Open AccessProperties of multiple G · A mismatches in stable oligonucleotide duplexes
Author(s) -
LANE Andrew,
EBEL Susanne,
BROWN Tom
Publication year - 1994
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1994.tb18672.x
Subject(s) - chemistry , glycosidic bond , base pair , crystallography , stereochemistry , stacking , nuclear magnetic resonance spectroscopy , duplex (building) , circular dichroism , nucleotide , guanine , oligonucleotide , base (topology) , dna , biochemistry , organic chemistry , gene , enzyme , mathematical analysis , mathematics
The solution structure of the deoxydecanucleotide [d( GA GT GA AC GA )]·[d( GA GT GA AC GA )] 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. 1 H‐NMR spectroscopy revealed that the N1H groups of the mismatched guanine residues are not hydrogen bonded, and 31 P‐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.