Conformations of the alternating (C-T)n sequence under neutral and low pH

The structures of the (C-T)n sequence at two different pHs have been analyzed by 500 MHz 2D-NMR using a modified DNA decamer d(CT[m5C]TCU[m5C]UCT) as a model system. The chemical modifications serve to perturb the monotonous C-T repeat, and consequently to yield a better chemical shift dispersion. The results reinforce our earlier suggestion that there are three major pH-dependent conformational species: two antiparallel-stranded (APS) duplexes at pH 7 and pH 3, and a different structure near pH 5. Structural refinement of the decamer duplexes at pH = 7.5 and pH = 2.9 using 2D-NOE data suggests that the C:T or C+:T base pairs are continuously stacked. Exchangeable proton NMR spectra at pH 7.5 and pH 2.9 are consistent with C:T or C+:T base pairing schemes in which a water molecule bridges the two bases.