一种新的DNA序列进化距离及其应用

为了研究核苷酸变异,通过DNA序列的同源率,建立了DNA序列进化的动力学方程,进而得到了一种新的物种间进化距离dy(选择进化距离).由于核苷酸替代模型有很多,选用其中的4种模型,计算出其相应的选择进化距离dy,该进化距离包含了4种模型下的p距离、替代率为常数的距离d和替代率服从Г分布的Г距离dG.进一步根据动力学方程的特点,将模型转化为一元线性回归问题,用最小二乘法求得选择模型中的动力学参数b和各核苷酸位点每年的平均替代速率r.以16个物种的线粒体基因序列为例,说明这种新的进化距离并通过构建不同进化距离下的基因进化树来对各进化距离进行比较.结果表明:选择进化距离dy是一种有效的构建进化距离的方法.     

基于混沌游走方法的Rh血型系统中RHD基因的分析

利用基于经典HP模型的蛋白质序列混沌游走方法（chaos game representation,CGR）,给出了RHD基因的蛋白质序列CGR图,可视作蛋白质序列二级结构的一个特征图谱描述．对临床上的血型鉴别有一定的参考价值．另外．还根据由Jeffrey在1990年提出的描绘DNA序列的CGR方法,给出了RHD基因的DNA序列的CGR图．并且根据RHD基因DNA序列的CGR图算出了尺日D基因相应的马尔可夫两步转移概率矩阵,从概率矩阵表可以看出RHD基因对编码氨基酸的三联子的第3个碱基的使用偏好性．     

增广Kalman滤波器在维生素C二步发酵中的应用

本文在维生素C二步发酵动力学模型研究的基础上,引进增广Kalman滤波器理论,将数学模型、发酵系统和实际操作等因素引起的偏差归为白噪声序列,用于发酵状态及模型参数的滤波处理。结果表明：滤波估计比模型计算的拟合精度大为提高。通过对模型参数的分析,加深了对该系统动力学特性的认识,为维生素c二步发酵过程的状态估计、状态预测及在线辨识奠定了理论基础。     

体外装配核小体过程组蛋白浓度依赖的动力学模型

为探索组蛋白浓度对核小体体外装配的影响,本研究表达纯化了4种组蛋白,通过控制实验反应体系中组蛋白的浓度,利用盐透析法在体外装配了核小体,检测分析了组蛋白浓度与核小体组装效率的关系。以此实验数据为基础,提出了核小体组装过程组蛋白浓度依赖性的动力学模型。实验结果发现,反应体系中组蛋白浓度与核小体生成量呈典型的线性关系。依据动力学理论模型,进行线性回归拟合,回归系数达到0.963;经计算601 DNA序列组装核小体的反应速率常数k为1.49×10^-5mL·h·μg^-1。CS1序列验证动力学模型的线性回归相关系数为0.989,反应速率常数为1.52×10^-5mL·h·μg^-1。该实验方法及动力学模型中反应速率常数k可用于评价相同长度的DNA序列组装核小体的能力、组蛋白与其突变体以及组蛋白变体之间形成核小体结构能力的差异。该动力学模型的建立为理解核小体装配、核小体定位、染色质结构等相关问题提供了理论指导。     

外显子与内含子序列的分形尺度参数可分性研究

近年来, 关于ＤＮＡ 序列的分形尺度特性的研究引起了研究者广泛的兴趣, 许多研究表明,ＤＮＡ 序列的外显子和内含子区域具有不同的分形尺度特性,这有可能成为区别外显子和内含子序列的特征之一。文中应用ＷＴＭＭ（ Ｗａｖｅｌｅｔ Ｔｒａｎｓｆｏｒｍ Ｍｏｄｕｌｕｓ Ｍａｘｉｍ） 方法分析ＤＮＡ 序列的分形结构,计算表征分形结构尺度特性的量化参数 Ｈｌｄｅｒ 指数。考虑到外显子序列的三联体编码特性, 计算了ＤＮＡ 序列及三个不同的相位序列分别在三种ＤＮＡ ｗａｌｋ 方式下得到的序列的Ｈｌｄｅｒ 指数,并将每个Ｈｌｄｅｒ 指数作为一维特征,考察外显子与内含子序列的分布。计算结果表明,只按单个分形尺度参数来看,外显子与内含子不具有可分性。在此基础上,从模式识别的角度出发, 将外显子与内含子视为由此构成的多维特征空间中的两个模式类, 由此设计基于ＬＬＭ（ＬｏｃａｌＬｉｎｅａｒ Ｍａｐ） 神经网络的分类器,并对分类器的错误率进行估计,实验结果表明外显子序列与内含子序列在此特征空间中具有聚类特性,从而表明以这一组分形尺度参数作为序列特征,外显子与内含子具有可分性。这一结果为研究外显子与内含子序列的识别算法提供了新的线索     

人、鼠、兔β-珠蛋白基因的信息分析

信息熵的计算是分析DNA分子结构和进化规律的有效方法之一。人们通过计算二联碱基水平的熵的偏离D_2揭示了DNA分子进化的方式,同时表明,D_2可作为进化指标。随着基因的核苷酸序列的不断确定,有可能进一步分析DNA的信息特性。本文就从三联碱基水平计算人、鼠、兔β-珠蛋白基因的各项熵值,并就这些结果在DNA的结构和进化特性上作些探讨。一、材料和方法我们用的材料是人、兔β-珠蛋白基因和鼠β~(maj)——珠蛋白基因,它们的核苷酸序列已完全确定。计算方法 (1)碱基实际出现概率的计算取DNA     

基于贝叶斯网络的DNA序列剪接位点预测

采用基于贝叶斯网络的建模方法,预测真核生物DNA序列中的剪接位点．分别建立了供体位点和受体位点模型,并根据两种位点的生物学特性,对模型的拓扑结构和上下游节点的选择进行了优化．通过贝叶斯网络的最大似然学习算法求出模型参数后,利用10分组交互验证方法对测试数据进行剪接位点预测。结果显示,受体位点的平均预测准确率为92．5％,伪受体位点的平均预测准确率为94．0％,供体位点的平均预测准确率为92．3％,伪供体位点的平均预测准确率为93．5％,整体效果要好于基于使用独立和条件概率矩阵、以及隐Markov模型的预测方法．表明利用贝叶斯网络对剪接位点建模是预测剪接位点的一种有效手段．     

牛乳腺核基质附着区多重顺式作用序列表明其功能的多样性

高等真核细胞的染色体DNA通过基质结合区(MAR)不时地与核基质特异性结合而组织成一种空间环状结构。为了研究以DNA套环形式附着于核基质上的DNA序列的特性,从处于泌乳期的乳腺组织中克隆了多个MAR DNA序列。体外结合实验表明,这些序列能够同核基质蛋白共结合成不溶性的复合物,这些复合物可较容易的通过离心去除。其中,两个MAR序列中包含有TL、CA—和GA—阻断以及ATTA基序。这两个序列中含有多个复制／转录因子的结合位点、增强子基序、多个完全的和非完全的反向重复序列以及潜在的DNA弯曲核心序列样结构。同一DNA序列中存在不同元件的组合可能说明在控制一系列细胞的发育过程中,它们可能发挥有正的或负的调控元件的功能。     

非编码保守DNA序列形成与演化机制

作为一种系统进化足迹,基因组非编码保守DNA序列受到极大关注。由于非编码保守DNA序列很可能与转录因子或特异蛋白质相互作用,直接参与调控基因表达或稳定染色体结构等重要的生命活动。因此,它极有可能成为基因组研究的下一个新浪潮。在总结对生物非编码保守DNA序列的认识过程的基础上,详细阐述了非编码保守DNA序列形成与演化的模型及其分子生物学机制,进一步展望了非编码保守DNA序列在生物学研究中的应用前景。     

DNA序列的多重分形Hurst分析

为了深入研究基因组序列的多重分形性质,首先选取12条较长的DNA序列,并根据此12条DNA序列的编码／非编码片段将DNA序列转换成相应的12条时间序列,其次对这12个时间序列进行多重分形Hurst分析,计算它们的Hurst指数,并且利用Hurst指数分析序列的自相似性,进一步将得到的Hurst指数与DNA一维游走模型相比较,发现12条序列均具有长程相关性,这说明DNA序列中确实存在着长程相关现象。     

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein–DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50–100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA.     

Plant chromatin -- epigenetics linked to ATP-dependent remodeling and architectural proteins

Studies in organisms belonging to different eukaryotic kingdoms have revealed that the structural state of chromatin is controlled by interactions of DNA, small RNAs and specific proteins, linked to a self-reinforcing complex network of biochemical activities involving histone and DNA modifications and ATP-dependent nucleosome remodeling. However, these findings must now be reinterpreted in light of the recent discovery of the highly dynamic character of interphase chromosomes exemplified by the constant flux of enzymatic and structural proteins through both eu- and heterochromatin and by short- and long-range chromosome movements in the nucleus. The available data on chromosome organization in Arabidopsis thaliana and links between proteins influencing chromatin structure and DNA and histone modifications documented in this model plant provide strong supportive evidence for the dynamic nature of chromosomes.     

Topological effects on the electrophoretic mobility of rigid rodlike DNA in polyacrylamide gels

The electrophoretic migration of rigid rodlike DNA structures with well defined topologies has been investigated in polyacrylamide (PA) hydrogels prepared by copolymerization of acrylamide and N, N'-methylenebisacrylamide. Previous studies have reported structural and dynamic characteristics of linear and branched DNA during electrophoresis in PA gels using a variety of experimental parameters. However, a thorough investigation aimed at establishing specific relationships between topological features of rigid rodlike DNA structures and their electrophoretic behavior is still needed. In order to study these topological effects on mobility, an intensive examination of the electrophoretic mobility of small linear and starlike DNA was performed. A series of model DNA structures with well-defined branched topologies were synthesized with varying molecular parameters, such as number of arms surrounding the branch point and arm length. The electrophoretic mobility of these structures was then contrasted with a series of data obtained using linear DNA of comparable molecular size. When large DNA stars (M >/= 60 bp) were compared with linear DNA of identical molecular weight, the Ferguson plots were quite different. However, small DNA stars (24-32 bp) and linear analogues had identical Ferguson plots. This indicates that a different motional mode or greater interaction with the gel exists for the larger DNA stars. When the total molecular weight of the DNA stars was held constant and the number of arms varied, the Ferguson plots for all the stars were identical. Additionally, a critical pore size was reached when the ratio of linear DNA mobility to star DNA mobility increased dramatically. Thus, while the incorporation of a single branch point can produce a large reduction in mobility, above a critical molecular size, the incorporation of additional branch points does not appear to provide further reduction in mobility. This finding is consistent with the transport properties of large synthetic star polymers, where a large reduction in their diffusion coefficient is observed when a single branch is added. When additional arms are incorporated, large synthetic stars do not display an appreciable further reduction in diffusion coefficient. The effect of arm length on mobility for rigid rod DNA stars was also studied. For four-arm DNA stars, the mobility was found to scale as an exponential function of the arm length. Finally, a recently proposed phenomenological model was used to successfully fit the mobility data for linear rigid rod DNA at various concentrations of PA.     

Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites

Using molecular dynamics simulations in explicit solvent, we investigated the behavior of a 50-bp DNA sequence containing the 434 bacteriophage operators OR1 and OR2 separated by an 8-bp spacer. Two simulations of 1 ns each were carried out, with DNA alone and with DNA complexed to dimers of the R1-69 DNA binding domain of the phage 434 cI repressor protein at the OR1 and OR2 sites. Strong correlations among average structural parameters are observed between our simulations and available experimental data for the bound OR1/OR2 subsites. In the free state, some differences appear between the three relevant fragments (OR1, the spacer, and OR2). Unbound OR1 exhibits a large, shallow major groove into which the base atoms protrude and is also bent toward the major groove. This structure is maintained because structural fluctuations are weak. Unbound OR2 resembles canonical B-DNA although the structural parameters show greater fluctuations, essentially due to a malleable step (the innermost CpA/TpG), absent in OR1. Complexation with the proteins slightly alters the base positions but strongly modifies the sugar and backbone motions. The most crucial repressor effects are changes in the flexibility of the OR1/OR2 sites. Structural fluctuations are enhanced for OR1, conferring a favorable energetic contribution to the OR1 binding, whereas they are reduced for OR2. Therefore, both structural and dynamic properties of DNA suggest OR1 is the most attractive site for the repressor, which may explain the different binding association constants observed for the OR1 and OR2 sites. Finally, we also investigated the impact of the protein on the DNA backbone dynamics and find that direct or indirect interactions facilitate the DNA structural variations required for achieving complementarity with the protein.     

Simulation of double-stranded branch point migration.

A structural and dynamic model has been developed for the branch point formed when two DNA double helices exchange strands during genetic recombination. This model, which generalizes most previous structural models, maintains the twofold symmetry inherent in the covalent and hydrogen bonded structure, yet has three degrees of freedom about virtual bonds, constituting a simplified junction. Using this structural model, a three-step dynamic model for branch point migration has been developed: longitudinal diffusion about the virtual bonds to achieve a structure in which the helix axes are approximately parallel; opening of the base pairs; and rotary diffusion about the helix axis to effect a migratory event. The model, which includes the possible role of electrostatic interactions, solves problems inherent in previous treatments. We find that no significant electrostatic torques arise that promote branch point migration. The absence of a kinetic mechanism to circumvent thermodynamic barriers due to mispairing suggests that an energy source is used for those situations in living systems.     

The DNA-binding domain in the Bacillus subtilis transition-state regulator AbrB employs significant motion for promiscuous DNA recognition

AbrB is a Bacillus subtilis protein responsible for regulating a diverse array of unrelated genes during periods of sub-optimal growth conditions. DNA binding by AbrB is unique in that sequence recognition is specific, yet no obvious consensus sequence of bound promoter regions is apparent. The N-terminal domain is a recently characterized representative of a novel class of DNA-binding proteins that possess a looped-hinge helix DNA-binding topology. Although the structural characterization of this DNA-binding topology contributed to an understanding of the architectural basis for recognition of DNA target sequences, specific mechanisms responsible for promiscuity in DNA sequence recognition still were not apparent. Analysis of (15)N backbone relaxation parameters shows that dynamic motion of regions directly linked to DNA binding show concerted motion on the microsecond-millisecond timescale. Furthermore, dynamic motion of the hinge region suggests that the DNA-binding region is capable of conformational orientations that allow it to accommodate DNA sequence variability in the cognate binding sites.     

Meta analysis of Chronic Fatigue Syndrome through integration of clinical, gene expression, SNP and proteomic data

The histone octamer induced bending of DNA into the super-helix structure in nucleosome core particle, is very unique and vital for DNA packing into chromatin. We collected 48 nucleosome crystal structures from PDB and applied a multivariate analysis on the nucleosome structural data. Based on the anisotropic nature of DNA structure, a principal conformational subspace (PCS) is derived from multiple properties to represent the most significant variances of nucleosome DNA structures. The coupling of base pair-oriented parameters with sugar phosphate backbone parameters presented in principal dimensionalities reveals two main deformation modes that have supplemented the existing physical model. By using sequence alignment-based statistics, a positiondependent conformational map for the super-helical DNA path is established. The result shows that the crystal structures of nucleosome DNA have much consistency in position-specific structural variations and certain periodicity is found to exist in these variations. Thus, the positions with obvious deformation patterns along the DNA path in nucleosome core particle are relatively conservative from the perspective of statistics.     

Presynaptic filament dynamics in homologous recombination and DNA repair

Homologous recombination (HR) is an essential genome stability mechanism used for high-fidelity repair of DNA double-strand breaks and for the recovery of stalled or collapsed DNA replication forks. The crucial homology search and DNA strand exchange steps of HR are catalyzed by presynaptic filaments-helical filaments of a recombinase enzyme bound to single-stranded DNA (ssDNA). Presynaptic filaments are fundamentally dynamic structures, the assembly, catalytic turnover, and disassembly of which must be closely coordinated with other elements of the DNA recombination, repair, and replication machinery in order for genome maintenance functions to be effective. Here, we reviewed the major dynamic elements controlling the assembly, activity, and disassembly of presynaptic filaments; some intrinsic such as recombinase ATP-binding and hydrolytic activities, others extrinsic such as ssDNA-binding proteins, mediator proteins, and DNA motor proteins. We examined dynamic behavior on multiple levels, including atomic- and filament-level structural changes associated with ATP binding and hydrolysis as evidenced in crystal structures, as well as subunit binding and dissociation events driven by intrinsic and extrinsic factors. We examined the biochemical properties of recombination proteins from four model systems (T4 phage, Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens), demonstrating how their properties are tailored for the context-specific requirements in these diverse species. We proposed that the presynaptic filament has evolved to rely on multiple external factors for increased multilevel regulation of HR processes in genomes with greater structural and sequence complexity.     

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.