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Developing model systems for the NMR study of substituent effects on the N—H···N hydrogen bond in duplex DNA
Author(s) -
Ishikawa Rei,
Kojima Chojiro,
Ono Akira,
Kainosho Masatsune
Publication year - 2001
Publication title -
magnetic resonance in chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.483
H-Index - 72
eISSN - 1097-458X
pISSN - 0749-1581
DOI - 10.1002/mrc.941
Subject(s) - chemistry , deoxyuridine , deoxyadenosine , hydrogen bond , substituent , stereochemistry , proton nmr , dna , nucleoside , base pair , crystallography , molecule , organic chemistry , biochemistry
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.