Deppdb — Dna Electrostatic Potential Properties Database: Electrostatic Properties of Genome Dna Elements

Abstract

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.

DEPPDB v.3: a portal to study electrostatic and other physical properties of genome DNA and its elements

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Motivation and Aim: DNA is a highly charged molecule and its electrostatic and other physical properties define its shape in the functional space and greatly influence its interactions with different proteins, especially regulating transcription, in particular RNA-polymerases and transcription factors. Methods and Algorithms: The electrostatic potential around the double-helical DNA molecule was calculated by the original method [1] using a specially developed program package [2,3]. Calculations of other physical properties are based on the di-and trinucleotide content.

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