Characterizing Single‐Molecule FRET Dynamics with Probability Distribution Analysis

Probability distribution analysis (PDA) is a recently developed statistical tool for predicting the shapes of single‐molecule fluorescence resonance energy transfer (smFRET) histograms, which allows the identification of single or multiple static molecular species within a single histogram. We used a generalized PDA method to predict the shapes of FRET histograms for molecules interconverting dynamically between multiple states. This method is tested on a series of model systems, including both static DNA fragments and dynamic DNA hairpins. By fitting the shape of this expected distribution to experimental data, the timescale of hairpin conformational fluctuations can be recovered, in good agreement with earlier published results obtained using different techniques. This method is also applied to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two‐state kinetic model with the observed smFRET distribution of unliganded KF and extraction of a millisecond fluctuation timescale, in good agreement with rates reported elsewhere. We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis‐testing models of conformational dynamics against experimental data.     

Dual‐Polarization Imaging of a Dual‐Fluorophore Ion Sensor: A Single‐Molecule Study

The fluorescence emission of the dual‐fluorophore Ca²⁺ ion sensor molecule, calcium‐green 2 (CG‐2), has been characterized using dual‐polarization imaging at the single‐molecule level. By comparing the fluorescence intensity of individual CG‐2 molecules in two mutually orthogonal polarization image channels, information about the relative orientation of the two constituent fluorophores in the molecule is obtained. Experimental results from polarization measurements are compared with those predicted from a geometric model based on coupled‐fluorophores that are randomly distributed in space. The results confirm previous optical spectroscopy‐based predictions of the orientation of CG‐2′s fluorophores, and the general applications of this dual‐polarization imaging approach for characterizing the optical properties of molecules containing multiple fluorophores is discussed.     

Sequencing Single DNA Molecules in Real Time

One's enough : The direct observation of a DNA‐polymerase‐based “sequencing engine” using single‐molecule detection recently allowed single‐molecule sequencing by synthesis in real time. Nucleotides with a fluorescent marker at the 5′‐phosphate unit and zero‐mode waveguides are crucial components of this approach, which at last promises low‐cost genome‐scale sequencing.

     

Mechanochemical Sensing: A Biomimetic Sensing Strategy

Existing biosensors employ two major components: analyte recognition and signal transduction. Although specificity is achieved through analyte recognition, sensitivity is usually enhanced through a chemical amplification stage that couples the two main units in a sensor. Although highly sensitive, the extra chemical amplification stage complicates the sensing protocol. In addition, it separates the two elements spatiotemporally, reducing the real‐time response of the biosensor. In this review, we discuss the new mechanochemical biosensors that employ mechanochemical coupling strategies to overcome these issues. By monitoring changes in the mechanical properties of a single‐molecule template upon analyte binding, single‐molecule sensitivity is reached. As chemical amplification becomes unnecessary in this single‐molecule mechanochemical sensing (SMMS) strategy, real‐time sensing is achieved.     

Single‐Molecule Mechanochemical Sensing Using DNA Origami Nanostructures

While single‐molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single‐molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7‐tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet‐derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single‐molecule sensing with improved throughput.     

Electron Transport through Single π‐Conjugated Molecules Bridging between Metal Electrodes

Understanding electron transport through a single molecule bridging between metal electrodes is a central issue in the field of molecular electronics. This review covers the fabrication and electron‐transport properties of single π‐conjugated molecule junctions, which include benzene, fullerene, and π‐stacked molecules. The metal/molecule interface plays a decisive role in determining the stability and conductivity of single‐molecule junctions. The effect of the metal–molecule contact on the conductance of the single π‐conjugated molecule junction is reviewed. The characterization of the single benzene molecule junction is also discussed using inelastic electron tunneling spectroscopy and shot noise. Finally, electron transport through the π‐stacked system using π‐stacked aromatic molecules enclosed within self‐assembled coordination cages is reviewed. The electron transport in the π‐stacked systems is found to be efficient at the single‐molecule level, thus providing insight into the design of conductive materials.     

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

We demonstrate the single‐molecule imaging of the catalytic reaction of a Zn²⁺‐dependent DNAzyme in a DNA origami nanostructure. The single‐molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high‐speed atomic force microscopy (AFM). This nanostructure‐based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single‐molecule level.     

Reversible Reconfiguration of DNA Origami Nanochambers Monitored by Single‐Molecule FRET

Today, DNA nanotechnology is one of the methods of choice to achieve spatiotemporal control of matter at the nanoscale. By combining the peculiar spatial addressability of DNA origami structures with the switchable mechanical movement of small DNA motifs, we constructed reconfigurable DNA nanochambers as dynamic compartmentalization systems. The reversible extension and contraction of the inner cavity of the structures was used to control the distance‐dependent energy transfer between two preloaded fluorophores. Interestingly, single‐molecule FRET studies revealed that the kinetics of the process are strongly affected by the choice of the switchable motifs and/or actuator sequences, thus offering a valid method for fine‐tuning the dynamic properties of large DNA nanostructures. We envisage that the proposed DNA nanochambers may function as model structures for artificial biomimetic compartments and transport systems.     

Nanopore‐Based Sequencing and Detection of Nucleic Acids

Nanopore‐based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single‐molecule detection. The technology allows the real‐time, selective, high‐throughput analysis of nucleic acids through both biological and solid‐state nanopores. In this Minireview, the background and latest progress in nanopore‐based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore‐based detection.     

A Molecular Tuning Fork in Single‐Molecule Mechanochemical Sensing

The separate arrangement of target recognition and signal transduction in conventional biosensors often compromises the real‐time response and can introduce additional noise. To address these issues, we combined analyte recognition and signal reporting by mechanochemical coupling in a single‐molecule DNA template. We incorporated a DNA hairpin as a mechanophore in the template, which, under a specific force, undergoes stochastic transitions between folded and unfolded hairpin structures (mechanoescence). Reminiscent of a tuning fork that vibrates at a fixed frequency, the device was classified as a molecular tuning fork (MTF). By monitoring the lifetime of the folded and unfolded hairpins with equal populations, we were able to differentiate between the mono‐ and bivalent binding modes during individual antibody‐antigen binding events. We anticipate these mechanospectroscopic concepts and methods will be instrumental for the development of novel bioanalyses.     

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

A single‐nucleotide polymorphism (SNP) detection method was developed by combining single‐base primer extension and salt‐induced aggregation of gold nanoparticles densely functionalized with double‐stranded DNA (dsDNA‐AuNP). The dsDNA‐AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single‐base protrusion at the outermost surface disperse stably, allowing detection of a single‐base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single‐stranded DNA on the AuNP surface, the resulting dsDNA‐AuNP works as a visual indicator of single‐base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single‐base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.     

Synthesis and Photophysics of Core‐Substituted Naphthalene Diimides: Fluorophores for Single Molecule Applications

The synthesis and photophysics of two new aminopropenyl naphthalene diimide (SANDI) dyes are reported. A general and convenient method for the synthesis of the precursor mono‐, di‐, and tetrabrominated 1,4,5,8‐naphthalene tetracarboxylic dianhydrides is described. The two core‐substituted SANDIs exhibit many of the photophysical properties required for fluorescence labeling applications including high photostability and high fluorescence quantum yields (>0.5) in the visible region of the spectrum. The emission wavelength is sensitive to the number of substituents on the NDI core, and the fluorescence decay times are in the range of ～8–12 ns for both compounds in the solvents investigated. Preliminary fluorescence emission data from single molecules of the compounds embedded in poly(methyl methacrylate) films are also reported and show that single molecules have very low yields of photobleaching, particularly the di‐substituted system. Furthermore, only a small proportion (<10 %) of the single molecules studied display fluorescence intermittencies or “blinks” in their photon trajectory. The compounds appear to be excellent candidates for applications at the single molecule level, for example, as FRET labels.     

Probing Deuterium Isotope Effect on Structure and Solvation Dynamics of Human Serum Albumin

The deuterium isotopic effect on the structure and solvation dynamics of the protein, human serum albumin (HSA), has been studied by using circular dichroism (CD), femtosecond up‐conversion, FRET, and single‐molecule spectroscopy. The CD spectra suggest that D₂O affects the structure of HSA, leading to a 20 % decrease in the helical structure. The FRET study indicates that the distance of C153 from the lone tryptophan residue of HSA is quite similar (≈21 Å) in H₂O and D₂O, and hence, the location of the probe in the protein remains the same in the two solvents. The single‐molecule study suggests that coumarin 153 (C153) binds almost exclusively (>96 %) to one site of HSA. Solvation dynamics of C153 in HSA is found to be markedly retarded in D₂O compared with H₂O. In H₂O, the solvation of C153 bound to HSA is found to be biexponential with one component of 7 ps (30 %) and a long component of 350 ps (70 %). In D₂O, we detected a short component of 4 ps (41 %) and a long component of 950 ps (59 %). Thus, the ultraslow component of the solvation dynamics of C153 bound to HSA in D₂O (950 ps) is 2.5‐fold slower than that in H₂O (350 ps). The marked deuterium isotope effect has been ascribed to water molecules confined in the protein environment and to a lesser extent to the structural modification of protein by D₂O.     

Multichannel Conductance of Folded Single‐Molecule Wires Aided by Through‐Space Conjugation

Deciphering charge transport through multichannel pathways in single‐molecule junctions is of high importance to construct nanoscale electronic devices and deepen insight into biological redox processes. Herein, we report two tailor‐made folded single‐molecule wires featuring intramolecular π–π stacking interactions. The scanning tunneling microscope (STM) based break‐junction technique and theoretical calculations show that through‐bond and through‐space conjugations are integrated into one single‐molecule wire, allowing for two simultaneous conducting channels in a single‐molecule junction. These folded molecules with stable π–π stacking interaction offer conceptual advances in single‐molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and π‐stacked columnar aggregates.     

Controlling Electrical Conductance through a π‐Conjugated Cruciform Molecule by Selective Anchoring to Gold Electrodes

Tuning charge transport at the single‐molecule level plays a crucial role in the construction of molecular electronic devices. Introduced herein is a promising and operationally simple approach to tune two distinct charge‐transport pathways through a cruciform molecule. Upon in situ cleavage of triisopropylsilyl groups, complete conversion from one junction type to another is achieved with a conductance increase by more than one order of magnitude, and it is consistent with predictions from ab initio transport calculations. Although molecules are well known to conduct through different orbitals (either HOMO or LUMO), the present study represents the first experimental realization of switching between HOMO‐ and LUMO‐dominated transport within the same molecule.     

Mechanism‐Guided Improvements to the Single Molecule Oxidation of Carbon Nanotube Sidewalls

Real‐time monitoring of carbon nanotube conductance during electrochemical and chemical etching reveals the electronic signatures of individual bond alteration events on the nanotube sidewall. Tracking the conductance of multiple single‐molecule experiments through different synthetic protocols supports putative mechanisms for sidewall derivatization. Insights gained from these mechanistic observations imply the formation of sidewall carboxylates, which are useful as handles for bioconjugation. We describe an electronic state required for efficacious chemical treatment. Such real‐time monitoring can improve carboxylate yields to 45 % or more. The experiments illustrate the power of molecular nanocircuits to uncover and direct the mechanisms of chemical reactions.     

Detection of structured single‐strand DNA via solid‐state nanopore

Nanopore is a single‐molecule analysis method which also employed electrophoresis has achieved promising single‐molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid‐state nanopores with desirable diameters to study the structured single‐strand DNA of C‐rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single‐strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single‐molecule information. The solid‐state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.     

Single‐Molecule Methods to Study Membrane Receptor Oligomerization

Membrane receptors control fundamental cellular processes. Binding of a specific ligand to a receptor initiates communication through the membrane and activation of signaling cascades. This activation process often leads to a spatial rearrangement of receptors in the membrane at the molecular level. Single‐molecule techniques contributed significantly to the understanding of receptor organization and rearrangement in membranes. Here, we review four prominent single‐molecule techniques that have been applied to membrane receptors, namely, stepwise photobleaching, Förster resonance energy transfer, sub‐diffraction localization microscopy and co‐tracking. We discuss the requirements, benefits and limitations of each technique, discuss target labeling, present a selection of applications and results and compare the different methodologies.