A DATABASE OF 32 DNA TRIPLETS TO STUDY TRIPLE HELICES BY MOLECULAR MECHANICS AND DYNAMICS

We present here a database of 32 deoxyribonucleotide triplets, that ca n be used as building blocks of triple helix forming deoxyribonucleoti des on a computer. This database is made of all the pairing schemes of the triplets ATT, GCC(+), ATA and GCG where the third base forms two hydrogen bonds with the purine of the first two Watson-Crick strands. The essential features of the known triple helices were preserved in t he resulting structures. A triple helix can be easily built from any c ombination of these basic triplets. Four homogeneous and alternate tri ple helices thus obtained were studied by molecular mechanics and dyna mics in vacuo. The results are in agreement with known experimental ob servations for ATT and suggest a possible structure for the GCG triple helix. In order to characterize the geometry of the structures obtain ed, the definitions of nucleic acid structure parameters (R.E. Dickers on et al., EMBO J. 8 (1989) 1-4) have been extended to triple helical polynucleotides.