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A structure based similarity measure for nucleic acid sequence comparison

Double strand DNA exhibits sequence dependent variations in three-dimensional conformation. Crystallographic studies have shown that regulatory proteins bind to DNA and may use these structural effects to indirectly recognize binding sites in a sequence specific manner. In this paper we describe a sequence similarity scoring measure based on the energetics of helix distortion. A set of preferred conformations is compiled from data in the Nucleic Acid Database ( NDB ) for 16 dinucleotide steps. These conformational parameters are combined with elastic force constants derived from solution studies of DNA to compute a log likelihood score for one sequence adopting the preferred conformation of another.