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Nucleic Acids Research, 1990, Vol. 18, No. 22 6621-6624
© 1990

MOLECULAR BIOLOGY

Formation of intramolecular triplex in homopurine-homopyrimidine mirror repeats with point substitutions

B.P. Belotserkovskii, A.G. Veselkov, S.A. Filippov1,{dagger}, V.N. Dobrynin1, S.M. Mirkin*,* and M. D. Frank-Kamenetskii

Institute of Molecular Genetics, Academy of Sciences of USSR Moscow 123182 1M.M.Shemyakin Institute of Bioorganic Chemistry Moscow, USSR

*To whom correspondence should be addressed

Received July 16, 1990. Revised October 13, 1990. Accepted October 13, 1990.

We have used two-dimensional gel electrophoresis to study the structural transition to the triplex H form of sequences 5'-AAGGGAGAAXGGGGTATAGGGGYAA-GAGGGAA-3' where X and Y are any DNA bases. The transition was observed at acid pH under superhelical stress. For X = Y = A or X = Y = G the sequences corresponded to homopurlne-homopyrimidine mirror repeats (H-palindrome) which are known to adopt the H form under acid pH and superhelical stress. We have shown that the H form is actually formed for all X and Y, though in cases other than X = Y = A and X = Y = G the transition requires larger negative superhelical stress. Different substitutions require different superhelicity levels for the transition to occur. Theoretical analysis of the data obtained made it possible to estimate the energy cost of triplex formation due to all possible mismatched base triads.

*Present address: Department of Genetics, University of Illinois at Chicago, 808 South Wood Street, Chicago, 1L 60612 USA

{dagger}Deceased


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