Fast and low-noise tunnelling current measurements for single-molecule detection in an electrolyte solution using insulator-protected nanoelectrodes

Sub-5 nm nanogap electrodes towards single-molecular biosensing

Nanogap electrodes (NGEs) with sub-5 nm gap has been widely used in single-molecule sensing and sequencing, with the characteristics of label-free, high sensitivity, rapid detection and low-cost. However, the fabrication of sub-5 nm gap electrodes with high controllability and reproducibility still remains a great challenge that impedes the experimental research and the commercialization of the nanogap device. Here, we review the common currently used fabrication methods of nanogap electrodes, such as gap narrowing deposition, mechanical controllable break junctions and the fabrication methods combined with nanopore or nanochannel. We then highlight the typical applications of nanogap electrodes in biological/chemical sensing fields, including single molecule recognition, single molecule sequencing and chemical kinetics analysis. Finally, the challenges of nanogap electrodes in single molecule sensing/sequencing are outlined and the future directions for sensing perspectives are suggested.

Cataloguing the proteome: Current developments in single-molecule protein sequencing

The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.

Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement

Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC₃) and nitrogenized graphene (C₃N) sandwiched stripe (BC₃/C₃N/BC₃) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C₃N stripe than the BC₃ one, which leads to their capture, elongation, and confinement along the center C₃N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise.

The Characterization of Electronic Noise in the Charge Transport through Single-Molecule Junctions

With the goal of creating single-molecule devices and integrating them into circuits, the emergence of single-molecule electronics provides various techniques for the fabrication of single-molecule junctions and the investigation of charge transport through such junctions. Among the techniques for characterization of charge transport through molecular junctions, electronic noise characterization is an effective strategy with which issues from molecule-electrode interfaces, mechanisms of charge transport, and changes in junction configurations are studied. Electronic noise analysis in single-molecule junctions can be used to identify molecular conformations and even monitor reaction kinetics. This review summarizes the various types of electronic noise that have been characterized during single-molecule electrical detection, including the functions of random telegraph signal (RTS) noise, flicker noise, shot noise, and their corresponding applications, which provide some guidelines for the future application of these techniques to problems of charge transport through single-molecule junctions.

Planar graphene/h-BN/graphene heterostructures for protein stretching and confinement

Protein stretching and confinement in nanochannels is critical for advancing single-molecule detection techniques. For standard nanochannels integrated with nano-sensors, reducing their cross-section is beneficial for reading highly localized signals with minimal error, but results in increasing difficulty for the initial capture of any chain molecules due to the entropy barrier. Using molecular dynamics simulations, we show that spontaneous protein stretching can be realized by a two-dimensional (2D) heterostructure composed of a hexagonal boron nitride (h-BN) nanoribbon stitched with two graphene (GRA) sheets (i.e., a sandwiched GRA/BN/GRA structure). Due to fast protein diffusion on its flat surface and adsorption potential difference between two 2D materials, this planar nanochannel permits effective capture and elongation of three representative intrinsically disordered proteins including amyloid-β (1-42), polyglutamine (42) and α-synuclein (61-95). Moreover, we found that the extremely narrow h-BN stripe can provide stronger confinement for a longer polyglutamine chain after being stretched. Our approach has the potential to facilitate the bona fide readout of single-molecule protein sequencing techniques.

Sensitive and Direct DNA Mutation Detection by Surface-Enhanced Raman Spectroscopy Using Rational Designed and Tunable Plasmonic Nanostructures

Efficient DNA mutation detection methods are required for diagnosis, personalized therapy development, and prognosis assessment for diseases such as cancer. To address this issue, we proposed a straightforward approach by combining active plasmonic nanostructures, surface-enhanced Raman spectroscopy (SERS), and polymerase chain reaction (PCR) with a statistical tool to identify and classify BRAF wild type (WT) and V600E mutant genes. The nanostructures provide enhanced sensitivity, while PCR offers high specificity toward target DNA. A series of positively charged plasmonic nanostructures including gold/silver nanospheres, nanoshells, nanoflowers, and nanostars were synthesized with a one-pot strategy and characterized. By changing the shape of nanostructures, we are able to vary the surface plasmon resonance from 551 to 693 nm. The gold/silver nanostar showed the highest SERS activity, which was employed for DNA mutation detection. We reproducibly analyzed as few as 100 copies of target DNA sequences using gold/silver nanostars, thus demonstrating the high sensitivity of the direct SERS detection. By means of statistical analysis (principal component analysis-linear discriminant analysis), this method was successfully applied to differentiate the WT and V600E mutant both from whole genome DNA lysed from cell line and from cell-free DNA collected from cell culture media. We further proved that this assay is capable of specifically amplifying and accurately classifying a real plasma sample. Thus, this direct SERS strategy combined with the active plasmonic nanostructures has the potential for wide applications as an alternative tool for sensitively monitoring and evaluating important clinical nucleotide biomarkers.

Strategies for Development of a Next-Generation Protein Sequencing Platform

Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.

Paving the way to single-molecule protein sequencing

Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.

Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution

Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO₂-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.