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

✍ Scribed by Rei Ishikawa; Chojiro Kojima; Akira Ono; Masatsune Kainosho

• Publisher: John Wiley and Sons
• Year: 2001
• Tongue: English
• Weight: 165 KB
• Volume: 39
• Category: Article
• ISSN: 0749-1581
• DOI: 10.1002/mrc.941

✦ Synopsis

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-2deoxyuridine 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 pK 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.