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Nucleic Acids Research, 1992, Vol. 20, No. 24 6455-6460
© 1992

CHEMISTRY

Solution conformation of an oligonucleotide containing a urea deoxyribose residue in front of a thymine

V. Gervais, A. Guy1, R. Téoule1 and G. V. Fazakerley*

Service de Biochimie et de Génétique Moléculaire, DBCM, Centre d'Etudes de Saclay 91191 Gif-sur-Yvette Cedex 1Laboratoires de Chimie/Radiobiochimie, Département de Recherche Fondamentale, Centre d'Etudes Nucléaires de Grenoble BP 85X, 38041 Grenoble Cedex, France

*To whom correspondence should be addressed

Received November 3, 1992. Revised November 26, 1992. Accepted November 26, 1992.

Urea residues are produced by ionizing radiation on thymine residues in DNA. We have studied an oligodeoxynucleotide containing a thymine opposite the urea residue, by one and two dimensional NMR spectroscopy. The urea deoxyribose exists as two isomers with respect to the orientation about the peptide bond. For the trans isomer we find that the thymine and urea site are positioned within the helix and are probably hydrogen bonded. The oligonucleotide adopts a globally B form structure although conformational changes are observed around the mismatch site. A minor species is observed, in which the urea deoxyribose and the opposite base adopt an extraheiicai position and this corresponds to the isomer cis for the peptide bond.


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