Investigating DNA remodeling in DNA mismatch repair
type: CreativeWork
description: Many DNA metabolic pathways, including DNA repair, require the transmission of signals across long stretches of DNA or between DNA molecules. Solutions to this signaling challenge involve various mechanisms: protein factors can travel between these sites, loop DNA between sites, or form oligomers that bridge the spatial gaps. How these paradigms have been used to explain DNA mismatch repair which involves several steps that require action-at-a-distance has not been previously explained. In this thesis, we describe these models in detail and how current data fits into these descriptions. We also outline regulation steps that remain unanswered in how action is communicated across long distances along a DNA contour in DNA mismatch repair. In eukaryotes, mismatch repair begins with MutS homolog (MSH) complexes detecting mismatches and recruiting the processivity clamp (PCNA)-stimulated endonuclease Mlh1-Pms1/PMS2 (yeast/human), which nicks the DNA distal to the mismatch location and a pre-existing single strand break, that may allow the pathway to distinguish between DNA strands. The Mlh1-Pms1/PMS2-generated nick allows downstream proteins to remove the mismatch. How the Mlh1-Pms1/PMS2 endonuclease operates across lengths of DNA to facilitate nicking DNA is critical for mismatch repair, but presents a key signaling challenge to the pathway. Using purified yeast proteins, we show that Mlh1-Pms1 uses ATP to compact DNA, a behavior which may act as a search mechanism for strand-discrimination signals, which may be hundreds of base pairs away from the mismatch and the site where Mlh1-Pms1/PMS2 nicks. When a pre-existing nick is encountered, compaction is suppressed and Mlh1-Pms1 instead stabilizes the site, protecting it from melting induced by PCNA’s loader, RFC. Phased nicking assays further reveal that the timing of Mlh1-Pms1 encountering a pre-existing nick relative to RFC/PCNA determines whether the complex remains suppressed or becomes activated. Together, these resul…
abstract: Many DNA metabolic pathways, including DNA repair, require the transmission of signals across long stretches of DNA or between DNA molecules. Solutions to this signaling challenge involve various mechanisms: protein factors can travel between these sites, loop DNA between sites, or form oligomers that bridge the spatial gaps. How these paradigms have been used to explain DNA mismatch repair which involves several steps that require action-at-a-distance has not been previously explained. In this thesis, we describe these models in detail and how current data fits into these descriptions. We also outline regulation steps that remain unanswered in how action is communicated across long distances along a DNA contour in DNA mismatch repair. In eukaryotes, mismatch repair begins with MutS homolog (MSH) complexes detecting mismatches and recruiting the processivity clamp (PCNA)-stimulated endonuclease Mlh1-Pms1/PMS2 (yeast/human), which nicks the DNA distal to the mismatch location and a pre-existing single strand break, that may allow the pathway to distinguish between DNA strands. The Mlh1-Pms1/PMS2-generated nick allows downstream proteins to remove the mismatch. How the Mlh1-Pms1/PMS2 endonuclease operates across lengths of DNA to facilitate nicking DNA is critical for mismatch repair, but presents a key signaling challenge to the pathway. Using purified yeast proteins, we show that Mlh1-Pms1 uses ATP to compact DNA, a behavior which may act as a search mechanism for strand-discrimination signals, which may be hundreds of base pairs away from the mismatch and the site where Mlh1-Pms1/PMS2 nicks. When a pre-existing nick is encountered, compaction is suppressed and Mlh1-Pms1 instead stabilizes the site, protecting it from melting induced by PCNA’s loader, RFC. Phased nicking assays further reveal that the timing of Mlh1-Pms1 encountering a pre-existing nick relative to RFC/PCNA determines whether the complex remains suppressed or becomes activated. Together, these resul…
author: Collingwood, Bryce William
language: eng
keywords: Biochemistry, DNA repair, Mismatch repair, Mlh1-Pms1, Chemistry
license: http://rightsstatements.org/vocab/InC/1.0/
date published: 2026-05
date modified: 2026-07-27T21:19:51Z
provider: Temple University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Temple University. Libraries