Solution Structure of a GA Mismatch DNA Sequence, d(CCATGAATGG)₂, Determined by 2D NMR and Structural Refinement Methods

GA mismatches in DNA have drawn attention because of their special repair mechanisms, stability, and variety of conformations. A symmetric 10-base oligodeoxyribonucleotide duplex, d(CCATGAATGG)₂, containing two GA mismatches has been investigated by one- and two-dimensional multinuclear NMR and molecular refinement procedures to ascertain the conformational details of the 5′-pyrimidine-GA-purine-3′ sequence. A molecular model established from the NMR results has a B-type right-handed helix with each of the bases retaining the normal anti-glycosidic torsional angles. Type I mismatched base pairs have GNH₂-AN7 and GN3-ANH₂ (edge-to-edge) hydrogen bonds, while type II base pairs have GN1H-AN1 and GO6-ANH₂ (face-to-face) bonds. The conformation at the GA mismatch site has type I GA base pairs and an unusual cross-strand stacking of the adjacent G5 and A6 bases, which causes significant overwinding of the helix at the mismatch site. Unusual shifts of the ³¹P resonances suggest that the phosphate linkage between G5 and A6 is no longer in the low-energy B_I conformation. One-dimensional imino and phosphorus NMR studies were carried out on a number of DNA sequences containing adjacent 5′-GA-3′ mismatched base pairs to investigate the sequence dependence of the conformations and base-pairing types. Type I and type II conformations have very different imino proton and ³¹P NMR spectral patterns that can be used to classify any sequence with adjacent GA mismatches by base-pairing and conformational type. The NMR results indicate that the conformation selected is dictated completely by the flanking sequence: 5′-pyrimidine-GA-purine-3′ sequences adopt the type I conformation, while 5′-purine-GA-pyrimidine-3′ sequences have the type II conformation.