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Nucleic Acids Research, 1992, Vol. 20, No. 8 1903-1908
© 1992

MOLECULAR BIOLOGY

Kinetic trapping of H-DNA by oligonucleotide binding

Boris P. Belotserkovskii, Maria M. Krasilnikova, Alexei G. Veselkov and Maxim D. Frank-Kamenetskii*

Institute of Molecular Genetics, Russian Academy of Sciences Moscow 123182, Russia

*To whom Correspondence should be addressed

Received January 24, 1992. Revised March 23, 1992. Accepted March 23, 1992.

Homopurine-homopyrimidine mirror repeats are known to adopt the H form under acidic pH and/or negative supercolling. In H-DNA, one half of the purine strand enters the triplex whereas the second half Is unstructured and can form duplex with complementary oligonucleotide. However, because the same oligonucleotide can form triplex with the homopurine-homopyrimidine insert, one could expect that oligonucleotide would make H-DNA thermodynamically less favorable, as was claimed by Lyamlchev et al. Nucl. Acids Res. 16, 2165– 2178 (1988). Now we show that complex between oligonucleotide and H-DNA, formed under conditions favorable for the H-form extrusion, is kinetically trapped in superhelical DNA and remains stable up much higher pH values than H-DNA alone. Experiments on chemical probing show that such complex exists for a plasmid with native superhelical density at pH7. We have also used this approach to demonstrate a pH-dependent structural transition in yeast telomeric sequence, d(C-ACACCCA)16.


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