam of a digitized and fully computerized Auger instrument across a surface while simultaneously collecting well-defined secondary electron signals provides information on localized properties that supplement the information usually obtained during standard AES and standard sputter depth profiling studies. Subtle changes in the "true" secondary electron spectrum may be used to produce very sensitive 1D and 2D maps of surface compositional changes and interfacial oxides. When, on the other hand, using the elastically backscattered electrons one can easily generate 1D and 2D maps of subsurface features.

Cota-Araiza, L.; Poppa, H.

1984-09-01

181

Characterization of interfacially electronic structures of gold-magnetite heterostructures using X-ray absorption spectroscopy.  

PubMed

Gold-magnetite heterostructures are novel nanomaterials which can rapidly catalyze the reduction reaction of nitroaromatics. In this study, the interfacially structural and electronic properties of various morphologies of Au-Fe3O4 heterostructures were systematically investigated using X-ray absorbance spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS). The effect of change in electronic structure and charge transfer on electrochemically catalytic activity of Au-Fe3O4 heterostructures was further evaluated by oxygen reduction reaction (ORR). The shifts in binding energy of Au4f and Fe2p peaks in XPS spectra indicate the charge transfer between the Au and Fe3O4 nanoparticles. The increase in d-hole population of Au seeds after the conjugation with iron oxides follows the order flower-like Au-Fe3O4 (FLNPs)>dumbbell-like Au-Fe3O4 (DBNPs)>Au seeds. In addition, the Fe(2+) valence state increases in Au-Fe3O4 heterostructures, which provides evidence to support the hypothesis of charge transfer between Au and Fe3O4 nanoparticles. The theoretical simulation of Au L3-edge XAS further confirms the production of Au-Fe and Au-O bonds at the interface of Au/Fe3O4 and the epitaxial linkage relationship between Au and Fe3O4 nanoparticles. In addition, the electron deficient of Au seeds increases upon increasing Fe3O4 nanoparticles on a single Au seed, and subsequently decreases the catalytic activity of Au in the Au-Fe3O4 heterostructures. The catalytic activity of Au-Fe3O4 toward ORR follows the order Au seeds>Au-Fe3O4 DBNPs>Au-Fe3O4 FLNPs, which is positively correlated to the extent of electronic deficiency of Au in Au-Fe3O4 heterostructures. PMID:24407694

Lin, Fang-hsin; Doong, Ruey-an

2014-03-01

182

A single-molecule force spectroscopy study of the interactions between lectins and carbohydrates on cancer and normal cells  

NASA Astrophysics Data System (ADS)

The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells.The interaction forces between carbohydrates and lectins were investigated by single-molecule force spectroscopy on both cancer and normal cells. The binding kinetics was also studied, which shows that the carbohydrate-lectin complex on cancer cells is less stable than that on normal cells. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c3nr00553d

Zhao, Weidong; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

2013-03-01

183

Light Sheet Microscopy for Single Molecule Tracking in Living Tissue  

PubMed Central

Single molecule observation in cells and tissue allows the analysis of physiological processes with molecular detail, but it still represents a major methodological challenge. Here we introduce a microscopic technique that combines light sheet optical sectioning microscopy and ultra sensitive high-speed imaging. By this approach it is possible to observe single fluorescent biomolecules in solution, living cells and even tissue with an unprecedented speed and signal-to-noise ratio deep within the sample. Thereby we could directly observe and track small and large tracer molecules in aqueous solution. Furthermore, we demonstrated the feasibility to visualize the dynamics of single tracer molecules and native messenger ribonucleoprotein particles (mRNPs) in salivary gland cell nuclei of Chironomus tentans larvae up to 200 µm within the specimen with an excellent signal quality. Thus single molecule light sheet based fluorescence microscopy allows analyzing molecular diffusion and interactions in complex biological systems. PMID:20668517

Ritter, Jörg Gerhard; Veith, Roman; Veenendaal, Andreas; Siebrasse, Jan Peter; Kubitscheck, Ulrich

2010-01-01

184

Single molecule imaging with longer x-ray laser pulses  

E-print Network

In serial femtosecond crystallography, x-ray laser pulses do not need to outrun all radiation damage processes because Bragg diffraction exceeds the damage-induced background scattering for longer pulses ($\\sim$ 50--100 fs). This is due to a "self-gating pulse" effect whereby damage terminates Bragg diffraction prior to the pulse completing its passage through the sample, as if that diffraction were produced by a shorter pulse of equal fluence. We show here that a similar gating effect applies to single molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of average structure separately to the diffraction from statistical fluctuations of the structure due to damage ("damage noise"). Our results suggest that sub-nanometer single molecule imaging with longer pulses, like those produced at currently operating facilities, should not yet be ruled out. The...

Martin, Andrew V; Caleman, Carl; Quiney, Harry M

2015-01-01

185

Photoactivatable DCDHF fluorophores for single-molecule imaging  

NASA Astrophysics Data System (ADS)

We have designed and studied the photophysics of a class of organic fluorophores termed "DCDHFs," which were originally used as push-pull chromophores for nonlinear optical applications. In this paper, we describe the general photophysics of many realizations of the DCDHF class of single-molecule emitters. Moreover, we have reengineered a red-emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low-intensity violet light. Photoactivation of the dark fluorogen leads to conversion of an azide to an amine, which shifts the absorption to long wavelengths. After photoactivation, the fluorophore is bright and photostable enough to be imaged on the singlemolecule level in living cells. This molecule and its relatives will provide a new class of bright photoactivatable fluorophores, as are needed for super-resolution imaging schemes that require active control of single-molecule emission.

Lord, Samuel J.; Conley, Nicholas R.; Lee, Hsiao-lu D.; Liu, Na; Samuel, Reichel; Twieg, Robert J.; Moerner, W. E.

2009-02-01

186

Visualizing cellular machines with colocalization single molecule microscopy.  

PubMed

Many of the cell's macromolecular machines contain multiple components that transiently associate with one another. This compositional and dynamic complexity presents a challenge for understanding how these machines are constructed and function. Colocalization single molecule spectroscopy enables simultaneous observation of individual components of these machines in real-time and grants a unique window into processes that are typically obscured in ensemble assays. Colocalization experiments can yield valuable information about assembly pathways, compositional heterogeneity, and kinetics that together contribute to the development of richly detailed reaction mechanisms. This review focuses on recent advances in colocalization single molecule spectroscopy and how this technique has been applied to enhance our understanding of transcription, RNA splicing, and translation. PMID:23970346

Larson, Joshua D; Rodgers, Margaret L; Hoskins, Aaron A

2014-02-21

187

Single-molecule imaging in live bacteria cells  

PubMed Central

Bacteria, such as Escherichia coli and Caulobacter crescentus, are the most studied and perhaps best-understood organisms in biology. The advances in understanding of living systems gained from these organisms are immense. Application of single-molecule techniques in bacteria have presented unique difficulties owing to their small size and highly curved form. The aim of this review is to show advances made in single-molecule imaging in bacteria over the past 10 years, and to look to the future where the combination of implementing such high-precision techniques in well-characterized and controllable model systems such as E. coli could lead to a greater understanding of fundamental biological questions inaccessible through classic ensemble methods. PMID:23267188

Ritchie, Ken; Lill, Yoriko; Sood, Chetan; Lee, Hochan; Zhang, Shunyuan

2013-01-01

188

Applications of optical trapping to single molecule DNA  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project focused on the methodologies required to integrate optical trapping with single molecule detection (SMD) so as to demonstrate high speed sequencing through optical micromanipulation of host substrates, nucleotide cleavage, and single molecule detection. As part of this effort, the new technology of optical tweezers was applied to the confinement and manipulation of microsphere handles containing attached DNA fragments. The authors demonstrated substrate optical trapping in rapid flow streams, the fluorescence excitation and detection of fluorescently labeled nucleotides in an optical trapping system, and the epifluorescent imaging of DNA fragments in flow streams. They successfully demonstrated optical trapping in laminar flow streams and completely characterized the trapping process as functions of fluid flow velocity, chamber dimension, trapping depth, incident laser power, and fluorescence measurement geometry.

Sonek, G.J.; Berns, M.W. [Univ. of California, Irvine, CA (United States). Beckman Laser Inst. and Medical Clinic; Keller, R.A. [Los Alamos National Lab., NM (United States). Chemical Science and Technology Div.

1997-12-01

189

Microfluidic Device for Single-Molecule Experiments with Enhanced Photostability  

PubMed Central

A microfluidic device made of PDMS addresses key limitations in single-molecule fluorescence experiments by providing high dye photostability and low sample sticking. Photobleaching is dramatically reduced by deoxygenation via gas diffusion through porous channel walls. Rapid buffer exchange in a laminar sheath flow followed by optical interrogation minimizes surface-sample contacts, and allows the in situ addition and combination of other reagents. PMID:19772358

Lemke, Edward A.; Gambin, Yann; Vandelinder, Virginia; Brustad, Eric M.; Liu, Hsiao-Wei; Schultz, Peter G.

2009-01-01

190

Single-Molecule Detection in Temperature-Controlled Microchannels  

Microsoft Academic Search

This paper reports a temperature-controlled microfluidic platform for single-molecule studies. Parallel microchannels are formed between glass and quartz, and are integrated with on-chip heaters and temperature sensors. Combined with surface derivatization and fluorescent labeling of biomolecules, temperature-dependent changes in the rates of fluorescence photobleaching are measured. The results demonstrate the potential of the device to provide an ideal environment for

Bin Wang; Jingyi Fei; R. L. Gonzalez; Qiao Lin

2007-01-01

191

Single-Molecule Covalent Chemistry in a Protein Nanoreactor  

Microsoft Academic Search

Covalent chemistry can be observed at the single-molecule level by using engineered protein pores as “nanoreactors”. By recording\\u000a the ionic current driven through single engineered alpha-hemolysin (?HL) pores in a transmembrane potential, individual bond-making\\u000a and bond-breaking steps that occur within the pore and perturb the current are monitored with sub-millisecond time-resolution.\\u000a Recently, a variety of covalent reactions of small molecules

Hagan Bayley; Tudor Luchian; Seong-Ho Shin; Mackay B. Steffensen

192

What Do We Measure With Single-Molecule Force Spectroscopy?  

Microsoft Academic Search

Single-molecule force spectroscopy is a powerful technique for studying detailed intra- and inter- molecular interactions by manipulating single biomolecules at the nanometer scale. Force is measured while one pulls on the molecules. However, relating the measured information to equilibrium thermodynamic properties is challenging. Jarzynksi's equality allows one to reconstruct the free energy surface as a function of molecular end-to-end distance^1,2.

Ching-Hwa Kiang; Nolan Harris; Eric Botello; Wei-Hung Chen

2008-01-01

193

Single molecule conformational memory extraction: p5ab RNA hairpin.  

PubMed

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L; Marqusee, Susan; Bustamante, Carlos; Dill, Ken

2014-06-19

194

Single-molecule studies of actin assembly and disassembly factors.  

PubMed

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

195

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, Benîot; Sels, Bert F.; Jacobs, Pierre A.; De Schryver, Frans C.; De Vos, Dirk E.; Hofkens, Johan

2007-01-01

196

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.

2011-12-01

197

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

198

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

199

Interfacial Charge Transport in Organic Electronic Materials: the Key to a New Electronics Technology  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The primary aim of this project is to obtain a basic scientific understanding of electrical transport processes at interfaces that contain an organic electronic material. Because of their processing advantages and the tunability of their electronic properties, organic electronic materials are revolutionizing major technological areas such as information display. We completed an investigation of the fundamental electronic excitation energies in the prototype conjugated polymer MEH-PPV. We completed a combined theoretical/experimental study of the energy relation between charged excitations in a conjugated polymer and the metal at a polymer/metal interface. We developed a theoretical model that explains injection currents at polymer/metal interfaces. We have made electrical measurements on devices fabricated using the conjugated polymer MEH-PPV a nd a series of metals.

Smith, D.L.; Campbell, I.H.; Davids, P.S.; Heller, C.M.; Laurich, B.K.; Crone, B.K.; Saxena, A.; Bishop, A.R.; Ferraris, J.P.; Yu, Z.G.

1999-06-04

200

Electronic Coupling Dependence of Ultrafast Interfacial Electron Transfer on Nanocrystalline Thin Films and Single Crystal  

SciTech Connect

The long-term goal of the proposed research is to understand electron transfer dynamics in nanoparticle/liquid interface. This knowledge is essential to many semiconductor nanoparticle based devices, including photocatalytic waste degradation and dye sensitized solar cells.

Lian, Tianquan

2014-04-22

201

Electronic band structures and optical properties of type-II superlattice photodetectors with interfacial effect.  

PubMed

The electronic band structures and optical properties of type-II superlattice (T2SL) photodetectors in the mid-infrared (IR) range are investigated. We formulate a rigorous band structure model using the 8-band k · p method to include the conduction and valence band mixing. After solving the 8 × 8 Hamiltonian and deriving explicitly the new momentum matrix elements in terms of envelope functions, optical transition rates are obtained through the Fermi's golden rule under various doping and injection conditions. Optical measurements on T2SL photodetectors are compared with our model and show good agreement. Our modeling results of quantum structures connect directly to the device-level design and simulation. The predicted doping effect is readily applicable to the optimization of photodetectors. We further include interfacial (IF) layers to study the significance of their effect. Optical properties of T2SLs are expected to have a large tunable range by controlling the thickness and material composition of the IF layers. Our model provides an efficient tool for the designs of novel photodetectors. PMID:22330471

Qiao, Peng-Fei; Mou, Shin; Chuang, Shun Lien

2012-01-30

202

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

203

Incorporating single molecules into electrical circuits. The role of the chemical anchoring group.  

PubMed

Constructing electronic circuits containing singly wired molecules is at the frontier of electrical device miniaturisation. When a molecule is wired between a pair of electrodes, the two points of contact are determined by the chemical anchoring groups, located at the ends of the molecule. At this point, when a bias is applied, electrons are channelled from a metallic environment through an extremely narrow constriction, essentially a single atom, into the molecule. The fact that this is such an abrupt change in the electron pathway makes the nature of the chemical anchoring groups critically important regarding the propagation of electrons from the electrode across the molecule. A delicate interplay of phenomena can occur when a molecule binds to the electrodes, which can produce profound differences in conductance properties depending on the anchoring group. This makes answering the question "what is the best anchoring group for single molecule studies" far from straight forward. In this review, we firstly take a look at techniques developed to 'wire-up' single molecules, as understanding their limitations is key when assessing a molecular wire's performance. We then analyse the various chemical anchoring groups, and discuss their merits and disadvantages. Finally we discuss some theoretical concepts of molecular junctions to understand how transport is affected by the nature of the chemical anchor group. PMID:25522058

Leary, Edmund; La Rosa, Andrea; González, M Teresa; Rubio-Bollinger, Gabino; Agraït, Nicolás; Martín, Nazario

2015-02-10

204

Spin-filtering transport and switching effect of MnCu single-molecule magnet  

NASA Astrophysics Data System (ADS)

Electron transport of a single-molecule magnet (SMM) device has been investigated using the first-principles calculations. The SMM based device is constructed by a SMM MnCu [MnCuCl(5-Br-sap)2(MeOH)] bridged between semi-infinite Au(100) electrodes with thiol groups connecting the molecule and the gold electrodes. Our results exhibit crucial features of spin filtering and Kondo resonance. The spin filtering remains robust, whereas the Kondo resonance highly depends on the contact geometry. Specifically, this Kondo resonance can be switched on or off by changing the contact distance. The mechanisms of these features are formulated in details.

Hao, H.; Zheng, X. H.; Dai, Z. X.; Zeng, Z.

2010-05-01

205

Single Molecule Energetics of F1-ATPase Motor  

PubMed Central

Motor proteins are essential in life processes because they convert the free energy of ATP hydrolysis to mechanical work. However, the fundamental question on how they work when different amounts of free energy are released after ATP hydrolysis remains unanswered. To answer this question, it is essential to clarify how the stepping motion of a motor protein reflects the concentrations of ATP, ADP, and Pi in its individual actions at a single molecule level. The F1 portion of ATP synthase, also called F1-ATPase, is a rotary molecular motor in which the central ?-subunit rotates against the ?3?3 cylinder. The motor exhibits clear step motion at low ATP concentrations. The rotary action of this motor is processive and generates a high torque. These features are ideal for exploring the relationship between free energy input and mechanical work output, but there is a serious problem in that this motor is severely inhibited by ADP. In this study, we overcame this problem of ADP inhibition by introducing several mutations while retaining high enzymatic activity. Using a probe of attached beads, stepping rotation against viscous load was examined at a wide range of free energy values by changing the ADP concentration. The results showed that the apparent work of each individual step motion was not affected by the free energy of ATP hydrolysis, but the frequency of each individual step motion depended on the free energy. This is the first study that examined the stepping motion of a molecular motor at a single molecule level with simultaneous systematic control of ?GATP. The results imply that microscopically defined work at a single molecule level cannot be directly compared with macroscopically defined free energy input. PMID:17158579

Muneyuki, Eiro; Watanabe-Nakayama, Takahiro; Suzuki, Tetsuya; Yoshida, Masasuke; Nishizaka, Takayuki; Noji, Hiroyuki

2007-01-01

206

Analytical tools for single-molecule fluorescence imaging in cellulo.  

PubMed

Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is typically obtained in a low signal-to-noise ratio (SNR) regime sometimes only marginally in excess of 1, in which a combination of detector shot noise, sub-optimal probe photophysics, native cell autofluorescence and intrinsically underlying stochasticity of molecules result in highly noisy datasets for which underlying true molecular behaviour is non-trivial to discern. The ability to elucidate real molecular phenomena is essential in relating experimental single-molecule observations to both the biological system under study as well as offering insight into the fine details of the physical and chemical environments of the living cell. To confront this problem of faithful signal extraction and analysis in a noise-dominated regime, the 'needle in a haystack' challenge, such experiments benefit enormously from a suite of objective, automated, high-throughput analysis tools that can home in on the underlying 'molecular signature' and generate meaningful statistics across a large population of individual cells and molecules. Here, I discuss the development and application of several analytical methods applied to real case studies, including objective methods of segmenting cellular images from light microscopy data, tools to robustly localize and track single fluorescently-labelled molecules, algorithms to objectively interpret molecular mobility, analysis protocols to reliably estimate molecular stoichiometry and turnover, and methods to objectively render distributions of molecular parameters. PMID:24626744

Leake, M C

2014-07-01

207

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

Täuber, Daniela; von Borczyskowski, Christian

2013-01-01

208

Diffusion of carbon nanotubes with single-molecule fluorescence microscopy  

NASA Astrophysics Data System (ADS)

Single walled carbon nanotubes (SWNTs) are a promising gene and drug delivery system since their physical dimensions mimic nucleic acids. Towards this aim, the hydrophobicity of SWNTs was averted by coating with ribonucleic acid (RNA) polymer [poly(rU)] or bovine serum albumin (BSA) and the consequent diffusion of these synthetic-biomolecular hybrids was studied by single-molecule fluorescence microscopy. The diffusion coefficient for SWNT-poly(rU) was measured at 0.374±0.045?m2/s and for SWNT-BSA it was 0.442±0.046?m2/s. Our diffusion study provides a fundamental guidance to gene delivery using SWNT as transporters.

Lu, Q.; Freedman, K. O.; Rao, R.; Huang, G.; Lee, J.; Larcom, L. L.; Rao, A. M.; Ke, P. C.

2004-12-01

209

Detection of pathogenic DNA at the single-molecule level  

NASA Astrophysics Data System (ADS)

We demonstrate ultrasensitive detection of pathogenic DNA in a homogeneous assay at the single-molecule level applying two-color coincidence analysis. The target molecule we quantify is a 100 nucleotide long synthetic single-stranded oligonucleotide adapted from Streptococcus pneumoniae, a bacterium causing lower respiratory tract infections. Using spontaneous hybridization of two differently fluorescing Molecular Beacons we demonstrate a detection sensitivity of 100 fM (10-13M) in 30 seconds applying a simple microfluidic device with a 100 ?m channel and confocal two-color fluorescence microscopy.

Yahiatène, Idir; Klamp, Tobias; Schüttpelz, Mark; Sauer, Markus

2011-03-01

210

DNA-psoralen interaction: A single molecule experiment  

NASA Astrophysics Data System (ADS)

By attaching one end of a single ?-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the ?-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particulary interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

Rocha, M. S.; Viana, N. B.; Mesquita, O. N.

2004-11-01

211

Single molecule detection and underwater fluorescence imaging with cantilevered near-field fiber optic probes  

E-print Network

Tapping-mode near-field scanning optical microscopy (NSOM) employing a cantilevered fiber optic probe is utilized to image the fluorescence from single molecules and samples in aqueous environments. The single molecule fluorescenceimages demonstrate...

Talley, Chad E.; Lee, M. Annie; Dunn, Robert C.

1998-04-03

212

Research Highlights 1. Combination of single-molecule FRET & optical tweezers  

E-print Network

Research Highlights 1. Combination of single-molecule FRET & optical tweezers Understanding as little as possible. Single-molecule fluorescence resonance energy transfer (FRET) is a powerful tool to combine single-molecule FRET and optical tweezers. Prior attempts, however, exposed great technical

Hohng, Sung Chul

213

Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time  

E-print Network

Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time-color detection capability in doing single- molecule fluorescence resonance energy transfer (FRET) experiments. Existing single-molecule three-color FRET techniques, however, suffer from severe photobleaching of Alexa

Hohng, Sung Chul

214

Single-Molecule Three-Color FRET Sungchul Hohng, Chirlmin Joo, and Taekjip Ha  

E-print Network

Single-Molecule Three-Color FRET Sungchul Hohng, Chirlmin Joo, and Taekjip Ha Physics Department (FRET) measured at the single-molecule level can reveal conform- ational changes of biomolecules and intermolecular interactions in physiologically relevant conditions. Thus far single-molecule FRET has been

Hohng, Sung Chul

215

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.  

PubMed

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy. PMID:21291281

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

216

Kinetic Measurements on Single-molecule Disulfide Bond Cleavage  

PubMed Central

We use single-molecule force clamp spectroscopy (SMFCS) to explore the reactivity of tris(2-carboxyethyl)phosphine (TCEP), 1, 4-DL-dithiothreitol (DTT) and hydrosulfide anion (HS-) on disulfide bonds within a mechanically stretched polypeptide. The single-bond level bimolecular nucleophilic substitution (SN2) events are recorded at a series of precisely-controlled temperatures so that the Arrhenius kinetic parameters, i.e. the height of the activation energy barrier (Ea) and the attempting frequency (A) of the chemical reactions, can be determined. The values of A are typically at the order of 107 M-1s-1, which is far lower than that predicted by the transition-state theory, in which A is given by kBT/h and around 1012 M-1s-1 at room temperature. Furthermore, Ea is derived to be 30-40 kJ/mol, which can be lowered by ~6-8% with every 100 pN mechanical force applied. The correlation of the A and Ea with the molecular structures reveals that the relative magnitude of these two parameters cannot be simply judged from the size of the molecule or the nucleophilicity of the attacking atom. The comparison of the influences on the reaction rate induced by force and temperature indicates an equivalent accelerating effect by every 50 pN or 10 K increment, giving for the first time the relationship between mechanical and thermal effects on a single-molecule SN2 chemical reaction. PMID:21341766

Liang, Jian; Fernández, Julio M.

2011-01-01

217

Single-molecule microscopy using tunable nanoscale confinement  

NASA Astrophysics Data System (ADS)

We present the design, construction and implementation of a modular microscopy device that transforms a basic inverted fluorescence microscope into a versatile single-molecule imaging system. The device uses Convex Lens- Induced Confinement (CLIC) to improve background rejection and extend diffusion-limited observation time. To facilitate its integration into a wide range of laboratories, this implementation of the CLIC device can use a standard flow-cell, into which the sample is loaded. By mechanically deforming the flow-cell, the device creates a tunable, wedge-shaped imaging chamber which we have modeled using finite element analysis simulations and characterized experimentally using interferometry. A powerful feature of CLIC imaging technology is the ability to examine single molecules under a continuum of applied confinement, from the nanometer to the micrometer scale. We demonstrate, using freely diffusing ?-phage DNA, that when the imposed confinement is on the scale of individual molecules their molecular conformations and diffusivity are altered significantly. To improve the flow-cell stiffness, seal, and re-usability, we have innovated the fabrication of thin PDMS-bonded flow-cells. The presented flow-cell CLIC technology can be combined with surface-lithography to provide an accessible and powerful approach to tune, trap, and image individual molecules under an extended range of imaging conditions. It is well-suited to tackling open problems in biophysics, biotechnology, nanotechnology, materials science, and chemistry.

McFaul, Christopher M. J.; Leith, Jason; Jia, Bojing; Michaud, François; Arsenault, Adriel; Martin, Andrew; Berard, Daniel; Leslie, Sabrina

2013-09-01

218

Multiplexed Single-molecule Force Proteolysis Measurements Using Magnetic Tweezers  

PubMed Central

The generation and detection of mechanical forces is a ubiquitous aspect of cell physiology, with direct relevance to cancer metastasis1, atherogenesis2 and wound healing3. In each of these examples, cells both exert force on their surroundings and simultaneously enzymatically remodel the extracellular matrix (ECM). The effect of forces on ECM has thus become an area of considerable interest due to its likely biological and medical importance4-7. Single molecule techniques such as optical trapping8, atomic force microscopy9, and magnetic tweezers10,11 allow researchers to probe the function of enzymes at a molecular level by exerting forces on individual proteins. Of these techniques, magnetic tweezers (MT) are notable for their low cost and high throughput. MT exert forces in the range of ~1-100 pN and can provide millisecond temporal resolution, qualities that are well matched to the study of enzyme mechanism at the single-molecule level12. Here we report a highly parallelizable MT assay to study the effect of force on the proteolysis of single protein molecules. We present the specific example of the proteolysis of a trimeric collagen peptide by matrix metalloproteinase 1 (MMP-1); however, this assay can be easily adapted to study other substrates and proteases. PMID:22871786

Adhikari, Arjun S.; Chai, Jack; Dunn, Alexander R.

2012-01-01

219

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

220

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

221

New Antifouling Platform Characterized by Single-Molecule Imaging  

PubMed Central

Antifouling surfaces have been widely studied for their importance in medical devices and industry. Antifouling surfaces mostly achieved by methoxy-poly(ethylene glycol) (mPEG) have shown biomolecular adsorption less than 1 ng/cm2 which was measured by surface analytical tools such as surface plasmon resonance (SPR) spectroscopy, quartz crystal microbalance (QCM), or optical waveguide lightmode (OWL) spectroscopy. Herein, we utilize a single-molecule imaging technique (i.e., an ultimate resolution) to study antifouling properties of functionalized surfaces. We found that about 600 immunoglobulin G (IgG) molecules are adsorbed. This result corresponds to ?5 pg/cm2 adsorption, which is far below amount for the detection limit of the conventional tools. Furthermore, we developed a new antifouling platform that exhibits improved antifouling performance that shows only 78 IgG molecules adsorbed (?0.5 pg/cm2). The antifouling platform consists of forming 1 nm TiO2 thin layer, on which peptidomimetic antifouling polymer (PMAP) is robustly anchored. The unprecedented antifouling performance can potentially revolutionize a variety of research fields such as single-molecule imaging, medical devices, biosensors, and others. PMID:24503420

2015-01-01

222

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

223

Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches  

PubMed Central

The cell membrane plays a key role in compartmentalization, nutrient transportation and signal transduction, while the pattern of protein distribution at both cytoplasmic and ectoplasmic sides of the cell membrane remains elusive. Using a combination of single-molecule techniques, including atomic force microscopy (AFM), single molecule force spectroscopy (SMFS) and stochastic optical reconstruction microscopy (STORM), to study the structure of nucleated cell membranes, we found that (1) proteins at the ectoplasmic side of the cell membrane form a dense protein layer (4 nm) on top of a lipid bilayer; (2) proteins aggregate to form islands evenly dispersed at the cytoplasmic side of the cell membrane with a height of about 10–12 nm; (3) cholesterol-enriched domains exist within the cell membrane; (4) carbohydrates stay in microdomains at the ectoplasmic side; and (5) exposed amino groups are asymmetrically distributed on both sides. Based on these observations, we proposed a Protein Layer-Lipid-Protein Island (PLLPI) model, to provide a better understanding of cell membrane structure, membrane trafficking and viral fusion mechanisms. PMID:24806512

Wang, Feng; Wu, Jiazhen; Gao, Jing; Liu, Shuheng; Jiang, Junguang; Jiang, Shibo; Wang, Hongda

2014-01-01

224

New assay for multiple single molecule enzyme kinetics  

NASA Astrophysics Data System (ADS)

A population of identical proteins has the same amino acid sequence, but there may be subtle differences in local folding that lead to variations in activity. Single molecule studies allow us to understand these subtle differences. Single molecule experiments are usually time consuming and difficult because only a few molecules are observed in one experiment. To address this problem, we have developed an assay where we can simultaneously measure the activity of multiple individual molecules of a protease, ?-chymotrypsin. The assay utilizes a synthetic chymotrypsin substrate that is non-fluorescent before cleavage by chymotrypsin, but is intensely fluorescent after. To study the activity of individual enzymes, the enzyme and substrate are encapsulated in micron-sized droplets of water surrounded by silicone oil. On average, each micro-droplet contains less than one enzyme. The fluorescence of these droplets is recorded over time using a microscope and a CCD camera system. Software tracks individual droplets over time and records fluorescence. The kinetics of individual chymotrypsin molecules is calculated through the increase of fluorescence intensity of the same individual droplet over time. The activity profiles of the individual enzymes and the bulk sample of the enzyme are very similar. This validates the assay and demonstrates that the average of a few individual molecules can be representative of the behavior of the bulk population.

Lee, Alan I.; Brody, James P.

2005-03-01

225

Association Kinetics from Single Molecule Force Spectroscopy Measurements  

PubMed Central

Abstract Single molecule force spectroscopy is often used to study the dissociation of single molecules by applying mechanical force to the intermolecular bond. These measurements provide the kinetic parameters of dissociation. We present what to our knowledge is a new atomic force microscopy-based approach to obtain the activation energy of the association reaction and approximate grafting density of reactive receptors using the dependence of the probability to form molecular bonds on probe velocity when one of the interacting molecules is tethered by a flexible polymeric linker to the atomic force microscopy probe. Possible errors in the activation energy measured with this approach are considered and resulting corrections are included in the data analysis. This new approach uses the same experimental setup as traditional force spectroscopy measurements that quantify dissociation kinetics. We apply the developed methodology to measure the activation energy of biotin-streptavidin association (including a contribution from the steric factor) and obtain a value of 8 ± 1 kT. This value is consistent with the association rate measured previously in solution. Comparison with the solution-derived activation energy indicates that kinetics of biotin-streptavidin binding is mainly controlled by the reaction step. PMID:19383484

Guo, Senli; Lad, Nimit; Ray, Chad; Akhremitchev, Boris B.

2009-01-01

226

Ambipolar transport in an electrochemically gated single-molecule field-effect transistor.  

PubMed

Charge transport is studied in single-molecule junctions formed with a 1,7-pyrrolidine-substituted 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) molecular block using an electrochemical gate. Compared to an unsubstituted-PTCDI block, spectroscopic and electrochemical measurements indicate a reduction in the highest occupied (HOMO)-lowest unoccupied (LUMO) molecular orbital energy gap associated with the electron donor character of the substituents. The small HOMO-LUMO energy gap allows for switching between electron- and hole-dominated charge transports as a function of gate voltage, thus demonstrating a single-molecule ambipolar field-effect transistor. Both the unsubstituted and substituted molecules display similar n-type behaviors, indicating that they share the same n-type conduction mechanism. However, the substituted-PTCDI block shows a peak in the source-drain current vs gate voltage characteristics for the p-type transport, which is attributed to a two-step incoherent transport via the HOMO of the molecule. PMID:22789617

Díez-Pérez, Ismael; Li, Zhihai; Guo, Shaoyin; Madden, Christopher; Huang, Helin; Che, Yanke; Yang, Xiaomei; Zang, Ling; Tao, Nongjian

2012-08-28

227

Keynote FIELD REGULATION OF SINGLE MOLECULE CONDUCTIVITY BY A CHARGED ATOM  

E-print Network

A new concept for a single molecule transistor is demonstrated (1). A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. One electron is sufficient to achieve gating because high gate efficiency is achieved. Because one electron achieves gating, compared to ~10^5 in a modern transistor, enormous speed, and minimal power consumption are implied.

Robert A. Wolkow

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

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

230

Force and Conductance Spectroscopy of Single Molecule Junctions  

NASA Astrophysics Data System (ADS)

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

Frei, Michael

231

Single molecule desorption studies on immobilized nanoclay particle surfaces.  

PubMed

AFM-based single molecule force spectroscopy was performed on sheetlike inorganic particles of Na-montmorillonite to study the pH-dependent adsorption and desorption behavior of polyelectrolytes in aqueous solutions. Polyallylamine macromolecules were covalently attached on gold-coated AFM cantilevers. Heterogeneous surfaces were formed by immobilizing the nanoclay sheets on mica-stripped ultraflat Au(111) surfaces using aminothiol chemistry. Because of the constant surface charge of the particles over a wide pH range, polymer line charge density was the only parameter that affected the adsorption and desorption behavior when the ionic concentration was kept constant. Polarization modulation infrared-reflection absorption spectroscopy (PM-IRRAS) was performed on cast polyallylamine films to study the pH-dependent charge density of polyallylamine molecules. A good correlation was found between the line charge density and the adsorption characteristics of polyallylamine. PMID:20230055

Ozkaya, Berkem; Ozcan, Ozlem; Thissen, Peter; Grundmeier, Guido

2010-06-01

232

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

233

Photoswitchable fluorophores for single-molecule localization microscopy.  

PubMed

Over the past decade, fluorescence microscopy has been revolutionized by the development of novel techniques that allow near-molecular resolution. Many such methods-collectively referred to as "single-molecule localization microscopy" (SMLM)-are based upon the repeated imaging of sparse stochastic subsets of the fluorophores in a sample. Active fluorophores are localized by finding the centers of their point spread functions, and a super-resolution image is constructed.Key to this strategy is the use of fluorophores that can be switched "on" and "off" in a controllable manner. Here we review the strengths and weaknesses of the wide variety of SMLM-compatible photoswitchable fluorophores and labeling strategies currently available. We also discuss their suitability for live-cell and multicolor imaging, as well as molecular counting. PMID:23086874

Finan, Kieran; Flottmann, Benjamin; Heilemann, Mike

2013-01-01

234

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

235

Inequivalence of statistical ensembles in single molecule measurements  

NASA Astrophysics Data System (ADS)

We study the role of fluctuations in single molecule experimental measurements of force-extension (f-?) curves. We use the wormlike chain (WLC) model to bring out the connection between the Helmholtz ensemble characterized by the free energy [F(?)] and the Gibbs ensemble characterized by the free energy [G(f)] . We consider the rigid rod limit of the WLC model as an instructive special case to bring out the issue of ensemble inequivalence. We point out the need for taking into account the free energy of transition when one goes from one ensemble to another. We also comment on the “phase transition” noticed in an isometric setup for semiflexible polymers and propose a realization of its thermodynamic limit. We present general arguments which rule out nonmonotonic force-extension curves in some ensembles and note that these do not apply to the isometric ensemble.

Sinha, Supurna; Samuel, Joseph

2005-02-01

236

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

237

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

238

Single molecule thermodynamics of ATP synthesis by F$_1$-ATPase  

E-print Network

F$_\\mathrm{o}$F$_1$-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F$_1$-motor (F$_1$-ATPase) and performs the reversible mechanochemical coupling. Isolated F$_1$-motor hydrolyzes ATP, which is accompanied by unidirectional rotation of its central $\\gamma$-shaft. When a strong opposing torque is imposed, the $\\gamma$-shaft rotates in the opposite direction and drives the F$_1$-motor to synthesize ATP. This mechanical-to-chemical free-energy transduction is the final and central step of the multistep cellular ATP-synthetic pathway. Here, we determined the amount of mechanical work exploited by the F$_1$-motor to synthesize an ATP molecule during forced rotations using methodology combining a nonequilibrium theory and single molecule measurements of responses to external torque. We found that the internal dissipation of the motor is negligible even during rotations far from a quasistatic process.

Shoichi Toyabe; Eiro Muneyuki

2015-01-16

239

Single molecule thermodynamics of ATP synthesis by F1-ATPase  

NASA Astrophysics Data System (ADS)

FoF1-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F1-motor (F1-ATPase) and performs the reversible mechanochemical coupling. The isolated F1-motor hydrolyzes ATP, which is accompanied by unidirectional rotation of its central ? -shaft. When a strong opposing torque is imposed, the ? -shaft rotates in the opposite direction and drives the F1-motor to synthesize ATP. This mechanical-to-chemical free-energy transduction is the final and central step of the multistep cellular ATP-synthetic pathway. Here, we determined the amount of mechanical work exploited by the F1-motor to synthesize an ATP molecule during forced rotations using a methodology combining a nonequilibrium theory and single molecule measurements of responses to external torque. We found that the internal dissipation of the motor is negligible even during rotations far from a quasistatic process.

Toyabe, Shoichi; Muneyuki, Eiro

2015-01-01

240

Single-molecule studies of group II intron ribozymes  

PubMed Central

Group II intron ribozymes fold into their native structure by a unique stepwise process that involves an initial slow compaction followed by fast formation of the native state in a Mg2+-dependent manner. Single-molecule fluorescence reveals three distinct on-pathway conformations in dynamic equilibrium connected by relatively small activation barriers. From a most stable near-native state, the unobserved catalytically active conformer is reached. This most compact conformer occurs only transiently above 20 mM Mg2+ and is stabilized by substrate binding, which together explain the slow cleavage of the ribozyme. Structural dynamics increase with increasing Mg2+ concentrations, enabling the enzyme to reach its active state. PMID:18772388

Steiner, Miriam; Karunatilaka, Krishanthi S.; Sigel, Roland K. O.; Rueda, David

2008-01-01

241

Single-Molecule Encoders for Tracking Motor Proteins on DNA  

NASA Astrophysics Data System (ADS)

Devices such as inkjet printers and disk drives track position and velocity using optical encoders, which produce periodic signals precisely synchronized with linear or rotational motion. We have implemented this technique at the nanometer scale by labeling DNA with regularly spaced fluorescent dyes. The resulting molecular encoders can be used in several ways for high-resolution continuous tracking of individual motor proteins. These measurements do not require mechanical coupling to macroscopic instrumentation, are automatically calibrated by the underlying structure of DNA, and depend on signal periodicity rather than absolute level. I will describe the synthesis of single-molecule encoders, data from and modeling of experiments on a helicase and a DNA polymerase, and some ideas for future work.

Lipman, Everett A.

2012-02-01

242

Enhancing Single Molecule Imaging in Optofluidics and Microfluidics  

PubMed Central

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

243

Visualizing Cyclic Peptide Hydration at the Single-Molecule Level  

NASA Astrophysics Data System (ADS)

The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin-water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface.

Chen, Yumin; Deng, Ke; Qiu, Xiaohui; Wang, Chen

2013-08-01

244

Visualizing Cyclic Peptide Hydration at the Single-Molecule Level  

PubMed Central

The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin–water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface. PMID:23955234

Chen, Yumin; Deng, Ke; Qiu, Xiaohui; Wang, Chen

2013-01-01

245

Linear trinuclear cobalt(ii) single molecule magnet.  

PubMed

The introduction of NaBPh4 into a methanolic solution of CoCl2·6H2O and 2-[(pyridine-2-ylimine)-methyl]phenol (Hpymp) afforded {[Co(II)3(pymp)4(MeOH)2][BPh4]2}·2MeOH () with a centro-symmetrically linear trinuclear structure. Magnetic analysis of exhibited significant intracluster ferromagnetic exchange (2.4 cm(-1)) and slow relaxation of magnetization in both zero and non-zero static fields below 5 K, giving the first [Co(II)3] single molecule magnet with an effective energy barrier of 17.2(3) cm(-1) under a 500 Oe dc field. PMID:25562308

Zhang, Yuan-Zhu; Brown, Andrew J; Meng, Yin-Shan; Sun, Hao-Ling; Gao, Song

2015-01-28

246

Visualizing cyclic peptide hydration at the single-molecule level.  

PubMed

The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin-water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface. PMID:23955234

Chen, Yumin; Deng, Ke; Qiu, Xiaohui; Wang, Chen

2013-01-01

247

DNA computing using single-molecule hybridization detection  

PubMed Central

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that require vast search spaces. However, the actual parallelism currently being achieved is at least a hundred million-fold lower than the number of DNA molecules used. This is due to the quantity of DNA molecules of one species that is required to produce a detectable output to the computations. In order to miniaturize the computation and considerably reduce the amount of DNA needed, we have combined DNA computing with single-molecule detection. Reliable hybridization detection was achieved at the level of single DNA molecules with fluorescence cross-correlation spectroscopy. To illustrate the use of this approach, we implemented a DNA-based computation and solved a 4-variable 4-clause instance of the computationally hard Satisfiability (SAT) problem. PMID:15388798

Schmidt, Kristiane A.; Henkel, Christiaan V.; Rozenberg, Grzegorz; Spaink, Herman P.

2004-01-01

248

DNA computing using single-molecule hybridization detection.  

PubMed

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that require vast search spaces. However, the actual parallelism currently being achieved is at least a hundred million-fold lower than the number of DNA molecules used. This is due to the quantity of DNA molecules of one species that is required to produce a detectable output to the computations. In order to miniaturize the computation and considerably reduce the amount of DNA needed, we have combined DNA computing with single-molecule detection. Reliable hybridization detection was achieved at the level of single DNA molecules with fluorescence cross-correlation spectroscopy. To illustrate the use of this approach, we implemented a DNA-based computation and solved a 4-variable 4-clause instance of the computationally hard Satisfiability (SAT) problem. PMID:15388798

Schmidt, Kristiane A; Henkel, Christiaan V; Rozenberg, Grzegorz; Spaink, Herman P

2004-01-01

249

What Do We Measure With Single-Molecule Force Spectroscopy?  

NASA Astrophysics Data System (ADS)

Single-molecule force spectroscopy is a powerful technique for studying detailed intra- and inter- molecular interactions by manipulating single biomolecules at the nanometer scale. Force is measured while one pulls on the molecules. However, relating the measured information to equilibrium thermodynamic properties is challenging. Jarzynksi's equality allows one to reconstruct the free energy surface as a function of molecular end-to-end distance^1,2. Using protein folding as an example, we studied the parameters that influence the unfolding process, such as pulling velocity, tempearture, and chemical denaturant concentration in the solution, to demonatrate that valuable equailibrium thermodynamic information can be obtained using this technique. 1. N. C. Harris, Y. Song, and C.-H. Kiang, Phys. Rev. Lett., 99 068101 (2007). 2.``Pulling Strings: Stretching Proteins Can Reveal How They Fold,'' Science News, 172 22 (2007).

Kiang, Ching-Hwa; Harris, Nolan; Botello, Eric; Chen, Wei-Hung

2008-03-01

250

Connecting Rare DNA Conformations and Surface Dynamics using Single-Molecule Resonance Energy Transfer  

PubMed Central

A mechanistic understanding of single-stranded DNA (ssDNA) behavior in the near-surface environment is critical to advancing DNA-directed self-assembled nanomaterials. A new approach is described that uses total internal reflection fluorescence microscopy to measure resonance energy transfer at the single-molecule level, providing a mechanistic understanding of the connection between molecular conformation and interfacial dynamics near amine-modified surfaces. Large numbers (>105) of ssDNA trajectories were observed, permitting dynamic correlation of molecular conformation with desorption and surface mobility. On the basis of dynamic behavior, molecules could be designated as members of the more common coiled population or a rare, weakly bound conformation. Molecules in the coiled state generally exhibited slow diffusion and conformational fluctuations that decreased with increasing average end-to-end distance. Lattice simulations of adsorbed self-avoiding polymers successfully predicted these trends. In contrast, the weakly bound conformation, observed in about 5% of molecules, had a large end-to-end distance but demonstrated conformational fluctuations that were much higher than predicted by simulations for adsorbed flexible chains. This conformation correlated positively with desorption events and led to fast diffusion, indicating weak surface associations. Understanding the role of the weakly bound conformation in DNA hybridization, and how solution conditions and surface properties may favor it, could lead to improved self-assembled nanomaterials. PMID:21942411

Kastantin, Mark; Schwartz, Daniel K.

2011-01-01

251

Probing peptide-inorganic surface interaction at the single molecule level using force spectroscopy.  

PubMed

We investigate the interaction between D-Ala-D-Ala peptide and a stainless steel (SS) surface by AFM force spectroscopy with view to understand the role and nature of interfacial processes at the single molecule level. For this purpose, force-distance curves were recorded between the D-Ala-D-Ala modified tip and the SS surface in NaHCO(3)-enriched medium. The SS surface was prepared in a way that allows iron oxide species, presumably FeOOH, to be formed and remains stable during AFM measurements. Dynamic force measurements show that the unbinding force linearly increases with the logarithm of the loading rate, as generally observed for receptor–ligand complexes. Our results reveal also the existence of two regimes, suggesting the presence of multiple energy barriers in the energy landscape. From these dynamic force spectroscopy measurements, the kinetic off-rate constant is determined. An average unbinding force in the range of 50-300 pN is obtained, depending on the loading rate. Accordingly, in a medium in which the electrostatic interactions are not dominating, the binding mechanism of the peptide and SS surface cannot be attributed to covalent bonds and may be due to a combination of van der Waals and hydrogen bonds. Our findings open up new way to probe peptide-inorganic surface interactions and to understand the mechanism of peptide specific binding which is of particular interest in the design of hybrid materials. PMID:21488141

Landoulsi, Jessem; Dupres, Vincent

2011-05-01

252

Probing van der Waals Forces at the Single-Molecule Level  

NASA Astrophysics Data System (ADS)

Single molecule junctions represent an attractive platform to understand and control functionality of materials and devices at the nanoscale. While their electronic transport properties have received tremendous attention thus far, measurements of mechanics are new and allow for a more complete understanding of the structure-function relationship of these atomic scale devices. Here we report simultaneous measurement of force and electrical conductance across Au-Bipyridine-Au junctions using a conducting atomic force microscope (AFM). We show that these junctions have two distinct structures each with a characteristic conductance. Using statistically relevant analysis, these two structures are found to have very different mechanical properties. Specifically, we find that the higher conductance junctions have a significantly larger rupture force and stiffness than the lower conducting junctions. They also have a larger rupture force than Au single-atom point contacts, suggesting multiple points of contact. Using density functional theory simulations we show that van der Waals (vdW) interactions between the pyridine ring and Au electrodes plays a key role in the junction mechanics. These measurements thus provide a quantitative characterization of vdW interactions at metal/organic interfaces at the single-molecule level [1].[4pt] [1] Aradhya, S. V., Frei, M., Hybertsen, M. S. & Venkataraman, L., Nature Materials, 11, 872-876 (2012).

Venkataraman, Latha

2013-03-01

253

Single Molecule Manipulation and Spectroscopy of Chlorophyll-a from Spinach  

NASA Astrophysics Data System (ADS)

Chlorophyll-a, a molecule produced from `Spinach', adsorbed on a Au(111) surface has been investigated by using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. Studies are carried out both on isolated single molecules and on self-assembled molecular layers. The tunneling I-V and dI-dV spectroscopy of chlorophyll-a elucidate electronic properties of single molecule, such as the HOMO-LOMO gap and molecular orbital states. Mechanical stability of the chlorophyll-a is examined by using STM lateral manipulation (1,2). Here, the STM tip is placed just a few angstrom separation from the molecule to increase the tip-molecule interaction. Then the tip is laterally scanned across the surface resulting in pulling of the molecule. The detailed molecule movement is directly monitored through the corresponding STM-tip height signals. Our results reveal that the spinach molecule is a promising candidate for environmental friendly nano-device applications. (1). S.-W. Hla, K.-H. Rieder, Ann. Rev. Phys. Chem. 54 (2003) 307-330. (2). S.-W. Hla, et al. Phys. Rev. Lett. 93 (2004), 208302. This work is financially supported by the US-DOE grant DE-FG02-02ER46012.

Benson, Jessica-Jones

2005-03-01

254

A Layer-by-Layer ZnO Nanoparticle-PbS Quantum Dot Self-Assembly Platform for Ultrafast Interfacial Electron Injection.  

PubMed

Absorbent layers of semiconductor quantum dots (QDs) are now used as material platforms for low-cost, high-performance solar cells. The semiconductor metal oxide nanoparticles as an acceptor layer have become an integral part of the next generation solar cell. To achieve sufficient electron transfer and subsequently high conversion efficiency in these solar cells, however, energy-level alignment and interfacial contact between the donor and the acceptor units are needed. Here, the layer-by-layer (LbL) technique is used to assemble ZnO nanoparticles (NPs), providing adequate PbS QD uptake to achieve greater interfacial contact compared with traditional sputtering methods. Electron injection at the PbS QD and ZnO NP interface is investigated using broadband transient absorption spectroscopy with 120 femtosecond temporal resolution. The results indicate that electron injection from photoexcited PbS QDs to ZnO NPs occurs on a time scale of a few hundred femtoseconds. This observation is supported by the interfacial electronic-energy alignment between the donor and acceptor moieties. Finally, due to the combination of large interfacial contact and ultrafast electron injection, this proposed platform of assembled thin films holds promise for a variety of solar cell architectures and other settings that principally rely on interfacial contact, such as photocatalysis. PMID:25163799

Eita, Mohamed; Usman, Anwar; El-Ballouli, Ala'a O; Alarousu, Erkki; Bakr, Osman M; Mohammed, Omar F

2015-01-01

255

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

256

Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface.  

PubMed

Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on spin transport. Going beyond investigations focused on physisorbed SMMs, in this work the robust grafting of terbium(III) bis(phthalocyaninato) complexes to a silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here by exploiting the surface sensitivity of X-ray circular magnetic dichroism, we evidence an enhancement of the magnetic bistability of this SMM, in contrast to the dramatic reduction of the magnetic hysteresis that characterizes monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices. PMID:25109254

Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G; Dalcanale, Enrico; Sessoli, Roberta

2014-01-01

257

Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface  

NASA Astrophysics Data System (ADS)

Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on spin transport. Going beyond investigations focused on physisorbed SMMs, in this work the robust grafting of terbium(III) bis(phthalocyaninato) complexes to a silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here by exploiting the surface sensitivity of X-ray circular magnetic dichroism, we evidence an enhancement of the magnetic bistability of this SMM, in contrast to the dramatic reduction of the magnetic hysteresis that characterizes monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices.

Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G.; Dalcanale, Enrico; Sessoli, Roberta

2014-08-01

258

Quantum tunneling of magnetization in lanthanide single-molecule magnets, bis(phthalocyaninato)terbium and bis(phthalocyaninato)-dysprosium anions  

Microsoft Academic Search

Magnetization versus field measurements were performed on single crystals of [(Pc)2TbIII0.02YIII0.98]^TBA+ and [(Pc)2DyIII0.02YIII0.98]^TBA+ (Pc: phthalocyaninato, TBA: tetrabutylammonium) at 0.04 K. The [(Pc)2TbIII] complex, the first lanthanide single-molecule magnet, exhibited clear staircase-like structures, which are assigned to resonant quantum tunneling between entangled states of the electron and nuclear spin systems.

Naoto Ishikawa; Miki Sugita; Wolfgang Wernsdorfer

2005-01-01

259

Interfacial electronic transport phenomena in single crystalline Fe-MgO-Fe thin barrier junctions  

SciTech Connect

Spin filtering effects in nano-pillars of Fe-MgO-Fe single crystalline magnetic tunnel junctions are explored with two different sample architectures and thin MgO barriers (thickness: 3–8 monolayers). The two architectures, with different growth and annealing conditions of the bottom electrode, allow tuning the quality of the bottom Fe/MgO interface. As a result, an interfacial resonance states (IRS) is observed or not depending on this interface quality. The IRS contribution, observed by spin polarized tunnel spectroscopy, is analyzed as a function of the MgO barrier thickness. Our experimental findings agree with theoretical predictions concerning the symmetry of the low energy (0.2?eV) interfacial resonance states: a mixture of ?{sub 1}-like and ?{sub 5}-like symmetries.

Gangineni, R. B., E-mail: rameshg.phy@pondiuni.edu.in [Department of Physics, School of Physical, Chemical and Applied Sciences, Pondicherry University, R. V. Nagar, Kalapet, Pondicherry 605 014 (India); SPINTEC, UMR 8191 CEA/CNRS/UJF-Grenoble 1/Grenoble INP, INAC, 17 rue des Martyrs, F-38054 Grenoble Cedex (France); Bellouard, C., E-mail: christine.bellouard@ijl.nancy-universite.fr; Duluard, A. [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); Negulescu, B. [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); UFR de Sciences et Techniques, Matériaux, microélectronique, acoustique, nanotechnologies (GREMAN), University François Rabelais, Parc de Grandmont, 37200 Tours (France); Baraduc, C.; Gaudin, G. [SPINTEC, UMR 8191 CEA/CNRS/UJF-Grenoble 1/Grenoble INP, INAC, 17 rue des Martyrs, F-38054 Grenoble Cedex (France); Tiusan, C., E-mail: coriolan.tiusan@phys.utcluj.ro [Institut Jean Lamour, UMR 7198, CNRS-Université de Lorraine, BP 239, 54506 Vandoeuvre (France); Department of Physics and Chemistry, Center of Superconductivity, Spintronics and Surface Science, Technical University of Cluj Napoca, Str. Memorandumului No. 28, RO-400114 Cluj-Napoca (Romania)

2014-05-05

260

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

261

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

262

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

263

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

264

Single Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics  

PubMed Central

We employ single-molecule fluorescence resonance energy transfer (smFRET) to study structural dynamics over the first two elongation cycles of protein synthesis, using ribosomes containing either Cy3-labeled ribosomal protein L11 and A- or P-site Cy5-labeled tRNA or Cy3 and Cy5 labeled tRNAs. Pre-translocation (PRE) complexes demonstrate fluctuations between classical and hybrid forms, with concerted motions of tRNAs away from L11 and from each other when classical complex converts to hybrid complex. EF-G·GTP binding to both hybrid and classical PRE complexes halts these fluctuations prior to catalyzing translocation to form the post-translocation (POST) complex. EF-G dependent translocation from the classical PRE complex proceeds via transient formation of a short-lived hybrid intermediate. A-site binding of either EF-G to the PRE complex or of aminoacyl-tRNA·EF-Tu ternary complex to the POST complex markedly suppresses ribosome conformational lability. PMID:21549313

Chen, Chunlai; Stevens, Benjamin; Kaur, Jaskarin; Cabral, Diana; Liu, Hanqing; Wang, Yuhong; Zhang, Haibo; Rosenblum, Gabriel; Smilansky, Zeev; Goldman, Yale E.; Cooperman, Barry S.

2011-01-01

265

Profiling of Short RNAs Using Helicos Single-Molecule Sequencing  

PubMed Central

The importance of short (<200 nt) RNAs in cell biogenesis has been well documented. These short RNAs include crucial classes of molecules such as transfer RNAs, small nuclear RNA, microRNAs, and many others (reviewed in Storz et al., Annu Rev Biochem 74:199–217, 2005; Ghildiyal and Zamore, Nat Rev Genet 10:94–108, 2009). Furthermore, the realm of functional RNAs that fall within this size range is growing to include less well-characterized RNAs such as short RNAs found at the promoters and 3? termini of genes (Affymetrix ENCODE Transcriptome Project et al., Nature 457:1028–1032, 2009; Davis and Ares, Proc Natl Acad Sci USA 103:3262–3267, 2006; Kapranov et al., Science 316:1484–1488, 2007; Taft et al., Nat Genet 41:572–578, 2009; Kapranov et al., Nature 466:642–646, 2010), short RNAs involved in paramutation (Rassoulzadegan et al., Nature 441:469–474, 2006), and others (reviewed in Kawaji and Hayashizaki, PLoS Genet 4:e22, 2008). Discovery and accurate quantification of these RNA molecules, less than 200 bases in size, is thus an important and also challenging aspect of understanding the full repertoire of cellular and extracellular RNAs. Here, we describe the strategies and procedures we developed to profile short RNA species using single-molecule sequencing (SMS) and the advantages SMS offers. PMID:22144202

Kapranov, Philipp; Ozsolak, Fatih; Milos, Patrice M.

2012-01-01

266

Multiplex single-molecule interaction profiling of DNA barcoded proteins  

PubMed Central

In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

Gu, Liangcai; Li, Chao; Aach, John; Hill, David E.; Vidal, Marc; Church, George M.

2014-01-01

267

A single-molecule view of gene regulation in cancer  

NASA Astrophysics Data System (ADS)

Single-cell analysis has revealed that transcription is dynamic and stochastic, but tools are lacking that can determine the mechanism operating at a single gene. Here we utilize single-molecule observations of RNA in fixed and living cells to develop a single-cell model of steroid-receptor mediated gene activation. Steroid receptors coordinate a diverse range of responses in higher eukaryotes and are involved in a wide range of human diseases, including cancer. Steroid receptor response elements are present throughout the human genome and modulate chromatin remodeling and transcription in both a local and long-range fashion. As such, steroid receptor-mediated transcription is a paradigm of genetic control in the metazoan nucleus. Moreover, the ligand-dependent nature of these transcription factors makes them appealing targets for therapeutic intervention, necessitating a quantitative understanding of how receptors control output from target genes. We determine that steroids drive mRNA synthesis by frequency modulation of transcription. This digital behavior in single cells gives rise to the well-known analog dose response across the population. To test this model, we developed a light-activation technology to turn on a single gene and follow dynamic synthesis of RNA from the activated locus. The response delay is a measure of time required for chromatin remodeling at a single gene.

Larson, Daniel

2013-03-01

268

FPGA for single-molecule recycling in a nanochannel  

NASA Astrophysics Data System (ADS)

Single-molecule (SM) trapping and detection experiments are important in studying biophysical processes on the molecular level. As an SM is too small for optical trapping, prolonged observation requires measurement of the position and active feedback to counteract diffusion. In previous work, a custom-built Field Programmable Gate Array (FPGA) circuit board was developed for SM detection and real-time electrokinetic trapping in a fused silica nanochannel. The FPGA was used as part of a feedback system to control the voltage for electrokinetic movement of solution along the nanochannel in response to the time stamps of individual photons from the excited SM. Other researchers have since shown that alternating the flow in a nanochannel can be used to recycle an SM through a stationary laser focus for repeated observations and that the times between each passage yield a measurement of the molecule's diffusion. Improved measurements could be obtained by use of an FPGA for more precisely timed flow control. Therefore, we are now adapting the FPGA for SM trapping to use algorithms tested in a Monte Carlo simulation of SM recycling in an attempt to extend existing capabilities. This presentation discusses the custom-built FPGA board, algorithms, and ongoing nanochannel experiments.

Behery, Sultan; Wang, Bo; Canfield, Brian K.; Davis, Lloyd M.

2013-03-01

269

Locked nucleic acid oligomers as handles for single molecule manipulation  

PubMed Central

Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments. PMID:25159617

Berezney, John P.; Saleh, Omar A.

2014-01-01

270

Alternative Spliceosome Assembly Pathways Revealed by Single Molecule Fluorescence Microscopy  

PubMed Central

SUMMARY Removal of introns from nascent transcripts (pre-mRNAs) by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered, with stable recruitment of U1 snRNP to the 5' splice site necessarilypreceding recruitment of U2 snRNP to the branch site to form the “pre-spliceosome”. Using Colocalization Single Molecule Spectroscopy (CoSMoS) to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we here demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5•U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist toassemble functional spliceosomes. These observations provide new insight into the mechanisms of cross-intron coordination of initial spliceosome assembly. PMID:24075986

Shcherbakova, Inna; Hoskins, Aaron A.; Friedman, Larry J.; Serebrov, Victor; Corrêa, Ivan R.; Xu, Ming-Qun; Gelles, Jeff; Moore, Melissa J.

2014-01-01

271

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

272

Single Molecule Views of Protein Movement on Single Stranded DNA  

PubMed Central

The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical and magnetic “tweezers”), in combination with ensemble methods, have been particularly useful for mechanistic studies of protein-nucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single stranded DNA. These include single stranded (ss)DNA binding (SSB) proteins, recombinases (RecA/Rad51) and helicases/translocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the ssDNA and the mechanistic and functional information that can result from detailed analysis of such movement. PMID:22404684

Ha, Taekjip; Kozlov, Alexander G.; Lohman, Timothy M.

2013-01-01

273

A Single Molecule Investigation of the Photostability of Quantum Dots  

PubMed Central

Quantum dots (QDs) are very attractive probes for multi-color fluorescence imaging in biological applications because of their immense brightness and reported extended photostability. We report here however that single QDs, suitable for biological applications, that are subject to continuous blue excitation from a conventional 100 W mercury arc lamp will undergo a continuous blue-switching of the emission wavelength eventually reaching a permanent dark, photobleached state. We further show that ?-mercaptoethanol has a dual stabilizing effect on the fluorescence emission of QDs: 1) by increasing the frequency of time that a QD is in its fluorescent state, and 2) by decreasing the photobleaching rate. The observed QD color spectral switching is especially detrimental for multi-color single molecule applications, as we regularly observe spectral blue-shifts of 50 nm, or more even after only ten seconds of illumination. However, of significant importance for biological applications, we find that even small, biologically compatible, concentrations (25 µM) of ?-mercaptoethanol has a significant stabilizing effect on the emission color of QDs, but that greater amounts are required to completely abolish the spectral blue shifting or to minimize the emission intermittency of QDs. PMID:22952963

Lagerholm, B. Christoffer

2012-01-01

274

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

275

Kinetics from Nonequilibrium Single-Molecule Pulling Experiments  

PubMed Central

Mechanical forces exerted by laser tweezers or atomic force microscopes can be used to drive rare transitions in single molecules, such as unfolding of a protein or dissociation of a ligand. The phenomenological description of pulling experiments based on Bell's expression for the force-induced rupture rate is found to be inadequate when tested against computer simulations of a simple microscopic model of the dynamics. We introduce a new approach of comparable complexity to extract more accurate kinetic information about the molecular events from pulling experiments. Our procedure is based on the analysis of a simple stochastic model of pulling with a harmonic spring and encompasses the phenomenological approach, reducing to it in the appropriate limit. Our approach is tested against computer simulations of a multimodule titin model with anharmonic linkers and then an illustrative application is made to the forced unfolding of I27 subunits of the protein titin. Our procedure to extract kinetic information from pulling experiments is simple to implement and should prove useful in the analysis of experiments on a variety of systems. PMID:12829459

Hummer, Gerhard; Szabo, Attila

2003-01-01

276

Multiplexed single-molecule measurements with magnetic tweezers  

SciTech Connect

We present a method for performing multiple single-molecule manipulation experiments in parallel with magnetic tweezers. We use a microscope with a low magnification, and thus a wide field of view, to visualize multiple DNA-tethered paramagnetic beads and apply an optimized image analysis routine to track the three-dimensional position of each bead simultaneously in real time. Force is applied to each bead using an externally applied magnetic field. Since variations in the field parameters are negligible across the field of view, nearly identical manipulation of all visible beads is possible. However, we find that the error in the position measurement is inversely proportional to the microscope's magnification. To mitigate the increased error caused by demagnification, we have developed a strategy based on tracking multiple fixed beads. Our system is capable of simultaneously manipulating and tracking up to 34 DNA-tethered beads at 60 Hz with {approx}1.5 nm resolution and with {approx}10% variation in applied force.

Ribeck, Noah [Physics Department, University of California, Santa Barbara, Santa Barbara, California 93106 (United States); Saleh, Omar A. [Materials Department and Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93106 (United States)

2008-09-15

277

Multiplexed single-molecule measurements with magnetic tweezers.  

PubMed

We present a method for performing multiple single-molecule manipulation experiments in parallel with magnetic tweezers. We use a microscope with a low magnification, and thus a wide field of view, to visualize multiple DNA-tethered paramagnetic beads and apply an optimized image analysis routine to track the three-dimensional position of each bead simultaneously in real time. Force is applied to each bead using an externally applied magnetic field. Since variations in the field parameters are negligible across the field of view, nearly identical manipulation of all visible beads is possible. However, we find that the error in the position measurement is inversely proportional to the microscope's magnification. To mitigate the increased error caused by demagnification, we have developed a strategy based on tracking multiple fixed beads. Our system is capable of simultaneously manipulating and tracking up to 34 DNA-tethered beads at 60 Hz with approximately 1.5 nm resolution and with approximately 10% variation in applied force. PMID:19044437

Ribeck, Noah; Saleh, Omar A

2008-09-01

278

Open quantum system approach to single-molecule spectroscopy  

NASA Astrophysics Data System (ADS)

In this paper, single-molecule spectroscopy experiments based on continuous laser excitation are characterized through an open quantum system approach. The evolution of the fluorophore system follows from an effective Hamiltonian microscopic dynamic where its characteristic parameters, i.e., its electric dipole, transition frequency, and Rabi frequency, as well as the quantization of the background electromagnetic field and their mutual interaction, are defined in an extended Hilbert space associated to the different configurational states of the local nanoenvironment. After tracing out the electromagnetic field and the configurational states, the fluorophore density matrix is written in terms of a Lindblad rate equation. Observables associated to the scattered laser field, such as optical spectrum, intensity-intensity correlation, and photon-counting statistics, are obtained from a quantum-electrodynamic calculation also based on the effective microscopic dynamic. In contrast with stochastic models, this approach allows one to describe in a unified way both the full quantum nature of the scattered laser field as well as the classical nature of the environment fluctuations. By analyzing different processes such as spectral diffusion, lifetime fluctuations, and light assisted processes, we exemplify the power of the present approach.

Budini, Adrián A.

2009-04-01

279

Quantum Dot Spin Valves Controlled by Single Molecule Magnets  

NASA Astrophysics Data System (ADS)

We explore theoretically for the first time the properties of a new class of spintronic nano-devices in which the electrical resistance of a non-magnetic quantum dot contacted by non-magnetic electrodes is controlled by transition metal-based single molecule nanomagnets (SMMs) bound to the dot. Although the SMMs do not lie directly in the current path in these devices, we show that the relative orientation of their magnetic moments can strongly influence on the electric current passing through the device. If the magnetic moment of one of the SMMs is reversed by the application of a magnetic field, we predict a large change in the resistance of the dot, i.e., a strong spin valve effect. The mechanism is resonant conduction via molecular orbitals extending over the entire system. The spin valve is activated by a gate that tunes the transport resonances through the Fermi energy. Detailed results will be presented for the case of Mn12 SMMs bound to a gold quantum dot.

Rostamzadeh Renani, Fatemeh; Kirczenow, George

2013-03-01

280

Single molecule activity measurements of cytochrome P450 oxidoreductase reveal the existence of two discrete functional states.  

PubMed

Electron transfer between membrane spanning oxidoreductase enzymes controls vital metabolic processes. Here we studied for the first time with single molecule resolution the function of P450 oxidoreductase (POR), the canonical membrane spanning activator of all microsomal cytochrome P450 enzymes. Measurements and statistical analysis of individual catalytic turnover cycles shows POR to sample at least two major functional states. This phenotype may underlie regulatory interactions with different cytochromes P450 but to date has remained masked in bulk kinetics. To ensure that we measured the inherent behavior of POR, we reconstituted the full length POR in "native like" membrane patches, nanodiscs. Nanodisc reconstitution increased stability by ?2-fold as compared to detergent solubilized POR and showed significantly increased activity at biologically relevant ionic strength conditions, highlighting the importance of studying POR function in a membrane environment. This assay paves the way for studying the function of additional membrane spanning oxidoreductases with single molecule resolution. PMID:24359083

Laursen, Tomas; Singha, Aparajita; Rantzau, Nicolai; Tutkus, Marijonas; Borch, Jonas; Hedegård, Per; Stamou, Dimitrios; Møller, Birger Lindberg; Hatzakis, Nikos S

2014-03-21

281

Single-Molecule Tracking in Living Cells Using Single Quantum Dot Applications  

PubMed Central

Revealing the behavior of single molecules in living cells is very useful for understanding cellular events. Quantum dot probes are particularly promising tools for revealing how biological events occur at the single molecule level both in vitro and in vivo. In this review, we will introduce how single quantum dot applications are used for single molecule tracking. We will discuss how single quantum dot tracking has been used in several examples of complex biological processes, including membrane dynamics, neuronal function, selective transport mechanisms of the nuclear pore complex, and in vivo real-time observation. We also briefly discuss the prospects for single molecule tracking using advanced probes. PMID:22896768

Baba, Koichi; Nishida, Kohji

2012-01-01

282

TOPICAL REVIEW: Electrical conduction through single molecules and self-assembled monolayers  

NASA Astrophysics Data System (ADS)

Although research on molecular electronics has drawn increasingly more attention in the last decade, the large spread in obtained results for the conduction rescaled to a single molecule indicates a strong dependence of the measured data on the experimental testbed used. We subdivided a generalized metal-molecule-metal junction into different components and discuss their influence on electrical transport measurements of a single organic molecule or an assembly of molecules. By relating the advantages and disadvantages of different experimental testbeds to the more general view of a molecular junction, we strive to explain the discrepancies between the obtained results on molecular conduction. The reported results on molecular conduction of molecules with an alkane backbone can be categorized into three groups with different resistance values, depending on the device area of the molecular junction and the nature of the contacts.

Akkerman, Hylke B.; de Boer, Bert

2008-01-01

283

Switching of a photochromic molecule on gold electrodes: single-molecule measurements  

NASA Astrophysics Data System (ADS)

We have studied the electronic changes caused by light-induced isomerization of a photochromic molecule between an open state (that absorbs in the UV to become closed) and a closed state (that absorbs in the visible to become open). Data obtained using a newly developed repetitive break junction method are interpreted in terms of single-molecule resistances of 526 ± 90 M? in the open form and 4 ± 1 M? in the closed form when the molecule is bound between two gold contacts via dithiol linkages. The corresponding ratio of open to closed resistance is in close agreement with the results of ab initio calculations, though the measured resistances are about half of the calculated values. Optical spectroscopy indicates that the photoisomerization occurs in both directions on small gold particles, evaporated thin gold films, and in the break junction experiments. http://stacks.iop.org/0957-4484/16/695

He, Jin; Chen, Fan; Liddell, Paul A.; Andréasson, Joakim; Straight, Stephen D.; Gust, Devens; Moore, Thomas A.; Moore, Ana L.; Li, Jun; Sankey, Otto F.; Lindsay, Stuart M.

2005-06-01

284

Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules  

NASA Astrophysics Data System (ADS)

Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins.

Bennett, Kochise; Biggs, Jason D.; Zhang, Yu; Dorfman, Konstantin E.; Mukamel, Shaul

2014-05-01

285

Local magnetic properties of a monolayer of Mn12 single molecule magnets.  

PubMed

The magnetic properties of a monolayer of Mn12 single molecule magnets grafted onto a silicon (Si) substrate have been investigated using depth-controlled beta-detected nuclear magnetic resonance. A low-energy beam of spin-polarized radioactive 8Li was used to probe the local static magnetic field distribution near the Mn12 monolayer in the Si substrate. The resonance line width varies strongly as a function of implantation depth as a result of the magnetic dipolar fields generated by the Mn12 electronic magnetic moments. The temperature dependence of the line width indicates that the magnetic properties of the Mn12 moments in this low-dimensional configuration differ from bulk Mn12. PMID:17488049

Salman, Z; Chow, K H; Miller, R I; Morello, A; Parolin, T J; Hossain, M D; Keeler, T A; Levy, C D P; MacFarlane, W A; Morris, G D; Saadaoui, H; Wang, D; Sessoli, R; Condorelli, G G; Kiefl, R F

2007-06-01

286

Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules  

SciTech Connect

Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins.

Bennett, Kochise, E-mail: kcbennet@uci.edu; Biggs, Jason D.; Zhang, Yu; Dorfman, Konstantin E.; Mukamel, Shaul, E-mail: smukamel@uci.edu [University of California, Irvine, California 92697-2025 (United States)

2014-05-28

287

Time-, Frequency-, and Wavevector-Resolved X-Ray Diffraction from Single Molecules  

E-print Network

Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broad-band X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and ...

Bennett, Kochise; Zhang, Yu; Dorfman, Konstantin E; Mukamel, Shaul

2014-01-01

288

Tuning the thermoelectric properties of a single-molecule junction by mechanical stretching.  

PubMed

We theoretically investigate, as a function of the stretching, the behaviour of the thermoelectric properties - the Seebeck coefficient (S), the electronic heat conductance (?el) and the figure of merit (ZT) - of a molecule-based junction composed of a benzene-1,4-dithiolate molecule (BDT) coupled to Au(111) surfaces at room temperature. We show that the thermoelectric properties of a single molecule junction can be tuned by mechanic stretching. The Seebeck coefficient is positive, indicating that it is dominated by the HOMO. Furthermore, it increases as the HOMO level, which is associated to the sulphur atom, tends towards energies close to the Fermi energy. By modelling the transmission coefficient of the system as a single Lorentzian peak, we propose a scheme to obtain the maximum ZT of any molecular junction. PMID:25612893

Torres, Alberto; Pontes, Renato B; da Silva, Antônio J R; Fazzio, Adalberto

2015-02-01

289

Single-molecule-magnet behavior and spin changes affected by crystal packing effects.  

PubMed

Five Mn 3Zn 2 heterometallic complexes have been synthesized and structurally and magnetically characterized. Spin ground states up to S = 6 have been observed for these complexes and are shown to depend on the cocrystallizing cation and on the terminal ligand. Large axial zero-field interactions ( D = -1.16 K) are the result of near-parallel alignment of the Mn (III) Jahn-Teller axes. High-frequency electron paramagnetic resonance, single-crystal magnetization hysteresis, and alternating current susceptibility measurements are presented to characterize [NEt 4] 3[Mn 3Zn 2(salox) 3O(N 3) 6X 2] [X (-) = Cl (-) ( 1), Br (-) ( 2)] and [AsPh 4] 3[Mn 3Zn 2(salox) 3O(N 3) 6Cl 2] ( 3) and reveal that 1 and 2 are single-molecule magnets ( U eff = 44 K), while 3 is not. PMID:18771258

Feng, Patrick L; Koo, Changhyun; Henderson, John J; Nakano, Motohiro; Hill, Stephen; del Barco, Enrique; Hendrickson, David N

2008-10-01

290

Frequency domain Fourier transform THz-EPR on single molecule magnets using coherent synchrotron radiation.  

PubMed

Frequency domain Fourier transform THz electron paramagnetic resonance (FD-FT THz-EPR) based on coherent synchrotron radiation (CSR) is presented as a novel tool to ascertain very large zero field splittings in transition metal ion complexes. A description of the FD-FT THz-EPR at the BESSY II storage ring providing CSR in a frequency range from 5 cm(-1) up to 40 cm(-1) at external magnetic fields from -10 T to +10 T is given together with first measurements on the single molecule magnet Mn(12)Ac where we studied DeltaM(S) = +/-1 spin transition energies as a function of the external magnetic field and temperature. PMID:19639156

Schnegg, Alexander; Behrends, Jan; Lips, Klaus; Bittl, Robert; Holldack, Karsten

2009-08-21

291

Single-molecule enzyme kinetics in the presence of inhibitors  

NASA Astrophysics Data System (ADS)

Recent studies in single-molecule enzyme kinetics reveal that the turnover statistics of a single enzyme is governed by the waiting time distribution that decays as mono-exponential at low substrate concentration and multi-exponential at high substrate concentration. The multi-exponentiality arises due to protein conformational fluctuations, which act on the time scale longer than or comparable to the catalytic reaction step, thereby inducing temporal fluctuations in the catalytic rate resulting in dynamic disorder. In this work, we study the turnover statistics of a single enzyme in the presence of inhibitors to show that the multi-exponentiality in the waiting time distribution can arise even when protein conformational fluctuations do not influence the catalytic rate. From the Michaelis-Menten mechanism of inhibited enzymes, we derive exact expressions for the waiting time distribution for competitive, uncompetitive, and mixed inhibitions to quantitatively show that the presence of inhibitors can induce dynamic disorder in all three modes of inhibitions resulting in temporal fluctuations in the reaction rate. In the presence of inhibitors, dynamic disorder arises due to transitions between active and inhibited states of enzymes, which occur on time scale longer than or comparable to the catalytic step. In this limit, the randomness parameter (dimensionless variance) is greater than unity indicating the presence of dynamic disorder in all three modes of inhibitions. In the opposite limit, when the time scale of the catalytic step is longer than the time scale of transitions between active and inhibited enzymatic states, the randomness parameter is unity, implying no dynamic disorder in the reaction pathway.

Saha, Soma; Sinha, Antara; Dua, Arti

2012-07-01

292

Single-molecule fluorescence probes dynamics of barrier crossing  

NASA Astrophysics Data System (ADS)

Kramers developed the theory on how chemical reaction rates are influenced by the viscosity of the medium. 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 to reactions as complex as protein folding. 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. Its duration, the transition path time, can now be determined from photon trajectories for single protein molecules undergoing folding/unfolding transitions. 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, which occurs for many small-molecule reactions. 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.

Chung, Hoi Sung; Eaton, William A.

2013-10-01

293

Nucleosome disassembly intermediates characterized by single-molecule FRET  

PubMed Central

The nucleosome has a central role in the compaction of genomic DNA and the control of DNA accessibility for transcription and replication. To help understanding the mechanism of nucleosome opening and closing in these processes, we studied the disassembly of mononucleosomes by quantitative single-molecule FRET with high spatial resolution, using the SELEX-generated “Widom 601” positioning sequence labeled with donor and acceptor fluorophores. Reversible dissociation was induced by increasing NaCl concentration. At least 3 species with different FRET were identified and assigned to structures: (i) the most stable high-FRET species corresponding to the intact nucleosome, (ii) a less stable mid-FRET species that we attribute to a first intermediate with a partially unwrapped DNA and less histones, and (iii) a low-FRET species characterized by a very broad FRET distribution, representing highly unwrapped structures and free DNA formed at the expense of the other 2 species. Selective FCS analysis indicates that even in the low-FRET state, some histones are still bound to the DNA. The interdye distance of 54.0 ? measured for the high-FRET species corresponds to a compact conformation close to the known crystallographic structure. The coexistence and interconversion of these species is first demonstrated under non-invasive conditions. A geometric model of the DNA unwinding predicts the presence of the observed FRET species. The different structures of these species in the disassembly pathway map the energy landscape indicating major barriers for 10-bp and minor ones for 5-bp DNA unwinding steps. PMID:19706432

Gansen, Alexander; Valeri, Alessandro; Hauger, Florian; Felekyan, Suren; Kalinin, Stanislav; Tóth, Katalin; Langowski, Jörg; Seidel, Claus A. M.

2009-01-01

294

Influence of the electron–phonon interfacial conductance on the thermal transport at metal/dielectric interfaces  

NASA Astrophysics Data System (ADS)

Thermal boundary conductance at a metal-dielectric interface is a quantity of prime importance for heat management at the nanoscale. While the boundary conductance is usually ascribed to the coupling between metal phonons and dielectric phonons, in this work we examine the influence of a direct coupling between the metal electrons and the dielectric phonons. The effect of electron–phonon processes is generally believed to be resistive and tends to decrease the overall thermal boundary conductance as compared to the phonon–phonon conductance ?p. Here, we find that the effect of a direct electron-phonon interfacial coupling ?e is to enhance the effective thermal conductance between the metal and the dielectric. Resistive effects turn out to be important only for thin films of metals that have a low electron–phonon coupling strength. Two approaches are explored to reach these conclusions. First, we present an analytical solution of the two-temperature model to compute the effective conductance which accounts for all the relevant energy channels, as a function of ?e, ?p and the electron–phonon coupling factor G. Second, we use numerical resolution to examine the influence of ?e on two realistic cases: a gold film on silicon or silica substrates. We point out the implications for the interpretation of time-resolved thermoreflectance experiments.

Lombard, J.; Detcheverry, F.; Merabia, S.

2015-01-01

295

Time resolved single molecule spectroscopy of semiconductor quantum dot/conjugated organic hybrid nanostructures  

NASA Astrophysics Data System (ADS)

Single molecule studies on CdSe quantum dots functionalized with oligo-phenylene vinylene ligands (CdSe-OPV) provide evidence of strong electronic communication that facilitate charge and energy transport between the OPV ligands and the CdSe quantum dot core. This electronic interaction greatly modify, the photoluminescence properties of both bulk and single CdSe-OPV nanostructure thin film samples. Size-correlated wide-field fluorescence imaging show that blinking suppression in single CdSe-OPV is linked to the degree of OPV coverage (inferred from AFM height scans) on the quantum dot surface. The effect of the complex electronic environment presented by photoexcited OPV ligands on the excited state property of CdSe-OPV is measured with single photon counting and photon-pair correlation spectroscopy techniques. Time-tagged-time-resolved (TTTR) single photon counting measurements from individual CdSe-OPV nanostructures, show excited state lifetimes an order of magnitude shorter relative to conventional ZnS/CdSe quantum dots. Second-order intensity correlation measurements g(2)(tau) from individual CdSe-OPV nanostructures point to a weak multi-excitonic character with a strong wavelength dependent modulation depth. By tuning in and out of the absorption of the OPV ligands we observe changes in modulation depth from g(2) (0) ? 0.2 to 0.05 under 405 and 514 nm excitation respectively. Defocused images and polarization anisotropy measurements also reveal a well-defined linear dipole emission pattern in single CdSe-OPV nanostructures. These results provide new insights into to the mechanism behind the electronic interactions in composite quantum dot/conjugated organic composite systems at the single molecule level. The observed intensity flickering , blinking suppression and associated lifetime/count rate and antibunching behaviour is well explained by a Stark interaction model. Charge transfer from photo-excitation of the OPV ligands to the surface of the CdSe quantum dot core, mixes electron/holes states and lifts the degeneracy in the band edge bright exciton state, which induces a well define linear dipole behaviour in single CdSe-OPV nanostructures. The shift in the electron energies also affects Auger assisted hole trapping rates, suppress access to dark states and reduce the excited state lifetime.

Odoi, Michael Yemoh

296

Noncovalent Cross-Linking of Casein by Epigallocatechin Gallate Characterized by Single Molecule Force Microscopy  

E-print Network

a compaction of the casein micelle. KEYWORDS: Epigallocatechin gallate; polyphenol; casein; single molecule, 7, 8). It has also been shown to increase the stability of the casein micelles to heat denaturationNoncovalent Cross-Linking of Casein by Epigallocatechin Gallate Characterized by Single Molecule

Williamson, Mike P.

297

Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA  

E-print Network

RNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce with the magnetic tweezers. We present atomic force microscopy images of dsRNA and demonstrate a new method single- molecule techniques, magnetic tweezers and atomic force microscopy (AFM), to measure its

Dekker, Nynke

298

A single-molecule characterization of p53 search on DNA  

E-print Network

A single-molecule characterization of p53 search on DNA Anahita Tafvizia,b , Fang Huangc,3 , Alan R (sent for review August 9, 2010) The tumor suppressor p53 slides along DNA while searching for its coordination with the core DNA- binding domain is highly debated. Here we use single-molecule techniques

299

High-density single-molecule analysis of cell surface dynamics in C. elegans embryos  

E-print Network

High-density single-molecule analysis of cell surface dynamics in C. elegans embryos Francois B in GFP::Actin embryos. Supplementary Figure 3 Tunable and high-density sampling of single molecule vs axial position, measured across the field of illumination in a GFP::Utrophin embryo during

Cai, Long

300

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

301

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

E-print Network

and infrared wavelengths and have been recently used to modify fluorescence from single quantum dots and single control over the fluorescent emission from single quantum dots6 and single molecules.7,8 It is knownDirectional Raman Scattering from Single Molecules in the Feed Gaps of Optical Antennas Dongxing

302

LETTER doi:10.1038/nature13761 Multiplex single-molecule interaction profiling of  

E-print Network

LETTER doi:10.1038/nature13761 Multiplex single-molecule interaction profiling of DNA-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes,2 In contrast with advances in massively parallel DNA sequencing1 , high-throughput protein analyses2

303

Single-Molecule Fluorescence Spectroscopy: New Probes of Protein Function and Dynamics  

NSDL National Science Digital Library

Single-molecule fluorescence methods provide new tools for the study of biological systems. Single-pair fluorescence resonance energy transfer has provided detailed information about dynamics and structure of the Ca2+-signaling protein calmodulin. Single-molecule polarization modulation spectroscopy has probed the mechanism by which calmodulin activates the plasma membrane Ca2+ pump

PhD Carey K. Johnson (University of Kansas Department of Chemistry)

2005-02-01

304

Probing the conductance superposition law in single-molecule circuits with parallel paths  

E-print Network

Probing the conductance superposition law in single-molecule circuits with parallel paths H.S. Hybertsen3 * According to Kirchhoff's circuit laws, the net conductance of two parallel components investigate the conductance superposition law for parallel components in single-molecule circuits

Venkataraman, Latha

305

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

E-print Network

Supplementary Information for: Complex RNA folding kinetics revealed by single molecule FRET (hidden states). The states are not associated with a single FRET value of the signal but to a value range emission process, which gives rise to the ob- served photon-by-photon trace in a single-molecule FRET

306

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models  

E-print Network

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models Bettina G a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified

307

Single-Molecule FRET Reveals the Native-State Dynamics of the IB Ankyrin Repeat Domain  

E-print Network

Single-Molecule FRET Reveals the Native-State Dynamics of the IB Ankyrin Repeat Domain Jorge A single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IB were labeled with FRET pairs showed slow fluctuations as if the IB AR domain

Komives, Elizabeth A.

308

Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments  

E-print Network

Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments Eyal. Introduction Forty years after Stryer and Haugland proposed to use fluorescence resonance energy transfer (FRET) as a molecular ruler,1 single-molecule fluorescence resonance energy transfer (smFRET) has become a widely used

Michalet, Xavier

309

How Does a Single Pt Nanocatalyst Behave in Two Different Reactions? A Single-Molecule Study  

E-print Network

How Does a Single Pt Nanocatalyst Behave in Two Different Reactions? A Single-Molecule Study Kyu ABSTRACT: Using single-molecule microscopy of fluoro- genic reactions we studied Pt nanoparticle catalysis-deacetylation and the other a reductive N- deoxygenation. These Pt nanoparticles show distinct catalytic kinetics in these two

Chen, Peng

310

Spectroelectrochemical investigation of intramolecular and interfacial electron-transfer rates reveals differences between nitrite reductase at rest and during turnover.  

PubMed

A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Fo?rster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (?520 ?M), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer. PMID:21863850

Krzemi?ski, ?ukasz; Ndamba, Lionel; Canters, Gerard W; Aartsma, Thijs J; Evans, Stephen D; Jeuken, Lars J C

2011-09-28

311

"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

312

Nanovesicle Trapping for Studying Weak Protein Interactions by Single-Molecule FRET  

PubMed Central

Protein–protein interactions are fundamental biological processes. While strong protein interactions are amenable to many characterization techniques including crystallography, weak protein interactions are challenging to study due to their dynamic nature. Single-molecule FRET can monitor dynamic protein interactions in real time, but are generally limited to strong interacting pairs because of the low concentrations needed for single-molecule detection. Here we describe a nanovesicle trapping approach to enable single-molecule FRET study of weak protein interactions at high effective concentrations. We describe the experimental procedures, summarize the application in studying the weak interactions between intracellular copper transporters, and detail the single-molecule kinetic analysis of bimolecular interactions involving three states. Both the experimental approach and the theoretical analysis are generally applicable for studying many other biological processes at the single-molecule level. PMID:20580959

Benítez, Jaime J.; Keller, Aaron M.; Chen, Peng

2010-01-01

313

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

314

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

PubMed

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 d(z)(2) 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 Fe(2+) 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 d(z)(2) 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 Fe(2+) 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. PMID:25106595

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

2014-08-01

315

Calix[4]arene Based Single-Molecule Magnets  

SciTech Connect

Single-molecule magnets (SMMs) have been the subject of much interest in recent years because their molecular nature and inherent physical properties allow the crossover between classical and quantum physics to be observed. The macroscopic observation of quantum phenomena - tunneling between different spin states, quantum interference between tunnel paths - not only allows scientists to study quantum mechanical laws in great detail, but also provides model systems with which to investigate the possible implementation of spin-based solid state qubits and molecular spintronics. The isolation of small, simple SMMs is therefore an exciting prospect. To date almost all SMMs have been made via the self-assembly of 3d metal ions in the presence of bridging/chelating organic ligands. However, very recently an exciting new class of SMMs, based on 3d metal clusters (or single lanthanide ions) housed within polyoxometalates, has appeared. These types of molecule, in which the SMM is completely encapsulated within (or shrouded by) a 'protective' organic or inorganic sheath have much potential for design and manipulation: for example, for the removal of unwanted dipolar interactions, the introduction of redox activity, or to simply aid functionalization for surface grafting. Calix[4]arenes are cyclic (typically bowl-shaped) polyphenols that have been used extensively in the formation of versatile self-assembled supramolecular structures. Although many have been reported, p-{sup t}But-calix[4]arene and calix[4]arene (TBC4 and C4 respectively, Figure 1A) are frequently encountered due to (a) synthetic accessibility, and (b) vast potential for alteration at either the upper or lower rim of the macrocyclic framework. Within the field of supramolecular chemistry, TBC4 is well known for interesting polymorphic behavior and phase transformations within anti-parallel bi-layer arrays, while C4 often forms self-included trimers. The polyphenolic nature of calix[n]arenes (where n = 4-8) also suggests they should be excellent candidates as ligands for the isolation of molecular magnets, but to date their use in the isolation of paramagnetic cluster compounds is rather limited. Herein we present the first Mn cluster and the first SMM to be isolated using any methylene bridged calix[n]arene - a ferromagnetically coupled mixed-valence [Mn{sub 2}{sup III}Mn{sub 2}{sup II}] complex housed between either two TBC4s or two C4s.

Karotsis, Georgios; Teat, Simon J.; Wernsdorfer, Wolfgang; Piligkos, Stergios; Dalgarno, Scott J.; Brechin, Euan K.

2009-06-04

316

Interfacial Properties of Ultrathin- Film Metal Electrodes: Studies by Combined Electron Spectroscopy and Electrochemistry  

E-print Network

(low energy ion scattering spectroscopy, X-ray photoelectron spectroscopy, Auger electron spectroscopy, and low energy electron diffraction) and electrochemistry (voltage efficiency, voltammetry, and coulometry). Mixed-metal preparation of Pt...

Cummins, Kyle

2012-07-16

317

Low Temperature STM Manipulation and Spectroscopy of Chlorophyll-a Single Molecules from Spinach  

NASA Astrophysics Data System (ADS)

We interrogate single chlorophyll-a, a molecule produced from Spinach, on Cu(111) surface to check its mechanical stability and electronic properties using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. The measured results of isolated single chlorophyll-a molecules are then compared with that of self-assembled molecular layer. The tunneling I/V and dI/dV spectroscopy techniques are used to probe the electronic properties of the chlorophyll-a molecule with atomic precision (1). These spectroscopic investigations elucidate properties of the single molecule such as the band gap and additional molecular orbital states. Mechanical stability of the chlorophyll-a molecule is examined using lateral manipulation techniques with the STM tip (2). In this procedure, the STM tip is placed in close proximity to the molecule (just a few angstrom separation) to increase the tip-molecule interaction. Then the tip is laterally moved across the surface, which results in pulling of the chlorophyll-a molecule to relocate to the specific surface sites. The detailed molecule movement during this manipulation is directly monitored through the corresponding STM-tip height signals. Our results highlight that the Spinach molecule is a promising candidate for environmental friendly nano-electronic device applications. (1) F. Moresco et al, Phy. Rev. Lett. 86, 672-675, (2001) (2) S-W. Hla, K-H. Rieder, Ann. Phy. Chem. 54, 307-330, (2003)

Benson, Jessica J.; Iancu, Violeta; Deshpande, Aparna; Hla, Saw-Wai

2004-04-01

318

Single Molecule Spectroscopy of Amino Acids and Peptides by Recognition Tunneling  

PubMed Central

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 and measuring the electron tunneling 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 tunneling technique, we are able to identify D, 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

2014-01-01

319

Electronic Structure and Vibrational Mode Study of Nafion Membrane Interfacial Water Interactions.  

PubMed

The structural, energetic, and mid-infrared spectral properties of water clusters interacting with a model perfluorosulfonate (Nafion) ionomer segment have been investigated by means of quantum chemical calculations. Density functional theory calculations were conducted to model interfacial water condensed in pores and channels of Nafion and helped shedding light on the structural and vibrational properties of hydrated Nafion membranes. The computational models consisted of a sodium counterion, the Nafion ionomer, and a cluster of water molecules positioned in three different regions of the ionomer. The orientations of the water molecules in the vicinity of the ionomer were examined to understand the appearance of O-H stretching bands that deviated from the typical bulk water values as well as the appearance of multiple free O-H stretching bands. The calculations revealed insights into the structure, orientation, and energetics of Nafion and water clusters in and around the membrane interface; the results show that hydrogen atoms at the water-ionomer interface hydrogen bond to the hydrophilic sulfonate group as well as to the hydrophobic fluorinated backbone. PMID:25412259

Kabrane, Joseph; Aquino, Adelia J A

2014-12-01

320

A starting point for fluorescence-based single-molecule measurements in biomolecular research.  

PubMed

Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research. PMID:25271426

Gust, Alexander; Zander, Adrian; Gietl, Andreas; Holzmeister, Phil; Schulz, Sarah; Lalkens, Birka; Tinnefeld, Philip; Grohmann, Dina

2014-01-01

321

One- and two-photon spectroscopy on single molecules of diphenyloctatetraene  

NASA Astrophysics Data System (ADS)

We report investigations on one- and two-photon excitation of single molecules of diphenyloctatetraene in n-tetradecane at cryogenic temperatures. Saturation intensities, count rates and linewidths of single molecules are compared with corresponding ensemble values obtained from statistical fine structure investigations. The single-molecule linewidths under one-photon excitation are generally two to three times narrower than in two-photon excitation spectra. This effect is discussed with respect to saturated spectral diffusion induced by the high power 1R light necessary for efficient two-photon absorption.

Walser, Daniel; Plakhotnik, Taras; Renn, Alois; Wild, Urs P.

1997-05-01

322

Single-Molecule STM Studies on Atomically-Flat Nanoparticles  

Microsoft Academic Search

The scanning tunneling microscope (STM) has been broadly applied to measure electronic characteristics of individual molecules supported in an inert monolayer matrix, which is typically grown on gold thin films on mica or bulk single crystal substrates. Although these substrates are excellent for electronic measurements, they have serious disadvantages for optical measurements because they are not optically transparent and the

D. H. Dahayanaka; D. W. Kelle; D. J. Wasielewski; E. S. Day; D. R. White; L. A. Bumm; C. M. Waite; J. L. Moore; R. L. Halterman

2006-01-01

323

The role of aromaticity and the pi-conjugated framework in multiporphyrinic systems as single-molecule switches.  

PubMed

A systematic analysis of electron-transport characteristics for monomer, dimer, and tetramer multiporphyrinic systems is presented, to provide a thorough understanding of the structural dependence of electron transport related to the aromatic nature of the contact structure. Theoretical investigation shows that the electron-transport characteristics can be controlled by manipulating the pi-conjugated framework in the multiporphyrinic systems through the arrangement of the inner hydrogen atoms. The designed pi-conjugated framework assigns the distinct aromaticity on the contact structure, and the large aromatic nature of the contact structure increases conductivity. The feature emerging from this study is that the aromaticity and pi-conjugated framework are important factors that control the electron-transport characteristics in molecular-scale electronic devices, such as single-molecule switches. PMID:18574801

Lee, Sang Uck; Belosludov, Rodion V; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2008-07-01

324

Single-molecule dynamics of lysozyme processing distinguishes linear and cross-linked peptidoglycan substrates.  

PubMed

The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20-50 s(-1) and rapid (200-400 s(-1)) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme's time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate. PMID:22239748

Choi, Yongki; Moody, Issa S; Sims, Patrick C; Hunt, Steven R; Corso, Brad L; Seitz, David E; Blaszczak, Larry C; Blaszcazk, Larry C; Collins, Philip G; Weiss, Gregory A

2012-02-01

325

Voltage tuning of vibrational mode energies in single-molecule junctions  

PubMed Central

Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been used to manipulate electronic structure and related functional properties of molecules, electrical control of vibrational mode energies has remained elusive. Here we use simultaneous transport and surface-enhanced Raman spectroscopy measurements to demonstrate large, reversible, voltage-driven shifts of vibrational mode energies of C60 molecules in gold junctions. C60 mode energies are found to vary approximately quadratically with bias, but in a manner inconsistent with a simple vibrational Stark effect. Our theoretical model instead suggests that the mode shifts are a signature of bias-driven addition of electronic charge to the molecule. These results imply that voltage-controlled tuning of vibrational modes is a general phenomenon at metal–molecule interfaces and is a means of achieving significant shifts in vibrational energies relative to a pure Stark effect. PMID:24474749

Li, Yajing; Doak, Peter; Kronik, Leeor; Neaton, Jeffrey B.; Natelson, Douglas

2014-01-01

326

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

327

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

328

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

329

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

E-print Network

-molecule fluorescence microscope to con- duct simultaneous multi-color excitation and detection is a key experimental for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact

Walter, Nils G.

330

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

331

Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR  

E-print Network

of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic...

Shuga, Joe; Zeng, Yong; Novak, Richard; Lan, Qing; Tang, Xiaojiang; Rothman, Nathaniel; Vermeulen, Roel; Li, Laiyu; Hubbard, Alan; Zhang, Luoping; Mathies, Richard A.; Smith, Martyn T.

2013-06-23

332

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

E-print Network

Theory of vibrational absorption sidebands in the Coulomb-blockade regime of single-driven vibrational nonequilibrium induces vibrational sidebands in single-molecule transistors which arise from tunneling processes accompanied by absorption of vibrational quanta. Unlike conventional sidebands

von Oppen, Felix

333

A microfluidic mixing system for single-molecule measurements Shawn H. Pfeil,1  

E-print Network

- ing face-type static O-ring seals, so pressure delivery fittings can remain in place while devices A microfluidic device intended for use with single- molecule detection is subject to a number of inescapable re

Fygenson, Deborah Kuchnir

334

The chemical dynamics of nanosensors capable of single-molecule detection  

E-print Network

Recent advances in nanotechnology have produced the first sensor transducers capable of resolving the adsorption and desorption of single molecules. Examples include near infrared fluorescent single-walled carbon nanotubes ...

Boghossian, Ardemis A.

335

Maximizing information content of single-molecule FRET experiments: multi-color FRET and FRET combined with force or torque.  

PubMed

Since its first demonstration about twenty years ago, single-molecule fluorescence resonance energy transfer (FRET) has undergone remarkable technical advances. In this tutorial review, we will discuss two technical advances that increase the information content of the single-molecule FRET measurements: single-molecule multi-color FRET and single-molecule FRET combined with force or torque. Our expectations for future developments will be briefly discussed at the end. PMID:23970315

Hohng, Sungchul; Lee, Sanghwa; Lee, Jinwoo; Jo, Myung Hyun

2014-02-21

336

SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY  

SciTech Connect

The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in Tuscany, provides an avenue for scientists from different disciplines to interact and brainstorm and promotes cross-disciplinary collaborations directed toward compelling biological problems.

Professor William Moerner

2010-07-09

337

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

Microsoft Academic Search

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. We also provide guidelines for choosing the right approach

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

2008-01-01

338

Central dogma at the single-molecule level in living cells  

Microsoft Academic Search

Gene expression originates from individual DNA molecules within living cells. Like many single-molecule processes, gene expression and regulation are stochastic, that is, sporadic in time. This leads to heterogeneity in the messenger-RNA and protein copy numbers in a population of cells with identical genomes. With advanced single-cell fluorescence microscopy, it is now possible to quantify transcriptomes and proteomes with single-molecule

Gene-Wei Li; X. Sunney Xie

2011-01-01

339

Self-contained Kondo effect in single molecules  

SciTech Connect

Kondo coupling of f and conduction electrons is a common feature of f-electron intermetallics. Similar effects should occur in carbon ring systems (metallocenes). Evidence for Kondo coupling in Ce(C{sub 8}H{sub 8}){sub 2} (cerocene) and the ytterbocene Cp*{sub 2}Yb(bipy) is reported from magnetic susceptibility and L{sub III}-edge x-ray absorption spectroscopy. These well-defined systems provide a new way to study the Kondo effect on the nanoscale, should generate insight into the Anderson Lattice problem, and indicate the importance of this often-ignored contribution to bonding in organometallics.

Booth, Corwin H.; Walter, Marc D.; Daniel, Million; Lukens, WayneW.; Andersen, Richard A.

2005-04-25

340

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

341

Spin-polarized transport through single-molecule magnet Mn6 complexes  

NASA Astrophysics Data System (ADS)

The coherent transport properties of a device, constructed by sandwiching a Mn6 single-molecule magnet between two gold surfaces, are studied theoretically by using the non-equilibrium Green's function approach combined with density functional theory. Two spin states of such Mn6 complexes are explored, namely the ferromagnetically coupled configuration of the six MnIII cations, leading to the S = 12 ground state, and the low S = 4 spin state. For voltages up to 1 volt the S = 12 ground state shows a current one order of magnitude larger than that of the S = 4 state. Furthermore this is almost completely spin-polarized, since the Mn6 frontier molecular orbitals for S = 12 belong to the same spin manifold. As such the high-anisotropy Mn6 molecule appears as a promising candidate for implementing, at the single molecular level, both spin-switches and low-temperature spin-valves.The coherent transport properties of a device, constructed by sandwiching a Mn6 single-molecule magnet between two gold surfaces, are studied theoretically by using the non-equilibrium Green's function approach combined with density functional theory. Two spin states of such Mn6 complexes are explored, namely the ferromagnetically coupled configuration of the six MnIII cations, leading to the S = 12 ground state, and the low S = 4 spin state. For voltages up to 1 volt the S = 12 ground state shows a current one order of magnitude larger than that of the S = 4 state. Furthermore this is almost completely spin-polarized, since the Mn6 frontier molecular orbitals for S = 12 belong to the same spin manifold. As such the high-anisotropy Mn6 molecule appears as a promising candidate for implementing, at the single molecular level, both spin-switches and low-temperature spin-valves. Electronic supplementary information (ESI) available: Calculated total and projected density of states of an isolated [Mn6O2(Et-sao)6{O2CPh(Me)2}2(EtOH)6] original SMM complex (Fig. S1). Calculated total and projected density of states of an isolated [Mn6O2(Me-sao)6{O2CPh(SH)}2(MeOH)6] model complex (Fig. S2). Transmission spectra calculated at different voltages corresponding to the S = 12 and S = 4 ground states for the Mn6-Au(111) layer system (Fig. S3). Cell parameters and Cartesian coordinates of the Mn6-Au(111) layer system. See DOI: 10.1039/c3nr00054k

Cremades, Eduard; Pemmaraju, C. D.; Sanvito, Stefano; Ruiz, Eliseo

2013-05-01

342

Alkaline-resistant titanium dioxide thin film displaying visible-light-induced superhydrophilicity initiated by interfacial electron transfer.  

PubMed

We synthesized a three-layer-type photocatalytic structure (TiO2/Cu(II)SiO2/SiO2), consisting of TiO2 on Cu(II)-grafted SiO2, which was deposited on a SiO2-coated glass substrate, and investigated its visible-light absorption and hydrophilic properties. Water contact angle measurements revealed visible-light-induced superhydrophilicity at the film surface that was initiated by interfacial electron transfer (IFET) at the interface of TiO2 and Cu(II)SiO2. Monitoring the oxidation state of Pb(2+) ions confirmed that the IFET-initiated holes diffused to the TiO2 surface, where they likely contributed to the hydrophilic conversion. We also demonstrated that layer-structured TiO2/Cu(II)SiO2/SiO2 was stable under alkaline conditions. Thus, we successfully synthesized alkaline-resistant TiO2 that displays visible-light-induced superhydrophilicity. PMID:23527699

Taguchi, Tsuyoshi; Ni, Lei; Irie, Hiroshi

2013-04-16

343

Transmission electron microscopy study of interfacial microstructure formed by reacting Al-Mg alloy with mullite at high temperature  

SciTech Connect

Transmission electron microscopy (TEM) has been used to study the interfacial microstructure formed by reacting Al-Mg alloy with mullite (Al{sub 6}Si{sub 2}O{sub 13}) at high temperature (> 900 C). The TEM study was used in order to understand the strong effect of Mg addition on the nature of the reaction between Al and mullite used to form Al/Al{sub 2}O{sub 3} composite. After reaction at 1,050 C, the formation of a layered structure between the Al-1% Mg alloy and mullite was observed. An alloy layer with a much higher concentration of Mg than the starting alloy was found present next to the initial mullite surface. Between the alloy layer and mullite, a dense and continuous layer made of small MgAl{sub 2}O{sub 4} (spinel) and Si particles was present. The layer apparently stopped further reaction between Al-Mg alloy and mullite by preventing transport of the metals to the reaction front and the Si reaction product away from the reaction front. The microstructure resulting from the initial reaction indicated the reaction proceeded by replacing Si atoms with Al and Mg atoms on mullite (210) lattice planes and forming MgAl{sub 2}O{sub 4} (311) lattice planes simultaneously.

Lu, P. [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Dept. of Materials Science and Engineering] [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Dept. of Materials Science and Engineering; Loehman, R.E.; Ewsuk, K.G.; Fahrenholtz, W.G. [Sandia National Lab., Albuquerque, NM (United States). Advanced Materials Lab.] [Sandia National Lab., Albuquerque, NM (United States). Advanced Materials Lab.

1999-08-10

344

Applications of Irreversible Thermodynamics: Bulk and Interfacial Electronic, Ionic, Magnetic, and Thermal Transport  

E-print Network

, however, that Mott's solution is the lowest order of a consistent asymptotic solution, with the ion and electron concentrations and fluxes going as power series in t^-k/2, where k = 1, 2, .... We find that this gives corrections to the "parabolic growth...

Sears, Matthew

2012-10-19

345

CRADA Final Report for CRADA No. ORNL99-0544, Interfacial Properties of Electron Beam Cured Composites  

SciTech Connect

Electron beam (EB) curing is a technology that promises, in certain applications, to deliver lower cost and higher performance polymer matrix composite (PMC) structures compared to conventional thermal curing processes. PMCs enhance performance by making products lighter, stronger, more durable, and less energy demanding. They are essential in weight- and performance-dominated applications. Affordable PMCs can enhance US economic prosperity and national security. US industry expects rapid implementation of electron beam cured composites in aircraft and aerospace applications as satisfactory properties are demonstrated, and implementation in lower performance applications will likely follow thereafter. In fact, at this time and partly because of discoveries made in this project, field demonstrations are underway that may result in the first fielded applications of electron beam cured composites. Serious obstacles preventing the widespread use of electron beam cured PMCs in many applications are their relatively poor interfacial properties and resin toughness. The composite shear strength and resin toughness of electron beam cured carbon fiber reinforced epoxy composites were about 25% and 50% lower, respectively, than those of thermally cured composites of similar formulations. The essential purpose of this project was to improve the mechanical properties of electron beam cured, carbon fiber reinforced epoxy composites, with a specific focus on composite shear properties for high performance aerospace applications. Many partners, sponsors, and subcontractors participated in this project. There were four government sponsors from three federal agencies, with the US Department of Energy (DOE) being the principal sponsor. The project was executed by Oak Ridge National Laboratory (ORNL), NASA and Department of Defense (DOD) participants, eleven private CRADA partners, and two subcontractors. A list of key project contacts is provided in Appendix A. In order to properly manage the large project team and properly address the various technical tasks, the CRADA team was organized into integrated project teams (IPT's) with each team focused on specific research areas. Early in the project, the end user partners developed ''exit criteria'', recorded in Appendix B, against which the project's success was to be judged. The project team made several important discoveries. A number of fiber coatings or treatments were developed that improved fiber-matrix adhesion by 40% or more, according to microdebond testing. The effects of dose-time and temperature-time profiles during the cure were investigated, and it was determined that fiber-matrix adhesion is relatively insensitive to the irradiation procedure, but can be elevated appreciably by thermal postcuring. Electron beam curable resin properties were improved substantially, with 80% increase in electron beam 798 resin toughness, and {approx}25% and 50% improvement, respectively, in ultimate tensile strength and ultimate tensile strain vs. earlier generation electron beam curable resins. Additionally, a new resin electron beam 800E was developed with generally good properties, and a very notable 120% improvement in transverse composite tensile strength vs. earlier generation electron beam cured carbon fiber reinforced epoxies. Chemical kinetics studies showed that reaction pathways can be affected by the irradiation parameters, although no consequential effects on material properties have been noted to date. Preliminary thermal kinetics models were developed to predict degree of cure vs. irradiation and thermal parameters. These models are continually being refined and validated. Despite the aforementioned impressive accomplishments, the project team did not fully realize the project objectives. The best methods for improving adhesion were combined with the improved electron beam 3K resin to make prepreg and uni-directional test laminates from which composite properties could be determined. Nevertheless, only minor improvements in the composite shear strength, and moderate improvements i

Janke, C.J.

2005-10-17

346

High-efficiency inverted organic solar cells with polyethylene oxide-modified Zn-doped TiO2 as an interfacial electron transport layer.  

PubMed

High efficiency inverted organic solar cells are fabricated using the PTB7:PC71BM polymer by incorporating Zn-doped TiO2 (ZTO) and 0.05 wt% PEO:ZTO as interfacial electron transport layers. The 0.05 wt% PEO-modified ZTO device shows a significantly increased power conversion efficiency (PCE) of 8.10%, compared to that of the ZTO (7.67%) device. PMID:24976080

Thambidurai, M; Kim, Jun Young; Ko, Youngjun; Song, Hyung-Jun; Shin, Hyeonwoo; Song, Jiyun; Lee, Yeonkyung; Muthukumarasamy, N; Velauthapillai, Dhayalan; Lee, Changhee

2014-08-01

347

Single-molecule protein arrays enabled by scanning probe block copolymer lithography  

PubMed Central

The ability to control the placement of individual protein molecules on surfaces could enable advances in a wide range of areas, from the development of nanoscale biomolecular devices to fundamental studies in cell biology. Such control, however, remains a challenge in nanobiotechnology due to the limitations of current lithographic techniques. Herein we report an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control. Scanning probe block copolymer lithography was used to synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins. The number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein. This was demonstrated with both gold nanoparticle and quantum dot labeling coupled with transmission electron microscopy imaging experiments. The immobilized proteins remain bioactive, as evidenced by enzymatic assays and antigen-antibody binding experiments. Importantly, this approach to generate single-biomolecule arrays is, in principle, applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods. PMID:22106270

Chai, Jinan; Wong, Lu Shin; Giam, Louise; Mirkin, Chad A.

2011-01-01

348

Studies of magnetic properties and HFEPR of octanuclear manganese single-molecule magnets.  

PubMed

A new octanuclear manganese cluster [Mn(8)(Hpmide)(4)O(4)(EtCOO)(6)](ClO(4))(2) (1) is achieved by employing Hpmide as the ligand, and this paper examines the synthesis, X-ray structure, high-field electron paramagnetic resonance (HFEPR), magnetization hysteresis loops and magnetic susceptibilities. Complex 1 was prepared by two different methods, and hence, was crystallized in two space groups: P3(2)21 for 1a and P3(1)21 for 1b. Each molecule possesses four Mn(II) and four Mn(III) ions. The metal-oxo framework of complex 1 consists of three face-sharing cubes with manganese ions on alternate corners. The four Mn(III) cations have their Jahn-Teller elongation axes roughly parallel to the c axis of the crystal lattice. The dc magnetic susceptibility measurements reveal a spin-frustration effect in this compound. The ac magnetic susceptibilities, as well as the magnetization hysteresis measurements, clearly establish that complex 1a is a single-molecule-magnet (SMM) with a kinetic energy barrier (10.4 cm(-1)) for spin reversal. HFEPR further confirms that complex 1a is a new SMM with a magnetoanisotropy and quantized energy levels. However, interpretation of the complete set of measurements in terms of a well defined spin ground state is not possible due to the spin frustration. PMID:20886147

Wu, Che-Chih; Datta, Saiti; Wernsdorfer, Wolfgang; Lee, Gene-Hsian; Hill, Stephen; Yang, En-Che

2010-11-14

349

Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level.  

PubMed

We describe a single-molecule-sensitive method to determine the rate of contact formation and dissociation between tryptophan and an oxazine derivative (MR121) on the basis of measurements of the photon distance distribution. Two short peptides (15 and 20 amino acids) derived from the transactivation domain of the human oncoprotein p53 were investigated. With the fluorophore attached at the N-terminal end of the flexible peptides, fluorescence of the dye is efficiently quenched upon contact formation with a tryptophan residue. The mechanism responsible for the efficient fluorescence quenching observed in the complexes is assumed to be a photoinduced electron-transfer reaction occurring predominantly at van der Waals contact. Fluorescence fluctuations caused by intramolecular contact formation and dissociation were recorded using confocal fluorescence microscopy with two avalanche photodiodes and the time-correlated single-photon-counting technique, enabling a temporal resolution of 1.2 ns. Peptides containing a tryptophan residue at positions 9 and 8, respectively, show contact formation with rate constants of 1/120 and 1/152 ns(-1), respectively. Whereas the rate constants of contact formation most likely directly report on biopolymer chain mobility, the dissociation rate constants of 1/267 and 1/742 ns(-1), respectively, are significantly smaller and reflect strong hydrophobic interactions between the dye and tryptophan. Fluorescence experiments on point-mutated peptides where tryptophan is exchanged by phenylalanine show no fluorescence quenching. PMID:12720444

Neuweiler, Hannes; Schulz, Andreas; Böhmer, Martin; Enderlein, Jörg; Sauer, Markus

2003-05-01

350

Emerging fabrication techniques for 3D nano-structuring in plasmonics and single molecule studies.  

PubMed

The application of new methods and techniques to fields such as biology and medicine is becoming more and more demanding since the request of detailed information down to single molecules is a scientific necessity and a technical realistic possibility. In this effort a key role is played by emerging fabrication techniques. One of the hardest challenges is to incorporate the third dimension in the design and fabrication of novel devices. Significantly, this means that conventional nano-fabrication methods, intrinsically useful for planar structuring, have to be substituted or complemented with new approaches. In this paper we show how emerging techniques can be used for 3D structuring of noble metals down to nanoscale. In particular, the paper deals with electroless deposition of silver, ion and electron beam induced deposition, focused ion beam milling, and two-photon lithography. We exploited these techniques to fabricate different plasmonics nanolenses, nanoprobes and novel beads for optical tweezers. In the future these devices will be used for the manipulation and chemical investigation of single cells with sensitivity down to a few molecules in label free conditions and native environment. Although this paper is only devoted to nanofabrication, we foresee that the fields of biology and medicine will directly gain substantial advantages from this approach. PMID:21562670

De Angelis, F; Liberale, C; Coluccio, M L; Cojoc, G; Di Fabrizio, E

2011-07-01

351

A versatile low-temperature setup for the electrical characterization of single-molecule junctions  

SciTech Connect

We present a modular high-vacuum setup for the electrical characterization of single molecules down to liquid helium temperatures. The experimental design is based on microfabricated mechanically controllable break junctions, which offer control over the distance of two electrodes via the bending of a flexible substrate. The actuator part of the setup is divided into two stages. The slow stage is based on a differential screw drive with a large bending range. An amplified piezoceramic actuator forms the fast stage of the setup, which can operate at bending speeds of up to 800 {mu}m/s. In our microfabricated break junctions this is translated into breaking speeds of several 10 nm/s, sufficient for the fast acquisition of large statistical datasets. The bandwidth of the measurement electronics has been optimized to enable fast dI/dV spectroscopy on molecular junctions with resistances up to 100 M{Omega}. The performance of the setup is demonstrated for a {pi}-conjugated oligo(phenylene-ethynylene)-dithiol molecule.

Martin, Christian A. [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands); Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Smit, Roel H. M.; Egmond, Ruud van; Ruitenbeek, Jan M. van [Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Zant, Herre S. J. van der [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands)

2011-05-15

352

Quantitative single-molecule detection of protein based on DNA tetrahedron fluorescent nanolabels.  

PubMed

A highly sensitive method for single-molecule quantitative detection of human IgG is presented by the employment of a new fluorescent nanolabel. In this method, fluorescent nanolabels were assembled by inserting SYBR Green I into DNA tetrahedron nanostructure. The bio-nanolabels were attached to the streptavidin-antihuman antibody by a specific reaction between biotin and streptavidin. The antibody was combined with the target antigen, human IgG, which was immobilized on the silanized glass subtrate surface. Finally, epi-fluorescence microscopy (EFM) coupled with an electron multiplying charge-coupled device was employed for fluorescence imaging. The fluorescent spots corresponding to single protein molecule on images were counted and further used for the quantitative detection. It was found that the new nanolabel shows good photostability, biocompatiblity and exhibits no blinking compared to traditional labels like fluorescence dyes and quantum dot (QDs). In addition, the number of fluorescence spots on the images has a linear relationship with the concentration of human IgG in the range of 3.0×10(-14) to 1.0×10(-12)mol L(-1). What is more, this method showed an excellent specificity and a low matrix effect. PMID:24840462

Ding, Yongshun; Liu, Xingti; Zhu, Jing; Wang, Lei; Jiang, Wei

2014-07-01

353

Engineering nanostructures by binding single molecules to single-walled carbon nanotubes.  

PubMed

Organic and hybrid organic-inorganic systems are promising candidates for low cost photovoltaics. Recently, perovskite-based systems have been attracting a large amount of research attention, where the highest performing devices employ a small molecule (2,2',7,7'-tetrakis(N,N-di-p-methoxyphenyl-amine)-9,9'-spirobifluorene) (Spiro-OMeTAD) hole transporter. Here, we demonstrate the production of single-walled carbon nanotube (SWNT)/single molecule nanostructures using a simple solution processing technique for effective and strong binding of Spiro-OMeTAD to individual polymer-wrapped SWNTs. These small molecules bind very strongly, which causes both large mechanical strain of the nanotubes and also improves the separation of individual SWNTs, thus improving the nanotube photoluminescence quantum efficiency by 1 order of magnitude compared to simple polymer-nanotube nanohybrids. Using absorption and photoluminescence measurements, we show that there is a dramatic variation in the electronic properties of the polymer-NT nanocomposites due to the band alignment formed with Spiro-OMeTAD. These self-assembled nanocomposites offer the potential for integration into high performance optoelectronic such as photovoltaic cells and light emission devices. PMID:25437329

Sharkey, J Joseph; Stranks, Samuel D; Huang, Jian; Alexander-Webber, Jack A; Nicholas, Robin J

2014-12-23

354

Observation and electric current control of a local spin in a single-molecule magnet  

PubMed Central

In molecular spintronics, the spin state of a molecule may be switched on and off by changing the molecular structure. Here, we switch on and off the molecular spin of a double-decker bis(phthalocyaninato)terbium(III) complex (TbPc2) adsorbed on an Au(111) surface by applying an electric current via a scanning tunnelling microscope. The dI/dV curve of the tunnelling current recorded onto a TbPc2 molecule shows a Kondo peak, the origin of which is an unpaired spin of a ?-orbital of a phthalocyaninato (Pc) ligand. By applying controlled current pulses, we could rotate the upper Pc ligand in TbPc2, leading to the disappearance and reappearance of the Kondo resonance. The rotation shifts the molecular frontier-orbital energies, quenching the ?-electron spin. Reversible switching between two stable ligand orientations by applying a current pulse should make it possible to code information at the single-molecule level. PMID:21364556

Komeda, Tadahiro; Isshiki, Hironari; Liu, Jie; Zhang, Yan-Feng; Lorente, Nicolás; Katoh, Keiichi; Breedlove, Brian K.; Yamashita, Masahiro

2011-01-01

355

Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers†  

PubMed Central

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use. PMID:22005669

Emory, Jason M.; Peng, Zhiyong; Young, Brandon; Hupert, Mateusz L.; Rousselet, Arnold; Patterson, Donald; Ellison, Brad; Soper, Steven A.

2012-01-01

356

Preparation of zinc sulfide nanocrystallites from single-molecule precursors  

NASA Astrophysics Data System (ADS)

Zinc sulfide nanocrystallites were prepared using Zinc(II) thiosemicarbazone complexes of the types Zn(L) 2 and ZnCl 2(LH) 2 (where, LH=thiosemicarbazones of cinnamaldehyde, 4-chlorobenzaldehyde, indol-3-carboxaldehyde and thiophene-2-carboxaldehyde) as single source precursors by solvothermal decomposition in ethylene glycol and ethylene diamine in few cases. The materials were characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), selected area electron diffraction, energy dispersive X-ray analysis and UV-vis and IR spectroscopy. Solvothermal decomposition in ethylene glycol resulted in the formation of hexagonal ZnS (JCPDS: 36-1450) as evident from the XRD patterns. However, XRD shows formation of hybrid material, ZnS 0.5EN in case of solvothermal decomposition in ethylenediamine. Infrared spectra authenticate the capping of ethylene glycol and ethylenediamine on ZnS and ZnS 0.5EN, respectively. TEM images showed formation of spherical nanoparticles for the materials obtained from ethylene glycol, whereas plate-like morphology is observed in case of materials obtained from ethylene diamine. The blue shift of absorption bands compared to bands of bulk materials in the UV-vis spectra supports the formation of smaller particles.

Palve, Anil M.; Garje, Shivram S.

2011-07-01

357

Interfacial electron transfer in metal cyanide-sensitized TiO2 nanoparticles.  

PubMed

Electroabsorption (Stark) spectroscopy has been used to study the charge-transfer absorption from a transition-metal-cyanide complex to a TiO2 nanoparticle. Transition-metal cyanide/TiO2(particle) systems were synthesized using FeII(CN)(6)4-, RuII(CN)6(4-), MoIV(CN)(8)4-, and WIV(CN)8(4-). On formation of the M(CN)n4-/TiO2(particle) system, a new metal-to-particle charge-transfer (MPCT) absorption band is observed in the 390-480 nm region. Analysis of the absorption spectra suggests that the TiO2 level involved in the MPCT transition resides at significantly higher energy than the bottom of the conduction band and that the electronic coupling between the two metal centers is the dominant factor determining the position of the MPCT band maximum. The average charge-transfer distances determined by Stark spectra range from 4.1-4.7 A. The observation of relatively short charge-transfer distances leads to the conclusion that the MPCT absorption is from the transition-metal cyanide center to a level that is localized on the Ti atom bound to a nitrogen end of the [O2Ti-N-C-M(CN)x] system. The electronic coupling, Hab, calculated for a two state model is similar to values observed in dinuclear metal complexes. PMID:17402776

Harris, James A; Trotter, Kevin; Brunschwig, Bruce S

2007-06-21

358

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

359

Mechanically-Adjustable and Electrically-Gated Single-Molecule Transistors  

NASA Astrophysics Data System (ADS)

We describe the fabrication and characterization of single-molecule transistors whose properties can be tuned in two independent ways to achieve systematic measurements of electron transport. The spacing between the source and drain electrodes can be adjusted with better than 1 pm stability using the mechanical breakjunction technique -- the electrodes are freely suspended above a flexible substrate, and their spacing can be varied by bending the substrate. In the same devices, we are also able to apply a gate voltage to the molecule. This is done by employing lithographic techniques to suspend the breakjunction only 40 nm above the substrate surface and using the substrate as an electrostatic back gate. With the independent in-situ variations provided by these two experimental ``knobs'', we are able to achieve a more detailed characterization of electron transport through the molecule than is possible with either technique separately. To demonstrate the device capabilities, we have studied transport through single C60 molecules at low temperature. We observe Coulomb blockaded transport and can resolve discrete energy levels of the molecule. We are able to mechanically tune the spacing between the electrodes (over a range of 5 å) to modulate the lead-molecule coupling, and we can electrostatically tune the energy levels on the molecule by up to 160 meV using the gate electrode. We will also present data of Kondo transport in single [Co(tpy-SH)2]^2+ molecules. We are able to vary the strength of the Kondo resonance in these devices by changing the spacing between the source and drain electrodes.

Champagne, Alexandre

2006-03-01

360

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

361

Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy.  

PubMed

Solution-based single-molecule fluorescence spectroscopy is a powerful experimental tool with applications in cell biology, biochemistry and biophysics. The basic feature of this technique is to excite and collect light from a very small volume and work in a low concentration regime resulting in rare burst-like events corresponding to the transit of a single molecule. Detecting photon bursts is a challenging task: the small number of emitted photons in each burst calls for high detector sensitivity. Bursts are very brief, requiring detectors with fast response time and capable of sustaining high count rates. Finally, many bursts need to be accumulated to achieve proper statistical accuracy, resulting in long measurement time unless parallelization strategies are implemented to speed up data acquisition. In this paper we will show that silicon single-photon avalanche diodes (SPADs) best meet the needs of single-molecule detection. We will review the key SPAD parameters and highlight the issues to be addressed in their design, fabrication and operation. After surveying the state-of-the-art SPAD technologies, we will describe our recent progress towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. The potential of this approach is illustrated with single-molecule Förster resonance energy transfer measurements. PMID:25309114

Michalet, Xavier; Ingargiola, Antonino; Colyer, Ryan A; Scalia, Giuseppe; Weiss, Shimon; Maccagnani, Piera; Gulinatti, Angelo; Rech, Ivan; Ghioni, Massimo

2014-11-01

362

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

NASA Astrophysics Data System (ADS)

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.

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

2012-09-01

363

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

PubMed Central

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

2012-01-01

364

Closing the Gap between Single Molecule and Bulk FRET Analysis of Nucleosomes  

PubMed Central

Nucleosome structure and stability affect genetic accessibility by altering the local chromatin morphology. Recent FRET experiments on nucleosomes have given valuable insight into the structural transformations they can adopt. Yet, even if performed under seemingly identical conditions, experiments performed in bulk and at the single molecule level have given mixed answers due to the limitations of each technique. To compare such experiments, however, they must be performed under identical conditions. Here we develop an experimental framework that overcomes the conventional limitations of each method: single molecule FRET experiments are carried out at bulk concentrations by adding unlabeled nucleosomes, while bulk FRET experiments are performed in microplates at concentrations near those used for single molecule detection. Additionally, the microplate can probe many conditions simultaneously before expending valuable instrument time for single molecule experiments. We highlight this experimental strategy by exploring the role of selective acetylation of histone H3 on nucleosome structure and stability; in bulk, H3-acetylated nucleosomes were significantly less stable than non-acetylated nucleosomes. Single molecule FRET analysis further revealed that acetylation of histone H3 promoted the formation of an additional conformational state, which is suppressed at higher nucleosome concentrations and which could be an important structural intermediate in nucleosome regulation. PMID:23637734

Gansen, Alexander; Hieb, Aaron R.; Böhm, Vera; Tóth, Katalin; Langowski, Jörg

2013-01-01

365

Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays  

PubMed Central

Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM) have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins. PMID:19865530

Eom, Kilho; Yang, Jaemoon; Park, Jinsung; Yoon, Gwonchan; Soo Sohn, Young; Park, Shinsuk; Yoon, Dae Sung; Na, Sungsoo; Kwon, Taeyun

2009-01-01

366

Novel plasmonic nanodevices for few/single molecule detection  

NASA Astrophysics Data System (ADS)

This paper reports the fabrication of two reproducible surface enhanced Raman scattering devices using; a) nanoPillar coupled with PC cavity by means of FIB milling and electron beam induced deposition techniques (Device 1), and b) plasmonic gold nanoaggregate structures using electro-plating and e-beam lithography techniques (Device 2). Device 1 consists of photonic crystal cavity as an optical source to couple the incident laser with a metallic tapered nanolens. Exploiting such approach it is possible to overcome the difficulties related to scattering and diffraction phenomena when visible laser (514 nm) illuminates nanostructures. The nanostructure is covered with HMDS and is selectively removed leaving HMDS polymer on nanoPillar only. A clear Raman scattering enhancement has been demonstrated for label-free detection of molecule in sub-wavelength regime. On the other hand, myoglobin protein is deposited on Device 2 using drop coating deposition method and is estimated that the substrate is able to detect the myoglobin concentration down to attomole.

De Angelis, F.; Das, G.; Patrini, M.; Candeloro, P.; Liberale, C.; Cojoc, G.; Mecarini, F.; Di Fabrizio, E.

2008-08-01

367

Single molecule transistor based nanopore for the detection of nicotine  

NASA Astrophysics Data System (ADS)

A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain (D), and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realised from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the presence of Nicotine in smoke which is usually performed using chemical chromatography techniques.

Ray, S. J.

2014-12-01

368

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

369

Interfacial electronic structure of copper phthalocyanine on a gold surface studied by synchrotron radiation photoemission  

NASA Astrophysics Data System (ADS)

We have studied copper phthalocyanine (CuPc) molecules deposited on a clean gold surface via synchrotron radiation photoemission. The persistent appearance of Au4f surface core-level emission in a series of depositions suggests columnar growth of the adsorbed molecules covering only one-fifth of the surface. Molecular adsorption reduced the line intensity of emission from the Au surface slightly and also produced a shortened core-level shift, which demonstrates weakened s-d hybridization of the surface band. Moreover, manifestation of excess charge in the C1s core, along with an induced component in the Au4f core, indicates that charge polarization occurred at the organic/metal contact. The interface introduces an electronic state 1.09 eV below the Fermi level. Further analysis reveals that only the carbon atoms in the benzene rings are affected upon adsorption, suggesting that the molecular plane lies flat on the surface without changing the nominal bent configuration.

Pi, Tun-Wen; Lee, Guan-Ru; Wei, Ching-Hsuan; Chen, Wen-Yen; Cheng, Chiu-Ping

2009-12-01

370

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.

371

Single molecule detection from a large-scale SERS-active Au79Ag21 substrate  

PubMed Central

Detecting and identifying single molecules are the ultimate goal of analytic sensitivity. Single molecule detection by surface-enhanced Raman scattering (SM-SERS) depends predominantly on SERS-active metal substrates that are usually colloidal silver fractal clusters. However, the high chemical reactivity of silver and the low reproducibility of its complicated synthesis with fractal clusters have been serious obstacles to practical applications of SERS, particularly for probing single biomolecules in extensive physiological environments. Here we report a large-scale, free standing and chemically stable SERS substrate for both resonant and nonresonant single molecule detection. Our robust substrate is made from wrinkled nanoporous Au79Ag21 films that contain a high number of electromagnetic “hot spots” with a local SERS enhancement larger than 109. This biocompatible gold-based SERS substrate with superior reproducibility, excellent chemical stability and facile synthesis promises to be an ideal candidate for a wide range of applications in life science and environment protection. PMID:22355629

Liu, Hongwen; Zhang, Ling; Lang, Xingyou; Yamaguchi, Yoshinori; Iwasaki, Hiroshi; Inouye, Yasushi; Xue, Qikun; Chen, Mingwei

2011-01-01

372

High-throughput single-molecule fluorescence spectroscopy using parallel detection  

PubMed Central

Solution-based single-molecule fluorescence spectroscopy is a powerful new experimental approach with applications in all fields of natural sciences. The basic concept of this technique is to excite and collect light from a very small volume (typically femtoliter) and work in a concentration regime resulting in rare burst-like events corresponding to the transit of a single-molecule. Those events are accumulated over time to achieve proper statistical accuracy. Therefore the advantage of extreme sensitivity is somewhat counterbalanced by a very long acquisition time. One way to speed up data acquisition is parallelization. Here we will discuss a general approach to address this issue, using a multispot excitation and detection geometry that can accommodate different types of novel highly-parallel detector arrays. We will illustrate the potential of this approach with fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence measurements obtained with different novel multipixel single-photon counting detectors. PMID:21625288

Michalet, X.; Colyer, R. A.; Scalia, G.; Kim, T.; Levi, Moran; Aharoni, Daniel; Cheng, Adrian; Guerrieri, F.; Arisaka, Katsushi; Millaud, Jacques; Rech, I.; Resnati, D.; Marangoni, S.; Gulinatti, A.; Ghioni, M.; Tisa, S.; Zappa, F.; Cova, S.; Weiss, S.

2011-01-01

373

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

PubMed

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

2013-11-01

374

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

375

Single molecule fluorescence spectroscopy of mutants of the Discosoma red fluorescent protein DsRed  

NASA Astrophysics Data System (ADS)

We studied the emission of mutants of the red fluorescent protein DsRed by room temperature single molecule fluorescence spectroscopy. Bulk samples of the DsRed variant E8 show mixed green and red fluorescence of equivalent intensities individually spectrally similar to arrested green and mature red fluorescent forms of DsRed. Investigations at the single molecule level indicate that, like DsRed, E8 is not monomeric at single molecule concentrations. The entities visualized are composed of green and red emitting proteins without a fixed ratio of green to red fluorescing units. We find indications for only weak, if any, fluorescence resonance energy transfer (FRET) between red and green chromophores within one E8 entity.

Blum, Christian; Subramaniam, Vinod; Schleifenbaum, Frank; Stracke, Frank; Angres, Brigitte; Terskikh, Alexey; Meixner, A. J.

2002-08-01

376

Conformational-Modulated Enzyme Catalysis: Generalized Michaelis-Menten Equation and Single Molecule Measurements  

NASA Astrophysics Data System (ADS)

The Michaelis-Menten (MM) equation is a basic rate equation to describe the substrate-dependence of enzymatic reactions; therefore, it is important to establish the validity of the MM-equation for complex enzymatic reactions and derive the correction terms when the MM equation fails. Indeed, single molecule experiments reveal complex catalytic behaviors induced by conformational dynamics and possible deviations from the MM rate equation. To model such complex catalytic reactions, we construct a generic kinetic network model characterized by multiple intermediates and multiple conformational sub-states and, by solving for the turnover rate of this network, we extend the MM equation into a general form. The generalized MM equation predicts that (i) the MM equation holds under detailed balance and (ii) the correction to the MM expression depends on the unbalanced conformational currents. Using these predictions, we can establish a relationship between the substrate-dependence of the turnover rate and the connectivity of the enzymatic network. To confirm these predictions, we propose several single molecule indicators to test the violations of detailed balance. However, these single molecule indicators may be difficult to resolve from noisy single molecule data. To address these issues, we propose information theory based data analysis methods to process single molecule time series, and apply the Baysian technique to analyze a single protein fluctuation experiment. [4pt] [1] Jianlan Wu and Jianshu Cao, ``Generalized Michaelis-Menten equation for conformation modulated monomeric enzymes,'' in Adv. Chem. Phys. (2011) [0pt] [2] Jianshu Cao, ``Michaelis-Menten Equation and Detailed Balance in Enzymatic Networks,'' JPC B, P5493 (2001) [0pt] [3] Jianshu Cao and Rob Silbey, ``Generic models of single molecule kinetics: self-consistent solutions,'' JPC B, 112, p12876 (2008) feature article [0pt] [4] Jim Witkoskie and Jianshu Cao, ``Analysis of the entire sequence of a single photon experiment on a Flavin Protein,'' JPC B, 112, p5988-5991 (2008)

Cao, Jianshu

2012-02-01

377

Polymer dielectric materials for organic thin-film transistors: Interfacial control and development for printable electronics  

NASA Astrophysics Data System (ADS)

Organic thin-film transistors (OTFTs) have been extensively studied for organic electronics. In these devices, organic semiconductor-dielectric interface characteristics play a critical role in influencing OTFT operation and performance. This study begins with exploring how the physicochemical characteristics of the polymer gate dielectric affects the thin-film growth mode, microstructure, and OTFT performance parameters of pentacene films deposited on bilayer polymer (top)-SiO2 (bottom) dielectrics. Pentacene growth mode varies considerably with dielectric substrate, and correlations are established between pentacene film deposition temperature, the thin-film to bulk microstructural phase transition, and OTFT device performance. Furthermore, the primary influence of the polymer dielectric layer glass transition temperature on pentacene film microstructure and OTFT response is shown for the first time. Following the first study, the influence of the polymer gate dielectric viscoelastic properties on overlying organic semiconductor film growth, film microstructure, and TFT response are investigated in detail. From the knowledge that nanoscopically-confined thin polymer films exhibit glass transition temperatures that deviate substantially from those of the corresponding bulk materials, pentacene (p-channel) and cyanoperylene (n-channel) films grown on polymer gate dielectrics at temperatures well-below their bulk glass transition temperatures (Tg(b)) have been shown to exhibit morphological/microstructural transitions and dramatic OTFT performance discontinuities at well-defined temperatures (defined as the polymer "surface glass transition temperature," or Tg(s)). These transitions are characteristic of the particular polymer architecture and independent of film thickness or overall film cooperative chain dynamics. Furthermore, by analyzing the pentacene films grown on UV-curable polymer dielectrics with different curing times (hence, different degrees of crosslinking), clear correlations between pentacene film deposition temperature, degree of polymer dielectric film crosslinking, and the corresponding pentacene film growth mode, phase composition, and carrier mobilities are established. Based on the results, TFT measurements have been demonstrated to represent a new and sensitive methodology to probe polymer surface viscoelastic properties as well as the degree of polymer dielectric film crosslinking. In the final study, the synthesis and dielectric properties of optimized crosslinked polymer blend (CPB) dielectrics for printable TFTs are reported. Novel silane crosslinking reagents with tuned reactivity enable the fabrication of CPB films having excellent quality and tunable thickness, fabricated both by spin-coating and gravure-printing. The CPB dielectric films fabricated by blending crosslinking reagent with poly(4-vinyl)phenol (PVP) require very low-curing temperatures (˜110°C), tenaciously adhere to a variety of TFT gate contact materials and exhibit excellent insulating properties with tunable capacitance values. The CPB film quality is correlated with the PVP-crosslinking reagent reactivity. Devices fabricated with both p- and n-channel organic semiconductors on the CPB dielectrics function at low operating voltages and the device performance is strongly correlated with the morphology and microstructure of the representative semiconductor films.

Kim, Choongik

378

Helicase-mediated changes in RNA structure at the single-molecule level  

PubMed Central

RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field. PMID:23353571

König, Sebastian L.B.; Liyanage, Pramodha S.; Sigel, Roland K.O.; Rueda, David

2013-01-01

379

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

PubMed

To enable studies of conformational changes within multimolecular complexes, we present a simultaneous, four-color single molecule fluorescence methodology implemented with total internal reflection illumination and camera-based, wide-field detection. We further demonstrate labeling histidine-tagged proteins noncovalently with Tris-nitrilotriacetic acid (Tris-NTA)-conjugated dyes to achieve single molecule detection. We combine these methods to colocalize 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; Anderson, Trevor; Piehler, Jacob; Erie, Dorothy A; Weninger, Keith

2010-11-01

380

Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light  

PubMed Central

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

381

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

382

Intersystem Crossing Mechanisms and Single Molecule Fluorescence: Terrylene in Anthracene Crystals  

SciTech Connect

Single molecule spectroscopy requires molecules with low triplet yields and/or short triplet lifetimes. The intersystem crossing (ISC) rate may be dramatically enhanced by the host matrix. Comparing the fluorescence intensity of single terrylene molecules in para-terphenyl, naphthalene, and anthracene crystals, we found a reduction of the saturation intensity by three orders of magnitude in the latter case. The fluorescence autocorrelation function indicates that the bottleneck state is the terrylene triplet. We propose a ping-pong mechanism between host and guest. This intermolecular ISC mechanism, which can open whenever the host triplet lies lower than the guest singlet, was overlooked in previous single molecule investigations.

Kol'chenko, M.A.; Nicolet, A.; Orrit, M. [Molecular Nano-Optics and Spins (MoNOS), Leiden Institute of Physics (LION), Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden (Netherlands); Kozankiewicz, B. [Molecular Nano-Optics and Spins (MoNOS), Leiden Institute of Physics (LION), Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden (Netherlands); Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, PL-02668 Warsaw (Poland)

2005-05-15

383

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

384

Single-Molecule Study of Transcriptional Pausing and Arrest by E. coli RNA Polymerase  

NASA Astrophysics Data System (ADS)

Using an optical-trap/flow-control video microscopy technique, we followed transcription by single molecules of Escherichia coli RNA polymerase in real time over long template distances. These studies reveal that RNA polymerase molecules possess different intrinsic transcription rates and different propensities to pause and stop. The data also show that reversible pausing is a kinetic intermediate between normal elongation and the arrested state. The conformational metastability of RNA polymerase revealed by this single-molecule study of transcription has direct implications for the mechanisms of gene regulation in both bacteria and eukaryotes.

Davenport, R. John; Wuite, Gijs J. L.; Landick, Robert; Bustamante, Carlos

2000-03-01

385

Plasmonic Enhancement of Single-Molecule Fluorescence Near a Silver Nanoparticle  

PubMed Central

In this short paper, we reported the enhanced fluorescence from a single fluorophore bound to a 50nm silver nanoparticle. We found that on average the Cy5 molecules bound to metal nanoparticles are approximately 15-fold brighter than that of free dyes, and that single molecule lifetimes are shorter as compared to free fluorophores. The increased emission rate is primarily the result of local plasmon enhancement. These results demonstrate that the use of fluorophore-metal interactions can increase the brightness and photostability of fluorophores for single molecule detection. PMID:17922175

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

2009-01-01

386

Understanding the physics of DNA using nanoscale single-molecule manipulation  

PubMed Central

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. PMID:23467419

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

2013-01-01

387

Microstructure, phase transition, and interfacial chemistry of Gd{sub 2}O{sub 3}/Si(111) grown by electron-beam physical vapor deposition  

SciTech Connect

The effects of growth temperature, film thickness, and oxygen flux on the microstructure, phase transition, and interfacial chemistry of gadolinium oxide (Gd{sub 2}O{sub 3}) films grown on Si(111) substrates by electron-beam physical vapor deposition were investigated using a combination of transmission electron microscopy (TEM), electron diffraction, scanning TEM, x-ray energy dispersive spectrometry, and electron energy loss spectrometry. The authors find that a low growth temperature (250 Degree-Sign C) and a high oxygen flux (200 sccm) led to a small grain size and a high porosity of the Gd{sub 2}O{sub 3} film. Lowering the oxygen flux to 50 sccm led to reduced film porosity, presumably due to the increased diffusion length of the Gd atoms on the surface. Increasing the growth temperature to 650 Degree-Sign C resulted in a film with large columnar grains and elongated pores at the grain boundaries. Thin films grown at 250 Degree-Sign C consisted of cubic Gd{sub 2}O{sub 3}, but thermodynamically less stable monoclinic phase formed as the film thickness increased. Lowering the oxygen flux apparently further promoted the formation of the monoclinic phase. Furthermore, monoclinic phase dominated in the films grown at 650 Degree-Sign C. Such phase transitions may be related to the stress evolution of the films at different temperatures, thicknesses, and oxygen fluxes. Enhanced Gd{sub 2}O{sub 3}/Si interfacial reaction was observed as the growth temperature, film thickness, and oxygen flux increased. Moreover, oxygen was found to play a crucial role in the Gd{sub 2}O{sub 3}/Si interfacial reaction and the formation of Gd-Si-O interface layers, which proceeded by the reaction of excess oxygen with Si followed by the intermixing of SiO{sub x} and Gd{sub 2}O{sub 3}.

Weng Xiaojun; Grave, Daniel A.; Hughes, Zachary R.; Wolfe, Douglas E.; Robinson, Joshua A. [Materials Research Institute and Electro-Optics Center, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Department of Materials Science and Engineering and Applied Research Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Electro-Optics Center and Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Department of Materials Science and Engineering and Applied Research Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Electro-Optics Center and Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

2012-07-15

388

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

389

Under the Microscope: Single Molecule Symposium at the University of Michigan, 2006ABSTRACT  

E-print Network

Under the Microscope: Single Molecule Symposium at the University of Michigan, 2006ABSTRACT techniques, including optical tweezers, atomic force microscopes, microneedles, and magnetic traps, is based the molecular mechanisms they engage in. Truly ground-breaking and insight- ful discoveries using these single

Walter, Nils G.

390

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

Microsoft Academic Search

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. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

Attila Nagy; Keir C Neuman

2008-01-01

391

Simulated data sets for single molecule kinetics: some limitations and complications of data analysis  

Microsoft Academic Search

When the fluorescence intensity of a chromophore attached to or bound in an enzyme relates to a specific reactive step in the enzymatic reaction, a single molecule fluorescence study of the process reveals a time sequence in the fluorescence emission that can be analyzed to derive kinetic and mechanistic information. Reports of various experimental results and corresponding theoretical studies have

Jue Shi; Ari Gafni; Duncan Steel

2006-01-01

392

Chapter 6: Efforts toward single molecule fluorescence imaging of 6.1 Abstract  

E-print Network

AChRs bearing a BODIPY fluorophore as an amino acid side chain were imaged in the membrane of Xenopus laevis into the nAChR by nonsense suppression in Xenopus oocytes, and single molecule imaging of these fluorescent transfer (FRET) studies. A recently expanded toolkit of tRNAs for nonsense suppression in Xenopus oocytes

Winfree, Erik

393

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

E-print Network

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy force microscopy (AFM), micro-needle manipulation1, biomembrane force probe2 and flow-induced stretching

Ritort, Felix

394

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

PubMed Central

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 certain color and brightness but instead have their own ‘personalities’ regarding spectroscopic parameters, redox properties, size and water solubility, photostability and several more. 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 which was later overcome using Trolox through reducing/oxidizing system, but a boon for super-resolution imaging due to the controllable photoswitching. Understanding photophysics is critical in design and interpreting single molecule experiments. PMID:22404588

Ha, Taekjip; Tinnefeld, Philip

2013-01-01

395

Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments  

E-print Network

experiments, corresponds to the ensemble of structures that have equal probability of reaching either, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction zipper with two barriers provide a structural interpretation of single molecule experimental data. Our

Thirumalai, Devarajan

396

Criteria for Downhill Protein Folding: Calorimetry, Chevron Plot, Kinetic Relaxation, and Single-Molecule  

E-print Network

chevron rollovers, the relaxation of the models considered is essen- tially single-exponential overCriteria for Downhill Protein Folding: Calorimetry, Chevron Plot, Kinetic Relaxation, and Single-Molecule Radius of Gyration in Chain Models With Subdued Degrees of Cooperativity Michael Knott and Hue Sun Chan

Chan, Hue Sun

397

Chemical mapping of a single molecule by plasmon-enhanced Raman scattering.  

PubMed

Visualizing individual molecules with chemical recognition is a longstanding target in catalysis, molecular nanotechnology and biotechnology. Molecular vibrations provide a valuable 'fingerprint' for such identification. Vibrational spectroscopy based on tip-enhanced Raman scattering allows us to access the spectral signals of molecular species very efficiently via the strong localized plasmonic fields produced at the tip apex. However, the best spatial resolution of the tip-enhanced Raman scattering imaging is still limited to 3-15?nanometres, which is not adequate for resolving a single molecule chemically. Here we demonstrate Raman spectral imaging with spatial resolution below one nanometre, resolving the inner structure and surface configuration of a single molecule. This is achieved by spectrally matching the resonance of the nanocavity plasmon to the molecular vibronic transitions, particularly the downward transition responsible for the emission of Raman photons. This matching is made possible by the extremely precise tuning capability provided by scanning tunnelling microscopy. Experimental evidence suggests that the highly confined and broadband nature of the nanocavity plasmon field in the tunnelling gap is essential for ultrahigh-resolution imaging through the generation of an efficient double-resonance enhancement for both Raman excitation and Raman emission. Our technique not only allows for chemical imaging at the single-molecule level, but also offers a new way to study the optical processes and photochemistry of a single molecule. PMID:23739426

Zhang, R; Zhang, Y; Dong, Z C; Jiang, S; Zhang, C; Chen, L G; Zhang, L; Liao, Y; Aizpurua, J; Luo, Y; Yang, J L; Hou, J G

2013-06-01

398

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

ScienceCinema

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

2011-04-13

399

Three-Color Alternating-Laser Excitation of Single Molecules: Monitoring Multiple Interactions and Distances  

PubMed Central

We introduce three-color alternating-laser excitation (3c-ALEX), a fluorescence resonance energy transfer (FRET) method that measures up to three intramolecular distances and complex interaction stoichiometries of single molecules in solution. This tool extends substantially the capabilities of two-color ALEX, which employs two alternating lasers to study molecular interactions (through probe stoichiometry S) and intramolecular distances (through FRET efficiency E), and sorts fluorescent molecules in multi-dimensional probe-stoichiometry and FRET-efficiency histograms. Probe-stoichiometry histograms allowed analytical sorting, identification, and selection of diffusing species; selected molecules were subsequently represented in FRET-efficiency histograms, generating up to three intramolecular distances. Using triply labeled DNAs, we established that 3c-ALEX enables 1), FRET-independent analysis of three-component interactions; 2), observation and sorting of singly, doubly, and triply labeled molecules simultaneously present in solution; 3), measurements of three intramolecular distances within single molecules from a single measurement; and 4), dissection of conformational heterogeneity with improved resolution compared to conventional single-molecule FRET. We also used 3c-ALEX to study large biomolecules such as RNA polymerase-DNA transcription complexes, and monitor the downstream translocation of RNA polymerase on DNA from two perspectives within the complex. This study paves the way for advanced single-molecule analysis of complex mixtures and biomolecular machinery. PMID:17040983

Lee, Nam Ki; Kapanidis, Achillefs N.; Koh, Hye Ran; Korlann, You; Ho, Sam On; Kim, Younggyu; Gassman, Natalie; Kim, Seong Keun; Weiss, Shimon

2007-01-01

400

Determining the elastic properties of aptamer-ricin single molecule multiple pathways  

Technology Transfer Automated Retrieval System (TEKTRAN)

Ricin and an anti-ricin aptamer showed three stable binding conformations with their special chemomechanical properties. The elastic properties of the ricin-aptamer single-molecule interactions were investigated by the dynamic force spectroscopy (DFS). The worm-like-chain model and Hook’s law were ...

401

The FASEB Journal Research Communication A single-molecule force spectroscopy nanosensor for  

E-print Network

The FASEB Journal · Research Communication A single-molecule force spectroscopy nanosensor for the viability of most human patho- genic bacteria and of the malaria parasite. Using atomic force microscopy, IPP is derived from the mevalonate pathway (Fig. 1A). In contrast, in most bacteria, algae

Bielefeld, Universität

402

Single-molecule denaturation and degradation of proteins by the AAA ClpXP protease  

E-print Network

Single-molecule denaturation and degradation of proteins by the AAA ClpXP protease Yongdae Shina,1 proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ

Lang, Matthew

403

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

404

Single-molecule spectroscopy of protein folding in a chaperonin cage  

E-print Network

Single-molecule spectroscopy of protein folding in a chaperonin cage Hagen Hofmanna , Frank for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms In the recent past, a large number of components have been identified that control and modulate protein folding

Lipman, Everett A.

405

Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies  

E-print Network

Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies for protein folding studies and has been extensively stud- ied, both experimentally (at the ensemble level concentration. It is shown that new infor- mation about different aspects of the protein folding reaction can

Croquette, Vincent

406

Silver nanoparticles self assembly as SERS substrates with near single molecule detection limit  

E-print Network

Silver nanoparticles self assembly as SERS substrates with near single molecule detection limit as an Advance Article on the web 15th July 2009 DOI: 10.1039/b904744a Highly sensitive SERS substrates distribution of Ag NPs aggregates as the deposition number increased. Surface-enhanced Raman scattering (SERS

Brolo, Alexandre G.

407

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

E-print Network

-time cor- relation analysis, which is based on time series analyses, and the Kullback­Liebler distance, which is based on infor- mation theory principles [Elements of Information Theory, Wiley, New York, 1991 years, optical single-molecule spec- troscopy has been proving instrumental in access- ing information

Xie, Xiaoliang Sunney

408

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

409

Probing Photoluminescence Dynamics in Colloidal Semiconductor Nanocrystal/Fullerene Heterodimers with Single Molecule Spectroscopy  

NASA Astrophysics Data System (ADS)

Single molecule optical spectroscopy (SMS) allows for the characterization of photoluminescence intensity and lifetime of a isolated colloidal semiconductor nanocrystal, which provide valuable information about its intrinsic structural defects and interactions with the external nanoenvironment. In this chapter, we describe the application of SMS for the study of photoluminescence blinking and photoinduced charge transfer in colloidal semiconductor nanocrystals.

Xu, Zhihua; Cotlet, Mircea

410

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

411

Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates  

E-print Network

on both RNA and DNA templates. During reverse transcription in vivo, HIV-1 RT replicates through various secondary structures on RNA and single-stranded DNA (ssDNA) templates without the need for a nucleic acid using a multiplexed single-molecule DNA flow- stretching assay. We observed that HIV-1 RT performs fast

Xie, Xiaoliang Sunney

412

Analysis of single-molecule FRET trajectories of transcription complexes based on Hidden-Markov Modelling  

E-print Network

Analysis of single-molecule FRET trajectories of transcription complexes based on Hidden resonance energy transfer (FRET) and alternating-laser excitation (ALEX) tools to probe RNAP structure. At Oxford, the Kapanides group improved the temporal resolution of the TIRF assay: by monitoring FRET (using

Goldschmidt, Christina

413

Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using Maximum Likelihood Calculated Lifetimes  

E-print Network

Accurate Single Molecule FRET Efficiency Determination for Surface Immobilized DNA Using Maximum of surface immobilized double-stranded DNA coupled with a tetramethylrhodmaine and Cy5 FRET pair were these methods for the case of immobilized SM in conjunction with SM fluorescence resonance energy transfer (sm-FRET

414

Single-molecule FRET experiments with a red-enhanced custom technology SPAD  

E-print Network

Single-molecule FRET experiments with a red-enhanced custom technology SPAD Francesco Panzerib-molecule fluorescence resonant energy transfer (smFRET) studies on freely diffusing molecules in a confocal geometry-to-acceptor distances covering the whole range of useful FRET values. Both intensity-based (s-ALEX) and lifetime

Michalet, Xavier

415

Engineering bright sub-10-nm upconverting nanocrystals for single-molecule imaging.  

PubMed

Imaging at the single-molecule level reveals heterogeneities that are lost in ensemble imaging experiments, but an ongoing challenge is the development of luminescent probes with the photostability, brightness and continuous emission necessary for single-molecule microscopy. Lanthanide-doped upconverting nanoparticles overcome problems of photostability and continuous emission and their upconverted emission can be excited with near-infrared light at powers orders of magnitude lower than those required for conventional multiphoton probes. However, the brightness of upconverting nanoparticles has been limited by open questions about energy transfer and relaxation within individual nanocrystals and unavoidable tradeoffs between brightness and size. Here, we develop upconverting nanoparticles under 10 nm in diameter that are over an order of magnitude brighter under single-particle imaging conditions than existing compositions, allowing us to visualize single upconverting nanoparticles as small (d = 4.8 nm) as fluorescent proteins. We use advanced single-particle characterization and theoretical modelling to find that surface effects become critical at diameters under 20 nm and that the fluences used in single-molecule imaging change the dominant determinants of nanocrystal brightness. These results demonstrate that factors known to increase brightness in bulk experiments lose importance at higher excitation powers and that, paradoxically, the brightest probes under single-molecule excitation are barely luminescent at the ensemble level. PMID:24633523

Gargas, Daniel J; Chan, Emory M; Ostrowski, Alexis D; Aloni, Shaul; Altoe, M Virginia P; Barnard, Edward S; Sanii, Babak; Urban, Jeffrey J; Milliron, Delia J; Cohen, Bruce E; Schuck, P James

2014-04-01

416

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

417

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

418

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

419

Long-Lived Intracellular Single-Molecule Fluorescence Using Electroporated Molecules  

PubMed Central

Studies of biomolecules in vivo are crucial to understand their function in a natural, biological context. One powerful approach involves fusing molecules of interest to fluorescent proteins to study their expression, localization, and action; however, the scope of such studies would be increased considerably by using organic fluorophores, which are smaller and more photostable than their fluorescent protein counterparts. Here, we describe a straightforward, versatile, and high-throughput method to internalize DNA fragments and proteins labeled with organic fluorophores into live Escherichia coli by employing electroporation. We studied the copy numbers, diffusion profiles, and structure of internalized molecules at the single-molecule level in vivo, and were able to extend single-molecule observation times by two orders of magnitude compared to green fluorescent protein, allowing continuous monitoring of molecular processes occurring from seconds to minutes. We also exploited the desirable properties of organic fluorophores to perform single-molecule Förster resonance energy transfer measurements in the cytoplasm of live bacteria, both for DNA and proteins. Finally, we demonstrate internalization of labeled proteins and DNA into yeast Saccharomyces cerevisiae, a model eukaryotic system. Our method should broaden the range of biological questions addressable in microbes by single-molecule fluorescence. PMID:24314075

Crawford, Robert; Torella, Joseph P.; Aigrain, Louise; Plochowietz, Anne; Gryte, Kristofer; Uphoff, Stephan; Kapanidis, Achillefs N.

2013-01-01

420

Self-Contained Kondo Effect in Single Molecules C. H. Booth,1  

E-print Network

Anderson lattice problem. The main difference between the Kondo effect in a bulk system and a nanoparticleSelf-Contained Kondo Effect in Single Molecules C. H. Booth,1 M. D. Walter,1 M. Daniel,1 W. W 94720, USA (Received 12 May 2005; published 19 December 2005) Kondo coupling of f and conduction

Booth, Corwin H.

421

Supporting Information to: Single-Molecule Electrocatalysis by Single-Walled Carbon Nanotubes  

E-print Network

S1 Supporting Information to: Single-Molecule Electrocatalysis by Single-Walled Carbon Nanotubes. Experimental Methods I.1. Purification of SWNTs. The single-walled carbon nanotubes were purchased from Carbon Nanotechnologies Incorporated (Purified HiPCO single-walled carbon nanotubes). These SWNTs have an average diameter

Chen, Peng

422

Single-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded Proteins  

E-print Network

of cold denaturation are still under debate, but the most common interpretation of the originSingle-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded that cold- denatured proteins are more expanded than heat- denatured proteins. To clarify the connection

Schuler, Ben

423

Toward ultra-stable fluorescent dyes for single-molecule spectroscopy  

NASA Astrophysics Data System (ADS)

The wide-spread use of fluorescent dyes in molecular diagnostics and fluorescence microscopy together with new developments such as single-molecule fluorescence spectroscopy provide researchers from various disciplines with an ever expanding toolbox. Single-molecule fluorescence spectroscopy relies to a large extent on extraordinary bright and photostable organic fluorescent dyes such as rhodamine- or cyanine- derivatives. While in the last decade singlemolecule equipment and methodology have significantly advanced and in some cases reached theoretical limits (e.g. detectors approaching unity quantum yields), instable emission ("blinking") and photobleaching become more and more the bottleneck of further development and spreading of single-molecule fluorescence studies. In recent years, agents and recipes have been developed to increase the photostability of conventional fluorescent dyes. Here, we investigate some of these strategies at the single-molecule level. In particular, we focus on the dye selection criteria for multi-color applications. We investigate fluorescent dyes from the rhodamine, carborhodamine, cyanine, and oxazine family and show that within one dye class the photophysical properties are very similar but that dyes from different classes show strikingly different properties. These findings facilitate dye selection and provide improved chemical environment for demanding fluorescence microscopic applications.

Kasper, Robert; Heilemann, Mike; Tinnefeld, Philip; Sauer, Markus

2007-07-01

424

Single-molecule vibrational spectroscopy adds structural resolution to the optical trap.  

PubMed

The ability to apply forces on single molecules with an optical trap is combined with the endogenous structural resolution of Raman spectroscopy in an article in this issue, and applied to measure the Raman spectrum of ds-DNA during force-extension. PMID:23332052

Ganim, Ziad

2013-01-01

425

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 5nm 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

426

Tetrairon(III) single-molecule magnet monolayers on gold: insights from ToF-SIMS and isotopic labeling.  

PubMed

To work as magnetic components in molecular electronics and spintronics, single-molecule magnets (SMMs) must be reliably interfaced with metals. The organization on gold of a Fe4 SMM carrying two acetyl-protected thiol groups has been studied by exploiting the surface sensitivity of time-of-flight secondary ion mass spectrometry (ToF-SIMS), additionally powered by the use of an isotopic labeling strategy. Deposition from millimolar dichloromethane solutions results in a higher surface coverage and better packed monolayers as compared with previous protocols based on more diluted solutions. Fe4 complexes are chemically tethered to the surface via a single Au-S bond while they still contain an intact SAc group. PMID:25000391

Totaro, Pasquale; Poggini, Lorenzo; Favre, Annaick; Mannini, Matteo; Sainctavit, Philippe; Cornia, Andrea; Magnani, Agnese; Sessoli, Roberta

2014-07-29

427

A novel 3D resolution measure for optical microscopes with applications to single molecule imaging  

NASA Astrophysics Data System (ADS)

The advent of single molecule microscopy has generated significant interest in imaging single biomolecular interactions within a cellular environment in three dimensions. It is widely believed that the classical 2D (3D) resolution limit of optical microscopes precludes the study of single molecular interactions at distances of less than 200 nm (1 micron). However, it is well known that the classical resolution limit is based on heuristic notions. In fact, recent single molecule experiments have shown that the 2D resolution limit, i.e. Rayleigh's criterion, can be surpassed in an optical microscope setup. This illustrates that Rayleigh's criterion is inadequate for modern imaging approaches, thereby necessitating a re-assessment of the resolution limits of optical microscopes. Recently, we proposed a new modern resolution measure that overcomes the limitations of Rayleigh's criterion. Known as the fundamental resolution measure FREM, the new result predicts that distances well below the classical 2D resolution limit can be resolved in an optical microscope. By imaging closely spaced single molecules, it was experimentally verified that the new resolution measure can be attained in an optical microscope setup. In the present work, we extend this result to the 3D case and propose a 3D fundamental resolution measure 3D FREM that overcomes the limitations of the classical 3D resolution limit. We obtain an analytical expression for the 3D FREM. We show how the photon count of the single molecules affects the 3D FREM. We also investigate the effect of deteriorating experimental factors such as pixelation of the detector and extraneous noise sources on the new resolution measure. In contrast to the classical 3D resolution criteria, our new result predicts that distances well below the classical limit can be resolved. We expect that our results would provide novel tools for the design and analysis of 3D single molecule imaging experiments.

Ram, Sripad; Abraham, Anish V.; Ward, E. Sally; Ober, Raimund J.

2007-02-01

428

Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives.  

PubMed Central

Single-molecule and macroscopic reactions of fluorescent nucleotides with myosin have been compared. The single-molecule studies serve as paradigms for enzyme-catalyzed reactions and ligand-receptor interactions analyzed as individual stochastic processes. Fluorescent nucleotides, called Cy3-EDA-ATP and Cy5-EDA-ATP, were derived by coupling the dyes Cy3.29.OH and Cy5.29.OH (compounds XI and XIV, respectively, in, Bioconjug. Chem. 4:105-111)) with 2'(3')-O-[N-(2-aminoethyl)carbamoyl]ATP (EDA-ATP). The ATP(ADP) analogs were separated into their respective 2'- and 3'-O-isomers, the interconversion rate of which was 30[OH(-)] s(-1) (0.016 h(-1) at pH 7.1) at 22 degrees C. Macroscopic studies showed that 2'(3')-O-substituted nucleotides had properties similar to those of ATP and ADP in their interactions with myosin, actomyosin, and muscle fibers, although the ATP analogs did not relax muscle as well as ATP did. Significant differences in the fluorescence intensity of Cy3-nucleotide 2'- and 3'-O-isomers in free solution and when they interacted with myosin were evident. Single-molecule studies using total internal reflection fluorescence microscopy showed that reciprocal mean lifetimes of the nucleotide analogs interacting with myosin filaments were one- to severalfold greater than predicted from macroscopic data. Kinetic and equilibrium data of nucleotide-(acto)myosin interactions derived from single-molecule microscopy now have a biochemical and physiological framework. This is important for single-molecule mechanical studies of motor proteins. PMID:10827983

Oiwa, K; Eccleston, J F; Anson, M; Kikumoto, M; Davis, C T; Reid, G P; Ferenczi, M A; Corrie, J E; Yamada, A; Nakayama, H; Trentham, D R

2000-01-01

429

Single molecule fluorescence correlation spectroscopy of single apoptotic cells using a red-fluorescent caspase probe.  

PubMed

The detection of single molecules in single cells has enabled biochemical analyses to be conducted with high sensitivity and high temporal resolution. In this work, detection of apoptosis was studied by single molecule fluorescence correlation spectroscopy (FCS) in single living cells. Caspase activity was assayed using a new red fluorogenic probe that avoids the spectral overlap of green fluorescent probes and cell autofluorescence. This new probe, 2SBPO-Casp, was synthesized by coupling a water-soluble Nile Blue derivative (2SBPO) to an aspartic acid residue. Upon apoptosis induction and caspase activation, free 2SBPO dye is shown to accumulate inside the cell after probe cleavage. In previous work in our lab, single molecule fluorescence in single apoptotic cells was detected 45 min after induction using a rhodamine 110-based probe. However, significant statistical analysis was needed to exclude false positives. The use of 2SBPO-Casp overcomes the autofluorescence problem and offers a steady fluorescence signal. In our single molecule FCS measurements, Ramos cells were determined apoptotic on the basis of their correlation coefficient value (R(2)). Cells that contain an R(2) ? 0.65 were identified as highly correlated and therefore determined to be apoptotic. Single apoptotic cells identified in this manner were found as early as 30 min after induction and the number of apoptotic cells reached a peak value at the 3rd hour, which is consistent with other techniques. Using single molecule techniques and a new apoptosis probe, the temporal dynamics were elucidated with better sensitivity and resolution than in previous studies. PMID:22314869

Dong, Meicong; Martinez, Michelle M; Mayer, Michael F; Pappas, Dimitri

2012-07-01

430

Interfacial failure Analysis of CdZnTe detectors by Scanning Acoustic Microscopy and Auger Electron Spectrum  

Microsoft Academic Search

The contacts of CdZnTe detectors are rather complicated in their structure and the common failures or instabilities observed depend largely on the quality of the contacts. However, few works has been reported on the failure analysis of the interfacial layers between the contact and CdZnTe surface. In this paper, scanning acoustic microscopy (SAM) has been adopted to characterize these contact

Zhang Qi; Sang Wenbin; Qin Kaifeng; Min Jiahua; Teng Jianyong; Xia Jun

2005-01-01

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