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J. Biol. Chem., Vol. 279, Issue 12, 11834-11842, March 19, 2004

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Comparative Kinetics of Nucleotide Analog Incorporation by Vent DNA Polymerase^*

Andrew F. Gardner, Catherine M. Joyce¶, and William E. Jack||

From the New England Biolabs Inc., Beverly, Massachusetts 01915 and the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520

Comparative kinetic and structural analyses of a variety of polymerases have revealed both common and divergent elements of nucleotide discrimination. Although the parameters for dNTP incorporation by the hyperthermophilic archaeal Family B Vent DNA polymerase are similar to those previously derived for Family A and B DNA polymerases, parameters for analog incorporation reveal alternative strategies for discrimination by this enzyme. Discrimination against ribonucleotides was characterized by a decrease in the affinity of NTP binding and a lower rate of phosphoryl transfer, whereas discrimination against ddNTPs was almost exclusively due to a slower rate of phosphodiester bond formation. Unlike Family A DNA polymerases, incorporation of 9-[(2-hydroxyethoxy)methyl]X triphosphates (where X is adenine, cytosine, guanine, or thymine; acyNTPs) by Vent DNA polymerase was enhanced over ddNTPs via a 50-fold increase in phosphoryl transfer rate. Furthermore, a mutant with increased propensity for nucleotide analog incorporation (Vent^A488L DNA polymerase) had unaltered dNTP incorporation while displaying enhanced nucleotide analog binding affinity and rates of phosphoryl transfer. Based on kinetic data and available structural information from other DNA polymerases, we propose active site models for dNTP, ddNTP, and acyNTP selection by hyperthermophilic archaeal DNA polymerases to rationalize structural and functional differences between polymerases.

Received for publication, July 29, 2003 , and in revised form, December 22, 2003.

^* 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.

^¶ Supported by National Institutes of Health Grant GM-28550.

^|| To whom correspondence should be addressed: New England Bio-labs Inc., 32 Tozer Rd., Beverly, MA 01915. Tel.: 978-927-5054; Fax: 978-921-1350; E-mail: jack{at}neb.com.

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