SEQUENCE EFFECTS ON DNA STEREODYNAMICS - CONFORMATIONAL BEHAVIOR OF D-GGTAGIACTACC CONTAINING IA MISMATCHED BASE-PAIRS

An oligonucleotide d-GGTAGIACTACC (GC58) containing tandem inosine-adenosine (IA) mismatched base pairs has been studied by H-1 and P-31 NMR spectroscopy. Unique assignments of H-1 and P-31 spins have been achieved by 2D HELCO technique. The NOESY spectrum in 90% H2O + 10% (H2O)-H-2 has been used to assign all the exchangeable protons. NMR results indicate that at concentrationse above 2.5 mM, the molecule adopts a duplex structure. Cross-strand nOes between the 1NH proton of 16 and H2 proton of A7 and that between H2 of 16 and H2 of A7 provide evidence for IA base pairing, with both bases in anti conformation. The observed nOe connectivities d(1), d(2), and d(3) all the way from C12 to A7 and from T3 to G1 are consistent with a right-handed B-DNA conformation. However, the molecule adopts a more extended conformation in the mismatch region to accommodate the bulky IA base pairs. NMR experiments at lower concentrations indicate the coexistence of a monomeric structure in equilibrium with the duplex. 2D ROESY experiments at 1 mM concentration show that the conformation at the ends of the monomer does not deviate much from the corresponding region of the duplex, but the nucleotides in the central region undergo significant structural changes. The stereodynamics of GC58 differs significantly from an analogous dodecamer d-GGTACIAGTACC (CG58). A subtle change caused by the transposition of bases flanking the IA mismatch pairs provides greater stability both to the duplex and to the monomer in case of CG58.