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.     

利用纳米孔研究DNA

脱氧核糖核酸 (DNA)和蛋白质是构成生命体最为重要的两类生物大分子 .随着科学技术的快速发展 ,越来越多的纳米技术被用来研究这些生物大分子 .文章详细介绍了近来利用纳米孔技术研究DNA的一些进展 .结合作者近期利用聚焦离子束 (FIB)制作纳米孔的工作 ,提出了利用纳米孔解离核小体的设想 .如果能够利用纳米孔将双螺旋DNA从组蛋白八聚体上剥离下来 ,并探测这一过程 ,将揭示核小体中包含的许多生物化学、物理信息 .文章对此进行了较为详细的分析 :处于电场中的核小体在电场的作用下 ,DNA分子穿越纳米孔 ,同时由于纳米孔的阻挡力 ,使组蛋白不能穿越 ,从而诱使DNA从组蛋白八聚体上分离下来 .通过准确检测DNA分子穿孔过程中引起的电流阻塞效应 ,可将DNA与组蛋白的相互作用的一些性质反映出来     

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     

染色质的DNA与组蛋白复合和分离的拉曼光谱研究

鸡红血球染色质的DNA与组蛋白复合和分离的拉曼光谱有明显的不同,这主要是由于金属钠、钙离子的影响和DNA与组蛋白的相互作用。本文初步阐明了上述染色质拉曼光谱的不同特征,并进一步表明了钠、钙离子与染色质中DNA和组蛋白的相互作用地点和模式,以及当DNA与组蛋白复合后它们相互作用的地点和模式。     

核酸和组蛋白的高分辨核磁共振研究

本文报道了不同来源的4种DNA和11种组蛋白的核磁共振研究新结果。发现真核生物DNA的核磁共振波谱明显不同;而真核生物组蛋白的波谱却相似。并讨论了放线菌素D与DNA,以及E.B(Ethidiumbromide)与DNA相互作用时质子峰变弱,和化学位移发生变化问题。     

钠离子浓度对核小体纤维结构影响的Monte Carlo模拟

通过核小体纤维模型的构建，利用Monto Carlo方法模拟其在各种钠离子浓度的溶液中结构变化的过程.模拟结果显示当溶液的钠离子浓度增大时，核小体由锯齿状结构转变为螺旋状结构.在常温所得到的核小体结构参数与实验结果接近，较好地解释了溶液中的钠离子浓度对核小体纤维结构的影响. 关键词： 核小体纤维 超螺旋结构 Monte Carlo方法 钠离子浓度     

MRG15与甲基化组蛋白H3K36相互作用研究

人源转录调控因子MRG15（MORF4 related gene on chromosome 15）是在胚胎发育,细胞增殖和衰老过程中具有重要作用的蛋白质. 在分子水平上,MRG15的chromo结构域能够与组蛋白H3甲基化的肽段H3K36me3相互作用. 为了确定二者的作用位点和方式,利用液体核磁共振的方法对MRG15 chromo结构域和H3K36me3多肽进行了研究. 对MRG15 chromo结构域进行归属,用化学位移扰动的方法研究了其与H3K36me3肽段的相互作用,确定了相互作用位点的关键氨基酸为H21,Y46,W49和W53,并计算了解离常数约为1 mmol/L. 研究结果对于阐明MRG15与组蛋白H3的结合和相互作用机制提供了重要的线索.     

抗生物素蛋白与DNA相互作用的单分子研究

抗生物素蛋白(avidin)在生物单分子实验中被广泛用于DNA与修饰表面的连接,同时avidin也可作为一种DNA载体用于基因治疗中.本文利用原子力显微镜(AFM)、动态光散射(DLS)、单分子磁镊(MT)技术系统地研究了avidin与DNA之间的相互作用,以及avidin引起DNA凝聚的机理.首先通过AFM对avidin-DNA复合体形貌进行观察,发现不但有avidin导致DNA凝聚的环状形貌,同时也存在avidin自身聚集引起的DNA凝聚现象,通过定量分析,发现其凝聚尺寸越来越小,而当avidin浓度大于2 ng·μL~(-1)时,其凝聚尺寸又突然变大.DLS实验结果也显示了同样的规律,伴随着avidin浓度的升高,DNA的粒径大小从大约170 nm减小到125 nm左右,其电泳迁移率由-2.76(10~(-4)cm~2·V~(-1)·s~(-1))变化到-0.1(10~(-4)cm~2·V~(-1)·~(-1)).此外,通过MT技术的力谱曲线变化,发现avidin导致的DNA凝聚与其他多价离子相比,长度的变化曲线几乎呈线性变化,偶尔存在少而小的阶跃,这种变化趋势与组蛋白的变化曲线更相似.因此可以判断,avidin导致DNA凝聚是由avidin与DNA的静电吸引和avidin自身聚集两种相互作用引起的.     

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.     

电离辐射诱导组蛋白乙酰化引起的染色质结构解聚研究

真核生物的DNA分子经高度压缩以染色质形式存在于细胞核中,染色质动态结构在DNA复制、基因转录和DNA修复等过程中起着重要的调控作用。核内染色质结构的原位高分辨解析和其结构变化定量表征一直受困于显微成像观测分辨率的限制。通过点击化学荧光标记EdU和STORM单分子定位显微成像,实验得到了细胞核内超分辨率染色质结构图像。基于提出的单分子团簇分析和最近邻距离算法分析发现,X射线辐照和TSA处理后的细胞核内核小体团簇数量显著增多,核小体团簇所占细胞核内的面积比相对于对照组增加,且团簇内平均EdU分子数降低。同时,重离子辐照活细胞在线成像实验获得的XRCC1招募动力学速率常数表明乙酰化处理使得DNA损伤密度降低。这些结果表明电离辐射和乙酰化处理均导致了染色质结构的松散化。STORM超分辨成像方法和分析算法及其获得的核小体团簇分布规律为染色质结构的松散提供了直接的定量表征数据支持。     

Guided-Wave Two-Dimensional Acousto-Optic Scanner Using Proton-Exchanged Lithium Niobate Waveguide

Two-dimensional scanning of a 0.6328 mum guided-light beam has been realized using noncolinear acousto-optic (AO) coplanar Bragg diffraction together with colinear AO guided-mode to substrate radiation-mode conversion in a Z-cut Xpropagation LiNbO3 proton-exchanged (PE) waveguide. The two surface acoustic (SAW) waves utilized are at the center frequencies of 500 and 200 MHz, propagating in the Y and X axes, respectively. Two-dimensional scanning of approximately 720 resolvable light beam spots, namely, 18 40 (horizontal vertical) scanning, has been demonstrated using a light beam of 1.0 mm aperture. The total number of resolvable beam spots can be greatly increased from 720 by simply utilizing SAW transducers of larger bandwidth and a light beam of greater aperture. It should also be possible to significantly increase the diffraction efficiency from 3 % by optimizing the parameters of the PE waveguide and the SAWs.     

Effect ofγ-radiation on the spectral luminescence characteristics of impure cadmium tungstate crystals

Results of a study of the effect of γ-radiation on the spectral luminescence properties of cadmium tungstate crystals doped with silver, bismuth, and molybdenum cations are presented. Spectral characteristics of the nondnnnoped crystals are briefly described. Absorption and photo and X-ray luminescence spectra of the crystals taken before and after exposure to γ-radiation (5.5·10⁴ Gy) are compared. It is found that the spectral characteristics of the crystals doped with silver, bismuth, and molybdenum cations do not change markedly after the exposure. The relation between the type of impurity-induced defects, individual characteristics of the impurity cations, and the character of the effect of γ-radiation on the spectral luminescence properties of impure crystals is analyzed (preliminarily). Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 64, No. 1, pp. 55–60, January–February, 1997.     

Femtosecond Transform-Limited Pulse Generation by Compensating for the Linear Chirp of SPM Spectra in Dispersion Shifted Fibers

A simple technique of pulse compression, based on the linear chirp compensation of self-phase modulation (SPM) spectra in dispersion shifted fibers, is demonstrated. The optimization procedure is carried out, for a short span of a single-mode fiber, using a parabolic law, which describes the behavior of the squared output pulse width versus the pump peak power in the case of Gaussian pulses. The experimental results give a minimum pulse duration of 233 fs, which is in good agreement with the model. Shorter and coherent pulses, down to 90 fs, have been obtained by inserting an interference filter at the optical output.     

Sorting of bending magnets for the SSRF booster

The Shanghai Synchrotron Radiation Facility(SSRF)booster ring,a full energy injector for the storage ring,is deigned to accelerate the electron beam energy from 150MeV to 3.5GeV that demands high extraction efficiency at the extraction energy with low beam loss rate when electrons are ramping.Closed orbit distortion(COD)caused by bending magnet field uniformity errors which affects the machine performance harmfully could be effectively reduced by bending magnet location sorting.Considering the affections of random errors in measurement,both ideal sorting and realistic sorting are studied based on measured bending magnet field uniformity errors and one reasonable combination of bending magnets which can reduce the horizontal COD by a factor of 5is given as the final installation sequence of the booster bending magnets in this paper.     

Measurement of nonlinear coefficient of optical fiber based on small chirped soliton transmission

We measure the waveform and phase curves of short optical pulses before and after transmission over different lengths of fibers by use of the pulse analyzer with the frequency-resolved optical gating (FROG),and numerically simulate pulse evolution under the experimental conditions.The nonlinear coefficient of the fiber is given by comparing the experimental results with the numerical ones.Difference between the experiment and numerical simulation is analyzed.     

Resonance scattering of canonical elastic shells in absorbing fluid medium

Resonance scattering of elastic spherical shell and cylindrical shell while the surrounding fluid medium has absorption is studied. The normal mode solution derived using exact elastic theory and the separation of variables is still applicable. However, the scattering form function has to be modified for the absorbing medium, otherwise the unreasonable result would be obtained. The backscattering form function in the absorbing medium is redefined, and the form function of elastic spherical and cylindrical shell with vacuum or solid matter filled is calculated in various absorption conditions. The results show that the absorption of surrounding fluid leads to notable attenuation of the coincidence resonances in the mid-frequency, but it has a little influence on the low-frequency resonance scattering induced by the filler inside the shell.     

Single-beam self-referenced phase-sensitive surface plasmon resonance sensor with high detection resolution

A versatile and low-cost single-beam self-referenced phase-sensitive surface plasmon resonance(SPR)sensing system with ultra-high resolution performance is presented.The system exhibits a root-mean-square phase fluctuation of ±0.0028.over a period of 45 min.i.e.a resolution of±5.2×10-9 refractive index units.The enhanced performance has been achieved through the incorporation of three design elements:a true single-beam configuration enabling complete self-referencing so that only the phase change associated with SPR gets detected,a differential measurement scheme to eliminate spurious signals not related to the sensor response,and the elimination of retardation drifts by incorporating temperature stabilization in the liquid crystal phase modulato .Our design should bring the detection sensitivity of non-labeling SPR biosensing closer to that achievable by conventional fluorescence-based techniques.     

Influences of SiO2 protective layers and annealing on the laser-induced damage threshold of Ta2O5 films

Ta2O5 films are prepared on BK7 substrates with conventional electron beam evaporation deposition.The effects of SiO2 protective layers and annealing on the laser-induced damage threshold (LIDT) of the films are investigated.The results show that SiO2 protective layers exert little influence on the electric field intensity(EFI)distribution,microstructure and microdefect density but increase the absorption slightly.Annealing iS effective on decreasing the microdefect density and the absorption of the films.Both SiO2 protective layers and annealing are beneficial to the damage resistance of the films and the latter is more effective to improve the LIDT.Moreover,the maximal LIDT of Ta2O5 films is achieved by the combination of SiO2 protective layers and annealing.     

A stereo matching algorithm using multi-peak candidate matches and geometric constraints

Gray cross correlation matching technique is adopted to extract candidate matches with gray cross correla- tion coefficients less than some certain range of maximal correlation coefficient called multi-peak candidate matches. Multi-peak candidates are extracted corresponding to three closest feature points at first. The corresponding multi-peak candidate matches are used to construct the model polygon. Correspondence is determined based on the local geometric relations between the three feature points and the multi-peak candidates. The disparity test and the global consistency checkout are applied to eliminate the remaining ambiguous matches that are not removed by the local geometric relational test. Experimental results show that the proposed algorithm is feasible and accurate.