Issue February 2002

category image Volume 19
No. 4 (p 571-730)
February 2002
ISSN 0739-1102

Unifying Themes in DNA Replication: Reconciling Single Molecule Kinetic Studies with Structural Data on DNA Polymerases (p. 571-584)

Structural data suggest that DNA polymerases, from at least three different families, employ common strategies for carrying out DNA replication. Universal features include a large conformational change in the enzyme-template complex and a conserved active-site geometry that imposes a sharp kink at the 5? end of the template strand. Recent single molecule experiments have shown that stretching the DNA template markedly alters the rate of DNA synthesis catalyzed by these motor enzymes. From these data, it was previously inferred that T7 DNA polymerase and two related enzymes convert two or four (depending on the enzyme) single-stranded (ss) template bases to double helix geometry in the polymerase active site during each catalytic cycle. We discuss structural data on related DNA polymerases, which suggest that only one (ss) template base is contracted to dsDNA geometry during the rate-limiting step of each replication cycle. Previous interpretations relied upon the global stretching curves for DNA polymers alone (with no reference to the enzyme or the structure of the transition state). In contrast, we present a structurally guided model that presumes the force dependence of the replication rate is governed chiefly by local interactions in the immediate vicinity of the enzyme?s active site. Our analysis reconciles single molecule kinetic studies with structural data on DNA polymerases.

Anita Goel1*
Tom Ellenberger2
Maxim D. Frank-Kamenetskii3
Dudley Herschbach4

1Department of Physics
Harvard-MIT Joint Division of Health Sciences and Technology
Harvard University
Cambridge, MA 02138, USA
2Department of Biological
Chemistry and Molecular Pharmacology
Harvard Medical School
Boston, MA 02115, USA
3Center for Advanced Biotechnology
Department of Biomedical Engineering
Boston University
Boston, MA 02215, USA
4Department of Chemistry and
Chemical Biology
Harvard University
Cambridge, MA 02138, USA
*goel@physics.harvard.edu

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