DNA Repair 2 (2003) 863–878 Initiation of repair of A/G mismatches is modulated by sequence context Ana M. Sanchez a , David E. Volk b , David G. Gorenstein b , R. Stephen Lloyd a,∗ a Sealy Center for Molecular Science and The Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555-1071, USA b Sealy Center for Structural Biology and The Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555-1157, USA Accepted 28 March 2003 Abstract The efficiency of DNA glycosylases to initiate base excision repair (BER) has been demonstrated to be modulated by the precise sequence context in which the lesion or mismatch is located. In the case of DNA containing an A/G mismatch, in which the recognition and excision of adenine from the mismatch is mediated by the Escherichia coli MutY enzyme, not only does the local sequence context affect the strength of base stacking interactions, but it also modulates the syn/anti conformation around the glycosyl bond of the bases in the mispair. Utilizing prior NMR data to identify DNA sequence contexts that adopt either an anti/anti or a syn/anti configuration at an A/G mismatch, we tested the hypothesis that the initial equilibrium of the mismatched base orientations would modulate the overall efficiency of glycosyl bond scission. By systematically varying the sequence context around a central A/G mismatch within a 30-mer duplex DNA, significant kinetic differences were observed that were consistent with this hypothesis. Since the relative efficiency of the kinetics fell into only two groupings, a NMR study was conducted on a DNA sequence context of unknown syn/anti conformation. These data established that the relative syn/anti conformation did not correlate with the excision efficiency, as well as there being a lack of correlation between kinetics and thermal stability of these DNAs. © 2003 Elsevier B.V. All rights reserved. Keywords: DNA repair; DNA glycosylases; MutY 1. Introduction Although high fidelity DNA replication is manda- tory for the ultimate survival of organisms, occasionally mismatched bases may be formed and lead to per- manent mutations during subsequent rounds of DNA duplication. Correction of these mismatches by DNA repair systems is critical for minimizing mutagenesis ∗ Corresponding author. Tel.: +1-409-772-2179; fax: +1-409-772-1790. E-mail address: rslloyd@utmb.edu (R.S. Lloyd). and for higher organisms, carcinogenesis. The removal of mispaired nucleotides involves several different DNA repair pathways, including base excision repair (BER) [1,2], and mismatch repair [3,4]. Overall, BER is responsible for the recognition, removal and re- placement of a single nucleotide or a very short patch of nucleotides that previously contained the damaged or mispaired base. The initial step of this process is cat- alyzed by DNA glycosylases that cleave the C1 ′ -N gly- cosyl bond to yield an apurinic/apyrimidinic (AP) site. One of the most abundant oxidative DNA lesions is 8-oxo-7,8-dihydroguanosine (8-oxoG), that is created 1568-7864/$ – see front matter © 2003 Elsevier B.V. All rights reserved. doi:10.1016/S1568-7864(03)00067-3