# Creation and Repair of Postreplicative DNA Gaps

> **NIH NIH RM1** · UNIVERSITY OF WISCONSIN-MADISON · 2020 · $1,241,989

## Abstract

PROJECT SUMMARY/ABSTRACT
 When a replication fork encounters a DNA lesion in a template strand, replication gives way to DNA repair
and recombination. These encounters define an interface in DNA metabolism that gives rise to much of the
DNA rearrangement, repeat expansion, and mutagenesis that defines genome instability. This is ultimately
manifested in tumor evolution in eukaryotes and the development of antibiotic resistance and increased
pathogenicity in bacteria. Recent investigation of events that occur at the fork have largely overlooked an
important genomic venue for repair – lesions left behind the fork in postreplicative gaps. The existence of these
gaps has been appreciated for over 5 decades, but progress has been limited by methodology that has been
inadequate to properly explore their general importance and repair. These gaps are primary substrates for
DNA synthesis by translesion DNA polymerases, recombinational DNA repair, and replicational template
switching, all processes linked with genomic instability.
 This proposal frames a multidisciplinary effort to explore how postreplicative gaps are generated, how often
they are formed, what circumstances trigger formation, what occurs within them, and how the various paths of
gap repair are prioritized and governed. The work is an outgrowth of advances in understanding three
enigmatic protein activities, RarA, Uup, and RadD. RarA, an AAA+ ATPase that functions at the replisome to
generate postreplicative gaps on the lagging strand, is one key.
 To tackle this problem, we bring together world-class expertise in biochemistry, genetics, molecular
biology, and biophysics. We will develop new methods, including novel single-molecule approaches towards
detecting and quantifying gaps, and characterizing the proteins acting on them. While driven by our
mechanistic questions, these methods will broadly benefit research in genomic maintenance.
 The five specific aims constitute a systematic attack on the problem. The mechanism of RarA protein is the
focus of Aim 1. Aim 2 provides the first effort to quantify gap formation in vivo and determine the factors that
trigger gap formation. Aim 3 explores the functions of Uup and RadD, two enzymes that suppress template
switching within gaps. Aim 4 explores how various pathways of gap repair are organized and governed. The
proposal is completed with Aim 5, an exploration of translesion DNA polymerases acting within gaps, a key
source of genomic mutagenesis.

## Key facts

- **NIH application ID:** 9930114
- **Project number:** 5RM1GM130450-02
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** Michael M. Cox
- **Activity code:** RM1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,241,989
- **Award type:** 5
- **Project period:** 2019-05-15 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9930114

## Citation

> US National Institutes of Health, RePORTER application 9930114, Creation and Repair of Postreplicative DNA Gaps (5RM1GM130450-02). Retrieved via AI Analytics 2026-06-11 from https://api.ai-analytics.org/grant/nih/9930114. Licensed CC0.

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