Enhanced Diffusion of Molecular Catalysts is Due to Convection

Intriguing reports of enhanced diffusion in enzymes and molecular catalysts have spurred significant interest in experimental and theoretical investigations, and the mechanism of this phenomenon is the topic of lively debate. Here we use time‐resolved diffusion NMR methods to measure the diffusion coefficients (D) of small molecule species involved in chemical reactions with high temporal resolution. We show the enhanced diffusion of small molecules cannot be explained by reaction velocity, and that apparent measurements of enhanced diffusion by small molecules appear to be caused by bulk fluid flow processes such as convection.     

Effect of the Side‐Chain‐Distribution Density on the Single‐Conjugated‐Polymer‐Chain Conformation

The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side‐chain‐distribution density on the conformation at the isolated single‐polymer‐chain level was investigated with regiorandom (rra‐) poly(3‐hexylthiophene) (P3HT) and poly(3‐hexyl‐2,5‐thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single‐molecule spectroscopy investigation. With single‐molecule fluorescence excitation polarization spectroscopy, we found that rra‐P3HTV single molecules form highly ordered conformations. In contrast, rra‐P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side‐chain‐distribution density, that is, the spaced‐out side‐chain substitution pattern, in rra‐P3HTV favors more ordered conformations compared to rra‐P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer‐chain conformation, even at the single‐molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.     

Growth and Origami Folding of DNA on Nanoparticles for High‐Efficiency Molecular Transport in Cellular Imaging and Drug Delivery

A novel three‐dimensional (3D) superstructure based on the growth and origami folding of DNA on gold nanoparticles (AuNPs) was developed. The 3D superstructure contains a nanoparticle core and dozens of two‐dimensional DNA belts folded from long single‐stranded DNAs grown in situ on the nanoparticle by rolling circle amplification (RCA). We designed two mechanisms to achieve the loading of molecules onto the 3D superstructures. In one mechanism, ligands bound to target molecules are merged into the growing DNA during the RCA process (merging mechanism). In the other mechanism, target molecules are intercalated into the double‐stranded DNAs produced by origami folding (intercalating mechanism). We demonstrated that the as‐fabricated 3D superstructures have a high molecule‐loading capacity and that they enable the high‐efficiency transport of signal reporters and drugs for cellular imaging and drug delivery, respectively.     

Thermally Driven Polymorphic Transition Prompting a Naked‐Eye‐Detectable Bending and Straightening Motion of Single Crystals

The amplification of molecular motions so that they can be detected by the naked eye (10⁷‐fold amplification from the ångström to the millimeter scale) is a challenging issue in the development of mechanical molecular devices. In this context, the perfectly ordered molecular alignment of the crystalline phase has advantages, as demonstrated by the macroscale mechanical motions of single crystals upon the photochemical transformation of molecules. In the course of our studies on thermoresponsive amphiphiles containing tetra(ethylene glycol) (TEG) moieties, we serendipitously found that thermal conformational changes of TEG units trigger a single‐crystal‐to‐single‐crystal polymorphic phase transition. The single crystal of the amphiphile undergoes bending and straightening motion during both heating and cooling processes at the phase‐transition temperatures. Thus, the thermally triggered conformational change of PEG units may have the advantage of inducing mechanical motion in bulk materials.     

Franck–Condon Blockade and Aggregation‐Modulated Conductance in Molecular Devices Using Aggregation‐Induced Emission‐Active Molecules

We report an effective modulation of the quantum transport in molecular junctions consisting of aggregation‐induced‐emission(AIE)‐active molecules. Theoretical simulations based on combined density functional theory and rate‐equation method calculations show that the low‐bias conductance of the junction with a single tetraphenylethylene (TPE) molecule can be completely suppressed by strong electron–vibration couplings, that is, the Franck‐Condon blockade effect. It is mainly associated with the low‐energy vibration modes, which is also the origin of the fluorescence quenching of the AIE molecule in solution. We further found that the conductance of the junction can be lifted by restraining the internal motion of the TPE molecule by either methyl substitution on the phenyl group or by aggregation, a mechanism similar to the AIE process. The present work demonstrates the correlation between optical processes of molecules and quantum transport in their junction, and thus opens up a new avenue for the application of AIE‐type molecules in molecular electronics and functional devices.     

Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria

Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.     

一种可绝对定量核酸的数字PCR微流控芯片

构建了一种新型的可进行核酸单分子扩增和核酸绝对定量的数字聚合酶链式反应(数字PCR)微流控芯片. 应用多层软光刻技术, 以聚二甲基硅氧烷(PDMS)作为芯片材料, 盖玻片作为基底制作了具有3层结构以及微阀控制功能的微流控芯片. 芯片的大小与载玻片相当, 可同时检测4个样品, 每个样品通入芯片后平均分配到640个反应小室, 每个小室的体积为6 nL. 以从肺癌细胞A549中提取的18sRNA为样品检测了该芯片的可行性. 将样品稀释数倍后通入芯片, 核酸分子随机分布在640个小室中并扩增. 核酸分子在芯片中的分布符合泊松分布原理, 当样品中待测核酸分子平均拷贝数低于0.5个/小室时, 则每个反应小室包含0个或1个分子. 经过PCR扩增后, 有模板分子的小室检测结果为阳性反应, 而无模板分子的小室为阴性反应, 最后通过计数阳性反应室的个数, 可绝对定量原始待测样品中的目标DNA分子拷贝数. 实验结果表明, 该数字 PCR芯片可实现DNA单分子反应和核酸绝对定量, 具有成本低、 灵敏度高、 节省时间和试剂以及操作简单等优点, 为数字PCR方法在普通实验室的应用提供了一种新途径, 可用于癌症及感染性疾病的早期诊断、 单细胞分析、 产前诊断以及各种细菌病毒的核酸检验等研究.     

Advances in Optical Single‐Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low‐abundance biomarkers is of fundamental importance, e.g., for early‐stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single‐molecule bioaffinity assays. While many review articles have highlighted the potentials of single‐molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real‐world applications as one should expect. This Review provides a theoretical background on single‐molecule—or better digital—assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single‐molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.     

Structure‐Dependent Electronic Nature of Star‐Shaped Oligothiophenes,Probed by Ensemble and Single‐Molecule Spectroscopy

We have investigated the photophysical properties of star‐shaped oligothiophenes with three terthiophene arms (meta to each other, S3 ) or six terthiophene arms (ortho‐, meta‐, and para‐arranged, S6 ) connected to an ethynylbenzene core to elucidate the relationship between their molecular structure and electronic properties by using a combination of ensemble and single‐molecule spectroscopic techniques. We postulate two different conformations for molecules S3 and S6 on the basis of the X‐ray structure of hexakis(5‐hexyl‐2‐thienlyethynyl)benzene and suggest the coexistence of these conformers by using spectroscopic methods. From the steady‐state spectroscopic data of compound S6 , we show that the exciton is delocalized over the core structure, but that the meta‐linkage in compound S3 prevents the electronic communication between the arms. However, in single‐molecule spectroscopic measurements, we observed that some molecules of compound S3 showed long fluorescence lifetimes (about 1.4 ns) in the fluorescence‐intensity trajectories, which indicated that π electrons were delocalized along the meta linker. Based on these observations, we suggest that the delocalized exciton is intensely sensitive towards the dihedral angle between the core and the adjacent thiophene ring, as well as to the substituted position of the terthiophene arms. Our results highlight that the fluorescence lifetimes of compounds S3 and S6 are strongly correlated with the spatial location of their excitons, which is mainly affected by their conformation, that is, whether the innermost thiophene rings are facing each other or not. More interestingly, we observed that the difference between the degrees of ring‐torsional flexibility of compounds S3 and S6 results in their sharply contrasting fluorescence properties, such as a change in fluorescence intensity as a function of temperature.     

Gold Nanorod Enhanced Fluorescence Enables Single‐Molecule Electrochemistry of Methylene Blue

Redox reactions are central to energy conversion and life metabolism. Herein we present electrochemical measurements with fluorescent readout of the redox‐sensitive dye Methylene Blue (MB), at the single‐molecule (SM) level. To overcome the low fluorescence quantum yield of MB we enhanced fluorescence by using individual gold nanorods to achieve the required sensitivity. By measuring the same molecule at different electrochemical potentials we determined the mid‐point potential of each single molecule through its redox‐induced fluorescence blinking dynamics.     

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.     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.     

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.     

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.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

Single‐Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm^?2) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme‐induced compositional heterogeneity within membranes, where NR within liquid‐ordered vs. liquid‐disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid‐lipid, lipid‐protein, and lipid‐dye interactions with single‐molecule, nanoscale resolution.     

Non‐hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single‐stranded DNA

The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label‐free, and economical non‐hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single‐stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single‐base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84‐mer, in which guanine to adenine single‐base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.     

Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number

Digital polymerase chain reaction (PCR) is a promising technique for estimating target DNA copy number. PCR solution is distributed throughout numerous partitions, and following amplification, target DNA copy number is estimated based on the proportion of partitions containing amplified DNA. Here, we identify approaches for obtaining reliable digital PCR data. Single molecule amplification efficiency was significantly improved following fragmentation of total DNA and bias in copy number estimates reduced by analysis of short intact target DNA fragments. Random and independent distribution of target DNA molecules throughout partitions, which is critical to accurate digital PCR measurement, was demonstrated by spatial distribution analysis. The estimated relative uncertainty for target DNA concentration was under 6% when analyzing five digital panels comprising 765 partitions each, provided the panels contained an average of 212 to 3,365 template molecules. Partition volume was a major component of this uncertainty estimate. These findings can be applied to other digital PCR studies to improve confidence in such measurements. Figure Digital PCR amplification plot (left) and panel read out (right) of HindIII-digested pIRMM69. pIRMM69 contains one HindIII restriction enzyme site outside the hmg and transgene fragments used as targets in PCR. Red boxes with white shade denote positive hits containing one or more target DNA molecules, and white boxes with grey shade refer to no target being amplified.     

Simultaneous Arrangement of up to Three Different Molecules on the Pore Surface of a Metal–Macrocycle Framework: Cooperation and Competition

Porous crystals are excellent materials with potential spatial functions through molecular encapsulation within the pores. Co‐encapsulation of multiple different molecules further expands their usability and designability. Herein we report the simultaneous arrangement of up to three different guest molecules, TTF (tetrathiafulvalene), ferrocene, and fluorene, on the pore surfaces of a porous crystalline metal–macrocycle framework (MMF). The position and orientation of adsorbed molecules arranged in the pore were determined by single‐crystal X‐ray diffraction analysis. The anchoring effect of hydrogen bonds between the hydroxy groups of the guest molecules and inter‐guest cooperation and competition are significant factors in the adsorption behaviors of the guest molecules. This finding would serve as a design basis of multicomponent functionalized nanospaces for elaborate reactions that are realized in enzymes.