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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >DEPPDB — DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA
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DEPPDB — DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA

机译：DEPPDB — DNA静电势性质数据库：基因组DNA的静电性质

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摘要

The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB — DNA Electrostatic Potential Properties Database — was developed to hold and provide all available information on the electrostatic properties of genome DNA combined with its sequence and annotation of biological and structural properties of genome elements and whole genomes. Genomes in DEPPDB are organized on a taxonomical basis. Currently, the database contains all the completely sequenced bacterial and viral genomes according to NCBI RefSeq. General properties of the genome DNA electrostatic potential profile and principles of its formation are revealed. This potential correlates with the GC content but does not correspond to it exactly and strongly depends on both the sequence arrangement and its context (flanking regions). Analysis of the promoter regions for bacterial and viral RNA polymerases revealed a correspondence between the scale of these proteins' physical properties and electrostatic profile patterns. We also discovered a direct correlation between the potential value and the binding frequency of RNA polymerase to DNA, supporting the idea of the role of electrostatics in these interactions. This matches a pronounced tendency of the promoter regions to possess higher values of the electrostatic potential.
机译：基因组DNA的静电特性会影响其与不同蛋白质的相互作用，特别是RNA聚合酶对转录的调控。开发了DEPPDB（DNA静电势特性数据库）来保存并提供有关基因组DNA静电特性的所有可用信息，并结合其序列以及对基因组元素和整个基因组的生物学和结构特性的注释。 DEPPDB中的基因组是按分类进行组织的。目前，该数据库包含根据NCBI RefSeq的所有完全测序的细菌和病毒基因组。揭示了基因组DNA静电势分布的一般性质及其形成原理。该电势与GC含量相关，但与GC含量不完全相关，并且强烈取决于序列排列及其上下文（侧翼区域）。对细菌和病毒RNA聚合酶启动子区域的分析显示，这些蛋白质的物理性质和静电分布图谱之间存在对应关系。我们还发现了潜在价值与RNA聚合酶与DNA的结合频率之间的直接相关性，支持了静电在这些相互作用中的作用的想法。这与启动子区域具有较高静电势值的明显趋势相匹配。

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