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.     

Peering into Biological Nanopore: A Practical Technology to Single‐Molecule Analysis

As a unique technique at the singe‐molecule level to explore the distribution and temporal order of events, nanopore technology has attracted increasing attention. In comparison to the previous applications in DNA sequencing, this Focus Review highlights the technical details of biological nanopores, especially α‐hemolysin, in the analysis of peptides and proteins. The instrument configurations, experimental interferences, and data analysis including the conformation of peptides and proteins and their interactions for single‐molecule detection are discussed.     

Pim Kinase Inhibitors Evaluated with a Single‐Molecule Engineered Nanopore Sensor

Protein kinases are critical therapeutic targets. Pim kinases are implicated in several leukaemias and cancers. Here, we exploit a protein nanopore sensor for Pim kinases that bears a pseudosubstrate peptide attached by an enhanced engineering approach. Analyte binding to the sensor peptide is measured through observation of the modulation of ionic current through a single nanopore. We observed synergistic binding of MgATP and kinase to the sensor, which was used to develop a superior method to evaluate Pim kinase inhibitors featuring label‐free determination of inhibition constants. The procedure circumvents many sources of bias or false‐positives inherent in current assays. For example, we identified a potent inhibitor missed by differential scanning fluorimetry. The approach is also amenable to implementation on high throughput chips.     

Thermodynamics for the Formation of Double‐Stranded DNA–Single‐Walled Carbon Nanotube Hybrids

For the first time, the thermodynamics are described for the formation of double‐stranded DNA (ds‐DNA)–single‐walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds‐DNAs d(A)₂₀–d(T)₂₀ and nuclear factor (NF)‐κB decoy. UV/Vis/near‐IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single‐stranded DNAs (ss‐DNAs), including d(A)₂₀ and d(T)₂₀, are also used for comparison. The d(A)₂₀–d(T)₂₀ shows a drastic change in its thermodynamic parameters around the melting temperature (T_m) of the DNA oligomer. No such T_m dependency was measured, owing to high T_m in the NF‐κB decoy DNA and no T_m in the ss‐DNA.     

Direct Measurement of Single‐Molecule DNA Hybridization Dynamics with Single‐Base Resolution

Herein, we report label‐free detection of single‐molecule DNA hybridization dynamics with single‐base resolution. By using an electronic circuit based on point‐decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal‐to‐noise ratio and bandwidth. These measurements reveal two‐level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base‐by‐base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base‐pair level. This measurement capability promises a label‐free single‐molecule approach to probe biomolecular interactions with fast dynamics.     

Square Wave Stripping Voltammetry of Unlabeled Single‐ and Double‐Stranded DNAs

We show that, in difference to previously applied electrochemical methods working with stationary electrodes, square wave voltammetry produces well‐developed peaks II_SW (specific for dsDNA) and III_SW yielded by ssDNA at hanging mercury drop electrode (HMDE) and solid amalgam electrodes (SAEs). Using these peaks various kinds of DNA structural transitions can be studied, including unwinding of dsDNA at negatively charged electrode surfaces. The sensitivity of the DNA analysis is much better than that obtained with guanine oxidation signals at carbon electrodes. Both carbon electrodes and SAEs appear attractive as transducers in label‐free RNA and DNA sensors.     

DNA Origami Directed Assembly of Gold Bowtie Nanoantennas for Single‐Molecule Surface‐Enhanced Raman Scattering

Metallic bowtie nanoarchitectures can produce dramatic electric field enhancement, which is advantageous in single‐molecule analysis and optical information processing. Plasmonic bowtie nanostructures were successfully constructed using a DNA origami‐based bottom‐up assembly strategy, which enables precise control over the geometrical configuration of the bowtie with an approximate 5 nm gap. A single Raman probe was accurately positioned at the gap of the bowtie. Single‐molecule surface‐enhanced Raman scattering (SM‐SERS) of individual nanostructures, including ones containing an alkyne group, was observed. The design achieved repeatable local field enhancement of several orders of magnitude. This method opens the door on a novel strategy for the fabrication of metal bowtie structures and SM‐SERS, which can be utilized in the design of highly‐sensitive photonic devices.     

High‐Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This “liquid biopsy” approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild‐type sequences. This review discusses high‐performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing‐ and amplification‐based methods to next‐generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis‐based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.     

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.     

Nanopore‐Based Confined Spaces for Single‐Molecular Analysis

The field of nanopore sensing at the single‐molecular level is in a “boom” period. Such nanopores, which are either composed of biological materials or are fabricated from solid‐state substrates, offer a unique confined space that is compatible with the single‐molecular scale. Under the influence of an electrical field, such single‐biomolecular interfaces can read single‐molecular information and, if appropriately fine‐tuned, each molecule plays its individual ionic rhythm to compose a “molecular symphony”. Over the past few decades, many research groups have worked on nanopore‐based single‐molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore‐based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.     

Label‐Free Detection of Nanomolar Unmodified Single‐ and Double‐Stranded DNA by Using Surface‐Enhanced Raman Spectroscopy on Ag and Au Colloids

Unlabelled single‐ and double‐stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations ≥10^?9 M by surface‐enhanced Raman spectroscopy. Under appropriate conditions the sequences spontaneously adsorbed to the surface of both Ag and Au colloids through their nucleobases; this allowed highly reproducible spectra with good signal‐to‐noise ratios to be recorded on completely unmodified samples. This eliminated the need to promote absorption by introducing external linkers, such as thiols. The spectra of model ssDNA sequences contained bands of all the bases present and showed systematic changes when the overall base composition was altered. Initial tests also showed that small but reproducible changes could be detected between oligonucleotides with the same bases arranged in a different order. The spectra of five ssDNA sequences that correspond to different strains of the Escherichia coli bacterium were found to be sufficiently composition‐dependent so that they could be differentiated without the need for any advanced multivariate data analysis techniques.     

Voltammetric Studies on the Recognition of a Copper Complex to Single‐ and Double‐Stranded DNA and Its Application in Gene Biosensor

A mixed‐ligands copper complex [Cu(phendione)(DAP)]SO₄ (phendione=1,10‐phenanthroline‐5,6‐dione, DAP=2,3‐diaminophenazine) was synthesized. Cyclic voltammetry showed that the complex underwent an obvious decrease of redox peak currents and positive shift of formal potential after interaction with double‐stranded DNA (dsDNA), suggesting that the copper complex behaved as a typical metallointercalator for dsDNA, The recognition properties of the copper complex to single‐stranded DNA (ssDNA) and dsDNA were assessed using surface‐based electrochemical methods and the results suggested that the complex had obviously different redox signals at ssDNA and dsDNA modified electrodes. The copper complex was further used as an electroactive indicator for the detection of cauliflower mosaic virus (CaMV) 35S promoter gene.     

Single‐Molecule Nanocatalysis Shows In Situ Deactivation of Pt/C Electrocatalysts during the Hydrogen‐Oxidation Reaction

By coupling a Pt‐catalyzed fluorogenic reaction with the Pt‐electrocatalyzed hydrogen‐oxidation reaction (HOR), we combine single‐molecule fluorescence microscopy with traditional electrochemical methods to study the real‐time deactivation kinetics of a Pt/C electrocatalyst at single‐particle level during electrocatalytic hydrogen‐oxidation reaction. The decay of the catalytic performance of Pt/C could be mainly attributed to the electrocatalysis‐induced etching or dissolution of Pt nanoparticles. Spontaneous regeneration of activity and incubation period of the Pt electrocatalyst were also observed at single‐particle level. All these new insights are practically useful for the understanding and rational design of highly efficient electrocatalysts for application in fuel cells.