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Nucleic Acids Research, 1984, Vol. 12, No. 19 7565-7580
© 1984

CHEMISTRY

Circular dkhroism measurements show that C·C+ base pairs can coexist with A·T base pairs between antiparallel strands of an oligodeoxynudeotide double-helix

Donald M. Gray+,, Tao Cui*, and Robert L. Ratliff

Program in Molecular Biology, University of Texas at Dallas Box 830688, Richardson, TX 75083 Genetics Group, Life Sciences Division, Los Alamos National Laboratory Box 1663, Los Alamos, NM 78545, USA

Received July 10, 1984. Revised September 17, 1984. Accepted September 17, 1984.

We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C·C+ base pairs at the ends of the oligomer. We found that both A·T and C·C+ base pairs formed in a coordinated fashion as the temperature and pH were lowered. The CD data of the helix form of the oligomer were consistent with the presence of paired oligomers, but not with hairpin loops. The pKa for formation of C·C+ base pairs between the C4 ends of the oligomer was higher than the pKa for formation of C·C+ base pairs in d(C8), indicating that the formation of C·C+ base pairs in the oligomer was Influenced by the presence of a paired A4T4 region. We conclude that A·T and C·C+ base pairs coexist in the self-complex of the oligomer and, therefore, that C·C+ base pairs can form between antiparallel DNA strands.

*On leave from the University of Science and Technology, Hefei, Anhui, The People's Republic of China

+To whome reprint requests should be addressed


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