Theoretical studies on conformation comparison of braid-like and triplex DNA

Based on the experimental data of scanning tunneling microscopy (STM), mode ls of three-stranded braid-like DNAs composed by three kinds of base triple ts AAA, TAT and GCA were constructed. We investigated the braid-like DNAs a nd their comparative tripler DNAs using a molecular mechanics method. The t hree strands of braid-like DNAs are proven equivalent, while those of tripl er DNAs are not. The conformational energies for braid-like DNAs were found to be higher than that for tripler DNAs. Each period in one strand of brai d-like DNA has 18 nucleotides, half of which are right-handed, while the ot her half are left-handed. Additional discussions concerning sugar puckering modes and the H-bonds are also included. (C) 1999 Elsevier Science B.V. Al l rights reserved.