Properties of multiple G · A mismatches in stable oligonucleotide duplexes

The solution structure of the deoxydecanucleotide [d(GAGTGAACGA)]·[d(GAGTGAACGA)] has been determined by NMR methods. This duplex, which contains six G · A mismatches and four Watson‐Crick base pairs, is thermodynamically more stable than a decamer where T · A base pairs are substituted for the G · A mismatches, and is less stable than the duplex that contains G · C base pairs. Circular‐dichroism spectroscopy indicates an overall B‐like conformation for the decamer, but stronger than usual base stacking. ¹H‐NMR spectroscopy revealed that the N1H groups of the mismatched guanine residues are not hydrogen bonded, and ³¹P‐NMR showed the presence of B_II phosphate conformations for the GpA steps. Detailed analysis of the NMR data showed that all nucleotides have anti glycosidic torsion angles and S type sugar puckers. The G · A mismatches pair in the amino form as originally proposed by Li et al. [Li, Y., Zon, G. & Wilson, W. D. (1991) Proc. Natl Acad. Sci. USA 88, 26–30], which results in extensive base‐base stacking between the tandem G · A base pairs and their nearest neighbours. The terminal G · A base pairs are less stable than the central base pairs and show evidence of an equilibrium between two conformations, one involving B_II phosphate.