Effects of Ionic Dependence of DNA Persistence Length on the DNA Condensation at Room Temperature

DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA.A series of experiments pointed out that,in the DNA condensation process by multivalent cations,the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration.At the same time,single molecule experiments carried out in solution with multivalent cations(such as spermidine,spermine)indicated that DNA persistence length strongly depends on the ionic concentration.In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation,a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided.The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations.With an increase in ion concentration,the first periodic oscillation contained in the autocorrelation function shifts,the number of segment contained in the first periodic oscillation decreases gradually.According to the experiments,the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further.The relation between long-axis length and ionic concentration matches the experimental results qualitatively.     

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.     

Counterion condensation in ionic micelles as studied by a combined use of SANS and SAXS

We report a combined use of small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) to the study of counterion condensation in ionic micelles. Small-angle neutron and X-ray scattering measurements have been carried out on two surfactants cetyltrimethylammonium bromide (CTABr) and cetyltrimethylammonium chloride (CTACl), which are similar but having different counterions. SANS measurements show that CTABr surfactant forms much larger micelles than CTACl. This is explained in terms of higher condensation of Br⁻ counterions than Cl⁻ counterions. SAXS data on these systems suggest that the Br⁻ counterions are condensed around the micelles over smaller thickness than those of Cl⁻ counterions.     

Chiral electrostatics breaks the mirror symmetry of DNA supercoiling

DNA supercoiling plays a fundamental role in regulating cellular activity and in the packaging of genetic material. In this communication, we analyse the effect of attractive chiral forces on the conformation of a closed circular DNA molecule, arising due to the helical patterns of charges on the DNA. We propose a model for closed loop DNA which uses the results of the recent theory of electrostatic interactions of a braid of two free-ended DNA molecules. Our model reproduces the known features of DNA supercoiling in an environment of low ionic strength. In high salt conditions, and in the presence of counterions that have high affinity to the DNA grooves, helix-specific forces significantly affect the conformation of the molecule by favouring a state characterized by a central left-handed braided section where there is close contact between distant portions of the loop. In such an environment we predict a previously unexplored possibility that nicked or topologically relaxed DNA molecules adopt a writhed state. This prediction suggests an alternative explanation for experiments in which it was assumed that the most stable topoisomer is always an open circle. Our results also give the first plausible explanation for the occurrence of tightly interwound molecules observed in cryo-electron microscopy and atomic force microscopy in a high ionic strength environment. We suggest several new experiments to test the predictions of this theory.     

Single Molecule Fluorescence Imaging and Its Application to the Study of DNA Condensation

Single molecule fluorescence imaging incorporated with optical tweezers and a laminar flow cell has been used to monitor the kinetic process of DNA condensation induced by spermidine. It was found that at least two steps were involved in the condensation process of the hydrodynamically-stretched linear DNA; a lag period followed by a rapid collapse of DNA. The lag time increased with the flow speed and the collapse time remained short within the range of the flow speed studied. The effect of salt concentration on the condensation process was examined, and the results suggest that the longer lag time observed in the higher salt buffer probably results from the displacement of bound cations and rearrangement of spermidine on the DNA. The flow-speed dependence of the lag time suggests that a nucleation event at the free end of the DNA, i.e. formation of a loop, may play a vital role in the kinetic process of condensation.     

Elastic stability of DNA configurations. I. General theory

Results are presented in the theory of the elastic rod model for DNA, among which are criteria enabling one to determine whether a calculated equilibrium configuration of a DNA segment is stable in the sense that it gives a local minimum to the sum of the segment's elastic energy and the potential of forces acting on it. The derived stability criteria are applicable to plasmids and to linear segments subject to strong anchoring end conditions. Their utility is illustrated with an example from the theory of configurations of the extranucleosomal loop of a DNA miniplasmid in a mononucleosome, with emphasis placed on the influence that nicking and ligation on one hand, and changes in the ratio of elastic coefficients on the other, have on the stability of equilibrium configurations. In that example, the configurations studied are calculated using an extension of the method of explicit solutions to cases in which the elastic rod modeling a DNA segment is considered impenetrable, and hence excluded volume effects and forces arising from self-contact are taken into account.     

Effects of oxaliplatin on DNA condensation

In this paper the interactions between DNA and anti-cancer drug oxaliplatin were investigated by using magnetic tweezers. The dynamics of DNA condensation due to oxaliplatin was traced under various forces. It is found that torsion constraint in DNA enhances the ability of oxaliplatin for shortening DNA. The transplatin helps oxaliplatin combine to DNA and increase the rate of DNA condensation. All these results are consistent to the previously proposed model and are helpful for further investigation of interaction between DNA and oxaliplatin.     

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.     

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。     

Counterion condensation theory of attraction between like charges in the absence of multivalent counterions

There is abundant experimental evidence suggesting the existence of attractive interactions among identically charged polyelectrolytes in ordinary salt solutions. The presence of multivalent counterions is not required. We review the relevant literature in detail and conclude that it merits more attention than it has received. We discuss also some recent observations of a low ionic strength attraction of negatively charged DNA to the region of a negatively charged glass nanoslit where the floor of the nanoslit meets the walls, again in the absence of multivalent ions. On the theoretical side, it has become clear that purely electrostatic interactions require the presence of multivalent counterions if they are to generate like-charge attraction. Any theory of like-charge attraction in the absence of multivalent counterions must therefore contain a non-electrostatic component. We point out that counterion condensation theory, which has predicted like-charge polyelectrolyte attraction in an intermediate range of distances in ordinary 1:1 salt conditions, contains both electrostatic and non-electrostatic elements. The non-electrostatic component of the theory is the modeling constraint that the counterions fall into two explicit populations, condensed and uncondensed. As reviewed in the paper, this physically motivated constraint is supported by strong experimental evidence. We proceed to offer an explanation of the nanoslit observations by showing in an idealized model that the line of intersection of two intersecting planes is a virtual polyelectrolyte. Since we have previously developed a counterion condensation theory of attraction of two like-charged polyelectrolytes, our suggestion is that the DNA is attracted to the virtual polyelectrolytes that may be located in the nanoslit where floor meets walls. We present the detailed calculations needed to document this suggestion: an extension of previous theory to the case of polyelectrolytes with like but not identical charges; the demonstration of counterion condensation on a plane with bare charge density greater than an explicitly exhibited critical value; a calculation of the free energy of the plane; a calculation of the interaction of a line charge polyelectrolyte with a like-charged plane; and the detailed demonstration that the line of intersection of two planes is a virtual polyelectrolyte.     

Investigations on the liquid crystalline phases of cation-induced condensed DNA

Viral and nonviral condensing agents are used in gene therapy to compact oligonucleotides and plasmid DNA into nanostructures for their efficient transport through the cell membranes. Whereas viral vectors are best by the toxic effects on the immune system, most of the nonviral delivery vehicles are not effective for use in clinical system. Recent investigations indicate that the supramolecular organization of DNA in the condensed state is liquid crystalline. The present level of understanding of the liquid crystalline phase of DNA is inadequate and a thorough investigation is required to understand the nature, stability, texture and the influence of various environmental conditions on the structure of the phase. The present study is mainly concerned with the physicochemical investigations on the liquid crystalline transitions during compaction of DNA by cationic species such as polyamines and metallic cations. As a preliminary to the above investigation, studies were conducted on the evolution of mesophase transitions of DNA with various cationic counterion species using polarized light microscopy. These studies indicated significant variations in the phase behaviour of DNA in the presence of Li and other ions. Apart from the neutralization of the charges on the DNA molecule, these ions are found to influence selectively the hydration sphere of DNA that in turn influences the induction and stabilization of the LC phases. The higher stability observed with the liquid crystalline phases of Li-DNA system could be useful in the production of nanostructured DNA. In the case of the polyamine, a structural specificity effect depending on the nature, charge and structure of the polyamine used has been found to be favoured in the crystallization of DNA.     

Effect of electroelastic anisotropy of DNA-like molecules on their tertiary structure

Under certain conditions, mechanical forces can cause an anisotropic molecule like DNA to assume a toroidal spatial structure. A simple model describing such a behavior is suggested. The model incorporates anisotropic elastic energy and external electrical forces. The steady-state structures formed by a macromolecule have been studied numerically using this model. There exist ranges of model parameters, namely, the anisotropy of the elastic tensor, magnitude and orientation of forces, and modulation periods, where molecules have toroidal, spherical, or extended structures. Estimates of parameters characteristic of these structures are consistent with experimental data. In particular, the toroidal structure dimension corresponds to experimental dimensions of toroidal globules produced as a result of so-called PSI condensation of DNA molecules. Zh. éksp. Teor. Fiz. 112, 2156–2168 (December 1997)     

Dynamic changes of nucleolar DNA configuration and distribution during the cell cycle in Allium sativum cells

To investigate the correlation between subnucleolar structure and function, the precise distribution and configuration of nucleolar DNA during the cell cycle of Allium sativum were determined using the NAMA-Ur DNA-specific staining technique. We showed that nucleolar DNA is present in two forms: compacted chromatin clumps and a decondensed DNA cloud. The form of the DNA within the nucleolus varied greatly as the cell cycle progressed. During telophase, chromosomes extended into the prenucleolar body. In early G1 phase, DNA was only located in the fibrillar centers in the form of the condensed chromatin clump, while in mid-G1, S and G2 phases, the two forms of DNA were distributed in the fibrillar centers (FC) and dense fibrillar component (DFC). In prophase of mitosis, nucleolar DNA, along with FC and DFC, was linked into a network structure and condensed into a large chromatin clump. The area of the DNA cloud in the dense fibrillar component changed during different phases of the cell cycle. Our results demonstrated that the configuration of nucleolar DNA undergoes a series of decondensations and condensations during the cell cycle to fulfill the function of the nucleoli during the different phases.     

On co-evolution and the importance of initial conditions

We present a generic threshold model for the co-evolution of the structure of a network and the binary state of its nodes. We focus on regular directed networks and derive equations for the evolution of the system toward its absorbing state. It is shown that the system displays a transition from a connected phase to a fragmented phase, and that this transition is driven by the initial configuration of the system, as different initial conditions may lead to drastically different final configurations. Computer simulations are performed and confirm the theoretical predictions.     

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     

A counterion condensation theory for the relaxation,rise, and frequency dependence of the parallel polarization of rodlike polyelectrolytes

We calculate the relaxation, rise, and frequency dependence of the parallel polarization of counterions condensed on rodlike polyelectrolytes and charged colloids. Emphasis is placed on an effective counterion mobility along the rod as strongly influenced by electrostatic interactions.     

DNA分子能带结构与电子态研究

DNA分子链内的巡游电子数与其结构和位形密切相关，可变的电子数会导致这类软物质费米面处能带结构的变化.在紧束缚近似下，计入电子 晶格的相互作用，计算了DNA分子不同巡游电子数下的能带结构及态密度，对碱基对不同排列情况下DNA分子可能的电属性进行了讨论. 关键词： DNA 态密度 电晶相互作用     

蒸汽冷凝过程的分子团聚模型及其对不凝性气体影响传热性能的解释

根据相变过程的微观物理机理和热力学特性,提出了冷凝传热过程中,近壁面蒸汽分子经由团聚阶段进而冷凝成宏观液滴的物理模型.并将团聚体分布与滴状冷凝传热性能相联系,从而研究不凝性气体对滴状冷凝传热过程的影响.在改进的Dillmann和Meier(DM)模型基础上,将分子团聚过程中的临界过饱和度与冷凝过程中的过冷度相联系,以及将团聚体的能量特性与液固界面物理化学特性相联系,将团聚模型与考虑固液界面效应的滴状冷凝传热模型相联系,建立了近壁面条件影响的分子团聚模型.利用模型计算了近壁面蒸汽中团簇体尺寸和分布,以及不凝性气体存在导致的蒸汽冷凝团聚体分布的变化,并结合滴状冷凝传热模型,定量解释了少量不凝性气体的存在,极大影响了冷凝传热性能的现象.模型计算结果与实验结果及文献中含不凝气的蒸汽冷凝传热实验数据进行了比较,两者符合较好,验证了所提出模型的合理性.     

纳米结构超疏水表面冷凝现象的三维格子玻尔兹曼方法模拟

采用三维多相流格子玻尔兹曼方法 (lattice Boltzmann method, LBM),对纳米结构超疏水表面液滴的冷凝行为进行模拟研究.通过Laplace定律和光滑表面的本征接触角理论对三维LBM模型进行定量验证.模拟分析了超疏水表面纳米阵列的几何尺寸和润湿性的局部不均匀性对冷凝液滴形核位置和最终润湿状态的影响规律.结果表明,较高的纳米阵列使液滴在纳米结构间隙的上部侧面和底部优先形核长大,通过采用上下不均匀的间隙可避免液滴在底部形核长大,而在上部侧面形核的冷凝液滴在生长过程中向上运动,其润湿状态由Wenzel态转变为Cassie态;较低的纳米阵列使液滴在纳米结构底部优先形核长大,液滴的最终润湿状态为Wenzel态;润湿性不均匀的纳米结构表面使液滴在阵列顶端亲水位置处优先形核长大,成为Cassie态.冷凝液滴在不同几何尺寸的纳米结构表面上的最终润湿状态的模拟结果与文献报道的实验结果符合良好.通过模拟还发现,冷凝液滴在生长过程中的运动行为与液滴统计平均作用力的变化有关.本文的LBM模拟再现了三维空间中液滴的形核、长大和润湿状态转变等物理现象.     

Diffusion-enhanced resonance energy transfer shows that linker-DNA accessibility decreases during salt-induced chromatin condensation

Accessibility of linker-DNA chromatin during salt-induced condensation of chicken erythrocytes chromatin was studied by diffusion-enhanced resonance energy transfer. A terbium complex was covalently bound to linker-DNA and fluorescein molecules bound to latex particles with diameters ranging from 14 to 2470 nm were used as acceptor. The accessibility of linker-DNA to molecules with a diameter superior to 14 nm diminished during condensation, but for an acceptor diameter of 14 nm or less, no accessibility variation was observed. It can be concluded that (1) linker-DNA is located inside the fiber when chromatin is in the condensed state, (2) chromatin condensation can prevent the approach to DNA due to steric hindrance, (3) salt-induced chromatin condensation is a gradual process, and (4) condensed chromatin models containing a central cavity are more likely.Abbreviations DTPA diethylene tetramine pentacetic acid - FDL-DERET fast diffusion limit of diffusion-enhanced resonance energy transfer - Pso-Tb psoralen-terbium complex - PAS paraamino salicylic acid - TREF time-resolved emission of fluorescence