Department of Biochemistry
4-403 BSB
Iowa City, IA 52242-1109 USA phone: 877-846-8569
or 319-335-7932
fax: (319) 335-9570
biochem@uiowa.edu
Department of Biochemistry
Faculty Profiles
M. Todd Washington, Ph.D.
Assistant Professor
Current Research
Legend: The “polymerase switch” model of DNA lesion bypass. Upon encountering a thymine dimer (left), DNA polymerase delta (the replicative polymerase) stalls, because it cannot insert a nucleotide opposite the lesion. The stalled DNA polymerase delta is replaced by DNA polymerase eta, which inserts correct nucleotides opposite both bases of the dimer and subsequently extends past the lesion. Upon encountering an abasic site (right), DNA polymerase delta inserts a nucleotide opposite the lesion in an error-prone manner and then stalls, because it cannot extend past the lesion. The stalled DNA polymerase delta is replaced by DNA polymerase zeta, which catalyzes the extension step.
Classical, replicative DNA polymerases synthesize DNA in a template-dependent fashion with remarkable efficiency and fidelity. They achieve rates as high as 1,000 nucleotide incorporations per second with error frequencies as low as one error per one million nucleotides incorporated. What these amazing enzymes cannot do, however, is replicate through DNA lesions that arise spontaneously or are formed upon attack by a plethora of DNA damaging agents including oxygen free radicals and radiation. Consequently, organisms have evolved specialized polymerases to replicate through lesions.
DNA polymerase eta is one such specialized polymerase. Inactivation of DNA polymerase eta in yeast leads to an increase in the frequency of ultraviolet (UV) radiation-induced mutations. This indicates that the replication of UV-induced lesions by this polymerase is error-free (i.e., not mutagenic). In vitro, DNA polymerase eta has the unprecedented ability to accurately replicate through a thymine dimer, a common UV-induced lesion. Furthermore, defects in human DNA polymerase eta are responsible for the cancer prone genetic disorder, the variant form of xeroderma pigmentosum.
DNA polymerase zeta is another specialized polymerase. Inactivation of DNA polymerase zeta in yeast leads to a dramatic decrease in the frequency of mutations induced by a wide range of DNA damaging agents. This indicates that the replication of numerous lesions by this polymerase is mutagenic. In vitro, DNA polymerase zeta has the remarkable ability to efficiently extend from primer-terminal mismatches containing template lesions. Thus, DNA polymerase zeta likely functions in the mutagenic replication of damaged DNA by extending from nucleotides inserted opposite lesions by other polymerases—often the classical, replicative polymerases themselves.
Our long-term goal is to understand the mechanisms of DNA polymerases involved in both mutagenic and error-free replication of DNA damage at the thermodynamic, kinetic, and structural level. We use a variety of approaches including equilibrium binding techniques, transient state kinetic analyses (both rapid chemical quench flow and fluorescence-based stopped flow methods), and the characterization of mutant proteins generated by site-directed mutagenesis. We hope that this work will contribute to our understanding of the origins of mutations and cancers and perhaps gain new insights into their prevention.
Comments or questions about our Web site? Contact the Webmaster.