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Nucleic Acids Research 2006 34(9):2528-2535; doi:10.1093/nar/gkl300
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Published online 10 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Kinetics of error generation in homologous B-family DNA polymerases

Matthew Hogg, Wendy Cooper, Linda Reha-Krantz1,* and Susan S. Wallace*

Department of Microbiology and Molecular Genetics, University of Vermont Burlington, Vermont 05405 1 Department of Biological Sciences, University of Alberta Edmonton, Alberta T6G 2E9, Canada

*To whom correspondence should be addressed. Tel: +1 802 656 2164; Fax: +1 802 656 8749; Email: Susan.Wallace{at}uvm.edu

*Correspondence may also be addressed to Linda Reha-Krantz. Tel: +1 780 492 5383; Fax: +1 780 492 9234; Email: linda.reha-krantz{at}ualberta.ca

Received January 31, 2006. Revised March 2, 2006. Accepted April 7, 2006.

The kinetics of forming a proper Watson–Crick base pair as well incorporating bases opposite furan, an abasic site analog, have been well characterized for the B Family replicative DNA polymerase from bacteriophage T4. Structural studies of these reactions, however, have only been performed with the homologous enzyme from bacteriophage RB69. In this work, the homologous enzymes from RB69 and T4 were compared in parallel reactions to determine the relative abilities of the two polymerases to incorporate correct nucleotides as well as to form improper pairings. The kinetic rates for three different exonuclease mutants for each enzyme were measured for incorporation of an A opposite T and an A opposite furan as well as for the formation of A:C and T:T mismatches. The T4 exonuclease mutants were all ~2- to 7-fold more efficient than the corresponding RB69 exonuclease mutants depending on whether a T or furan was in the templating position and which exonuclease mutant was used. The rates for mismatch formation by T4 were significantly reduced compared with incorporation opposite furan, much more so than the corresponding RB69 mutant. These results show that there are kinetic differences between the two enzymes but they are not large enough to preclude structural assumptions for T4 DNA polymerase based on the known structure of the RB69 DNA polymerase.


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Home page
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M. Hogg, P. Aller, W. Konigsberg, S. S. Wallace, and S. Doublie
Structural and Biochemical Investigation of the Role in Proofreading of a beta Hairpin Loop Found in the Exonuclease Domain of a Replicative DNA Polymerase of the B Family
J. Biol. Chem., January 12, 2007; 282(2): 1432 - 1444.
[Abstract] [Full Text] [PDF]


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