CONFORMATIONAL PROPERTIES OF DNA HAIRPINS WITH TTT AND TTTT LOOPS

The DNA hairpins d[CGATCG-T(n)-CGATCG] (n = 3, 4) have been studied by NMR in order to gain information on hairpin conformation and flexibil ity. Resonance assignments were made using a combination of DQF-COSY, DQF-COSY{P-31}, NOESY, and H-1-P-31-COSY. These data also provide appr oximate coupling constant information which points out exceptionally f lexible regions of the phosphate backbone. The data for both hairpins reveal substantial flexibility within the loop segments. For n = 4, NO ESY data alone are insufficient to distinguish between two loop-foldin g motifs, although coupling constant data favor a conformation in whic h T(b) is folded toward the minor groove and is highly exposed to solv ent. This is in agreement with chemical shift data and susceptibility to modification by KMnO4. The phosphate backbone between T(c) and T(d) is exceptionally flexible, undergoing a facile exchange between (beta (t),gamma+) and (beta+,gamma(t)) conformers. A similar flexible phosph ate is observed between T(c) and C7 when n = 3. Differences in stem co nformation and dynamics in both hairpins are restricted to the two bas e pairs adjacent to the stem-loop junction. The C7pG8 stem phosphate a ppears to flip easily between (zeta-,alpha-) and (zeta-,alpha(t)) conf ormers when n = 4 but not when n = 3. Hairpin loop size thus affects t he conformational flexibility of the adjacent stem segment.