Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG•C+ triplets

The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR. H-1 NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds, Determination of the C-13 chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants ((1)J(CH)) conclusively showed that the Hoogsteen cytosine residues are protonated at N3, The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 Angstrom). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+ triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine, Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximate to 60 degrees and y approximate to 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.