THEORETICAL PREDICTION OF SEQUENCE-DEPENDENT DNA SUPERSTRUCTURES AND THEIR IMPLICATIONS IN RECOGNITION MECHANISMS WITH PROTEINS

Superstructures of biologically relevant DNA fragments were obtained from the sequence by integrating the theoretically evaluated local deviations from the canonical B-DNA structure produced by the differential interactions in the 16 different dinucleotide steps. The theoretical model was tested on 450 multimeric oligonucleotides different for sequence, periodicity, and length, and reproduced their electrophoretic behaviors with surprisingly good approximation. A very good agreement was also obtained between the theoretical and experimental gel electrophoretic mobility changes following point mutations in a Sv40 DNA tract. The application to the set of the 177 different nucleosomal DNA tracts of Satchwell et al. revealed a very significant distribution pattern of the curvature phases along the sequence, which accounts for the main features of the nucleosome structure. This distribution allowed the localization of virtual nucleosome positions near the Sv40 origin of replication using the correlation function with the corresponding curvature diagrams in good agreement with the experimental map.