Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA.
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.
Osypov
Alexander A
AA
Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino 142290, Russia. aosypov@gmail.com
Krutinin
Gleb G
GG
Kamzolova
Svetlana G
SG
D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics*; D008956:Models, Chemical; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods; D013329:Structure-Activity Relationship
D004247:DNA; D012321:DNA-Directed RNA Polymerases