Abasic site stabilization by aromatic DNA base surrogates: High-affinity
binding to a base-flipping DNA-methyltransferase
I. Singh, C. Beuck, A. Bhattacharya, W. Hecker, V. S. Parmar, E. Weinhold, and O. Seitz
Bioorganic Laboratory, Department of Chemistry, University
of Delhi, Delhi 110 007, India; Institut f�r Organische Chemie, RWTH
Aachen, Prof.-Pirlet-Strasse 1, 52 056 Aachen, Germany; Max-Planck-Institut
f�r Molekulare Physiologie, Otto-Hahn-Strasse 11, 44 227 Dortmund, Germany;
Institut f�r Chemie der Humboldt-Universit�t zu Berlin, Brook-Taylor-Str.2,
D-12489 Berlin, Germany
Abstract: DNA-methyltransferases catalyze the sequence-specific
transfer of the methyl group of S-adenosylmethionine to target
bases in genomic DNA. For gaining access to their target embedded within
a double-helical structure, DNA-methyltransferases (DNA-MTases) rotate
the target base out of the DNA helix. This base-flipping leads to the
formation of an apparent abasic site. MTases such as cytosine-specific
MHhaI and MHaeIII and also the repair enzyme uracil DNA
glycosylase (UDG) insert amino acid side chains into the opened space
and/or rearrange base-pairing. The adenine-specific DNA MTase MTaqI
binds without amino acid insertion. This binding mode allows for a substitution
of the orphaned thymine with larger DNA base surrogates without steric
interference by inserted amino acid side chains. DNA containing pyrenyl,
naphthyl, acenaphthyl, and biphenyl residues was tested in MTaqI
binding studies. The synthesis of DNA building blocks required the formation
of a C-glycosidic bond, which was established by using protected
1-chloro-2-deoxy- ribose as glycosyl donor and organocuprates as glycosyl
acceptors. It is shown that all of the base surrogates enhanced the
binding affinity to MTaqI. Incorporation of pyrene increased
the binding affinity by a factor of 400. Interestingly, there is a correlation
between the observed order of dissociation constants and the ability
of a base surrogate to stabilize abasic sites in model duplexes.
*Lecture presented at the symposium "Chemistry of nucleic acids", as part of the 39th IUPAC Congress and 86th Conference of the Canadian Society for Chemistry: Chemistry at the Interfaces, Ottawa, Canada, 10-15 August 2003. Other Congress presentations are published in this issue, pp. 1295-1603.
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