High throughput single molecule tracking for analysis of rare populations and events

High throughput single molecule tracking methods were developed to perform quantitative analyses of rare molecular populations. An optimization strategy for single molecule tracking at interfaces is described that allowed tracking of ~10(6) unique trajectories. These large statistical datasets were analyzed in order to identify and characterize distinct molecular populations based on their characteristic dynamic behavior (residence time or surface diffusion) and/or their spatial distribution. Cumulative (i.e. integrated) probability distributions were found to be several orders of magnitude more sensitive to rare populations than were raw probability distributions. Mapping using Accumulated Probe Trajectories (MAPT) was used to characterize molecular populations associated with rare surface heterogeneities. Importantly, large sample sizes were found to result in a dramatic enhancement in the ability to identify rare populations and to resolve their dynamic and spatial parameters.     

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.     

Electronic states of pyrene single crystal and of its single molecule inserted in a molecular vessel of cyclodextrin

Highly purified single crystals of pyrene were made by a gas phase crystal growth method from 180 times of zone-refined pyrene. The absorption spectra of the single crystal have been transformed from the reflection spectra between 2.5 and at 2, and room temperature. The dry powder of β-cyclodextrin including pyrene single molecule were prepared in vacuum to investigate the electronic states of the isolated molecule. The absorption spectra of the single molecule show similar spectra to those of the single crystal. The pyrene molecule keeps its electronic character even in the single crystal.     

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.     

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.     

Crystal packing and charge transport in single crystals of chrysene derivatives: Impact of halogenation

Crystal packing has strong influence on the charge mobility for organic semiconductors, so the elucidation of the structure-property relationship is important for the design of high-performance organic semiconductors. Halogen substitution has been shown to be a promising strategy to alter the crystal structure without significantly changing the molecular size in previous reports. This paper studies the influence of halogenation on charge transport in single crystals of chrysene derivatives from a theoretical standpoint. The structure-property relationship is first rationalized by investigating the reorganization energy and electronic coupling from the density functional theory calculations. Based on the Marcus charge transfer theory, the mobilities in the molecular monolayer are then calculated with the random walk simulation technique from which the angular resolution anisotropic mobilities are obtained on the fly. It is shown that the mobilities become much larger for holes than those for electrons in the molecular monolayer when the halogenation occurs. Furthermore, the intra-layer charge transport is little influenced by the inter-layer pathways in the single crystals of the halogenated chrysene derivatives, while the opposite case is shown for the crystal of the nonhalogenated chrysene derivative. The reason for the variations of charge transport is discussed theoretically.     

Substrate-mediated intermolecular interactions: a quantitative single molecule analysis

Long-range intermolecular interactions mediated by the surface are believed to be responsible for many effects in surface science, including molecular ordering, formation of nanostructures, and aligning reactive intermediates in catalysis. Here, we use scanning tunneling microscopy to probe the weak substrate-mediated interactions in benzene overlayers on Au{111} at 4 K. Using an automated procedure to monitor single molecule motion, we are able to quantify the substrate-mediated interaction strength. We explain quantitatively both the kinetics of the benzene motion and the thermodynamics that determine the packing structures benzene adopts in this system in light of these substrate-mediated interactions.     

Exponentially modified Gaussian relevance to the distributions of translocation events in nanopore-based single molecule detection

Nanopore technique plays an important role in single molecule detection, which illuminates the properties of an individual molecule by analyzing the blockage durations and currents. However, the traditional exponential function is lack of efficiency to describe the distributions of blockage durations in nanopore experiments. Herein, we introduced an exponentially modified Gaussian （EMG） function to fit the duration histograms of both simulated events and experimental events. In comparison with the traditional exponential function, our results demonstrated that the EMG provides a better fit while covers the entire range of the distributions. In particular, the fitted parameters of EMG could be directly used to discriminate the sequence length of the oligonucleotides at single molecule level.     

Enhancement factor distribution around a single surface-enhanced Raman scattering hot spot and its relation to single molecule detection

We provide the theoretical framework to understand the phenomenology and statistics of single molecule (SM) signals arising in surface enhanced Raman scattering (SERS) under the presence of so-called electromagnetic hot spots. We show that most characteristics of the SM-SERS phenomenon can be tracked down to the presence of a tail-like (power law) distribution of enhancements and we propose a specific model for it. We analyze, in the light of this, the phenomenology of SM-SERS and show how the different experimental manifestations of the effect reported in the literature can be analyzed and understood under a unified "universal" framework with a minimum set of parameters.     

Specific molecule localization in microchannel laminar flow and its application for non-immobilized-probe analysis

Microfluidic systems enable superior control of fluidics. We have developed a novel size-separation method utilizing secondary flow within a microchannel. Using confocal fluorescence microscopy and computer simulation, we confirmed that separation occurred as a result of specific molecular localization in the curving part of the microchannel. Maximum separation efficiency was achieved by optimizing microchannel design and flow rate for individual separation targets. In addition, more effective separation was achieved by use of plural microchannel curves. This method was used for sequence-selective DNA sensing. Double-stranded DNA formed by hybridization between target DNA and a complementary probe had different elution profiles from those of the single-stranded non-complementary sequence. Moreover, the response depends on the length of the DNA molecules. This method does not require immobilization of either probe or target DNA, because all reactions occurred in the solution phase. Such features may reduce experimental error and the difference between data from different operators.     

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.     

Electrochemical electron transfer and its relation to charge transport in single molecule junctions

Ability to control charge transport at nanometer scale lies in the heart of design of fast reliable electronic devices. Molecular electronics thrive to use functional molecules for such transport. If the molecule contains redox center(s), a diode-like or transistor-like behavior can be easily explored by controlling not only the voltage difference between two metallic contacts of the molecular junction but also the potential of one of the contacting electrodes with respect to some reference. Thus, one needs to understand the relationship between electrochemical electron transfer and charge transport in metal–molecule–metal junctions. This review presents latest theoretical approaches toward understanding of such relationship and discusses pivotal experimental works to validate them. Tunneling and hopping pathways may operate in parallel (two-channel model), but experimental conditions dictate the channel preference.     

Vibrations of a single adsorbed organic molecule: anharmonicity matters!

Vibrational spectroscopy is a powerful tool to identify molecules and to characterise their chemical state. Inelastic electron tunnelling spectroscopy (IETS) combined with scanning tunnelling microscopy (STM) allows the application of vibrational analysis to a single molecule. Up to now, IETS was restricted to small species due to the complexity of vibration spectra for larger molecules. We extend the horizon of IETS for both experiment and theory by measuring the STM-IETS spectra of mercaptopyridine adsorbed on the (111) surface of gold and comparing it to theoretical spectra. Such complex spectra with more than 20 lines can be reliably determined and computed leading to completely new insights. Experimentally, the vibrational spectra exhibit a dependence on the specific adsorption site of the molecules. Theoretically, this dependence is only accessible if anharmonic contributions to the interaction potentials are included. These joint experimental and theoretical advances open new perspectives for structure determination of organic adlayers.     

Multidimensional optical spectroscopy of a single molecule in a current-carrying state

The nonlinear optical signals from an open system consisting of a molecule connected to metallic leads, in response to a sequence of impulsive pulses, are calculated using a superoperator formalism. Two detection schemes are considered: coherent stimulated emission and incoherent fluorescence. The two provide similar but not identical information. The necessary superoperator correlation functions are evaluated either by converting them to ordinary (Hilbert space) operators which are then expanded in many-body states, or by using Wick's theorem for superoperators to factorize them into nonequilibrium two point Green's functions. As an example we discuss a stimulated Raman process that shows resonances involving two different charge states of the molecule in the same signal.     

Chemical contrasting in a single polymer molecule AFM experiment

We developed a simple contrasting procedure to improve the AFM visualization of single positively charged polymer chains deposited on substrates of a relatively high roughness via the decoration of the molecules with hexacyanoferrate anions or negatively charged clusters of cyanide-bridged complexes.     

Glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908: function of a halogenase and a haloperoxidase/perhydrolase

Glycopeptides are important clinical emergency antibiotics consisting of a glycosylated and chlorinated heptapeptide backbone. The understanding of the biosynthesis is crucial for development of new glycopeptides. With balhimycin as a model system, this work focuses on the investigation of the putative halogenase gene (bhaA) and the putative haloperoxidase/perhydrolase gene (bhp) of the balhimycin biosynthesis gene cluster. An in-frame deletion mutant in the haloperoxidase/perhydrolase gene bhp (OP696) did not produce balhimycin. Feeding experiments revealed that bhp is involved in the biosynthesis of beta-hydroxytyrosine, a precursor of balhimycin. A bhaA in-frame deletion mutant (PH4) accumulated glycosylated but nonchlorinated balhimycin variants. The mutants indicated that only the halogenase BhaA is required for chlorination of balhimycin. Nonglycosylated and/or nonhalogenated metabolites can serve as starting points for combinatorial approaches for novel glycopeptides.