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J. Biol. Chem., Vol. 277, Issue 32, 28491-28497, August 9, 2002
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From the Sequences of four or more AT base pairs without a
5'-TA-3' step, so-called A-tracts, influence the global properties of
DNA by causing curvature of the helix axis if phased with the helical repeat and also influence nucleosome packaging. Hence it is interesting to understand this phenomenon on the molecular level, and numerous studies have been devoted to investigations of dynamical and structural features of A-tract DNA. It was early observed that anomalously slow
base pair-opening kinetics were a striking physical property unique to
DNA A-tracts (Leroy, J. L., Charretier, E., Kochoyan, M., and
Gueron, M. (1988) Biochemistry 27, 8894-8898).
Furthermore, a strong correlation between DNA curvature and anomalously
slow base pair-opening dynamics was found. In the present work
it is shown, using imino proton exchange measurements by NMR
spectroscopy that the main contribution to the dampening of the base
pair-opening fluctuations in A-tracts comes from the C5 methylation of
the thymine base. Because the methyl group has been shown to have a
very limited effect on the DNA curvature as well as the structure of
the DNA helix, the thymine C5 methyl group stabilizes the helix directly. Empirical potential energy calculations show that methylation of the tract improves the stacking energy of a base pair with its
neighbors in the tract by 3-4 kcal/mol.
The Influence of the Thymine C5 Methyl Group on
Spontaneous Base Pair Breathing in DNA*
,
i
Sponer§¶
, and**
Department of Biochemistry and Biophysics,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
the § J. Heyrovský Institute of Physical
Chemistry, Academy of Sciences of the Czech Republic, Dolej
kova
3, 182 23 Prague 8, Czech Republic, and the ¶ Institute of
Biophysics and National Center for Biomolecular Research, Academy
of Science of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
*
This work was supported by the Swedish Natural Science
Research Council, by the Magnus Bergvall Foundation, by the Harald Jeansson Foundation (to M. L.), and by Ministry of Education of the
Czech Republic Grant LN00A016 (National Center for Biomolecular Research) (to J. S.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence and direct questions regarding the
energy calculations may be addressed. Tel.: 420-5-415-17-133; Fax: 420-5-412-12-179; E-mail: sponer@ibp.cz.
**
To whom correspondence may be addressed. Tel: 46-8-16-24-47; Fax:
46-8-15-55-97; E-mail: leijon@dbb.su.se.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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