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1.
Processes of DNA condensation induced by multivalent cations: Approximate annealing experiments and molecular dynamics simulations
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The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes. 相似文献
2.
Condensation of extended DNA into compact structures is encountered in a variety of situations, both natural and artificial.
While condensation of DNA has been routinely carried out by the use of multivalent cations, cationic lipids, detergents, and
polyvalent cationic polymers, the use of molecular crowding agents in condensing DNA is rather striking. In this work, we
have studied the dynamics of plasmid DNA condensed in the presence of a molecular crowding agent, polyethylene glycol (PEG).
Steady-state and time-resolved fluorescence of the recently established condensation-indicating DNA binder, YOYO-1 [G. Krishnamoorthy,
G. Duportail, and Y. Mely (2002), Biochemistry 41, 15277–15287] was used in inferring the dynamic aspects of DNA condensates. It is shown that DNA condensed by PEG is more
flexible and less compact when compared to DNA condensed by binding agents such as polyethyleneimine. The relevance of such
differences in dynamics toward functional aspects of condensed DNA is discussed. 相似文献
4.
Y. Sh. Mamasakhlisov 《Journal of Contemporary Physics (Armenian Academy of Sciences)》2010,45(2):94-97
A theory of DNA condensation by multivalent cations in the presence of an external stretching force is presented. It is shown
that in the mean-field approximation the system is described by the Zimm-Bragg model with effective parameters of growth of
ordered phase and cooperativity. Within the frames of the proposed model the experimental results on stretching of a double-stranded
DNA of λ-phage are interpreted. Possible scenarios of homo- and heteropolymeric behavior of DNA during condensation are analyzed.
A possible mechanism restricting the growth of linear size of DNA is proposed. 相似文献
5.
A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-square-radius, are also explicitly calculated, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition. 相似文献
6.
K. Kassapidou J.R.C. van der Maarel 《The European Physical Journal B - Condensed Matter and Complex Systems》1998,3(4):471-476
The persistence length DNA hexagonal-cholesteric phase transition upon dilution and/or increase in solvent ionic strength
is investigated with polarized light microscopy. The ionic strength dependence of the transition follows Lindemann criterion
, i.e., the hexagonal lattice melts when the root-mean-square fluctuations in transverse order exceed 10% of the interaxial spacing.
The spacings are derived from density and the fluctuations are estimated with a theory of undulation enhanced electrostatic
interactions. Additional support for this theory is given by the DNA equation of state and anisotropic neutron radiation scattering
from magnetically aligned cholesteric samples just below the phase transition.
Received: 17 November 1997 / Revised: 21 January 1998 / Accepted: 25 February 1998 相似文献
7.
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. 相似文献
8.
We present a model of nonspecific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence length, site occupancy, and cooperativity. Cooperativity leads to nonmonotonic variation of the persistence length with protein concentration, and to an unusual shape of the binding isotherm. The results are in qualitative agreement with recent single molecule experiments on nucleoid protein HU-DNA complexes. 相似文献
9.
We construct a system of magnetic tweezers and apply it to study the interaction between histones and DNA. The condensation of DNA by purified histones at low ionic strengths is directly monitored by recording the length of the DNA as a function of elapsed time. It is found that DNA condensates in a dynamic manner. The binding of hist, ones to DNA is energetically favoured, but the ten,sion applied on DNA tends to unravel the DNA-histone complex, The competition between the two processes determiners the rate of the DNA condensation. 相似文献
10.
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. 相似文献
11.
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. 相似文献
12.
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。 相似文献
13.
Zhang F Skoda MW Jacobs RM Zorn S Martin RA Martin CM Clark GF Weggler S Hildebrandt A Kohlbacher O Schreiber F 《Physical review letters》2008,101(14):148101
Negatively charged globular proteins in solution undergo a condensation upon adding trivalent counterions between two critical concentrations C and C, C 相似文献
14.
Caliskan G Hyeon C Perez-Salas U Briber RM Woodson SA Thirumalai D 《Physical review letters》2005,95(26):268303
We determine the persistence length l(p) for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P(r) obtained from small angle x-ray scattering intensity data to the asymptotic form of the calculated P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length. 相似文献
15.
Reisner W Beech JP Larsen NB Flyvbjerg H Kristensen A Tegenfeldt JO 《Physical review letters》2007,99(5):058302
We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around 100 x 100 nm in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion. 相似文献
16.
Recent experiments revealed the unusual strong spin effects with high spin selective transmission of electrons in double-stranded DNA. We propose a new mechanism that the strong spin effects could be understood in terms of the combination of the ehiral structure, spin-orbit coupling, and especially spin-dependent Anderson localization. The presence of chiral structure and spin-orbit coupling of DNA induce weak Fermi energy splitting between two spin polarization states. The intrinsic Anderson localization in generic DNA molecules may result in remarkable enhancement of the spin selective transport. In particular, these two spin states with energy splitting have different localization lengths. Spin up/down channel may have shorter/longer localization length so that relatively less/more spin up/down electrons may tunnel through the system. In addition, the strong length dependence of spin selectivity observed in experiments can be naturally understood. Anderson localization enhanced spin selectivity effect may provide a deeper understanding of spin-selective processes in molecular spintronics and biological systems. 相似文献
17.
We report single-DNA-stretching experiments showing that the protein Fis, an abundant bacterial chromosome protein of E. coli, mediates a dramatic DNA condensation to zero length. This condensation occurs abruptly when DNA tension is reduced below a protein-concentration-dependent threshold f* < 1 pN. Following condensation, reopening under larger forces proceeds via a series of discrete jumps, indicating that Fis is able to stabilize DNA crossings. Our experiments suggest that Fis may play a role in vivo stabilizing the "loop-domain" structure of the bacterial chromosome. 相似文献
18.
《中国科学:物理学 力学 天文学(英文版)》2010,(6)
We report the studies of ultrafast dynamics of azobenzene cations using femtosecond photoionization-photofragmentation spectroscopy. In our experiment,a femtosecond pump pulse first prepares an ensemble of azobenzene cations via photoionization of neutrals. A delayed probe pulse then brings the evolving ionic system to higher states that ultimately undergo ion fragmentation. The dynamics is followed by monitoring either the parent-ion depletion or fragment-ion formation as a function of the pump-probe delay time. The observed transients for azobenzene cations are characterized by a constant ion depletion modulated by a rapidly damped oscillatory signal with a period of about 1 ps. Theoretical calculations suggest that the oscillation arises from a vibration motion along the twisting inversion coordinate involving displacements in CNNC and phenyl-ring torsions. The oscillation is damped rapidly with a time constant of about 1.2 ps,suggesting that energy dissipation from the active mode to bath modes takes place on this time scale. 相似文献
19.
The statistical-thermodynamic analysis of the compact structure (globule) of a flexural stiff macromolecule in the two-dimensional square lattice model is proposed. It is shown that the anisotropy of monomer direction distribution increases with increasing rigidity. The temperature dependence of the globule size turns out to be non-monotonic under fixed pressure. 相似文献
20.
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters. 相似文献