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     

Supercoiling induces denaturation bubbles in circular DNA

We present a theoretical framework for the thermodynamic properties of supercoiling-induced denaturation bubbles in circular double-stranded DNA molecules. We explore how DNA supercoiling, ambient salt concentration, and sequence heterogeneity impact on the bubble occurrence. An analytical derivation of the probability distribution to find multiple bubbles is derived and the relevance for supercoiled DNA discussed. We show that in?vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs. Single DNA plasmid imaging experiments clearly demonstrate the existence of bubbles in free solution.     

Fluctuations in order–disorder transitions in the DNA–ligand complexes with various binding mechanisms

The melting of the DNA–ligand complex is considered theoretically for the ligands binding with the DNA by two mechanisms. The obtained results describe the experimentally observed behavior of such quantities as the denaturation degree and the correlation length depending on the concentration of ligands. It is shown that the heat and cold denaturations of the DNA–ligand complexes exhibit the same cooperativity, as the heat denaturation of the pure DNA. At the same time, the temperature range of the cold denaturation is essentially narrower than the interval for the heat denaturation of the pure DNA and the DNA–ligand complexes.     

DNA melting induced by alcohols: Role of the solvent properties

Summary The isothermal denaturation of calf thymus DNA, induced by the presence of some monohydric alcohols in the solution, was investigated. Measurements were performed at a temperature (67.2°C) at which the denaturation, in the absence of alcohols, is about 20% and melting profiles at varying temperatures were also recorded. Results show that with increasing alcohol concentration and alkyl group size DNA denaturation first reaches a maximum and then falls back. This behaviour, ascribed to ?unusual? water properties as inferred also from compressibility measurements, indicates that hydrophobic and electrostatic effects are connected in a complex way. Partially supported by Consiglio Nazionale delle Ricerche, Italy.     

核黄素与鲱鱼精DNA相互作用的荧光光谱

荧光光谱法研究了核黄素(RF)与鲱鱼精DNA的相互作用.考查了离子强度、温度及磷酸盐对RF-DNA体系的影响.结果表明,DNA的存在使得RF的荧光光谱发生了规律性猝灭,其猝灭机制为静态猝灭;运用Stern-Volmer方程对实验数据进行了分析,得到了猝灭常数为2.82×103L·mol-1、结合位点数为1.17.核黄素...     

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.     

盐离子对DNA延伸力的影响

在Ahsan等给出的描述DNA分子弹性的两状态虫链模型的基础上,考虑到盐离子浓度对静电自由能的影响,得到了延伸力随盐浓度的变化规律,结果表明:在低力和高力范围延伸力受盐浓度的影响较小,相变延伸范围随盐浓度的增加非线性增加,与实验测量一致.     

Phase diagram of mechanically stretched DNA: The salt effect

The cations, in the form of salt, present in a solution containing DNA play a crucial role in the opening of the two strands of DNA. We use a simple non-linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified to incorporate the solvent effect and the presence of these cations in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.     

光谱法研究普利沙星与小牛胸腺DNA的结合作用

利用紫外光谱,荧光光谱及流体动力学方法,研究了普利沙星与小牛胸腺DNA的作用机理。讨论了不同浓度普利沙星与DNA作用的紫外光谱,荧光光谱,磷酸盐效应以及离子强度对两者相互作用的影响,测量了DNA的热变性温度和粘度。从紫外光谱图上看出DNA发生了明显的减色效应, 说明普利沙星可能与DNA发生作用。普利沙星的荧光光谱发生了有规律的猝灭,最大发射峰发生红移, 猝灭常数为3.1×104 L·mol-1, 为静态猝灭,表明普利沙星与DNA结合生成了二元复合物。磷酸盐效应表明普利沙星与DNA的磷酸基团不发生静电作用。普利沙星引起了DNA的热变性温度略微升高(≤7℃)和DNA粘度略微下降, 表明普利沙星与DNA之间不存在插入作用, 只是在DNA的外部发生沟槽作用。     

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).     

Thermal denaturation of fluctuating DNA driven by bending entropy

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 fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-square-radius, are also explicitly calculated, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition.     

Small-angle neutron scattering study of structural evolution of different phases in protein solution

Small-angle neutron scattering (SANS) has been used to study the structural evolution of different phases in protein solution leading to crystallization, denaturation and gelation. The protein solution under crystallization mostly consists of monomers and dimers, and higher-mers are not observed as they are perhaps formed in very small numbers. The onset and the rate of crystallization strongly depend on the salt concentration. Protein denaturation on addition of surfactant occurs due to the formation of micelle-like clusters along the unfolded polypeptide chains of the protein. The structure of such protein-surfactant complex is found to be independent of the size of the micelles in their pure surfactant solutions. The structure of temperature-induced protein gels shows a fractal structure. Rheology of these gels shows a strong dependence on varying pH or protein concentration, whereas the structure of such gels is found to be similar.      

盐离子对双链DNA分子弹性影响的研究P

在DNA延伸过程中,考虑到氢键相互作用以及盐浓度(Na+)对氢键和堆积作用的影响,给出了修正的ZZO模型,得到了力-延伸曲线随盐浓度的变化规律.结果表明:随盐浓度的增加,延伸相变力非线性增加,并最终趋于稳定,理论计算结果与实验测量一致.     

荧光光谱法研究蛋白质构象的电磁-温度协同效应

长期以来电磁生物效应受到人们普遍关注，近年来从各个角度进行了相关研究。电磁－温度协同效应是当前的热点。本研究通过电磁场及温度协同对蛋白质影响的研究，发现蛋白质在电磁场作用下的不可逆变性，而且这种变性也遵循Arrhenius规律，并进一步得出电磁－温度协同作用的蛋白质变性模型。本文从分子反应动力学的角度解释了电磁－温度协同效应，并对非热效应作了一定的探讨。     

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.     

Phase behavior and selectivity of DNA-linked nanoparticle assemblies

We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies [J. Am. Chem. Soc. 125, 1643 (2003)]; Science 289, 1757 (2000)]]. The binding of DNA-coated nanoparticles by dissolved DNA linkers can be described by exploiting an analogy with quantum particles obeying fractional statistics. In accordance with experimental findings, we predict that the phase-separation temperature of the nanocolloids increases with the DNA coverage of the colloidal surface. Upon the addition of salt, the demixing temperature increases logarithmically with the salt concentration. Our analysis suggests an experimental strategy to map microscopic DNA sequences onto the macroscopic phase behavior of the DNA-nanoparticle solutions. Such an approach should enhance the efficiency of methods to detect (single) mutations in specific DNA sequences.     

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.     

Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations

Protein XPA plays critical roles in nucleotide excision repair pathway. Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site. Here, we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations. The results demonstrated strong salt concentration dependence of the diffusion mechanisms. At low salt concentrations, the one-dimensional diffusion with rotational coupling is the dominant mechanism. At high salt concentrations, the diffusion by three-dimensional mechanism becomes more probable. At wide range of salt concentrations, the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature. This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions. In addition, we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA, which increases the exposure extent of the sites for the binding of other repair proteins.     

氯盐溶液近红外光谱分析研究

氯盐近红外光谱分析在生物医学上有着十分重要的意义。在室温下对氯化钠,氯化钾,氯化钙水溶液的近红外光谱采集分析表明,氯盐溶液浓度的变化会影响水分子的氢键而使得水溶液的近红外光谱发生变化。通过选择合理波长区间以及温度变化影响为零的波长点(等吸光点),减小温度的干扰对溶液近红外光谱影响,采用偏最小二乘法建立了氯盐溶液的浓度模型用于预测氯盐的离子浓度。分析氯盐溶液中氯盐阳离子的离子半径大小、离子电荷数和离子在水中络合效应等因素对水的近红外光谱所造成的影响以及产生影响因素的原因。实验结果表明,温度和浓度都会影响溶液的近红外光谱,氯盐溶液浓度较低时,温度的影响占主导地位;氯盐浓度高时,浓度的影响占主导地位。氯盐在水溶液中形成络合物,并与氯盐阳离子共同作用对水的氢键产生影响,对于浓度相同种类不同的氯盐溶液, 形成的络合物和阳离子破坏效应对水的氢键的破坏作用为: CaCl₂>NaCl>KCl。最终建立的样品浓度模型校正集的决定系数(R2)=99.97%,交叉验证均方误差(RMSECV)=4.51,剩余预测偏差(RPD)=62.7,满足日常生化检测精度要求。     

Quantum perspective on the localized strand separation and cyclization of DNA double helix

We apply Heisenberg model to study local strand separation and cyclization of double-stranded DNA molecule. By mapping the conformational properties of DNA onto the Heisenberg spin system, we show that denaturation can be viewed as a quench-induced quantum phase transition (QPT) at a finite non-zero temperature. These phase transitions lead to the formation of kinks in Heisenberg model that, in turn, correspond to sharp bends in helical axes of double-stranded DNA molecule. In this scenario we study the cyclization of DNA fragments of short length. Our results are in agreement with the reported observation that there is 1 open bp per circle of about 70 bp. Also we have computed the probability of the formation of kinks in circles of various sizes and have observed that beyond 100 bp it decreases sharply which is in agreement with experimental result.