Usability of BioCon2 for nucleic acid structures in database.

With the specific three-dimensional structure, DNA/RNA molecules express the specific structural and catalytic functions. The knowledge integration based on three dimensional structures can be used to explain biochemical observations, to predict biological functions and to design drugs specific to a given complex system. In the large RNAs, the helical stems close to each other with specific arrangement. The polymorphic nature of multiple stranded helical structure of nucleic acid relates a promising technique of achieving base sequence specific recognition and hence artificial gene regulation. The database cataloging the interaction motifs of nucleic acid moieties has been developed. Skew matrix, a kind of kink parameter, affords the structural description between the adjacent moieties. The program BioCon2 for estimating these skew matrix and cataloguing for multiple stranded helices has been developed. New version allows for the good properties, i.e., impregnable and flexible presentation of multiple helices. The tentative database including these parameters with the species and physical properties of the surrounding nucleic acid components and amino acids has been constructed.