Towards Next Generation Protein Sequencing.

Understanding the structure and function of proteins is a critical objective in the life sciences. Protein sequencing, a central aspect of this endeavor, was first accomplished through Edman degradation in the 1950s. Since the late 20 century, mass spectrometry has emerged as a prominent method for protein sequencing.

Single-Molecule Exchange inside a Nanocage Provides Insights into the Origin of π-π Interactions.

The attractive interactions between aromatic rings, also known as π-π interactions, have been widely used for decades. However, the origin of π-π interactions remains controversial due to the difficulties in experimentally measuring the weak interactions between π-systems. Here, we construct an elaborate system to accurately compare the strength of the π-π interactions between phenylalanine derivatives via molecular exchange processes inside a protein nanopore.

Peptide sequencing based on host-guest interaction-assisted nanopore sensing.

Direct protein sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose an alternative method for peptide sequencing based on enzymatic cleavage and host-guest interaction-assisted nanopore sensing. We serendipitously discovered that the identity of any proteinogenic amino acid in a particular position of a phenylalanine-containing peptide could be determined via current blockage during translocation of the peptide through α-hemolysin nanopores in the presence of cucurbit[7]uril.

High-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes.

The hollow and tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for making nanopores. However, the heterogeneity of SWCNTs hinders the fabrication of robust and reproducible carbon-based nanopore sensors. Here we develop a modified density gradient ultracentrifugation approach to separate ultrashort (≈5-10 nm) SWCNTs with a narrow conductance range and construct high-resolution nanopore sensors with those tubes inserted in lipid bilayers.

Enhancement of Domain Wall Pinning in High-Temperature Resistant SmCo Type Magnets by Addition of YO.

In this study, the effects of YO addition on the magnetic properties, microstructure and magnetization reversal behavior of Sm(CoFeCuZr) magnet were investigated. By addition of YO, the coercivity was increased from 21.34 kOe to 27.

Construction of a pH-Mediated Single-Molecule Switch with a Nanopore-DNA Complex.

A molecular switch is one of the simplest examples of artificial molecular machines. Even so, the development of molecular switches is still at its very early stage. Currently, building single-molecule switches mostly rely on the molecular junction technique, but many of their performance characteristics are device-dependent.

A Nanopore Sensing Assay Resolves Cascade Reactions in a Multienzyme System.

Enzymatic cascade reactions are widely used to synthesize complex molecules from simple precursors. The major underlying mechanism of cascade reactions is substrate channelling, where intermediates of different enzymatic steps are not in equilibrium with the bulk solution. Here, we report a nanopore sensing assay that allows accurate quantification of all the reaction intermediates and the product of an artificial three-enzyme system.

High-fidelity biosensing of dNTPs and nucleic acids by controllable subnanometer channel PaMscS.

Current tools for dNTP analysis mainly rely on expensive fluorescent labeling, mass spectrometry or electrochemistry. Single-molecule assay by protein nanopores with an internal diameter of ca. 1-3.

Correction: A bifunctional DNA probe for sensing pH and microRNA using a nanopore.

Correction for 'A bifunctional DNA probe for sensing pH and microRNA using a nanopore' by Yun Zhang , , 2020, , 7025-7029, DOI: 10.1039/D0AN01208D.

A bifunctional DNA probe for sensing pH and microRNA using a nanopore.

We have developed a bifunctional probe based on triplex molecular beacons for the measurement of environmental pH and quantification of microRNA-10b using a nanopore. The probe responds sharply to solution pH changes in the range of 6.0-7.

Simultaneous Sensing of Multiple Cancer Biomarkers by a Single DNA Nanoprobe in a Nanopore.

Both vascular endothelial growth factor (VEGF) and matrix metallopeptidase-9 (MMP-9) are key biomarkers in tumor angiogenesis. Determination of the overexpression of the two biomarkers would provide valuable information on the progression of tumor growth and metastasis, but their simultaneous quantification by a single probe is unprecedented. Here, we develop a triplex DNA-based nanoprobe for simultaneously quantifying VEGF and MMP-9 using an α-hemolysin nanopore.

Probing Conformational Polymorphism of DNA Assemblies with Nanopores.

Single-stranded DNA (ssDNA) can be designed to assemble into duplexes and other high-order structures through Watson-Crick hydrogen bonds. Incorporation of unnatural nucleobases or binding with small molecules can also introduce new interactions that give rise to novel DNA assemblies. However, the methods for determining the conformational properties of DNA assemblies are still very limited.

Measuring Enzymatic Activities with Nanopores.

Nanopores have become powerful and versatile tools for measuring single molecules since their emergence in the mid-1990s. They can be used to sense a wide variety of analytes including metal ions, small organic molecules, DNA/RNA, proteins, etc. to monitor chemical reactions, and to sequence DNA.

A Dual-Response DNA Probe for Simultaneously Monitoring Enzymatic Activity and Environmental pH Using a Nanopore.

Both protease overexpression and local pH changes are key signatures of cancer. However, the sensitive detection of protease activities and the accurate measurement of pH in a tumor environment remain challenging. Here, we develop a dual-response DNA probe that can simultaneously monitor protease activities and measure the local pH by translocation through α-hemolysin (αHL).

Measuring Binding Constants of Cucurbituril-Based Host-Guest Interactions at the Single-Molecule Level with Nanopores.

Cucurbiturils are one type of widely used macrocyclic host compound in supramolecular chemistry. Their peculiar properties have led to applications in a wide variety of research areas such as fluorescence spectroscopy, drug delivery, catalysis, and nanotechnology. However, the solubilities of cucurbiturils are rather poor in water and many organic solvents, which may cause accuracy problems when measuring binding constants with traditional methods.

Investigating the effect of mono- and multivalent counterions on the conformation of poly(styrenesulfonic acid) by nanopores.

Polyelectrolytes are useful materials that have many technical, medical, physiological and biological applications. The properties of polyelectrolytes are determined not only by their chemical composition but also by their conformational states. However, the conformations of polyelectrolytes in solution are very difficult to characterize.

Enhanced Sensitivity in Nanopore Sensing of Cancer Biomarkers in Human Blood via Click Chemistry.

Cancer biomarkers are expected to be indicative of the occurrence of certain cancer diseases before the tumors form and metastasize. However, many biomarkers can only be acquired in extremely low concentrations, which are often beyond the limit of detection (LOD) of current instruments and technologies. A practical strategy for nanopore sensing of cancer biomarkers in raw human blood down to the femtomolar level is developed here.

Multiplexed discrimination of microRNA single nucleotide variants through triplex molecular beacon sensors.

Herein, we develop a new nanopore sensing strategy for the selective detection of microRNAs and single nucleotide variants (SNVs) based on triplex molecular beacon sensors. This sensing system shows very high specificity in discriminating microRNA SNVs and can be applied for the simultaneous detection of several microRNAs of the same family in a mixture.

Ultrasensitive detection of thiophenol based on a water-soluble pyrenyl probe.

We report a simple pyrene-based fluorescent probe, sodium 8-(2,4-dinitrophenoxy)pyrene-1,3,6-trisulfonate (HPTS-DNP), for the ultrasensitive and visual detection of thiophenol in 100% aqueous media. The sensing mechanism of this method is based on nucleophilic aromatic substitution on HPTS-DNP caused by thiophenol to afford a highly fluorescent product, 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS). The extremely low fluorescence background of HPTS-DNP and high quantum yield of HPTS ensure the superior sensing performance toward thiophenol, including rapid responses, off-on detection mode and excellent sensitivity.

Rapid and selective DNA-based detection of melamine using α-hemolysin nanopores.

We have developed a rapid and selective approach for the detection of melamine based on simple DNA probes and α-hemolysin nanopores. The limit of detection can be as low as 10 pM.

Simultaneous Quantification of Multiple Cancer Biomarkers in Blood Samples through DNA-Assisted Nanopore Sensing.

Protein biomarkers in blood have been widely used in the early diagnosis of disease. However, simultaneous detection of many biomarkers in a single sample remains challenging. Herein, we show that the combination of a sandwich assay and DNA-assisted nanopore sensing could unambiguously identify and quantify several antigens in a mixture.

Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing.

A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin.