Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA.cntdot.dC mismatch site
- 3 July 1984
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 23 (14) , 3218-3226
- https://doi.org/10.1021/bi00309a016
Abstract
Deoxyadenosine-deoxycytidine pairing at symmetrically related dA.cntdot.dC mismatch sites in the d(C1-G2-C3-G4-A5-A6-T6-T5-C4-A3-C2-G1) self-complementary duplex (12-mer AC) was investigated by proton and phosphorus NMR studies in aqueous solution. Base pairing is maintained on either side of the mismatch site in the 12-mer AC duplex at low temperature. The proton chemical shifts and NOE (nuclear overhauser effect) measurements rule out models in which the H-2 proton of adenosine at the mismatch site is stacked over adjacent dG.cntdot.dC base pairs. A comparison of the H-exchange kinetics in the d-(C-G-C-G-A-A-T-T-C-G-C-G) duplex (12-mer) with standard dG.cntdot.dC base pairs at position 3 from either end with the 12-mer AC duplex, which contains dA.cntdot.dC mismatches at these positions, demonstrates kinetic destabilization at dG.cntdot.dC base pair 4 adjacent to the mismatch site and at dA.cntdot.dT base pairs 5 and 6 far from this site. This contrasts with previous H-exchange studies on the 12-mer GT and 12-mer GA duplexes where the kinetic destabilization was localized to base pair 4, which is adjacent to the mispairing site. The melting temperature of the 12-mer AC duplex in 0.1 M phosphate is .apprx. 30.degree. C lower than the corresponding value for the 12-mer duplex. This indicates that the overall duplex stability is affected to a greater degree on replacing 2 dG.cntdot.dC base pairs by dA.cntdot.dC pairs compared to replacement by either dG.cntdot.dT or dG.cntdot.dA pairs. Perturbations in the phosphodiester backbone of the 12-mer AC duplex can be readily detected by the observation of a downfield-shifted resolved phosphorus resonance assigned tentatively to a phosphate at the mismatch site.This publication has 9 references indexed in Scilit:
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