4 research outputs found
Recommended from our members
A pre-catalytic non-covalent step governs DNA polymerase β fidelity
DNA polymerase beta (pol beta) selects the correct deoxyribonucleoside triphosphate for incorporation into the DNA polymer. Mistakes made by pol beta lead to mutations, some of which occur within specific sequence contexts to generate mutation hotspots. The adenomatous polyposis coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the underlying mechanism is not fully understood. In previous work, we demonstrated that a somatic colon cancer variant of pol beta, K289M, misincorporates deoxynucleotides at significantly increased frequencies over wild-type pol beta within a mutation hotspot that is present several times within the APC gene. Kinetic studies provide evidence that the rate-determining step of pol beta catalysis is phosphodiester bond formation and suggest that substrate selection is governed at this step. Remarkably, we show that, unlike WT, a pre-catalytic step in the K289M pol beta kinetic pathway becomes slower than phosphodiester bond formation with the APC DNA sequence but not with a different DNA substrate. Based on our studies, we propose that precatalytic conformational changes are of critical importance for DNA polymerase fidelity within specific DNA sequence contexts.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State
We examine the DNA
polymerase β (pol β) transition
state (TS) from a leaving group pre-steady-state kinetics perspective
by measuring the rate of incorporation of dNTPs and corresponding
novel β,γ-CXY-dNTP analogues, including individual β,γ-CHF
and -CHCl diastereomers with defined stereochemistry at the bridging
carbon, during the formation of right (R) and wrong (W) base pairs.
Brønsted plots of log <i>k</i><sub>pol</sub> versus
p<i>K</i><sub>a4</sub> of the leaving group bisphosphonic
acids are used to interrogate the effects of the base identity, the
dNTP analogue leaving group basicity, and the precise configuration
of the C-X atom in <i>R</i> and <i>S</i> stereoisomers
on the rate-determining step (<i>k</i><sub>pol</sub>). The
dNTP analogues provide a range of leaving group basicity and steric
properties by virtue of monohalogen, dihalogen, or methyl substitution
at the carbon atom bridging the β,γ-bisphosphonate that
mimics the natural pyrophosphate leaving group in dNTPs. Brønsted
plot relationships with negative slopes are revealed by the data,
as was found for the dGTP and dTTP analogues, consistent with a bond-breaking
component to the TS energy. However, greater multiplicity was shown
in the linear free energy relationship, revealing an unexpected dependence
on the nucleotide base for both A and C. Strong base-dependent perturbations
that modulate TS relative to ground-state energies are likely to arise
from electrostatic effects on catalysis in the pol active site. Deviations
from a uniform linear Brønsted plot relationship are discussed
in terms of insights gained from structural features of the prechemistry
DNA polymerase active site