# Structural and Mechanistic Studies of DNA Repair

> **NIH NIH R35** · UNIVERSITY OF KANSAS MEDICAL CENTER · 2020 · $84,347

## Abstract

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Oxidative stress is a prevalent and dangerous cellular condition resulting in deleterious modifications to the
structure of DNA. These modifications promote mutagenesis and consequently the development of numerous
human maladies, including cancer. The base excision repair (BER) pathway is the cells primary defense against
oxidative DNA damage and is a vital guardian of genome stability. While the roles of individual enzymes during
a classical BER cycle are largely established, it remains enigmatic how these enzymes function together in a
multi-protein/DNA complex to facilitate the channeling of toxic DNA repair intermediates between each protein.
In addition, it is poorly understood how deviations in the classical BER pathway affect the DNA repair process
and genome stability. These deviancies range from mismatched-, damaged-, and ribo-nucleotides inserted by a
DNA polymerase, to the coordinated repair of “dirty” or damaged DNA ends that block BER. These scenarios
become particularly biologically relevant during times where there is an increase in genome instability (i.e., in
cancer cells and/or during therapeutic treatments). The overarching goal of the parental grant is to understand
the molecular mechanisms of each BER component individually and to place these activities within the larger
BER co-complex with damaged DNA repair intermediates. Elegant biophysical approaches are required to
elucidate these BER complexities and to provide both a foundation for interpreting the biological response and
the subsequent development of therapeutic treatments. To meet this goal, we utilize a comprehensive approach
of time-lapse X-ray crystallography, neutron crystallography, small angle neutron scattering, molecular dynamic
simulations, enzyme kinetics, and single-molecule total internal reflection microscopy. Specific to this research
supplement, we have established a three-color single-molecule TIRFM system to characterize the multiprotein
BER complex. Using this approach, Dr. Fausto Varela will determine how OGG1 and APE1 coordinate on the
DNA during the repair of 8-oxoG. Simultaneously, he will learn new technical expertise, publish impactful
research, and acquire the key preliminary data for a competitive postdoctoral fellowship. Furthermore, the results
gleaned from the proposed experiments with OGG1 will directly complement the parental grant and ongoing
experiments in the lab looking at substrate channeling between APE1 and pol β, which are two downstream
enzymes in BER.

## Key facts

- **NIH application ID:** 9943840
- **Project number:** 3R35GM128562-02S1
- **Recipient organization:** UNIVERSITY OF KANSAS MEDICAL CENTER
- **Principal Investigator:** Bret D Freudenthal
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $84,347
- **Award type:** 3
- **Project period:** 2018-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9943840

## Citation

> US National Institutes of Health, RePORTER application 9943840, Structural and Mechanistic Studies of DNA Repair (3R35GM128562-02S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9943840. Licensed CC0.

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