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.     

利用原子力显微镜研究在单分子水平上DNA与组蛋白的相互作用

核小体是DNA被压缩成染色质的第一级压缩结构. 为了更深刻描述DNA与组蛋白的相互作用,利用透析方法将DNA和组蛋白构建成核小体,并且应用原子力显微镜进行单分子水平上的观察. 实验结果表明利用透析方法得到了核小体的“串珠型排列”,并且对在两种不同的结合条件下DNA与组蛋白的相互作用进行了观察和比较.     

DNA在熵受限管道中穿越过程的计算机模拟

利用Metropolis Monte-Carlo动力学方法结合键长涨落算法，模拟了单链DNA分子在电场作用下穿越熵受限管道的动力学过程.结果表明，DNA分子穿越管道时将经历无规迁移、受限迁移及快速迁移等几个显著不同的阶段.平均迁移率随外场增加而增大并最终达到饱和值μ0，受限时间的对数与所加场强的倒数之间基本满足线性关系.模拟结果不仅与文献所给的实验结果基本一致，而且还可以提供实验不能直接观察到的DNA分子较为详细的穿越过程.     

DNA诱导金纳米粒子自组装及其SERS表征

首先将巯基DNA分子与金纳米粒子偶联,并用琼脂糖凝胶电泳分离出含不同DNA分子数目的金纳米粒子,最后将修饰有互补DNA链的Au纳米粒子进行组装,得到组装体(五聚体)。透射电子显微镜(TEM)研究表明,DNA-Au纳米组装体被成功地获得;表面增强拉曼光谱(SERS)研究表明,与未组装的金纳米粒子相比,DNA-Au纳米组装体具有更强的SERS活性。     

消光式核壳二聚体传感器的设计与光谱特性分析

根据ITO/Au纳米核壳二聚体粒子在生物医学领域的应用合理性,设计了一种实时检测生物液体的核壳二聚体探针消光式传感器;由偶极子理论推导出输出波长与外界环境折射率关系;利用MATLAB设计ITO/Au纳米核壳二聚体粒子结构;采用软件DDSCAT7.3结合离散偶极近似法,利用二聚体有效半径模拟计算了300~950nm可见光到红外光波段不同核壳比、二聚体间距、以及不同介质折射率的消光光谱;根据传感芯片折射率与偶极共振、耦合八级共振的响应关系得出ITO/Au二聚体的折射率灵敏特性。与传统Ag/Au核壳纳米粒子相比,ITO/Au纳米核壳二聚体结构引入了可作为传感芯片灵敏性自参考参数的耦合八级共振峰,同时ITO/Au二聚体结构的折射率灵敏度可达到419nm/RIU。这些工作及其结果对制作消光式传感器具有重要的意义。     

应用分子梳技术对DNA与组蛋白相互作用的研究

利用分子梳技术对λ DNA和组蛋白的相互作用进行了研究. 通过这种简单有效的方法，我们将λ DNA分子拉伸到26—28 μm，相当于其原长（约162 μm）的16—17倍. 当组蛋白与DNA结合后，DNA分子发生凝聚现象，复合体的拉伸长度明显变短，其峰值分布在10—14 μm之间. DNA 组蛋白复合体的拉伸长度与组蛋白的浓度、与碱基对和荧光染料的比例有显著的关系. 关键词： 分子梳 组蛋白 DNA 荧光显微     

DNA单分子弹性理论

随着单分子操纵技术的发明与发展，人们已经可以对单个生物大分子施以力或力矩，并测量它们的物理性质，DNA单分子的力学实验表明，在分子尺度上理解生物大分子的生化过程，力与能量是同等重要的结构与功能参数。一个梯子模型被用来描述双链DNA的外力拉伸曲线，在这个模型中，DNA是由许多碱基对(梯子的横杆，横杆之间存在吸引势)连接两条聚核苷酸虫链(梯子的两侧)形成的高分子，利用路径积分法得出的理论曲线与实验曲线吻合得很好，对于单链DNA，用分立的杂化高分子链统计理论的母函数方法来计算其弹性行为，得出与实验相符合的外力引起的解链相变结果。此外，对于抑瘤蛋白p53识别序列DNA微环弹性进行分析，发现其弹性模量只是通常随机序列的三分之一。     

生物软物质研究的新进展

文章对近年来中科院物理研究所软物质物理实验室生物软物质研究的部分新进展做一简略介绍,包括DNA单分子研究,DNA与组蛋白的相互作用动力学研究,生物分子马达的运动机制研究,解旋酶与DNA的结合以及解旋DNA的动力学研究,朊病毒片段聚集的分子动力学研究,蛋白质折叠动力学的脉冲升温-时间分辨光谱研究,光合细菌外周捕光天线膜蛋白的拓扑结构研究等.     

拉曼光谱法研究不同环境温度下脉冲电场对胰岛素二级结构影响及理论模型分析

近年来,弱电磁辐射生物效应已受到人们的普遍关注.前期研究发现脉冲电场与环境温度对胰岛素分子的构象产生协同效应.因此,文章首先应用拉曼光谱法研究了不同环境温度下脉冲电场对胰岛素分子二级结构的影响,得到胰岛素分子α螺旋结构含量的变化;并运用蛋白质螺旋-线团结构转变模型对实验结果进行定量分析,得到的理论模型可以较好地刻画不同环境温度下,脉冲电场对胰岛素分子α螺旋结构含量的影响.脉冲电场的作用及热力学环境的改变,使蛋白质螺旋结构向无规线团结构发生转变,可以解释脉冲电场作用下,胰岛素分子α螺旋结构含量随环境温度升高而下降的原因.研究结果为进一步研究弱电磁辐射对生物大分子二级结构的非热效应机理提供了一定的实验依据及理论参考.     

单分散“核-卫星”金纳米结构的DNA控制组装：一种新型的纳米分级组装模块

报道了一种单分散“核-卫星”纳米金簇状结构的构造方法,不但可以有效调节卫星粒子的数目,还能实现核与卫星粒子间距离的准确控制. 利用DNA分子高度可控的程序化自组装性能,通过合理控制组装过程中核与卫星粒子表面的DNA修饰密度以及不同金纳米粒子的化学计量比,实现了单分散核-卫星结构的高产率组装,结合使用凝胶电泳这一高效的纳米分离技术实现了目标产物的分离. 该方法保证了卫星粒子表面极低的DNA覆盖率,使其与蛋白分子中的巯基基团具有较强的化学亲和作用,使得金纳米粒子在蛋白功能化石墨烯表面的二维层次化自组装得以实现.     

Water wettability in nanoconfined environment

Water confined in nanoscale space behaves quite differently from that in the bulk.For example,in biological aquaporins and in carbon nanotubes,the traversing water molecules form a single file configuration.Water would stay in vapor state in extremely hydrophobic narrow nanopores owing to the physicochemical interactions between the water molecules and the surface of the nanopore.A spontaneous wet-dry transition has been identified in both biological and artificial nanopores.The nanopore is either fulfilled with liquid water or completely empty.Based on this mechanism,the wetting and dewetting processes inside nanopores have been further developed into highly efficient nanofluidic gates that can be switched by external stimuli,such as light irradiation,electric potential,temperature,and mechanical pressure.This review briefly covers the recent progress in the special wettability in nanoconfined environment,water transportation through biological or artificial nanochannels,as well as the smart nanofluidic gating system controlled by the water wettability.     

离子浓度及表面结构对岩石孔隙内水流动特性的影响

酸性环境引发的岩石孔隙表面溶解增加了孔隙内水溶液的盐离子浓度,破坏了孔隙的表面结构.本文采用分子动力学模拟的方法研究了纳米级岩石孔隙内水溶液的流动特性,分析了盐离子浓度和孔隙表面结构对水流速度分布的影响及原因.研究结果表明:纳米级岩石孔隙内的水溶液流动符合泊肃叶流动特性,流速呈"抛物线"分布;随盐离子浓度增加,水溶液内部氢键网络变得更为致密,水黏度随其呈线性增长;水溶液中离子浓度越大,孔隙表面对水流动的阻力越大,最大流速越小,速度分布的"抛物线"曲率半径越大;岩石孔隙表面结构的破坏改变了流动表面的粗糙程度,增加了孔隙表面对H2O分子的吸引力.随表面结构破坏程度的增大,水溶液在近壁区域的密度增大,流速降低;当表面破坏程度达到50%时,水溶液在近壁区域出现了明显的负边界滑移现象.     

Concentration polarization in translocation of DNA through nanopores and nanochannels

In this Letter we provide a theory to show that high-field electrokinetic translocation of DNA through nanopores or nanochannels causes large transient variations of the ionic concentrations in front and at the back of the DNA due to concentration polarization (CP). The CP causes strong local conductivity variations, which can successfully explain the nontrivial current transients and ionic distributions observed in molecular dynamics simulations of nanopore DNA translocations as well as the transient current dips and spikes measured for translocating hairpin DNA. Most importantly, as the future of sequencing of DNA by nanopore translocation will be based on time-varying electrical conductance, CP, must be considered in experimental design and interpretation--currently these studies are mostly based on the incomplete pore conductance models that ignore CP and transients in the electrical conductance.     

DNA in nanopores: counterion condensation and coion depletion

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.     

Ionic capillary evaporation in weakly charged nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.     

MD模拟方法研究圆柱形纳米微孔的吸附平衡

本文用MD（分子动力学）模拟方法对圆柱形纳米微孔中的Lennard-Jones流体的物理吸附平衡及界面现象进行了研究。模拟中引入新型势模型,采用了计数法计算平衡压力,预测了在不同孔径下（直径为 3～5nm）的吸附等温线,分析了毛细凝聚理论用于纳米微孔吸附的局限性。并比较了同一纳米尺度的窄缝形微孔和圆柱形微孔吸附的差异。     

聚丙烯腈基碳纤维原丝在纺丝过程中纳米孔变化规律与机理研究

应用小角X射线散射等方法, 系统、定量地测试表征了聚丙烯腈基碳纤维原丝中纳米孔的尺寸、形状、体积分数、单位体积中纳米孔绝对数量以及纤维总孔洞率等形态结构参量, 并对这些参量在水洗、水洗牵伸、热致密化、高压蒸汽牵伸及热稳定化等工艺过程中的变化规律及原因进行了研究. 结果表明, 纺丝过程中牵伸及高温热处理均可使纤维总孔洞率逐步下降. 纳米孔尺寸体积分数V_i测试表明, 对于小于10 nm³的小纳米孔和大于10³ nm³的较大纳米孔, 两者的V_i在纺丝初期水洗牵伸工艺中分别为0.217和0.369, 而在纺丝后期热稳定化处理后发生大幅度改变, 分别为0.948 与0.015. 其原因并不是在高压蒸汽牵伸及热稳定处理中较小纳米孔含量的增加, 而是较大纳米孔含量的大幅度减少. 纳米孔形状研究表明, 纺丝工艺中的多次牵伸处理均使纳米孔的长短轴比加大, 而大于玻璃化温度的热处理均使纳米孔长短轴比收缩, 并且对于较小纳米孔来说这种收缩更为显著.     

Nanobubbles in solid-state nanopores

From conductance and noise studies, we infer that nanometer-sized gaseous bubbles (nanobubbles) are the dominant noise source in solid-state nanopores. We study the ionic conductance through solid-state nanopores as they are moved through the focus of an infrared laser beam. The resulting conductance profiles show strong variations in both the magnitude of the conductance and in the low-frequency noise when a single nanopore is measured multiple times. Differences up to 5 orders of magnitude are found in the current power spectral density. In addition, we measure an unexpected double-peak ionic conductance profile. A simple model of a cylindrical nanopore that contains a nanobubble explains the measured profile and accounts for the observed variations in the magnitude of the conductance.     

Highly Efficient Power Conversion from Salinity Gradients with Ion-Selective Polymeric Nanopores

A polymeric nanopore membrane with selective ionic transport has been proposed as a potential device to convert the chemical potential energy in salinity gradients to electrical power.However,its energy conversion efficiency and power density are often limited due to the challenge in reliably controlling the size of the nanopores with the conventional chemical etching method.Here we report that without chemical etching,polyimide(PI) membranes irradiated with GeV heavy ions have negatively charged nanopores,showing nearly perfect selectivity for cations over anions,and they can generate electrical power from salinity gradients.We further demonstrate that the power generation efficiency of the PI membrane approaches the theoretical limit,and the maximum power density reaches 130mW/m2 with a modified etching method,outperforming the previous energy conversion device that was made of polymeric nanopore membranes.