Effect of spermine and DNase on DNA release from bacteriophage T5

Bacterial viruses (bacteriophages) consist of nucleic acid protected by a protein envelope called capsid. At the start of infection, the phage genome is translocated into the bacterial cytoplasm. In vitro (and also in vivo), this DNA release can be triggered by binding a specific receptor protein to the phage tail. The force responsible for the release arises from energy stored in the capsid due to strong confinement of the DNA. We show that this force can be modified by adding molecules like spermine that affect DNA conformation. The tetravalent cation spermine can reduce the pressure inside the capsid and induce condensation of the released DNA. We examine the effect of spermine on DNA ejection from phage T5 by using light scattering and gel electrophoresis to measure the amount of DNA remaining in the capsid at the end of ejection. We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid.     

Physical Approaches to the Study of DNA

New micromanipulation techniques now enable physicists and biologists to study the behavior of single biomolecules such as DNA. In particular, it is possible to measure the elastic response of individual DNA molecules to changes in the double helix's supercoiling. The force versus extension diagram for torsionally relaxed DNA is continuous and allows one to evaluate the persistence length of the polymer. When the molecule is supercoiled, however, stretching leads to the buildup of torsional stress in the double helix's axis. When the twist energy thus generated increases beyond a critical value, the molecule is locally destabilized and changes conformation. This structural transition occurs at stretching forces which can be exerted in vivo by molecular motors and at degrees of supercoiling found in the cell, and may have implications for DNA structure and function within the nucleus.     

Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes.     

Long range correlation and possible electron conduction through DNA sequences

Long range correlation analysis and charge conductivity investigation are applied to sequences in 16 chromosomes in the Saccharomyces cerevisiae genome. DNA sequence data are analyzed via Hurst’s analysis and Detrended Fluctuation Analysis (DFA) analysis. Super diffusive nature of mapping sequences are evident with the measured Hurst exponent H to be around the value of 0.60 for all sequences in the 16 chromosomes. The DFA result is consistent with the result from the Hurst analysis. Tight binding models are applied for the investigation of charge conduction through DNA sequences. The overall averaged transmission coefficients, 〈T_N〉_av, calculated from sixteen chromosomes are shown to be significantly different from values calculated from random as well as periodic sequences. Sequences from the S. cerevisiae genome promise better charge conduction ability than random sequences. Finally, delocalized electronic wave function patterns are also shown through calculations using the tight binging model. Slightly delocalized electronic wavefunctions are seen on sequences in sixteen chromosomes, as compared with those obtained from random sequences on the same eigenenergies.     

X射线和过氧化氢引起的Hela细胞染色质损伤的微区拉曼光谱研究

我们成功地用微区拉曼光谱探针技术获得了培养单个活体 Hela 细胞核中染色质的拉曼光谱。从光谱中我们看到正常 Hele 细胞核蛋白的二级结构为 a 螺旋,DNA 为 A 型构象。经10~(-3)moI/L 过氧化氢处理20分钟及8Gy x 射线照射后的 Hela 细胞核蛋白的二级结构出现反平行β折叠,DNA 出现 B 型构象。这种结果与我们的假设是相符合的。     

Finite-Size Conformational Transitions：A Unifying Concept Underlying Chromosome Dynamics

Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization, from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.     

Chromosome evolution with naked eye: palindromic context of the life origin

Based on the representation of the DNA sequence as a two-dimensional (2D) plane walk, we consider the problem of identification and comparison of functional and structural organizations of chromosomes of different organisms. According to the characteristic design of 2D walks we identify telomere sites, palindromes of various sizes and complexity, areas of ribosomal RNA, transposons, as well as diverse satellite sequences. As an interesting result of the application of the 2D walk method, a new duplicated gigantic palindrome in the X human chromosome is detected. A schematic mechanism leading to the formation of such a duplicated palindrome is proposed. Analysis of a large number of the different genomes shows that some chromosomes (or their fragments) of various species appear as imperfect gigantic palindromes, which are disintegrated by many inversions and the mutation drift on different scales. A spread occurrence of these types of sequences in the numerous chromosomes allows us to develop a new insight of some accepted points of the genome evolution in the prebiotic phase.     

Helix coil mixing in twist-storing polymers

Twist-storing polymers respond with elastic energy penalty to coherent or random twisting along the local chain axis away from its equilibrium, which can be straight (as in “ribbons”) or helical (as in DNA and other biopolymers). Here we study the equilibrium conformation of such polymers, focusing on the thermodynamic balance between twist and writhe, resulting from the competition between the random coil entropy and the potential energy stored in superhelical portions of the polymer chain. Two macroscopic variables characterise such a chain, the end-to-end distance R and the link number Lk, which is a topological invariant of a given polymer with clamped ends. We find that with increasing link number Lk, the chain accommodates its excess twist in growing plectonemes, unless forced out of this state by stretching its end-to-end distance R. We calculate the force-extension relation, which exhibits crossovers between different deformation regimes. Received 16 November 2000 and Received in final form 6 February 2001     

The karyotype and sex chromosomes of Praomys tullbergi (Muridae, Rodentia): a detailed characterization

Here we present the first detailed characterization of Praomys tullbergi karyotype, enlightening several chromosome features such as constitutive heterochromatin, telomeric and LINE-1 sequences. The combination of these approaches provided some interesting insights about the genome organization of this African species, which is one of the tullbergi complex elements, a group of species belonging to Murinae (Rodentia, Muridae). Evolutionary considerations on Praomys chromosomes were also achieved, namely, the autosomal complement and the X chromosome from P. tullbergi seem to be derivative chromosomes, most probably resulting from extensive reshufflings during the course of evolution. This conclusion came from the fact that the majority of the chromosomes telomeric sequences are located interstitially, seeming footprints of evolutionary chromosome rearrangements. The detailed analysis of Praomys tullbergi X chromosome suggests that chromosome rearrangements and/or centromere transpositions and addition/elimination of heterochromatin must have been the main evolutionary events that shaped this chromosome.     

共轭聚合物单分子构象和能量转移特性研究

利用基于宽场显微光学系统的单分子散焦成像技术测量了不同构象poly[2,7-(9,9-dioctylfluorene)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole](PFO-DBT)共轭聚合物单分子的光物理与动力学特性.通过分析共轭聚合物单分子的荧光轨迹和对应的发射偶极取向变化识别共轭聚合物单分子发光单元,发现延伸构象下的单分子呈现多发色团发光特性,而折叠构象下的单分子保持高效链间能量转移,呈现单个发色团发光特性.共轭聚合物单分子构象对能量转移效率的影响可用于研究基于共轭聚合物的光电器件和分子器件.     

重离子诱导的质粒DNA双链断裂分布研究

利用能量为7．2MeV／u氖离子束辐照体外质粒DNA:pUC18，采用恒场凝胶电泳结合多功能荧光成像系统研究了pUC18双链断裂片段的分布。证实了双链断裂片段分布的非随机性，结果还发现DNA断裂后片段的交联现象，而且交联片段的分布也是非随机的。DNA is considered to be the most important and sensitive target in biological systems. In addition to the base damage, DNA strand breaks are the major lesion in the genome due to exposure to ionizing radiation. Mutation can be introduced to DNA as a result of enzymatic processing of DNA lesions or post irradiation replication. However, the mechanisms of radiation induced mutations are not well clarified at the molecular level. To study the effect on the simple plasmid DNA of heavy ion is even predominant or more feasible. Plasmid pUC18 DNA was prepared and irradiated by neon beam (7.199 MeV/u). The fragment distributions were determined by quantifying the ethidium bromide fluorescence. It can be seen that the shape of the intensity distributions is vastly different for the used radiation Dose. The distribution produced shows an excess of fragments particularly in 3 000 and 10 000 Gy the size range between 20—40 kbp and 20—50 bp. This clustering of double stranded fragments might be influenced by the higher order chromatin structure of genomic DNA. If so, DNA loop structures could correspond to the size range for which we observed DSB clustering. Further studies aim at elucidating the heterogeneity of DSB induction within the genome and investigate the influence of chromatin structure on the non random fragment distribution.     

Synthesis and luminescence properties of dye-doped deoxyribonucleic acid films

Dye-doped deoxyribonucleic acids (DNA)–tetradecyltrimethylammonium (TTA) films have been prepared. Rhodamine 6G, known as laser dyes, can be spontaneously doped by immersing the DNA–TTA film in rhodamine 6G-acetonitrile solutions. It is surmised that rhodamine 6G monomers and dimers diffuse within the hydrophobic TTA sites, and then monomers presumably intercalate between adjacent base pairs of DNA. Optical absorption spectra reveal that rhodamine 6G molecules in the sample undergo an unusual transformation from the dimer state to the monomer state with the elapse of time. Rhidamine 6G molecules doped in DNA–TTA show enhanced photostability and concentration quenching than those in PMMA. The environment, conformation and chemical stability of rhodamine 6G are different between DNA–TTA and PMMA, and are presumably modified by the intercalation.     

Mechanism and Properties of Non-Thermally Biological Effect of the Millimeter Waves

The electromagnetic features of biomacromolecules are foundation of interaction between the millimeter waves and living systems. Therefore we first reveal the electromagnetic features of biomacromolecules, for example, protein, DNA and lipid. Next we calculate the rotational energy-spectra of these biomacromolecules by quantum mechanical theory. The transitions of electrons between the rotational energy-levels can result in radiations or absorptions of millimeter waves. Thus we propose the mechanism and properties of non-thermally biological effect of the millimeter waves, i.e., the millimeter waves are absorbed by these biomacromolecules which can result in rotation and changes of conformations of these molecules, thus the energy of the millimeter waves are to be transformed as the mechanical energy of the conformation changes of the biomacromolecules, but not as thermal energy of motions of these biomacromolecules to increase their temperature. This mechanism is verified by experiments of conformation changes of the protein and amino acid molecules exposed under the millimeter waves. These rotations of conformations of these molecules can results in obvious biological effects. We study the features of the biological effects.PACS numbers: 33.20.-Eat, 33.10.-n, 78.30.-j; 87.50. Hi     

DNA 环化时间的半经验计算方法

DNA 分子是生命遗传信息的主要物质载体。DNA 环化是DNA 不同位置所携带信息的 一种协同实现方式。典型的例子是转录调控，增强子通过DNA 环化与启动子相互作用，从而 实现了对基因表达水平的调控。因此，破译DNA 的环化动力学是解读基础生命过程的重要课 题。本文在介绍DNA 结构和力学性质的基础上，综述DNA 环化时间的计算方法。在生理条件 下，DNA 的主要性质特点是弯折柔性强，而扭转和拉伸刚性强；据此，DNA 环化可视作自发 的熵减过程。运用热力学统计理论，可获得计算DNA 环化时间的半经验公式。公式中的参数可 由单分子光谱共聚焦技术测得的数据确定。该公式表明，空间拓扑决定了环化概率，DNA 长度 决定了环化时间。该公式适用于计算DNA 上的顺式元件之间、顺式元件与启动子之间的相互作 用。其优点在于避开了DNA 结构和细胞核环境的复杂性。     

A novel family of space-filling curves in their relation to chromosome conformation in eukaryotes

Spatial conformation of DNA chains during interphase in eukaryotic cell nucleus is relatively dense, yet unknotted and exhibits self-similar fractal properties. In this respect it resembles the space-filling curves of Hilbert, but differs in the experimentally accessible contact probability of distant loci. Here we construct space-filling curves with fractal domain boundaries of dimension close to that of the embedding space and show how these match the statistical properties and the contact probability of the DNA conformation. The present mathematical model should shed light on the statistical ensemble of unknotted dense polymers and ease the modeling of genome folding and related biological processes.     

Thionine Interaction to DNA: Comparative Spectroscopic Studies on Double Stranded Versus Single Stranded DNA

Interaction of thionine with double stranded and single stranded calf thymus DNA has been studied by absorbance, fluorescence, competition dialysis, circular dichroism and isothermal titration calorimetry. Binding to the native double stranded DNA conformation induced strong quenching in fluorescence spectrum of thionine. Linear Scatchard plots indicated the binding to be of one type and the affinity values evaluated to be of the order of 10⁵ M⁻¹ with double stranded DNA. Fluorescence quenching was much weaker with single stranded DNA and the binding affinity was about one order lower. Ferrocyanide quenching studies revealed that the fluorescence emission of dye molecules bound to the double stranded DNA was quenched much less compared to those bound to the single stranded DNA. Furthermore, there was significant emission polarization for the bound dye molecules and strong energy transfer from the DNA base pairs to the dye molecules indicating intercalative binding to ds DNA. Salt dependence of the binding phenomenon revealed that electrostatic forces played a significant role in the binding process. The intercalation of the dye molecules to double stranded DNA and simple stacking to single strands was proved from these fluorescence techniques. Support to the fluorescence results have been derived from absorption, circular dichroic and dialysis results. Calorimetric studies suggested that the binding to ds DNA conformation was both enthalpy and entropy favoured while that to ss DNA was predominantly entropy favoured.     

DNA-based tunable THz oscillator

The intrinsic helix conformation of the DNA strands is known to be the key ingredient of control of the electric current through the molecule by the perpendicular (gate) electric field. We show theoretically that Bloch oscillations in periodic systems with helical conformation are also strongly affected by such lateral field; the oscillation frequency splits into a manifold of several generally non-commensurate frequencies leading to a complicated pattern of the charge motion. For model parameters typical for the DNA the frequency of such oscillations falls in the THz domain, suggesting a possibility to design a DNA-based nano-scale source of THz radiation.     

Theoretical investigation on surface‐enhanced Raman evidence for conformation transition of dimercaptoazobenzene adsorbed on gold nanoclusters

Probing and controlling the configurations and mechanical motions of the azobenzenes adsorbed on the metal substrates are preliminary for their applicability in various functional devices. In this work, we presented a detailed investigation of Raman properties of the dimercaptoazobenzene (DMAB) bound to gold nanoclusters using density functional calculations. It is demonstrated that the spectral features of the trans conformation of DMAB are quite different from the cis conformation, and the Raman intensities of the trans‐DMAB are much larger. Magnitude of chemical enhancement for the adsorbed trans‐DMAB is found to be close to or less than that for the adsorbed cis‐DMAB for the molecule–cluster complexes. This change trend can be, to a large extent, governed by the energy difference between the highest occupied energy level of the molecule and the lowest unoccupied energy level of the gold. Moreover, it is further demonstrated that differences in Raman intensities of the two conformations can be amplified for the cluster–molecular–cluster junctions, and thus chemical enhancement is much larger for the trans conformation than the cis conformation, possibly facilitating the experimental identification of the trans/cis DMAB. Copyright © 2012 John Wiley & Sons, Ltd.