DNA分子力学性质的测量

利用单分子实验技术测量了DNA分子的力学性质.通过生化手段将单根DNA分子连在顺磁小球与玻璃侧壁之间,利用磁铁对顺磁球施加力进而拉伸DNA.图像分析得到小球运动的轨迹以及DNA的长度,利用均分定理可以求得施加的外力.测量发现在外力作用下DNA分子的力学反应与高分子物理学的蠕虫状链模型符合良好.     

用液流操纵单个DNA分子形成纳米悬链线图形

首先用液流拉伸单分子DNA,使其吸附在修饰过的云母基片上.然后让二次液流沿着垂直于已拉伸的DNA的方向流过云母片,用原子力显微镜(AFM)观测,可见DNA单分子片段在基片上形成了一些纳米尺度的悬链线.提出一种“S悬桥”模型能定量地解释这一现象.该研究工作揭示,在DNA的单分子操作中,经典的弹性力学理论足以描述和控制DNA分子二维图形的形成 关键词： DNA 单分子DNA操纵 原子力显微镜(AFM) 纳米悬链线     

用单分子磁镊研究顺铂导致的DNA凝聚

本文报道了用单分子磁镊研究抗癌药顺铂导致的DNA凝聚过程.结果表明,当拉力比较小时,DNA凝聚的长度-时间曲线是连续缩短和阶跃缩短并存的复杂曲线.而当拉力较大但又不足以阻止DNA的凝聚时,凝聚曲线为连续缩短的双曲线.增加顺铂浓度只会增大凝聚速度而不会改变反应曲线的形状.实验结果与下列成环凝聚模型一致：在水溶液中顺铂能够与DNA形成双臂加合物,也能形成单臂加合物.当顺铂使DNA长链上相距较远的碱基间发生远程交联时,形成小环,导致DNA凝聚.小环间的进一步交联会引起DNA的完全凝聚.DNA凝聚产物十分稳定. 关键词： 顺铂 DNA凝聚 单分子操纵 抗癌药     

单链DNA在受限环境中伸展的Monte Carlo模拟

将MonteCarlo方法和键长涨落算法相结合,模拟了受限于两平行平面间的单链DNA分子在外力作用下的伸展以及撤除外力以后弛豫的动力学过程,研究了受限程度对DNA分子的伸展长度及弛豫过程的影响.结果表明,随着受限程度的增加,DNA分子链的构象更加伸展,这主要是由于随着平面间距的减少,DNA分子不同链段之间流体力学相互作用将会被平面屏蔽所致,受限程度不同时DNA分子的弛豫过程进一步证实了这一点.DNA分子的伸展长度(即末端距)随着流速的变化关系与文献给出的实验结果及其对此所做的理论分析是基本一致的.     

拉直的单个DNA分子的全内反射荧光实时成像研究

全内反射荧光(TIRF)成像技术利用穿透深度仅200 nm左右的隐失波来激发诱导荧光,探测灵敏度和图像信噪比大大提高,成为单分子研究的有力工具。分子梳技术利用DNA末端与固体表面的结合力和周围流体流动产生的侧向力将DNA分子拉伸并平铺在表面上。结合这两种技术,对分子梳拉直的单个DNA分子进行了清晰的实时荧光成像,发现TIRF成像条件下DNA分子与荧光探针YOYO-1组成的复合体可自然避免发生光敏断裂现象;实时监测了单个DNA-YOYO-1复合体的光漂白过程,通过对激发光照射时间与探测器曝光时间进行同步控制,可大幅降低光漂白程度,为拉直的单个DNA分子的长时间实时观察和成像研究优化了实验条件,为实时、可视化地研究其与蛋白质相互作用的动力学过程奠定了基础。     

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

通过建立DNA高分子的粗粒化模型,采用分子动力学方法模拟其穿孔行为,研究了不同的孔内非均匀外力对DNA高分子穿孔的影响.外力及高分子链内部势能在分子水平下对单体的综合作用很复杂,某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况.研究还发现,穿孔行为是否成功与孔口力的大小有关,在成功穿孔的情况下,非均匀外力相比于恒力情况穿孔时间至少减少了1/2.这些结果对理解DNA复杂的穿孔机理提供了新的视角.     

单分子技术研究T7解旋酶的解旋与换链

单分子荧光共振能量转移(smFRET)和磁镊(MT)技术目前广泛应用于研究分子马达.相较于常规技术,其具有高精度及动态观测的优点.本文研究对象为T7解旋酶,是六聚体解旋酶的典型代表.研究表明,这种解旋酶主要消耗脱氧胸苷三磷酸(dTTP)提供能量,且仅能沿着5′-3′单向进行行走和解旋工作.目前对于六聚体解旋酶的解旋和换链机制的认知仍然存在着诸多问题,因此本文主要以此作为切入点开展研究.首先通过运用smFRET技术研究T7解旋酶在不同DNA底物上的解旋现象,发现其需要3′-尾链参与到解旋工作中,但其为单链或双链结构并无明显区别;通过改变脱氧核糖核酸(DNA)序列中的GC含量,发现T7解旋酶随着序列中GC含量的升高会更容易在解旋过程中发生回退现象,导致解旋长度明显缩短;通过进一步分析发生回退先的实验数据,发现T7解旋酶除了可以瞬时回退到叉形DNA岔口或脱落外,还可以缓慢回退到叉形DNA岔口;运用MT技术研究该解旋酶,同样发现这种缓慢回退现象的存在.根据T7解旋酶解旋DNA遵循的单向性和极性,其只能沿着5′到3′方向进行行走和解旋.因此,本文推测这种缓慢回退的现象可能是解旋酶从5′-链转移至3′-链上,即发生换链过程;最后,本文提出了T7解旋酶在解旋过程中进行换链的模型,将有助于进一步理解环状六聚体解旋酶行使其功能的分子机制.     

一种改进型单分子操纵装置及其应用

改进了单分子横向磁镊装置,可以直接用于观察单个DNA分子的伸长和扭转并随时更换样品池内的溶液,还可以同时操纵多个DNA分子,大大提高实验效率.此方法可以提供01到40pN范围的拉力,足以满足大部分单分子DNA实验的要求.用该装置实时观测到了DNA分子在拉力作用下的伸长以及在旋转磁场作用下的扭转,并成功地观察到了分子马达拉动DNA的动力学过程,从而验证了该装置的实用性. 关键词： 横向磁镊 单分子操纵 DNA拉伸 DNA扭转     

DNA分子链电子结构特性研究

在单电子紧束缚近似下，建立了一维无序二元DNA分子链模型，计算了链长为2×10⁴个碱基对的DNA分子链的电子态密度、局域化特性，并探讨了碱基对的不同组分、格点能量无序度对电子局域态的影响.结果表明：由于DNA分子链中格点能量无序及碱基对的不同组分的存在，其电子波函数呈现出局域化的特性，而局域长度作为衡量电子局域化程度的一个尺度，受碱基对的组分及格点能量无序度的影响. 关键词： DNA分子链 电子结构 电子局域态 局域长度     

碱基序列对DNA分子电子结构的影响

将DNA分子看成一维二元随机序列，利用负本征值理论计算其态密度，针对碱基对分布和相对含量等参量，讨论了DNA分子的电子结构.结果表明碱基对分布和相对含量都对电子能态结构影响较大，说明碱基序列对DNA分子的电子结构影响很大. 关键词： DNA分子 电子态密度 碱基对     

外力诱导吸附高分子单链的拉伸分子动力学研究

采用拉伸分子动力学方法研究聚乙烯单链在真空中从一个强吸附表面被拉伸的动力学过程. 当聚乙烯单链从中间1/3处被拉伸时,通过理想弹簧可测量其平均力〈f〉,发现在拉力与拉伸距离的曲线上出现了两个平台,这与实验结果非常一致,同时研究了在这个过程中链的形状变化情况,发现形状变化经历了四个阶段. 当聚乙烯单链的一端与吸附表面成一定倾斜角拉伸时,发现通过理想弹簧测量到的平均吸附力〈f〉与倾斜角θ在θ>20°的范围里总保持线性关系,并且其斜率随着拉伸速度的增加而增 关键词： 拉伸分子动力学 聚乙烯链 吸附现象     

Transport properties of a ladder with two random dimer chains

We investigate the transport properties of a ladder with two random dimer (RD) chains. It is found that there are two extended states in the ladder with identical RD chains and a critical state regarded as an extended state in the ladder with pairing RD chains. Such a critical state is caused by the chiral symmetry. The ladder with identical RD chains can be decoupled into two isolated RD chains and the ladder with pairing RD chains can not. The analytic expressions of the extended states are presented for the ladder with identical RD chains.     

Quantum Monte Carlo study of hard-core bosons in Creutz ladder with zero flux

The quantum phase of hard-core bosons in Creutz ladder with zero flux is studied.For a specific regime of the parameters(t_x=t_p,t_y0),the exact ground-state is found analytically,which is a dimerized insulator with one electron bound in each rung of the ladder.For the case t_x,t_y,t_p0,the system is exactly studied using quantum Monte Carlo(QMC)method without a sign problem.It is found that the system is a Mott insulator for small t_p and a quantum phase transition to a superfluid phase is driven by increasing t_p.The critical t~c _pis determined precisely by a scaling analysis.Since it is possible that the Creutz ladder is realized experimentally,the theoretical results are interesting to the cold-atom experiments.     

Measurement of Binding Force between Microtubule-Associated Protein and Microtubule

Microtubule-associated proteins （MAPs） are important proteins in cells. They can regulate the organization, dynamics and function of microtubules. We measure the binding force between microtubule and a new plant MAP, i.e. AtMAP65-1, by dual-optical tweezers. The force is obtained to be 14.6 ± 3.5 pN from the data statistics and analysis. This force measurement is helpful to understand the function and mechanism of MAPs from the mechanical point of view and lays the groundwork for future measurements of the mechanical properties of other biological macro-molecules.     

快速简便的杂交检测DNA

Southern杂交作为黄金标准,已广泛运用于DNA的检测上。但是,经典的southern杂交和近年来一些DNA检测方法存在放射性污染,操作繁琐,耗时,对实验仪器设备要求高等问题。本文利用异硫氰酸荧光素(FITC)标记的dUTP合成DNA探针建立了快速检测DNA的液相杂交方法。该方法包括探针制备、液相杂交、电泳分离和信号检测四个步骤,并在此基础上对FITC-双链和FITC-单链探针的杂交效果作了比较。结果显示,使用FITC标记的两种探针都能取得良好的实验结果,但单链探针较双链的检测灵敏度高;双链DNA探针可以检测出0.8 μg(3.64×10-13 mol)的质粒,而单链DNA探针可以检测出0.38 μg(1.82×10-13 mol)的质粒DNA,在检出效率上是前者的2.1倍。整个检测过程操作简便,可在3 h内完成,可较好地解决了其他DNA检测方法存在的费时费力的问题。     

AFM‐Based Single Molecule Force Spectroscopy of Polymer Chains: Theoretical Models and Applications

Abstract

In recent years, remarkable advances in research of the mechanical and structural properties of single polymer chains have been achieved thanks to atomic force microscope (AFM)‐based single molecule force spectroscopy (SMFS). This technique offers great possibilities to investigate the mechanical properties of a single polymer chain by static/dynamic force‐extension measurements at the mesoscale level. Data are analyzed with the help of appropriate theoretical models, such as statistical mechanics models for freely jointed chains (FJC) or worm‐like chains (WLC), which can well describe the moderate entropy‐controlled stretch of most polymers, and with semiclassical models, which are being modified using quantum mechanics principles to account for entropic and enthalpic contributions to stretching in the high‐force Hookean regime. In this article we review the theoretical models of single chain stretching, the latest progress in force‐extension measurements by static and dynamic AFM modes for polymer chains dispersed in different solvents and subjected to a force that may induce their conformational transformations, as well as relevant applications.     

Inference of DNA sequences from mechanical unzipping: an ideal-case study

The performances of Bayesian inference to predict the sequence of DNA molecules from fixed-force unzipping experiments are investigated. We show that the probability of misprediction decreases exponentially with the amount of collected data. The decay rate is calculated as a function of biochemical parameters (binding free energies), the sequence content, the applied force, the elastic properties of a DNA single strand, and time resolution.     

Bubbles in DNA by random force

We model single strand binding (SSB) proteins as agents exerting randomly oriented force on the bonds in DNA unzipping. The fluctuating force is found to unzip the double stranded DNA (dsDNA) via opening of bubbles along the chain.     

Conformation and aggregation of poly-L-proline in solution

Although a large number of physical techniques have been successfully used to investigate many of the properties of poly-L-proline, the work reported here has used a combination of osmometry, light scattering, viscometry, and sedimentation studies to reveal a new aspect of this model biopolymer. Experiments were made both on solutions (propionic acid) of poly-L-proline Form I and Form II and on solutions (propionic acid with a threefold dilution of n-propanol) in which Form II was in the process of converting to Form I. The results indicate that an increase in the measured molecular weight accompanies known optical activity and intrinsic viscosity changes which occur as Form II becomes Form I. It appears that the molecular weight determined at infinite dilution for poly-L-proline I is approximately twice that found for poly-L-proline II, and evidence for concentration-promoted aggregation beyond the level of a dimer has been noted in these Form I solutions. Based on these facts and on the information obtained about the particle shapes, it is proposed that this association occurs by a side-to-side binding of two macro-molecules. Discussion is directed toward how these experimental findings can be incorporated into the established concept of the Form I conformation. Light, scattering experiments were also performed on solutions (propionic acid 3 M in LiBr) in which the high-salt, or collapsed, form of poly-L-proline had been generated from either Form II or Form I material. These results showed that the dissolved particles are composed of single chains and are significantly smaller in size than found in solutions of either form and it appears possible that in the collapsed form poly-L-proline might be represented by rodlike macromolecules possessing trans-peptide bonds and a conformation with a relatively small helical pitch.     

A steered molecular dynamics study on the elastic behaviour of knotted polymer chains

In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.