Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5' -5' ends. The defect-free duplex shows a plateau in the force-extension curve at 120pN in which large segments with inclined and paired bases (“S-DNA”) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching.     

Dynamics of force-induced DNA slippage

We study the base pairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied shear force f: reptationlike dynamics at f=f(c) with a rupture time tau scaling as N3 with its length N, drift-diffusion dynamics for f(c)相似文献   

Theoretical Study on Effects of Salt and Temperature on Denaturation Transition of Double-stranded DNA

We investigate the statistical mechanics properties of a nonlinear dynamics model of the denaturation of the DNA double-helix and study the effects of salt concentration and temperature on denaturation transition of DNA. The specific heat, entropy, and denaturation temperature of the system versus salt concentration are obtained. These results show that the denaturation of DNA not only depends on the temperature but also is influenced by the salt concentration in the solution of DNA, which are in agreement with experimental measurement.     

盐对DNA相变影响的非线性特性研究

在Prohofsky，Peyrard-Bishop等提出的描述DNA双螺旋分子结构模型以及实验测量的基础上 , 给出了与盐(指NaCl)浓度有关的哈密顿模型, 得到了非线性动力学方程及扭结孤波解.并 由此求出了DNA变性相变所需要的Peierls相变力. 进一步讨论了盐浓度对相界面和相变力的 影响, 得到的结果与实验测量一致. 关键词： DNA 盐浓度 相界面 相变力     

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, P approximately l(-c). If excluded volume effects are fully taken into account, c = 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.     

New results on the melting thermodynamics of a circular DNA chain

We investigate the impact of supercoil period and nonzero supercoil formation energy on the thermal denaturation of a circular DNA. Our analysis is based on a recently proposed generalization of the Poland-Scheraga model that allows the DNA melting to be studied for plasmids with circular topology, where denaturation is accompanied by formation of supercoils. We find that the previously obtained first-order melting transition persists under the generalization discussed. The dependence of the size of the order-parameter jump at the transition point and the associated melting temperature are obtained analytically.     

Why is the DNA denaturation transition first order?

We study a model for the denaturation transition of DNA in which the molecules are considered as being composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d = 2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.     

Ashkin-Teller Formalism for Elastic Response of DNA Molecule to External Force and Torque

We propose an Ashkin-Teller-like model for elastic response of DNA molecule to external force and torque. The base-stacking interaction is described in a simple and uniform way. We obtain the phase diagram of dsDNA, and in particular, the transition from 13 form to the S state induced by stretching and twisting. The elastic response of the ssDNA is presented also in a unified formalism. The close relation of dsDNA molecule structure with elastic response is shown clearly. The calculated folding angle of the dsDNA molecule is 59.2°.     

EuVO_4的制备与发光性能的研究

利用固相反应法制备了EuVO4样品,利用X射线衍射,傅里叶红外光谱,激发光谱与发射光谱等测试手段对其粉末的晶型、结构、发光性质进行了研究.XRD结果表明,随着反应温度的升高,V2O5和Eu2O3在600℃左右开始反应,700℃左右反应基本完成,生成物属四方晶系,与EuVO4标准图谱一致,说明固相反应主产物是EuVO4;红外光谱证明,V=O键的伸缩振动变弱,并向低波数移动,O-V-O的反对称伸缩振动明显增强;激发光谱的主要变化是Eu-O电荷迁移带随着反应温度的升高而消失,产生出强度很强的323 nm处的7F0-5H3跃迁;发射光谱结果表明,随着V2O5和Eu2O3向EuVO4转变,最佳激发波长也由275 nm逐渐向323 nm移动,同时出现了467,592和616 nm处的发射峰.它们分别归属于VO3-4的蓝色发射、Eu3+的磁偶极跃迁和电偶极跃迁,实现了同一物质同时产生蓝色荧光和红色荧光,而且VO3-4-对Eu3+的发光有较好的促进作用.     

Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium

When a single DNA molecule is stretched beyond its normal contour length, a force-induced melting transition is observed. Ethidium binding increases the DNA contour length, decreases the elongation upon melting, and increases the DNA melting force in a manner that is consistent with the ethidium-induced changes in duplex DNA stability known from thermal melting studies. The DNA stretching curves map out a phase diagram and critical point in the force-extension-ethidium concentration space. Intercalation occurs between alternate base pairs at low forces and between every base pair at high forces.     

Direct observation of large temperature fluctuations during DNA thermal denaturation

In this Letter, we report direct measurement of large low frequency temperature fluctuations in double stranded DNA when it undergoes a denaturation transition. The fluctuation, which occurs only in the temperature range where the denaturation occurs, is several orders more than the expected equilibrium fluctuation. It is absent in single stranded DNA of the same sequence. The fluctuation at a given temperature also depends on the wait time and vanishes in a scale of a few hours. It is suggested that the large fluctuation occurs due to coexisting denaturated and closed base pairs that are in dynamic equilibrium due to the transition through a potential barrier in the scale of 25-30kBT0 (T0=300 K).     

Depinning with dynamic stress overshoots: mean field theory

An infinite-range model of an elastic manifold pulled through a random potential by a force F is analyzed focusing on inertial effects. When the inertial parameter M is small, there is a continuous depinning transition from a small- F static phase to a large- F moving phase. When M is increased to M(c), a novel tricritical point occurs. For M>M(c), the depinning transition becomes discontinuous with hysteresis. Yet, the distribution of discrete "avalanche"-like events as the force is increased in the static phase for M>M(c) has an unusual mixture of first-order-like and critical features. The results may be relevant for the onset of crack propagation and for dynamics of geological faults.     

Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.     

Bell's expression and the generalized Garg form for forced dissociation of a biomolecular complex

The dissociation of a biomolecular complex under the action of constant force, constant loading rate, and periodic force is studied theoretically. We show that the celebrated Bell expression provides a good approximation for the bond dissociation rate when F/F(c)<1, where F(c) is the maxima slope of the binding potential along the reaction coordinate. When 1-F/F(c) <1 the dissociation rate is better described by a generalized Garg form in which the potential derivative is expanded near F(c). We also show that a constant-force experiment is suitable for extracting the activation energy of the bond, a constant loading experiment is suitable to extract F(c), while time-periodic force can be applied to extract both bond dissociation rates at zero force and F(c).     

Nonequilibrium phase transitions associated with DNA replication

Thermodynamics governing the synthesis of DNA and RNA strands under a template is considered analytically and applied to the population dynamics of competing replicators. We find a nonequilibrium phase transition for high values of polymerase fidelity in a single replicator, where the two phases correspond to stationary states with higher elongation velocity and lower error rate than the other. At the critical point, the susceptibility linking velocity to thermodynamic force diverges. The overall behavior closely resembles the liquid-vapor phase transition in equilibrium. For a population of self-replicating macromolecules, Eigen's error catastrophe transition precedes this thermodynamic phase transition during starvation. For a given thermodynamic force, the fitness of replicators increases with increasing polymerase fidelity above a threshold.     

Physical Approaches to the Study of DNA

New micromanipulation techniques now enable physicists and biologists to study the behavior of single biomolecules such as DNA. In particular, it is possible to measure the elastic response of individual DNA molecules to changes in the double helix's supercoiling. The force versus extension diagram for torsionally relaxed DNA is continuous and allows one to evaluate the persistence length of the polymer. When the molecule is supercoiled, however, stretching leads to the buildup of torsional stress in the double helix's axis. When the twist energy thus generated increases beyond a critical value, the molecule is locally destabilized and changes conformation. This structural transition occurs at stretching forces which can be exerted in vivo by molecular motors and at degrees of supercoiling found in the cell, and may have implications for DNA structure and function within the nucleus.     

Evidence of mechanically activated processes in slow granular flows

We study how a shear band in a granular medium dramatically changes the mechanical behavior of the material further in the non sheared region. To this end, we carry out a microrheology experiment, where a constant force F is applied to a small rod immersed outside the shear band. In the absence of a shear band, a critical force F(c) is necessary to move the intruder. When a shear band exists, the intruder moves even for a force F less than the critical force F(c). We systematically study how the creep velocity V(creep) of the rod varies with F(c) - F and with the distance to the shear band, and show that the behavior can be described by an Eyring-like activated process.     

Torsion and entropy driven denaturation of DNA

A unified theory of the denaturation transition having torsion energy as the control parameter has been formulated here in the framework of the mapping of a DNA molecule onto a Heisenberg spin system. The torsion energy incorporates the torque, tension and temperature, the latter being associated with the twist angle. The denaturation transition can be mapped onto the quantum phase transition induced by a quench when the temperature effect is incorporated in the quench time and torsion takes the role of the external field. The denaturation transition occurs when the entanglement entropy of the spin system vanishes.     

Elasticity of strongly stretched ssDNA

We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discrete persistent chain, whose ground state is a zigzag rather than a straight line configuration. This mimics the underlying molecular architecture and helps to explain the experimentally observed saturation of the stretching curve at very high force.