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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 elements
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DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome dna elements

机译：DEPPDB-DNA静电势特性数据库。基因组dna元素的静电特性

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摘要

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB- DNA Electrostatic Potential (and other Physical) Properties Database- provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.
机译：基因组DNA的静电性质对其与不同蛋白质的相互作用特别是与转录有关非常重要。 DEPPDB- DNA静电势（和其他物理）特性数据库-提供有关基因组DNA的静电和其他物理特性的信息，并结合其序列以及对基因组及其元素的生物学和结构特性的注释。基因组以分类学为基础进行组织，以支持比较和进化研究。目前，根据NCBI RefSeq，DEPPDB包含所有完全测序的细菌，病毒，线粒体和质体基因组，以及一些模型真核基因组。启动子，调控位点，结合蛋白等的数据来自已建立的数据库和文献。该数据库辅以分析工具。用户序列计算可用。案例研究发现静电补充了大肠杆菌质粒BNT2启动子功能中的DNA弯曲，可能影响宿主环境的代谢转换。转录因子结合位点被吸引到高电位区域，证实了静电在蛋白质-DNA相互作用中的普遍重要性超出了经典的启动子-RNA聚合酶的识别和调控。其他基因组元素，例如终止子，也显示出静电特性。最有趣的是基因起始，表现出生物分类学上的相关性。讨论了基因组静电特性研究的必要性。

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