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°.     

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c = 4 nu-1/2 such that the transition is second order with c = 1.85 < 2 in d = 3. We show that a finite stretching force F destabilizes DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments.     

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.     

DNA与组蛋白相互作用的布朗动力学研究

在真核生物中,DNA按左手手征性的方式,缠绕在组蛋白八聚体的周围,形成稳定的核小体结构.文章作者运用布朗动力学,数值模拟了DNA与组蛋白相互作用最终形成核小体的动力学过程,揭示了DNA与组蛋白相互作用的详细图景,并提出了组蛋白八聚体旋转模型,以解释这一过程.文章作者还计算了组成核小体的DNA在受到拉伸力时,组蛋白被从核小体中剥离下来的动力学过程,得到了组装和剥离过程的详细图像,给出了与前人单分子实验一致的拉伸力与拉伸长度的关系曲线和拉伸台阶.此外,还通过建立的组蛋白手征性模型,模拟了核小体手征性的形成过程,发现DNA的缠绕方向强烈依赖于组蛋白的手征性,显示出环境温度对核小体手征性有重要影响.     

Direct observation of multiple pathways of single-stranded DNA stretching

We observed multiple pathways of stretching single-stranded polydeoxynucleotides, poly(dA). Poly(dA) has been shown to undergo unique transitions under mechanical force, and such transitions were attributed to the stacking characteristics of poly(dA). Using single-molecule manipulation studies, we found that poly(dA) has two stretching pathways at high forces. The previously observed pathway has a free energy that is less than what is expected of single-stranded DNA with a random sequence, indicating the existence of a novel conformation of poly(dA) at large extensions. We also observed stepwise transitions between the two pathways by pulling the molecule with constant force, and found that the transitions are cooperative. These results suggest that the unique mechanical property of poly(dA) may play an important role in biological processes such as gene expression.     

Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting

We propose a physics method to study the effect of laser field and mechanical force on the melting process of double-stranded deoxyribonucleic acid （DNA）. A two-dimensional lattice model is established for DNA molecules stuck on the surface, and the stretching energy of the hydrogen bond and stacking energy for each DNA molecule are calculated by using a nonlinear potential. A real-time algorithm is employed to deal with the dynamics process of DNA melting. Numerical results explain the experimental observations. The spatial distribution of the laser field determines the sequences of DNA melting. The simulation has shown the dependence of the final number of melted DNA on the laser field and mechanical force.     

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.     

Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

Stretching of semiflexible polymers with elastic bonds

A semiflexible harmonic chain model with extensible bonds is introduced and applied to the stretching of semiflexible polymers or filaments. The semiflexible harmonic chain model allows to study effects from bending rigidity, bond extension, discrete chain structure, and finite length of a semiflexible polymer in a unified manner. The interplay between bond extension and external force can be described by an effective inextensible chain with increased stretching force, which leads to apparently reduced persistence lengths in force-extension relations. We obtain force-extension relations for strong- and weak-stretching regimes which include the effects of extensible bonds, discrete chain structure, and finite polymer length. We discuss the associated characteristic force scales and calculate the crossover behaviour of the force-extension curves. Strong stretching is governed by the discrete chain structure and the bond extensibility. The linear response for weak stretching depends on the relative size of the contour length and the persistence length which affects the behaviour of very rigid filaments such as F-actin. The results for the force-extension relations are corroborated by transfer matrix and variational calculations.PACS: 87.15.-v Biomolecules: structure and physical properties - 87.15.Aa Theory and modeling; computer simulation - 87.15.La Mechanical properties     

Elasticity theory of a twisted stack of plates

We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a macroscopic elasticity theory of DNA to four. We derive an effective twist-stretch energy in terms of the macroscopic stretch along and relative excess twist about the DNA molecular axis. In addition to the bulk stretch and twist moduli found previously, we obtain a twist-stretch modulus with the following remarkable properties: 1) it vanishes when the radius of the helical curve following the geometric center of each plate is zero, 2) it vanishes with the elastic constant K₂₃ that couples compression normal to the plates to a shear strain, if the plates are perpendicular to the molecular axis, and 3) it is nonzero if the plates are tilted relative to the molecular axis. This implies that a laminated helical structure carved out of an isotropic elastic medium will not twist in response to a stretching force, but an isotropic material will twist if it is bent into the shape of a helix. Received: 4 July 1997 / Received in final form: 16 October 1997 / Accepted: 21 October 1997     

Extension of a DNA molecule by local heating with a laser

Thermal convection and thermophoresis induced by mum-scale local heating are shown to elongate a single DNA molecule. An infrared laser used as a point heat source is converged into a dispersion solution of DNA molecules, which is observed under a fluorescent microscope. The thermal convection around the laser focus manifests as extensional flow for the long DNA chain. A simulation of thermal convection that reproduces the experimental condition provides numerical support for the stretching caused by thermal convection. This DNA elongation technique is a novel method for manipulating the intact single DNA molecules, and it can be applied to a "lab on a chip".     

Interaction of Au nanowires with impurities

We report the results of our first-principles studies of the interaction between an infinite monoatomic gold nanowire and a carbon-monoxide molecule. We show that the gold monoatomic nanowire is capable of absorbing the CO molecule at the distances of about 1.8 ? and forms a bond with the carbon atom. Further, we find that dissociation of the CO molecule as the source of gold nanowire contamination with carbon, which is widely discussed in literature as the possible reason for the striking stability of gold nanowires under stretching, is thermodynamically unfavored.     

Relaxation dynamics of semiflexible polymers

We study the relaxation dynamics of a semiflexible chain by introducing a time-dependent tension. The chain has one of its ends attached to a large bead, and the other end is fixed. We focus on the initial relaxation of the chain that is initially strongly stretched. Using a tension that is self-consistently determined, we obtain the evolution of the end-to-end distance with no free parameters. Our results are in good agreement with single molecule experiments on double stranded DNA.     

Elastic properties of a single-stranded charged homopolymeric ribonucleotide

We have investigated the elastic properties of poly(U), homopolymeric single-stranded RNA molecules that lack any base pairing and stacking interactions and conform to a random-coil structure. Using single-molecule stretching experiments we show that the elastic properties are described by a wormlike chain model for polymer elasticity rather than by a freely jointed chain model as is commonly used for single-stranded DNA. At low [Na+], introduction of a scale-dependent persistence length is required to account for electrostatic contributions.     

CALCULATIONS OF STRETCHING VIBRATIONAL ENERGY LEVELS OF THE CH3I MOLECULE BY A NONLINEAR MODEL

A nonlinear model, i.e. the quantized discrete self-trapping equation, is applied to calculate the highly excited CH stretching vibrational energy levels of the CH₃I molecule in the liquid phase at the electronic ground state up to n=8. The obtained results agree well with the experimental data and with those obtained from local mode model calculations. We note that the dominant feature of the methyl CH stretching vibrational energy levels of the CH₃I molecule is a pattern of local mode pairs. When n≥7, all the vibrational energy of the CH₃ group can nearly be localized on a single CH bond.     

WF6分子伸缩振动能谱的非线性模型计算

利用一个四参数非线性模型对处于电子基态下的XY6型分子的X-Y键的伸缩振动进行了描述,并将其应用于计算WF6分子中W-F键的伸缩振动能级.计算中引入的模型Hamilton算符所包含的描述WF键非谐振动的参数λ和描述WF键之间的偶极-偶极相互作用参数ε1,ε2由实验值得出,波函数 |ψn〉按形式为|n,α〉=|n1〉|n22〉|n3〉|n4〉|n5〉|n6〉的基函数集展开,从而把复杂的Hamilton方程转化为简单的矩阵代数方程.结果显示该非线性模型能够较好地描述了WF6分子的振动(计算误差在0.6 cm-1之内),同时合理地预测了一些至今还未观测到的能级值.     

IR spectra of chloromethyl derivatives of dioxans and dioxolans

A cyclic structure is demonstrated for the chloroacetals produced from chloroacetaldehyde and polyhydric alcohols. The stretching frequency of the chloromethyl group is not affected by the dioxan and dioxolan rings, or by the number of chlorine atoms in the molecule.     

Vibrational spectroscopy of Cm-C/Cb-Cb stretching vibrations of copper tetramesityl porphyrin: An algebraic approach

Using Lie algebraic techniques and simpler expressions of the matrix elements of Majorana and Casimir operators given by us, we obtain an effective Hamiltonian operator which conveniently describes stretching vibrations of biomolecules. For a copper tetramesityl porphyrin molecule, the higher excited vibrational levels are calculated by applying the U(2) algebraic approach.     

CO在尖晶石结构CuCr2O4(111)表面上的吸附理论研究

采用密度泛函理论，研究了CO在具有尖晶石结构的过渡金属氧化物CuCr2O4(100)表面上的吸附. 几何构型优化结果表明，CO倾向于以碳端吸附在Cu原子上，吸附能达到133.2 kJ/mol. 吸附在五配位的Cr原子上也比较稳定，吸附能为57.5 kJ/mol. 吸附后，C-O键伸长，振动频率出现红移，表明分子被活化. 同时分析了吸附前后态密度的变化，探讨了CO与底物的成键机理.     

Three-wave interaction between interstrand modes of the DNA

We consider the regime in which the bands of the torsional acoustic (TA) and hydrogen-bond-stretch (HBS) modes of DNA interpenetrate each other. We propose a simple model accommodating the helix structure of DNA and, within its framework, find a three-wave interaction between the TA and HBS modes. The phenomenon could be useful for studying the action of microwave radiation on a DNA molecule. Thus, using Zhang’s mechanism of the interaction between the system of electric dipoles of a DNA molecule and microwave radiation, we show that the latter could bring about torsional vibrations that maintaining HBS vibrations. We show an estimate of the microwave power density necessary for generating the HBS mode, which significantly depends on the viscous properties of the ambient medium.