Nucleic Acids Research Advance Access originally published online on August 8, 2008
Nucleic Acids Research 2008 36(16):5319-5334; doi:10.1093/nar/gkn512
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Nucleic Acids Research, 2008, Vol. 36, No. 16 5319-5334
© 2008 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 |
Interactions between branched DNAs and peptide inhibitors of DNA repair
1Center for Microbial Sciences and Department of Biology and 2Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
*To whom correspondence should be addressed. Tel: +1 619 594 4490; Fax: +1 619 594 5676; Email: asegall{at}sunstroke.sdsu.edu
Received May 8, 2008. Revised July 23, 2008. Accepted July 25, 2008.
The RecG helicase of Escherichia coli unwinds both Holliday junction (HJ) and replication fork DNA substrates. Our lab previously identified and characterized peptides (WRWYCR and KWWCRW) that block the activity of RecG on these substrates. We determined that the peptides bind HJ DNA and prevent the binding of RecG. Herein, we present further evidence that the peptides are competitive inhibitors of RecG binding to its substrates. We have generated structural models of interactions between WRWYCR and a junction substrate. Using the fluorescent probe 2-aminopurine, we show that inhibitors interact with highest affinity with HJs (Kd = 14 nM) and 
4- to 9-fold more weakly with replication fork substrates. The fluorescence assay results agree with the structural model, and predict the molecular basis for interactions between HJ-trapping peptides and branched DNA molecules. Specifically, aromatic amino acids in the peptides stack with bases at the center of the DNA substrates. These interactions are stabilized by hydrogen bonds to the DNA and by intrapeptide interactions. These peptides inhibit several proteins involved in DNA repair in addition to RecG, have been useful as tools to dissect recombination, and possess antibiotic activity. Greater understanding of the peptides’ mechanism of action will further increase their utility.
Present addresses: Kevin V. Kepple, Invitrogen Corp., Carlsbad, CA, USA Namita Patel, Applied Biosystems, San Francisco, CA, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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