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J. Biol. Chem., Vol. 283, Issue 14, 8829-8836, April 4, 2008

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Mechanisms of Base Selection by the Escherichia coli Mispaired Uracil Glycosylase^*

Pingfang Liu¹, Jacob A. Theruvathu, Agus Darwanto, Victoria Valinluck Lao, Tod Pascal, William Goddard, III, and Lawrence C. Sowers²

From the Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California 92354 and the Department of Chemistry, California Institute of Technology, Pasadena, California 91125

The repair of the multitude of single-base lesions formed daily in cells of all living organisms is accomplished primarily by the base excision repair pathway that initiates repair through a series of lesion-selective glycosylases. In this article, single-turnover kinetics have been measured on a series of oligonucleotide substrates containing both uracil and purine analogs for the Escherichia coli mispaired uracil glycosylase (MUG). The relative rates of glycosylase cleavage have been correlated with the free energy of helix formation and with the size and electronic inductive properties of a series of uracil 5-substituents. Data are presented that MUG can exploit the reduced thermodynamic stability of mispairs to distinguish U:A from U:G pairs. Discrimination against the removal of thymine results primarily from the electron-donating property of the thymine 5-methyl substituent, whereas the size of the methyl group relative to a hydrogen atom is a secondary factor. A series of parameters have been obtained that allow prediction of relative MUG cleavage rates that correlate well with observed relative rates that vary over 5 orders of magnitude for the series of base analogs examined. We propose that these parameters may be common among DNA glycosylases; however, specific glycosylases may focus more or less on each of the parameters identified. The presence of a series of glycosylases that focus on different lesion properties, all coexisting within the same cell, would provide a robust and partially redundant repair system necessary for the maintenance of the genome.

Received for publication, August 27, 2007 , and in revised form, January 18, 2008.

^* This work was supported in part by National Institutes of Health Grants GM50351 and CA112293. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S11.

¹ Current address: Laboratory of Complex Diseases, Harvard University, Cambridge, MA.

² To whom correspondence should be addressed: Alumni Hall for Basic Science, Rm. 101, 11021 Campus St., Loma Linda, CA 92354. Tel.: 909-558-4480; Fax: 909-558-4035: E-mail: lsowers{at}llu.edu.

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