UNCONVENTIONAL HELICAL PHASING OF REPETITIVE DNA MOTIFS REVEALS THEIRRELATIVE BENDING CONTRIBUTIONS

A novel, multiple DNA phasing analysis is described in which three seq uence motifs associated with bent DNA are clustered together in oligom ers of identical base composition, but with different phasing relation ships of these motifs to each other. Synthetic oligonucleotides contai ning different combinations of AAAAA(A), GGGCCC and GAGAG sequence mot ifs were ligated and analyzed by gel mobility and cyclization experime nts to determine their global curvature, These assays were used to obt ain relative bending contributions of the analyzed sequence motifs. Th e experimental results also provide a rigorous test of predictive mode ls for DNA bending. We report, using molecular modeling, that none of the most widely used dinucleotide (nearest neighbor) models can accura tely describe the conformational properties of these DNA sequences and that more complex models, at least at the trinucleotide level, are re quired.