Benmei Wei

Regulation of DNA self-assembly and DNA hybridization by chiral molecules with corresponding biosensor applications.

Chirality is one of the fundamental biochemical properties in a living system, and a lot of biological and physiological processes are greatly influenced by the chirality of molecules. Inspired by this phenomenon, we study the covalent assembly of DNA on chiral molecule modified surfaces and further discuss the hybridization of DNA on chiral surfaces with nucleic acids. Take methylene blue (MB) modified DNA as a model molecule, we show that the peak current of the L-NIBC (NIBC, N-isobutyryl-L(D)-cysteine) modified gold surface (L-surface) is larger than the D-surface because of a stronger interaction between short-chain DNA and the L-surface; however, the D-surface has a higher hybridization efficiency than the L-surface. Moreover, we apply this result to actual application by choosing an electrochemical DNA (E-DNA) sensor as a potential platform. Furthermore, we further amplify the difference of hybridization efficiency using the supersandwich assay. More importantly, our findings are successfully employed to program the sensitivity and limit of detection.

Imparting biomolecules to a metal-organic framework material by controlled DNA tetrahedron encapsulation

Recently, the incorporation of biomolecules in Metal-organic frameworks (MOFs) attracts many attentions because of controlling the functions, properties and stability of trapped molecules. Although there are few reports on protein/MOFs composites and their applications, none of DNA/MOFs composite is reported, as far as we know. Here, we report a new composite material which is self-assembled from 3D DNA (guest) and pre-synthesized MOFs (host) by electrostatic interactions and hydrophilic interactions in a well-dispersed fashion. Its biophysical characterization is well analyzed by fluorescence spectroscopy, quartz crystal microbalance (QCM) and transmission electron microscopy (TEM). This new composite material keeps 3D DNA nanostructure more stable than only 3D DNA nanostructure in DI water at room temperature, and stores amounts of genetic information. It will make DNA as a guest for MOFs and MOFs become a new platform for the development of DNA nanotechnology.

Nanopore-Based DNA-Probe Sequence-Evolution Method Unveiling Characteristics of Protein–DNA Binding Phenomena in a Nanoscale Confined Space

Almost all of the important functions of DNA are realized by proteins which interact with specific DNA, which actually happens in a limited space. However, most of the studies about the protein-DNA binding are in an unconfined space. Here, we propose a new method, nanopore-based DNA-probe sequence-evolution (NDPSE), which includes up to 6 different DNA-probe systems successively designed in a nanoscale confined space which unveil the more realistic characteristics of protein-DNA binding phenomena. There are several features; for example, first, the edge-hindrance and core-hindrance contribute differently for the binding events, and second, there is an equilibrium between protein-DNA binding and DNA-DNA hybridization.

Stereochemistry-Guided DNA Probe for Single Nucleotide Polymorphisms Analysis

Single nucleotide polymorphisms (SNPs) are the most abundant genetic polymorphisms and are responsible for many genetic diseases and cancers. In general, SNPs detection is performed by a single probe system (SPS), in which a single probe specifically hybridizes to one target. However, with the use of this method it is hard to improve the hybridization specificity and single mismatched discrimination factors (DF). In addition, the multiprobe system (MPS) requires complex probe designs and introduces at least one auxiliary probe except for the probe complementary to the target, resulting in a complicated detection system. Faced with these difficulties, we perform the SNP detection using a d/l-tryptophan (Trp) guided DNA probe and regulate the DF of electrochemical DNA (E-DNA) sensors by molecular chirality. We show that the DF of the d-Trp incubated E-DNA sensor (d-sensor) is larger than that of the l-sensor. More importantly, we achieve the high specificity by coupling d-Trp and l-Trp incubated E-DNA sensors, and the median DF is 7.21. Furthermore, the specificity of SNP detection can be further improved by supersandwich assay, and the median DF is enlarged to 37.23, which is comparable to that obtained with a multiprobe detection system.

Integrated Solid-state Nanopore Electrochemistry Array for Sensitive, Specific, and Label-free Biodetection

Nanopore ionic current measurement is currently a prevailing readout and offers considerable opportunities for bioassays. Extending conventional electrochemistry to nanoscale space, albeit noteworthy, remains challenging. Here, we report a versatile electrochemistry array established on a nanofluidic platform by controllably depositing gold layers on the two outer sides of anodic aluminum oxide (AAO) nanopores, leading to form an electrochemical microdevice capable of performing amperometry in a label-free manner. Electroactive species ferricyanide ions passing through gold-decorated nanopores act as electrochemical indicator to generate electrolytic current signal. The electroactive species flux that dominates current signal response is closely related to the nanopore permeability. Such well-characteristic electrolytic current-species flux correlation lays a premise for quantitative electrochemical analysis. As a proof-of-concept demonstration, we preliminarily verify the analytical utility by detection of nucleic acid and protein at picomolar concentration levels. Universal surface modification and molecule assembly, specific target recognition and reliable signal output in nanopore enable direct electrochemical detection of biomolecules without the need of cumbersome probe labeling and signal amplification.

Correction to “Stereochemistry-Guided DNA Probe for Single Nucleotide Polymorphisms Analysis”

ACS Appl. Mater. Interfaces 2016, 8 (25), 15911−15916. DOI: 10.1021/acsami.6b03896 I the original paper, there was an error regarding the author affiliations. The affiliation of all the authors should have read as follows: Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China. The correct affiliation is shown above. Addition/Correction