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J Biol Chem, Vol. 274, Issue 11, 6957-6962, March 12, 1999

High Base Pair Opening Rates in Tracts of GC Base Pairs

Utz DornbergerDagger , Mikael Leijon§, and Hartmut FritzscheDagger

From the Dagger  Institut für Molekularbiologie, Friedrich-Schiller-Universität, Winzerlaer Strasse 10, D-07745 Jena, Germany and the § Department of Biophysics, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden

Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.

Copyright © 1999 by The American Society for Biochemistry and Molecular Biology, Inc.
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