Developing model systems for the NMR study of substituent effects on the N?H���N hydrogen bond in duplex DNA

The substitution effects on various parameters, which may influence the hydrogen bond strengths of Watson–Crick-type base pairs, were investigated for DNA dodecamers containing 5-substituted-2′-deoxyuridine derivatives. In doing so, a series of [3-15N]-2′-deoxyuridine derivatives, including thymidine, 2′-deoxyuridine, 5-bromo-2′-deoxyuridine, 5-fluoro-2′-deoxyuridine and 5-cyano-2′-deoxyuridine, and [ul-15N]-2′-deoxyadenosine, were synthesized and incorporated into the DNA dodecamer, d(CGCGA* ATX* CGCG)2, where X* and A* were a [3-15N]-2′-deoxyuridine derivative and [ul-15N]-2′-deoxyadenosine, respectively. The imino proton chemical shift and the spin coupling constant between the imino proton and nitrogen [1J(N,H)] were measured for the Watson–Crick-type A*–X* base pair of all five duplexes. The substitution with an electron-withdrawing group results in downfield shift of the imino proton and a concomitant decrease in magnitude of the 1J(N,H) value, and a good, linear correlation was found between the two effects. These substitution effects on the NMR parameters were linearly correlated with the pKa values of the 2′-deoxyuridine derivatives and also with the theoretically calculated hydrogen bond energy. The linear correlations found here indicate that the DNA oligomers with 5-substituted-2′-deoxyuridine provide a good model to study the nature of the hydrogen bond in Watson–Crick-type base pairs.