Nucleic Acids Research, 1992, Vol. 20, No. 8 1933-1941
© 1992
CHEMISTRY |
The pH dependent configurations of the C.A mispair in DNA
Service de Biochimie et de GÉné Motéculaire, DÉpartement de Biologie Cellulaire et MolÉculaire, Centre d'Etudes de Saclay 91191 Gif-sur-Yvette Cedex 1Laboratoire de Physicochimie MacromolÉculaire, Institut Gustave Roussy F-94800 Villejuif, France 2Division of Pediatrics, City of Hope National Medical Center Duarte, CA 91010, USA
*To whom correspondence should be addressed
Received January 20, 1992. Revised March 20, 1992. Accepted March 20, 1992.
The structure of the cytosine-adenine mispair in a 7 base pair duplex has been investigated by proton NMR spectroscopy. At low pH, the predominant structure is protonated on the A residue and assumes a wobble conformation consistent with previous findings. The C residue of the mispair is found in a C2'-C3' endo eqllibrium. This is confirmed by molecular dynamics calculations which suggest that the conformation of the protonated wobble is flexible and not as rigid as a normal base pair. As the solution pH is raised, a structural transition is observed with an apparent pK of 7.54 at 23°C. At higher pH the predominant structure is one in which both the C and A residues are Intrahelical. Evidence is presented that this structure corresponds to a reverse wobble in which the two bases are held together by one hydrogen bond. This structure is much less stable than the protonated form and even at low temperature single strands are observed in slow exchange with the neutral duplex form.