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Nucleic Acids Research, 1984, Vol. 12, No. 21 8269-8279
© 1984

CHEMISTRY

Helix opening in deoxyribonucleic add from a proton nuclear magnetic resonance study of imino and araino protons in d(CG)3

G.Victor Fazakerley1, Gijs A. van der Marel2, Jacques H. van Boom2 and Wilhelm Guschlbauer1

1Service de Biochimie, Bat. 142, Département de Biologie, Centre d'Etudes Nucléaires de Saclay F-91191 Gif-sur-Yvette Cédex, France 2Gorlaeus Laboratories, State University of Leiden P.O. Box 9502. NL-2300RA Leiden. The Netherlands

Received July 31, 1984. Revised October 9, 1984. Accepted October 9, 1984.

All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first tine. As a function of temperature the cytidine amino protons and the amino protons behave very similarly, their relaxation is dominated by exchange with solvent above 30C. The guanosine amino protons, however, show that helix opening can only be described by a multistate model. The most rapid process observed is probably a twist about the helix axis which lengthens or breaks the guanosine amino hydrogen bond and allows rotation of the amino group. The second fastest process is a scissor opening into the major groove which gives rise to solvent exchange with the imino and cytidine amino protons. The slowest process observed is the complete base pair opening in which the guanosine amino protons also exchange with solvent. For the ammonium salt of the oligonucleotide, a specific amnoniun ion complex is observed which at low temperature may catalyze exchange of the guanosine amino protons with the protons of the amonium ion, but retards exchange with solvent. The complex appears to be specific for the sequence d(CpG).


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