相关论文: Protein-mediated Loops and Phase Transition in Non…

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between…

Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…

Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…

Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…

A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…

A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…

DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…

It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…

DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…

In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…

DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…

We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…

As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…