# Watching cooperative interactions between base and nucleotide excision repair proteins

> **NIH NIH R35** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2024 · $906,257

## Abstract

Title: Watching cooperative interactions between base and nucleotide excision repair proteins.
PI: Bennett Van Houten, PhD
Abstract/Summary
This highly innovative project seeks to answer several fundamental questions regarding how DNA
repair proteins work to protect the human genome from environmentally-induced DNA damage. This
project uses an integrated approach combining biochemistry, single molecule analysis and highly
innovative chemoptogenetic cell biology tools to study with high temporal and spatial resolution
molecular hand-offs during DNA repair. We posit that key nucleotide excision repair proteins including
UV-DDB, XPA, and XPC-RAD23B work in a dynamic way with specific base excision repair proteins to
process oxidized bases in the context of chromatin. Specially, we will follow purified DNA repair
proteins and/or proteins labeled from nuclear extracts as they interact at sites of damage on naked
DNA and chromatinized DNA using a DNA tightrope optical platform. Building on preliminary data and
premise that UV-DDB can change the register of specific lesions in the context of the nucleosome, we
will test the paradigm shifting hypothesis that UV-DDB working in concert with other NER proteins is a
general damage sensor and can stimulate APE1 and 11 mammalian DNA glycosylases activities on
their respective oxidized DNA substrates. This project will develop and validate new genomic tools to
place 8-oxoG adducts at defined sites throughout the genome to assess the how chromatin structure
and chromatin remodelers effects repair. We will also develop and use several high-resolution
fluorescent approaches including single particle tracking protocols (based on Halo- and SNAP-tags) to
watch individual repair proteins arrive and process damage sites in real-time in living cells. Finally, we
posit that UV-DDB and XPC-RAD23B work with thymine DNA glycosylase to alter methylation patterns
in cells and ultimately change gene expression profiles. Together these approaches will give an
unprecedented view of the complex process of DNA damage processing during repair and answer
several key questions regarding damage recognition that have been intractable in the absence of
super-resolution approaches. Completion of this project will have a long and lasting impact on the field.

## Key facts

- **NIH application ID:** 10798337
- **Project number:** 5R35ES031638-05
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** Bennett Van Houten
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $906,257
- **Award type:** 5
- **Project period:** 2020-06-01 → 2028-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10798337

## Citation

> US National Institutes of Health, RePORTER application 10798337, Watching cooperative interactions between base and nucleotide excision repair proteins (5R35ES031638-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10798337. Licensed CC0.

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