CAS OpenIR  > 中科院上海应用物理研究所2004-2010年
碱基水平DNA离散化模型的动力学研究
Alternative TitleThe Discrete Model of Single DNA Molecule at the Base Level
雷晓玲
Subtype博士
Thesis Advisor方海平
2005
Degree Grantor中国科学院上海应用物理研究所
Place of Conferral中国科学院上海应用物理研究所
Degree Discipline粒子物理与原子核物理
KeywordDna单分子 弹性力学 单分子操纵 离散化模型 碱基水平
Abstract许多重要的生物学功能如DNA的复制、基因的表达及DNA与蛋白质的相互作用等都涉及到DNA的弹性力学性质。在DNA的重组反应中,RecA蛋白会沿着DNA链模板聚合,在这个过程中DNA分子被拉伸到1.5倍其表观长度。而且理论推测DNA链中心轴线的热扰动对RecA蛋白的聚合有重要意义。在蛋白质对基因的调控过程中,特定蛋白质要捆绑到特定的DNA序列上去,它们之间的识别机制与DNA序列及DNA序列本身的力学性质有很大关系。长链DNA分子会缠绕到组蛋白上形成核小体,继而形成高度紧密的染色体,在这个过程中,会伴随DNA分子的拉伸和扭曲等变形。研究DNA的弹性力学性质不仅有助于研究其生物学功能,正如HonsFruenfelder等所说,还可以开拓物理学新的研究领域。近十年来,单分子操纵技术得到迅猛发展。随着单分子DNA拉伸、解链、扭曲以及DNA与蛋白质相互作用等实验的开展,单分子DNA独特的弹性力学性质逐步展现在人们的面前。这些实验所测量到的特殊DNA结构如S一DNA和P一DNA更激发起生物学家和物理学家的浓厚兴趣。但是,目前开展的实验大多数集中在DNA轴向弹性和扭曲的测量,得到的信息仍是DNA轴向成千上万个碱基对的平均值。最近上海应用物理研究所的周星飞等基于原子力显微镜测量了D琳雄和的压弹性卜给出DN人片段在几十个碱基对范围的压弹性信息,将DNA的弹性测量提高到一个新的高度。这项实验工作给理论工作提供了新的机遇,它要求理论工作能够理解更局域,包括碱基水平DNA分子的动力学机制。几十年以来已经发展了许多模型来研究DNA的弹性,'主要分为三类:统计模型、原子尺度的模型和碱基水平的模型。长度在微米级DNA片段的行为主要用统计模型来描述。如蠕虫链模型,主要描述DNA在小力区的行为。原子尺度的模型包括分子动力学方法,主要集中研究短片段DNA分子(几个到十几个纳米)在短期(几十个纳秒)的结构和动力学行为。碱基水平的模型是一种比较局域化的方法,主要用扭曲、滑移和倾斜等直观的参数来描述相邻碱基对之间的相对运动和趋向,能够提供特殊片段生物学功能的.机械解释。典型的工作如,德国马普大学的Mergell等人在2003年提出的一个碱基水平DNA的统一模型,模型中用G一B势描述相邻碱基对之间的堆积能。他们用该模型详细研究了DNA的驻留长度和拉弹性等性质,但是得到的B一到S一DNA的转变平台在14。皮牛左右,这与单分子操纵实验得到的数据有较大差距。而且该模型没有考虑氢键作用,无法模拟DNA的压弹性测量。近年来周海军、张扬和欧阳钟灿等提出的梯子模型,通过引入碱基堆积作用,可以统一的描述DNA在拉伸区域的弹性力学性质。尽管该模型是统计模型,但是其对碱基理解的思想仍适合推广到碱基水平系统的研究。在本文我们正是基于他们的模型,建立了一个新的碱基水平DNA的离散化弹性模型。在该模型中,我们进一步考虑了氢键作用和磷酸骨架的弹性性质,计算模拟的DN丸的拉伸和解链结果与实验工作符合很好。关于DNA的压弹性·在没有引入任何新的参数条件下,所得结果和实验工作吻合很好。本文首先详细介绍了目前常见的几种DNA单分子操纵仪器,如光镊、磁镊、玻璃微针和原子力显微镜等技术,分析其优缺点。在此基础之上分析目前开展的几种DNA操纵实验及其结果。然后介绍目前普遍应用到的几种理论模型,着重介绍周海军等提出的梯子模型,在此之上提出我们的碱基水平DNA离散化弹性模型。基于我们的碱基水平DNA离散化弹性模型,本文首先详细讨论了单个DNA分子轴向的拉弹性,并且按照从简单到复杂的原则,详细分析了不同碱基对体系的拉伸结果。研究结果表明DNA碱基对一个一个相继打开形成DNA拉伸曲线的B一到S一DNA转变平台。模拟结果还发现DNA分子大沟与小沟结构对DNA的拉弹性的影响很小,不同超螺旋程度下DNA的拉伸结果符合单分子操纵实验得到的变化趋势。我们的模型暴露了DNA拉伸过程的序列相关性问题(即DNA拉弹性实验所得到的poly(Gc)与年DNA的B一到S一DNA转变平台一致问题),对于该问题本论文从GC与AT含量及次近邻相互作用方面作了初步的探索。本文还研究了DNA片段的压弹性。为了确定氢键的参数设置,首先进行DNA片段的解链过程研究。研究结果表明氢键和碱基堆积作用主要影响DNA片段的解链过程,特别是氢键主要影响其力曲线的变化趋势。GC含量的实验模拟结果表明,GC含量与DNA片段解链力的大小成正比,这一点与实验结果相吻合。基于此,开展了DNA径向压弹性的模拟,模拟结果和实验结果非常吻合。研究结果表明DNA分子的径向压弹性必须考虑DNA双螺旋的大沟与小沟结构,并且在此基础之上原子力显微镜的针尖半径、序列等因素都影响DNA的压弹性。我们的离散化DNA弹性模型同时建立了统计模型和原子模型的桥梁。通过进行大规模计算,结果可以和统计模型进行比较。我们的模型可以通过大规模的原子尺度模拟加以对照。这项工作正在进行中。
Other AbstractThe elastic properties of single DNA molecules has been attracted great attention in the past fifteen years because of its great importance to numerous biological processes, such as DNA replication, gene expression, and site-specific interactions between DNA and proteins. With the development of single molecular manipulation technology, the elasticity of single DNA molecule has been extensively studied. The special elasticity property of DNA has been exposed with the stretching, unzipping, compressing and interaction with protein of DNA, especially the S-DNA and P-DNA transition inspire the interesting of biologist and physicist.Theoretical approaches have been widely used to exploit the molecular structures from the observed data of elasticity. Up to now, most of the theoretical models can be classified into three categories: statistical models, atomic-scale modelling and mesoscopic models. The elastic behaviors of a long DNA chain, with a typical length of several micrometers, are frequently described by statistical models. Two well-known statistical models are the freely jointed chain (FJC) and worm-like chain (WLC) models, which can describe the behavior of single DNA molecules stretched at low force. Atomic-scale modelling, including molecular dynamics simulations, in con-trast, focuses on the structural and dynamic behavior of very small segments of biomacromolecules in very short duration. Mesoscopic models, more local, describes the relative location and orientation of the neighboring base pairs in terms,of intuitive parameters such as twist, rise; slide, roll, etc.- It provides a mechanical interpretation of the biological function of particular sequences. Recently, Mergell et al. proposed a generic mesoscopic model at the base-pair level. Using the Gay-Berne potential to represent the stacking energy between the neighboring base pairs, they study the persistence length and the stretching property, but the B- to S-DNA transition occurs at approximately 140 pN that is not favor with the experimental data. Based on bending and base stacking interactions, Zhou et al. proposed a Ladder Model to provide a unified description in the stretching force regime (0 < F < 100 pN). The result shows that base-stacking interactions dominate the elasticity of DNA and, hence, are of vital biological significance. Based on the Ladder Model, we proposed a discrete elasticity model of DNA at the base level, and partly single molecular manipulation experiments have been detailed studied.In this thesis, firstly some single molecular manipulation devices were introduced, such as optical tweezers, magnetic tweezers, glass microneedles and atomic force microscopy, then some single DNA molecular manipulation experiments were further described. Secondly, we propose our discrete elasticity model of DNA at the base level based on the Ladder Model. Using our discrete model, we carefully investigate the stretching elasticity of DNA in the axis direction from easy to complex systems (according their base pairs number), which are four, thirty and seventy base-pair systems. It shows that the B- to S-DNA transition plateau was due to the base pairs unwound one by one. We also notice that the major and minor groove have little influence to the stretching elasticity of DNA, and the stretching force-extension relationship for different supercoiling degree agreed with the experimental data. The sequence-dependent question (that is the B- to S-DNA transition plateau is different for poly(GC) and poly (AT)) in the stretching process emerged during our simulation, and we simple discussed this question from the GC content and the hypo-neighbor interaction. But it is still an open question, and we will focus on it in the future.In addition to the stretching of DNA, the unzipping process is also discussed. It shows that the hydrogen bonding and the base stacking potential dominate the unzipping of DNA, especially the hydrogen bonding. The GC content simulation results show that the GC content is in direction proportion with the unzipping force that agrees with the experimental data. Last but not the least, in this thesis we try to simulate the compression elasticity of single DNA molecule in radial direction. The simulation result quite agrees with the experimental data. We notice that the major and minor groove must be considered in the compressing elasticity simulation. The compressing property of single DNA molecule strongly depends on the local structure of DNA, and the radius of AFM tip and different sequences have influence to the compressing elasticity of single DNA molecule.
Language中文
Document Type学位论文
Identifierhttp://ir.sinap.ac.cn/handle/331007/7416
Collection中科院上海应用物理研究所2004-2010年
Recommended Citation
GB/T 7714
雷晓玲. 碱基水平DNA离散化模型的动力学研究[D]. 中国科学院上海应用物理研究所. 中国科学院上海应用物理研究所,2005.
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