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‐ 15 N]‐2′‐deoxyuridine derivatives, including thymidine, 2′‐deoxyuridine, 5‐bromo‐2′‐deoxyuridine, 5‐fluoro‐2′‐deoxyuridine and 5‐cyano‐2′‐deoxyuridine, and [ ul ‐ 15 N]‐2′‐deoxyadenosine, were synthesized and incorporated into the DNA dodecamer, d(CGCGA* ATX* CGCG) 2 , where X* and A* were a [3‐ 15 N]‐2′‐deoxyuridine derivative and [ ul ‐ 15 N]‐2′‐deoxyadenosine, respectively. The imino proton chemical shift and the spin coupling constant between the imino proton and nitrogen [ 1 J(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 1 J(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 p K a 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. Copyright © 2001 John Wiley & Sons, Ltd.