Related papers: Melting a stretched DNA
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
We perform a single molecule force spectroscopy study to characterize the role of the size (molecular weight) and concentration of depleting agents on DNA condensation and on the stabilization of the double-helix structure, showing that…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
Motivated by experiments in which single DNA molecules are stretched and twisted we consider a perturbative approach around very high forces, where we determine the writhe distribution in a simple, analytically tractable model. Our results…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
We study the unzipping of double stranded DNA (dsDNA) by applying a pulling force at a fraction $s$ $(0 \le s \le 1)$ from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…