Characterization of a single molecule DNA switch in free solution

We have studied a donor-acceptor fluorophore-labeled DNA switch where the acceptor is Alexa-647, a carbocyanine dye, in solution at the single molecule level to elucidate the fluorescence switching mechanism. The acceptor, which is in an initial high fluorescence trans state, undergoes a photoisomerization reaction resulting in two additional states during its sub-millisecond transit across the probe volume. These two states are assigned to a nonfluorescent triplet trans state that strongly quenches the donor emission and a singlet cis state that blocks the fluorescence resonance energy transfer (FRET) pathway and gives rise to donor-only fluorescence. The formation of these states is faster than the transit time, so that all three states are approximately equally populated under our experimental conditions. The acceptor dye can stick to the DNA in all these states, with the rate of unsticking determining the rate of isomerization into the other states. Measurement of the rate of change of the FRET signal therefore provides information about the fluorophore-DNA intramolecular dynamics. These results explain the large zero peak in the proximity ratio, often seen in single molecule FRET experiments, and suggest that photoinduced effects may be important in single molecule FRET experiments using carbocyanine dyes. They also suggest that for fast photoinduced switching the interactions of the acceptor dye with the DNA and other surfaces should be prevented.     

Direct visualization of abasic sites on a single DNA molecule using fluorescence microscopy

A new method was developed to allow direct visualization of damaged sites on individual DNA molecules. Fluorescence in situ hybridization on extended DNA molecules was modified to detect a single abasic site. Abasic sites were specifically labeled with a biotinylated aldehyde-reactive probe and fluorochrome-conjugated streptavidin. The light emitted by a single fluorochrome-DNA complex was calibrated. The number of abasic sites on the DNA molecule was estimated by counting each fluorochrome-DNA complex. The present study directly visualized and characterized the abasic sites of single DNA molecules.     

High-throughput single molecule screening of DNA and proteins

We report a novel imaging technology for real time comprehensive analysis of molecular alterations in cells and tissues appropriate for automation and adaptation to high-throughput applications. With these techniques it should eventually be possible to perform simultaneous analysis of the entire contents of individual biological cells with a sensitivity and selectivity sufficient to determine the presence or absence of a single copy of a targeted analyte (e.g., DNA region, RNA region, protein), and to do so at a relatively low cost. The technology is suitable for DNA and RNA through sizing or through fluorescent hybridization probes, and for proteins and small molecules through fluorescence immunoassays. This combination of the lowest possible detection limit and the broadest applicability to biomolecules represents the final frontier in bioanalysis. The general scheme is based on novel concepts for single molecule detection (SMD) and characterization recently demonstrated in our laboratory. Since minimal manipulation is involved, it should be possible to screen large numbers of cells in a short time to facilitate practical applications. This opens up the possibility of finding single copies of DNA or proteins within single biological cells for disease markers without performing polymerase chain reaction or other biological amplification.     

Neutravidin coated surfaces for single DNA molecule analysis

We present a novel approach for single DNA molecule analysis using neutravidin coated surfaces. DNA molecules are elongated and reversibly immobilized on neutravidin coated surfaces with pH and salt controls. We demonstrate restriction enzyme reactions for optical mapping and ligation for tethered DNA molecules.     

Imaging of tautomerism in a single molecule

Fluorescence imaging is used to visualize directly the transfer of two inner hydrogen atoms in single porphycene molecules. This reaction leads to a chemically equivalent but differently oriented structure and hence results in a rotation of the transition dipole moments. By probing single immobilized molecules with an azimuthally polarized laser beam in the focal spot of a confocal microscope we observe ring-like emission patterns, possible only for a chromophore with two nearly orthogonal transition dipole moments. Numerical simulations of the observed emission patterns yield a value of 72 degrees for the angle between the S0-S1 transition moments in the two tautomeric forms.     

DNA-psoralen interaction: a single molecule experiment

By attaching one end of a single lambda-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 lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly 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.     

高岭石与水分子相互作用的理论研究

为从微观角度深入探讨单个水分子与高岭石最易解理晶面不同暴露末端的作用特点,本工作通过密度泛函理论的计算方法对不同吸附形态的水分子与不同暴露末端的稳定作用构型进行几何结构与电子结构分析.吸附能的计算结果表明水分子在铝氧八面体羟基作为暴露末端的表面上最稳定的吸附方式为水分子的氧原子和氢原子分别与相邻两个羟基的氢原子和氧原子...     

Driving the Bloch vector of a single molecule: towards a triggered single photon source

We propose the method of rapid adiabatic passage to prepare a single molecule in its fluorescing excited state. Spontaneous emission from this state gives rise to a single photon. Since the adiabatic passage can be performed on command, the molecule can be used as a triggered single photon source. Preliminary experiments and quantum Monte-Carlo simulations demonstrate the feasibility of this scheme.     

Using a nanopore for single molecule detection and single cell transfection

We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity.     

The fluctuating enzyme: a single molecule approach

The excess of structural degrees of freedom in a protein enzyme opens questions about the conformational homogeneity. We studied single horseradish peroxidase enzyme turnovers by fluorescence spectroscopy. Application of a two-state dynamic model to the measured data shows exponential product dissociation kinetics, but a large distribution of rates for the enzyme to form the enzyme-product complex. The experiments show that in addition to the peroxidative cycle thermodynamic fluctuation phenomena on a wide range of time scales affect enzyme activity.     

Marked differences in volume phase transitions between gel and single molecule in DNA

Volume phase transitions of a DNA gel and a single giant DNA chain caused by spermidine(3+) (SPD(3+)) were investigated. The change in volume for the single DNA (VV(0) approximately 10(-5)) was four orders of magnitude greater than that for the DNA gel ( approximately 10(-1)), while the critical SPD(3+) concentration for the gel (1.8 mM) was one order of magnitude greater than that of the single DNA (0.12-0.25 mM) at the same pH 6.86. We tried to describe mean-field theories with virial expansion, which is valid for the coil-globule transition of a single polymer chain, for the volume phase transitions to explain the reason why such marked differences appeared. Considering the degree of the ordering of Kuhn segments arising from the gel network structure together with the chain length of cross-linked polymer chains, the volume phase transitions were described and then the significant differences were reproduced quantitatively. We concluded that the network structure plays a significant role in the volume phase transition of the gel.     

Distribution of single DNA molecule electrophoretic mobilities in semidilute and dilute hydroxyethylcellulose solutions

The distribution of center of mass electrophoretic mobility mobilities and normalized migration time of up to 1080 lambda DNA molecules per experiment were measured in both semidilute hydroxyethylcellulose HEC/0.5 x Tris-borate-EDTA (TBE) solutions and dilute HEC/0.5 x TBE solution by high-speed video microscopy. Measurements were made microscopically over a short migration distance in homogeneous DNA HEC/0.5 x TBE solution and after electrophoretic migration of a plug of DNA through 7 cm. Video at 120 frames/s (semidilute HEC solution) and 236 frames/s (dilute HEC solution) allowed visualization with adequate resolution for single molecule mobility measurements. The electrophoretic migration times and band shapes predicted from the measurements corresponded well with those measured by conventional capillary electrophoresis (CE) in both semidilute and dilute HEC. In semidilute solution, the band width predicted by a square root of time scaling is in good agreement with the results of conventional CE. However, in dilute solution the precision of the measurements was not good enough to allow scaled estimates of band widths.     

DNA curtains and nanoscale curtain rods: high-throughput tools for single molecule imaging

Single molecule visualization of protein-DNA complexes can reveal details of reaction mechanisms and macromolecular dynamics inaccessible to traditional biochemical assays. However, these techniques are often limited by the inherent difficulty of collecting statistically relevant information from experiments explicitly designed to look at single events. New approaches that increase throughput capacity of single molecule methods have the potential for making these techniques more readily applicable to a variety of biological questions involving different types of DNA transactions. Here we show that nanofabricated chromium barriers, which are located at strategic positions on a fused silica slide otherwise coated with a supported lipid bilayer, can be used to organize DNA molecules into molecular curtains. The DNA that makes up the curtains is visualized by total internal reflection fluorescence microscopy (TIRFM) allowing simultaneous imaging of hundreds or thousands of aligned molecules. These DNA curtains present a robust experimental platform portending massively parallel data acquisition of individual protein-DNA interactions in real time.     

Effect of surface orientation on the segregation kinetics of Sb from a Cu single crystal

In a previous theoretical study it has been suggested that the bulk vacancy formation energy near a surface depends on the orientation of the surface. It has been suggested also that this dependency of the vacancy formation energy would influence the bulk diffusion coefficient near the surface. The experimental results presented in this paper support this hypothesis. The experimental results were obtained by measuring the bulk‐to‐surface segregation of Sb for a Cu(111) single crystal with 0.088 at.% Sb and for a Cu(110) single crystal with 0.082 at.% Sb. The experimental results were fitted with the vacancy‐modified Darken model and it was clear that the bulk diffusion coefficient beneath the (110) surface is higher than the bulk diffusion coefficient beneath the (111) surface. Copyright © 2003 John Wiley & Sons, Ltd.     

Influence of intrachain hydrogen bonding on the cyclization of a polystyrene chain

Cyclization of a polystyrene chain (M_n = 10,600; M_w/M_n = 1.09) both ends labeled with 4-(1-pyrenyl)butanoamide groups was studied in cyclohexane between 25 and 95°C. The amide groups (peptide bonds) at both ends can form an intrachain hydrogen bond between the amide hydrogen at one chain end and the carbonyl oxygen at the other. The presence of two sets of conformers, random coils, and chains cyclized through hydrogen bonding, complicates the data analysis. The pyrene excimer kinetics of this polymer is well described by a model composed of two monomers (hydrogen bonded and nonbonded chains) and one excimer, in equilibrium. The cyclization rate constant for hydrogen-bonded chains is larger than the one for nonhydrogen-bonded chains. The pyrene excimer binding energy (ca. 1.6 kcal/mol) is lower than the published value for nonhydrogen-bonded chains (～ 9 kcal/mol), suggesting that intrachain hydrogen bonding hinders the stabilization of the excimer. © 1994 John Wiley & Sons, Inc.     

Conductance of a single molecule C60-SnPc heterojunction

Geometries of molecule-molecule interfaces strongly influence the current passing from one molecule to another. The contact conductance of molecule-molecule junctions which consist of fullerene and tin phthalocyanine molecules is investigated with a low-temperature scanning tunneling microscope. Two types of molecules are deposited onto Cu(111). Fullerene molecules are transferred to tips through controlled contact of STM tips on molecules. The molecule-molecule junctions are formed by approachi...     

Excluded volume effects on the intrachain reaction kinetics

On the basis of the recently developed optimized Rouse-Zimm theory of chain polymers with excluded volume interactions, we calculate the long-time first-order rate constant k(1) for end-to-end cyclization of linear chain polymers. We first find that the optimized Rouse-Zimm theory provides the longest chain relaxation times tau(1) of excluded volume chains that are in excellent agreement with the available Brownian dynamics simulation results. In the free-draining limit, the cyclization rate is diffusion-controlled and k(1) is inversely proportional to tau(1), and the k(1) values calculated using the Wilemski-Fixman rate theory are in good agreement with Brownian dynamics simulation results. However, when hydrodynamic interactions are included, noticeable deviations are found. The main sources of errors are fluctuating hydrodynamic interaction and correlation hole effects as well as the non-Markovian reaction dynamic effect. The physical natures of these factors are discussed, and estimates for the magnitudes of required corrections are given. When the corrections are included, the present theory allows the prediction of accurate k(1) values for the cyclization of finite-length chains in good solvents as well as the correct scaling exponent in the long-chain limit.