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Molecular & Cellular Proteomics 5:858-867, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Proteomic Approach to Identification of Proteins Reactive for Abasic Sites in DNA ^*

Robert A. Rieger, Elena I. Zaika^,,¶, Weiping Xie^||, Francis Johnson, Arthur P. Grollman^,, Charles R. Iden^,** and Dmitry O. Zharkov^,

From the Department of Pharmacology, Laboratory of Chemical Biology, and ^|| Proteomic Center, Stony Brook University, Stony Brook, New York 11794 and the Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine and Novosibirsk State University, Novosibirsk 630090, Russia

Apurinic/apyrimidinic (AP) sites, a prominent type of DNA damage, are repaired through the base excision repair mechanism in both prokaryotes and eukaryotes and may interfere with many other cellular processes. A full repertoire of AP site-binding proteins in cells is presently unknown, preventing reliable assessment of harm inflicted by these ubiquitous lesions and of their involvement in the flux of DNA metabolism. We present a proteomics-based strategy for assembling at least a partial catalogue of proteins capable of binding AP sites in DNA. The general scheme relies on the sensitivity of many AP site-bound protein species to NaBH₄ cross-linking. An affinity-tagged substrate is used to facilitate isolation of the cross-linked species, which are then separated and analyzed by mass spectrometry methods. We report identification of seven proteins from Escherichia coli (AroF, DnaK, MutM, PolA, TnaA, TufA, and UvrA) and two proteins from bakers’ yeast (ARC1 and Ygl245wp) reactive for AP sites in this system.

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