PROPERTIES OF MULTIPLE G-CENTER-DOT-A MISMATCHES IN STABLE OLIGONUCLEOTIDE DUPLEXES

The solution structure of the deoxydecanucleotide [d(GAGTGAACGA)].[d(G AGTGAACGA)] has been determined by NMR methods. This duplex, which con tains six G.A mismatches and four Watson-Crick base pairs, is thermody namically more stable than a decamer where T.A base pairs are substitu ted for the G.A mismatches, and is less stable than the duplex that co ntains G.C base pairs. Circular-dichroism spectroscopy indicates an ov erall B-like conformation for the decamer, but stronger than usual bas e stacking. H-1-NMR spectroscopy revealed that the N1H groups of the m ismatched guanine residues are not hydrogen bonded, and P-31-NMR showe d the presence of B-II phosphate conformations for the GpA steps. Deta iled analysis of the NMR data showed that all nucleotides have anti gl ycosidic torsion angles and S type sugar puckers. The G.A mismatches p air in the amino form as originally proposed by Li et al. [Li, Y., Zon , G. and Wilson, W. D. (1991) Proc, Natl Acad, Sci. USA 88, 26-30], wh ich results in extensive base-base stacking between the tandem G.A bas e pairs and their nearest neighbours. The terminal G.A base pairs are less stable than the central base pairs and show evidence of an equili brium between two conformations, one involving B-II phosphate.