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Pure Appl. Chem., 2004, Vol. 76, No. 7-8, pp. 1563-1570

Abasic site stabilization by aromatic DNA base surrogates: High-affinity binding to a base-flipping DNA-methyltransferase

I. Singh, Christine Beuck, Anupam Bhattacharya, Walburga Hecker, V. S. Parmar, E. Weinhold and O. Seitz

Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India; Institut für Organische Chemie, RWTH Aachen, Prof.-Pirlet-Strasse 1, 52 056 Aachen, Germany; Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44 227 Dortmund, Germany; Institut für Chemie der Humboldt-Universität 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.