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Use of 2-Aminopurine and Tryptophan Fluorescence as Probes in Kinetic Analyses of DNA Polymerase β

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Departments of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
Cite this: Biochemistry 2002, 41, 37, 11226–11235
Publication Date (Web):August 16, 2002
https://doi.org/10.1021/bi025837g
Copyright © 2002 American Chemical Society

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    Abstract

    Although the use of 2-aminopurine (2-AP) as a probe in stopped-flow analyses of DNA polymerase β (Pol β) had provided important mechanistic insight, the conditions used were limited by the location of 2-AP and the use of a combination of tryptophan (Trp) and 2-AP fluorescence. This study examined different DNA substrates to identify several factors that can affect the observed signal in stopped-flow experiments. Both Trp and 2-AP emissions were separately excited and monitored. It was found that both probes show a fast phase and a slow phase of fluorescence changes, but the direction and the amplitude vary greatly between the two probes and between different DNA substrates. Detailed analyses suggested that the location of 2-AP in the template has a significant impact on the fluorescence properties of 2-AP and that a location opposite the incoming dNTP, which has been used in all such studies in the past, is not optimal. In particular, the results show that placing 2-AP one base after the templating base greatly enhances the signal intensity, which suggests a significant change in base stacking interactions at this position during nucleotide incorporation. These results allowed us to derive an improved set of conditions which were then used to reevaluate results from previous reports. It also allows greater freedom in the type of base pairs studied, since 2-AP is not the templating base in the nascent base pair. Kinetic constants were determined for dNTP and catalytic Mg2+. The results obtained from stopped-flow experiments were compared to results from chemical quench. Stopped flow of incorrect dNTP incorporation and the reverse reaction are also reported, which provide useful information to the mechanism of Pol β.

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     This work was supported by NIH Grant GM43268. This is paper 10 in the series DNA Polymerase β. For paper 9, see ref 1.

     Department of Chemistry.

    *

     To whom correspondence should be addressed at the Department of Chemistry [telephone (614) 292-3080; fax (614) 292-1532; e-mail [email protected]].

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