Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution.

Nuclear Overhauser enhancements (NOEs) have been observed between some of the nonexchangeable protons of the self-complementary octanucleoside heptaphosphate d(G-G-T-A-T-A-C-C) in conditions under which duplex formation takes place. Comparison of inter- and intraresidue NOEs has made possible the assignment of all the aromatic and 1'- and 2'-ribosyl signals. In particular, and with the exception of the 5' terminal, NOEs of comparable magnitude are observed between H-8 of purines or H-6 of pyrimidines and pairs of anomeric protons. There are the H-1's of the nucleotide containing the relevant aromatic proton and those of the adjacent residue in the 5' direction. Differentially evolving NOEs are also generated between aromatic protons and the C-2' methylene protons on both the same residue and on the neighboring 5' residue. The relative magnitudes of these NOEs are discussed in terms of overall helical geometry and are consistent with a generally accepted B-type DNA model (R. Chandrasekaran and S. Arnott, personal communications).