The conformational and physico-chemical DNA properties

The sequence-dependent conformational and physico-chemical properties of DNA may be complementary to the probabilistic properties predominantly considered up to now. Essentially, the increasing volume of experimental data supports the evidence that transcription factor binding sites functioning is to a large extent determined by conformational features of DNA (Starr et al. 1995; Meierhans et al., 1997). A growing number of crystallographic and physico-chemical studies during the last decade propose the local non-similarity of conformational and physico-chemical DNA properties and their dependence on nucleotide context (Suzuki et al., 1997, Grzeskowiak, 1996; Frank et al., 1997). Numerous experimental studies of B-DNA helix enable to determine a considerable number of mean values of conformational and physico-chemical parameters of di- and trinucleotides (Gartenberg and Crothers, 1988; Sugimoto et al., 1996; Suzuki et al., 1996; Bolshoy et al., 1991; Gorin et al., 1995; Gotoh and Tagashira, 1981; Satchwell et al., 1986).

We have accumulated the values of conformational and physico-chemical B-DNA properties in a PROPERTY database. Each PROPERTY entry describes the only B-DNA property, either "conformational" or "physico-chemical". This property is entitled by the field PN; its quantitative value assigned to each dsDNA dinucleotide step can be found in the field DINUCLEOTIDE; the field PU contains the property unit. The field RN links to the database REFERENCE citing the literature sources, out of which the property values were taken. A marked dependence of conformational and physico-chemical DNA parameters on the local nucleotide context suggests the potential importance of these parameters for the functioning of DNA sites. To demonstrate the importance of B-DNA properties, each PROPERTY entry contains the field WW of the "GALLERY" type linking to the Web-page with the property histograms comparing random DNA and transcription factor binding site sequences.