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We describe here a method for detecting the translocation of individual DNA molecules through nanopores created in graphene membranes. The devices consist of 1–5-nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graph ...

We review an approach for the characterization of single-stranded DNA based on the statistical identification of single bases via transverse electronic transport while DNA translocates in a nanopore or nanochannel. We describe the theoretical methods used to demonstrate this met ...

We have developed a two-level computational model that enables us to calculate electrostatic fields created by a semiconductor membrane submerged in electrolytic solution and investigate the effects of these fields on the dynamics of a polymer translocating through a nanopore in the ...

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can af ...

Small holes in membranes or nanocapillaries can be employed to detect single molecules in solution. In fact, the resistive-pulse technique based on nanopores allows for determination of length, charge, and folding state of deoxyribonucleic acid (DNA). Here, we describe the experiment ...

The translocation of long-chain molecules, such as DNA or peptides, through membranes is an integral process for the function of living cells. During the translocation process, a number of interactions of electrostatic or hydrophobic nature govern the translocation velocity. Most of t ...

Nanopore-based DNA analysis is an extremely attractive area of research due to the simplicity of the method, and the ability to not only probe individual molecules, but also to detect very small amounts of genomic material. Here, we describe the materials and methods of a novel, nanopore-based, si ...

Solid-state nanopores are emerging as robust single molecule electronic measurement devices and as platforms for confining biomolecules for further analysis. The first silicon nitride nanopore to detect individual DNA molecules was fabricated using ion beam sculpting (IBS), a m ...

We present here an overview on unfolding of biomolecular structures as DNA double strands or protein folds. After some theoretical considerations giving orders of magnitude about transport timescales through pores, forces involved in unzipping processes … we present our experime ...

In the past decade, there have been extensive studies aimed at exploring the potential of protein nanopores to sequence single strands of DNA using resistive pulse sensing. The high speed of DNA electrophoretically driven through these pores (∼l μs/base) necessitates high bandwidth mea ...

The use of nanopores is a powerful new frontier in single-molecule sciences. Nanopores have been used effectively in exploring various biophysical features of small polypeptides and proteins, such as their folding state and structure, ligand interactions, and enzymatic activity. In ...

Single-nanometer-scale pores have demonstrated the capability for the detection, identification, and characterization of individual molecules. This measurement method could soon extend the existing commercial instrumentation or provide solutions to niche applica ...

Here we describe novel procedures for production of DNA-based nanowires. This include synthesis and characterization of the one-to-one double-helical complex of poly(dG)–poly(dC), triple-helical poly(dG)–poly(dG)–poly(dC) and G4-DNA, which is a quadruple-helical form of DNA. All ...

The purpose of this chapter is to provide detailed instructions for the preparation and atomic force microscopy (AFM) imaging of linear chains of quadruplex DNA (a.k.a. “G-wire DNA”). Successful self-assembly of long chain quadruplex DNA requires pure concentrated guanine-rich oligo ...

Guanine-rich DNA, which is widely distributed in the human genome, can fold into a supramolecular structure called the G-wire. The G-wire possesses promising characteristics as a functional element for various applications in vitro and in vivo. Here, we describe the preparative procedu ...

Helical handedness and the twist and tilt parameters of the base pairs in duplex DNA can be affected by base sequence variation and change in environmental conditions as occurs in the transformation between right-handed B-DNA and left-handed Z-DNA. For duplexes of DNA with oligonucleotide ...

A few cellular compartments maintain acidic environments in their interiors that are crucial for their proper function. Alteration in steady state organelle pH is closely linked to several diseases. Although a few probes exist to measure pH of cell compartments, each has several associa ...

We here present a protocol for the metallization of DNA scaffolds by palladium. The method is based on the initial slow precipitation of palladium oxide onto DNA strands. A reduction step follows to create conductive metallic nanowires. The slow oxide precipitation approach enables the fo ...

The site-specific insertion of organic and inorganic molecules into DNA nanostructures can provide unique structural and functional capabilities. We have demonstrated the inclusion of two types of molecules. The first is a diphenylphenanthroline (dpp, 1) molecule that is site spe ...

Programed molecular structures allow us to research and make use of physical, chemical, and biological effects at the nanoscale. They are an example of the “bottom-up” approach to nanotechnology, with structures forming through self-assembly. DNA is a particularly useful molecule for t ...