用单分子技术研究抗癌药物顺铂对DNA结构的影响

文章作者用磁镊与原子力显微镜研究了抗癌药物顺铂对单个DNA分子结构的影响.当顺铂浓度较低时,DNA链变得柔软,驻留长度从～52 nm显著缩短到～15 nm;当顺铂浓度较高时,DNA表现出凝聚现象.基于单分子拉伸和原子力显微镜(AFM)成像两方面的实验结果,文章作者提出一个顺铂导致的DNA变软(softening)-成环(looping)-缩短(shortening)-凝聚(condensing)模型(简写为SLSC模型)来解释观察到的DNA凝聚,并认为通过远程交联使DNA形成小环结构是铂类抗癌药物作用的重要特征.     

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.     

重金属Cu2+增强农药甲萘威对ctDNA作用的光谱法研究

运用荧光光谱和紫外吸收光谱研究了在Cu2 的参与下农药甲萘威与小牛胸腺DNA(ctDNA)的相互作用.实验结果表明,甲萘威可以嵌入小牛胸腺DNA的双链中形成DNA加合物,从而使甲萘威的荧光光谱发生猝灭.通过计算这种猝灭为静态猝灭.当有Cu2 的参与下,甲萘威的猝灭常数增大,结合位点数n也有很大的增加.通过对热力学函数的计算和分析,在有Cu2 参与时,金属离子可能在甲萘威分子与ctD-NA分子间起"离子架桥作用",使甲萘威分子与ctDNA分子间静电相互作用增强,故△H对△G的贡献增大.     

紫外光谱法研究药物与DNA作用方式——药物对DNA碱变性的影响

抗癌药顺铂(CDDP)的抗癌机理研究表明,DNA是顺铂进攻的靶子,并且通过与DNA中鸟嘌呤中N7配位,通过形成链内交联作用使DNA功能受损。二氯二茂钛也具有抗癌活性,并且它作用的靶子也是DNA。我们曾报道了它能使DNA—EB的荧光强度降低。目前有关它与DNA作用的细节仍很不清楚。β-榄香烯是中药莪术中抗癌的有效成分,由于它只含有C和H两种元素而引起了人们的重视。曾有报道,     

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.     

一种实现冷原子(或冷分子)囚禁的可控制纵向光学双阱

提出了一种新颖的实现冷原子(或冷分子)囚禁的可控制纵向光学双阱方案，它由一个二元π相位板及一会聚透镜所组成，其π相位板由两个面积相等的具有0和π相位的同心圆环组成. 当一平面光波通过此光学系统时将在光轴上透镜焦点两侧形成一个光学双阱，如果调节入射到二元π相位板上光束横截面的半径大小，即可实现从光学双阱到单阱的连续演变，或由单阱到双阱的连续变化. 介绍了本方案产生可控制光学双阱的基本原理，给出了形成光学双阱的最佳几何参数，研究了双阱、单阱及其演化过程的光阱参数、光强分布等与光学系统参数间的关系. 该方案不仅可用于双样品原子(分子)的光学囚禁及其全光型玻色-爱因斯坦凝聚(BEC)的实现，而且可用于研究超冷原子(或分子)物质波的干涉，或构成双层2D光阱列阵，甚至用于制备新颖的双层2D光学晶格. 关键词： 二元π相位板 可控制光学双阱 双样品囚禁 光学晶格     

基于变温紫外分光光度法研究温度对DNA凝聚过程影响

荧光单分子实验结果表明温度能够促进DNA凝聚,随着温度升高,精胺(亚精胺)-DNA凝聚体系中DNA凝聚构象趋于更加紧致、有序。为探究温度对不同高价离子-DNA凝聚体系的影响,利用自行搭建的变温紫外分光光度计,通过系统研究荧光单分子实验中采用的精胺(亚精胺)-DNA凝聚体系及去离子水中DNA在260 nm处特征吸收值随温度变化情况,确定了DNA凝聚构象与其260 nm处特征吸收值之间的对应关系为：DNA凝聚构象越紧致、有序,其对应的260 nm处紫外吸收值越低。在此基础上,系统地研究了DNA凝聚实验中常用四种钴胺化合物-DNA凝聚体系随温度变化情况,结果表明三氯六胺合钴与精胺(亚精胺)类似,其对应的DNA凝聚体系在260 nm特征吸收值,随着温度升高而逐渐降低,即DNA凝聚构象趋于更加紧致、有序。而三(乙二胺)氯化钴、反式双(乙二胺)氯化钴、五胺氯化钴的情况却不同,与其对应的DNA凝聚体系在260 nm特征吸收值,随着温度升高,呈现先增加,再降低,然后再增加的规律。     

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     

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。     

Effect of Torsion on Cisplatin-Induced DNA Condensation

We investigate the effect of torsion on DNA condensation with the covalently closed circular DNA as the torsionconstrained system, using an atomic force microscope. It is found that there are two stages in the DNA condensation process under torsional constraint. At the early stage, the low torsion will accelerate DNA condensation by promoting the formation of micro-loops or intersection structures; while at the later stage, the increasing torsion will slow it down by preventing the crosslinking of cisplatin and DNA since the DNA molecule becomes more rigid. Our results show the important role of torsion in DNA condensation and sheds new light on the mechanism for DNA condensation.     

Stretching DNA: Role of electrostatic interactions

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find the extension scales as where is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out. Received 13 October 1998 and Received in final form 9 June 1999     

The interactions of cisplatin and DNA studied by atomic force microscopy

The interactions of the several linear DNA fragments and cisplatin at different concentrations and incubation time have been studied by atomic force microscopy. When equal volume of 2 mM cisplatin and 5 ng/μl 1134 bp DNA fragment were incubated for 30 min, 1 h, 2 h and 3 h, the observed DNA were gradually changed from the extended chains to the bending structures, the worm-like structures and flat particles. The formation of these structures can be attributed to the coordination and electrostatic interactions by binding of cisplatin on DNA. When longer DNA fragments such as pBR322/pstI DNA (4361 bp) and λ DNA (48502 bp) were used for interacting with cisplatin in the same condition, the observed DNA molecules tended to form many loop structures. The differences of the interactions between long and short DNA can be ascribed to the strong intramolecular interactions within the long DNA fragment. When the relative low concentration of cisplatin (100 μmol/l) was used in the experiments, the observed DNA tended to bend along its chains. Furthermore, the measured contour length and the calculated persistent length of cisplatin–DNA were gradually decreased with the incubated time. All of these AFM results revealed that the cisplatin–DNA interactions in vitro can be influenced by the concentration and the initial state of cisplatin, the length of DNA fragment and the reaction time.     

Density functional study of the pressure tensor for inhomogeneous Lennard—Jones fluids

Based on classical density functional theory,an expression of the pressure tensor for inhomogeneous fluids is presented.This takes into account greater correlation between particles,especially for systems that are geometrically confined or involve an interface.The density and pressure components of Lennard-Jones fluids confined in hard and softened nano-cavities are calculated.A comparison between the results of this work and IK expression suggests that the agreement depends on temperature.The interfacial tension for hard sphere fluids agrees well with the Monte Carlo result when the bulk density is not too large.The results of the solid-fluid interfacial tension for Lennard-Jones fluids demonstrate that different types of external potentials modulate the interfacial tension in different manners.     

On Mechanism of Intermediate-Sized Circular DNA Compaction Mediated by Spermine: Contribution of Fluorescence Lifetime Correlation Spectroscopy

The compaction of DNA plays a role in the nuclei of several types of cells and becomes important in the non-viral gene therapy. Thus, it is in the scope of research interest. It was shown, that spermine-induced compaction of large DNA molecules occurs in a discrete "all-or-non" regime, where the coexistence of free and folded DNA molecules was observed. In the case of intermediate-sized DNA molecules (approximately 10 kbp), so far, it was stated that the mechanism of folding is continuous. Here, we show, that neither a standard benchmark technique-dynamic light scattering, nor a single molecule technique such as fluorescence correlation spectroscopy, can decide what kind of mechanism is undertaken in the compaction process. Besides, we introduce an application of a new approach-fluorescence lifetime correlation spectroscopy. The method takes an advantage of a subtle lifetime change of an intercalating dye PicoGreen during the titration with spermine and based on that, it reveals the discrete mechanism of the process. Furthermore, we show that it allows for observation of the equilibrium state transition dynamics.     

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space, Monte Carlo simulations of DNA compaction in free space, in confined spherical space without crowders and in confined spherical space with crowders were performed separately. The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions. In addition,effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii. In confined spherical space without crowders, the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly. In contrast, with the addition of crowders to the confined spherical space, effects of temperature on the phase transition of DNA compaction become insignificant, whereas the phase transition at different temperatures strongly depends on the size of crowder, and the critical volume fraction of crowders pertains to the diameter of crowder linearly.     

Effects of drawing tension on the photosensitivity of Sn-Ge- and B-Ge-codoped core fibers

The influence of drawing tension on the formation of Bragg gratings in B-Ge- and Sn-Ge-codoped core fibers is investigated by transmission and stress measurements. With increasing drawing tension, the axial stress is reduced in the B-Ge-codoped core but increased in the Sn-Ge-codoped core. A higher drawing tension leads to a photosensitivity enhancement and an increase of the core stress during the grating formation in B-Ge-codoped fibers. For Sn-Ge-codoped fibers, increased drawing tension results in an UV-induced stress decrease accompanied by a reduction of the photosensitivity. The results are discussed on the basis of an UV-induced compaction of the core network.     

Rigid random surfaces at large d

A model of two-dimensional random surfaces with extrinsic curvature energy is studied in the limit where the dimension of bulk space d is large. The large-d effective potential is constructed. For large surface tension the ground state is homogeneous and its properties are studied. For small enough surface tension, non-perturbative instabilities which break translation invariance in the plane of the membrane are shown to occur for large but finite wavelength. The relationships between this model, the bosonic string, the Liouville model and lattive random surface models are discussed.