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Nucleic Acids Research Advance Access originally published online on February 6, 2007
Nucleic Acids Research 2007 35(5):1478-1487; doi:10.1093/nar/gkm018
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Nucleic Acids Research, 2007, Vol. 35, No. 5 1478-1487
© 2007 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping

Stuart R.W. Bellamy, Kuakarun Krusong and Geoff S. Baldwin*

Division of Molecular Biosciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London, SW7 2AZ, UK

*To whom correspondence should be addressed. Tel: +(44) 20 7594 5228; Fax: +(44) 20 7584 2056; Email: g.baldwin{at}imperial.ac.uk

Received November 10, 2006. Revised December 20, 2006. Accepted January 2, 2007.

Uracil DNA glycosylase (UNG) is the primary enzyme for the removal of uracil from the genome of many organisms. A key question is how the enzyme is able to scan large quantities of DNA in search of aberrant uracil residues. Central to this is the mechanism by which it flips the target nucleotide out of the DNA helix and into the enzyme-active site. Both active and passive mechanisms have been proposed. Here, we report a rapid kinetic analysis using two fluorescent chromophores to temporally resolve DNA binding and base-flipping with DNA substrates of different sequences. This study demonstrates the importance of the protein–DNA interface in the search process and indicates an active mechanism by which UNG glycosylase searches for uracil residues.

Present address: Stuart R.W. Bellamy, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK Kuakarun Krusong, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand


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