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Nucleic Acids Research, 1988, Vol. 16, No. 14 6465-6475
© 1988

Articles

The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme

David L. Sloane, Myron F. Goodman1 and Harrison Echols

Department of Molecular Biology, University of California-Berkeley Berkeley, CA 94720 1Department of Biological Sciences, University of Southern California Los Angeles, CA 90089, USA

Received March 2, 1988. In common with other DNA polymerases, DNA polymerase III holoenzyme of E. coli selects the biologically correct base pair with remarkable accuracy. DNA polymerase III is particularly useful for mechanistic studies because the polymerase and editing activities reside on separate sub-units. To investigate the biochemical mechanism for base insertion fidelity, we have used a gel electrophoresis assay to measure kinetic parameters for the incorporation of correct and incorrect nucleotides by the polymerase ({alpha}) subunit of DNA polymerase III. As judged by this assay, base selection contributes a factor of roughly 104–105 to the overall fidelity of genome duplication. The accuracy of base selection is determined mainly by the differential KM of the enzyme for correct vs. incorrect deoxynucleoside triphosphate. The misinsertion of G opposite template A is relatively efficient, comparable to that found for G opposite T. Based on a variety of other work, the G:A pair may require a special correction mechanism, possibly because of a syn-anti pairing approximating Watson-Crick geometry. We suggest that precise recognition of the equivalent geometry of the Watson-Crick base pairs may be the most critical feature for base selection.


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