CONFORMATIONS OF NICKED AND GAPPED DNA STRUCTURES BY NMR AND MOLECULAR DYNAMIC SIMULATIONS IN WATER

We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the b ase in front of the gap is a guanine. The continuous strand has the se quence 5'(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that th e global conformation is very close to canonical B-form DNA, but it di splays enhanced local flexibility. For the gap structure, we observe o nly one species in which the extra G is well stacked into the helix. T he two half-helices around this residue also show a B-form conformatio n. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely, Using dista nce constraints, MD calculations show that the nick conformation is ve ry close to a duplex with no lesion but is indeed more flexible in the central part, The gapped structure shows two families of conformation s. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two ca ses.