相关论文: Structural Rigidity of Paranemic (PX) and Juxtapos…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully…
The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…
The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…