Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein

Mark Hedglin, Patrick J. O'Brien

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Spontaneous DNA damage occurs throughout the genome, requiring that DNA repair enzymes search each nucleotide every cell cycle. This search is postulated to be more efficient if the enzyme can diffuse along the DNA, but our understanding of this process is incomplete. A key distinction between mechanisms of diffusion is whether the protein maintains continuous contact (sliding) or whether it undergoes microscopic dissociation (hopping). We describe a simple chemical assay to detect the ability of a DNA modifying enzyme to hop and have applied it to human alkyladenine DNA glycosylase (AAG), a monomeric enzyme that initiates repair of alkylated and deaminated purine bases. Our results indicate that AAG uses hopping to effectively search both strands of a DNA duplex in a single binding encounter. This raised the possibility that AAG might be capable of circumnavigating blocks such as tightly bound proteins. We tested this hypothesis by binding an EcoRI endonuclease dimer between two sites of DNA damage and measuring the ability of AAG to act at both damaged sites in a single binding encounter. Remarkably, AAG bypasses this roadblock in ∼50% of the binding events. We infer that AAG makes significant excursions from the surface of the DNA, allowing reorientation between strands and the bypass of a bound protein. This has important biological implications for the search for DNA damage because eukaryotic DNA is replete with proteins and only transiently accessible.

Original languageEnglish (US)
Pages (from-to)427-436
Number of pages10
JournalACS chemical biology
Volume5
Issue number4
DOIs
StatePublished - Apr 16 2010

Fingerprint

3-methyladenine-DNA glycosylase
DNA Glycosylases
DNA Repair
Repair
DNA
DNA Damage
Proteins
Enzymes
Deoxyribonuclease EcoRI
DNA Repair Enzymes
Humulus
Cell Cycle
Nucleotides

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Medicine

Cite this

@article{5a43b12ccb1a4125a9e470e0ca1cf7d3,
title = "Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein",
abstract = "Spontaneous DNA damage occurs throughout the genome, requiring that DNA repair enzymes search each nucleotide every cell cycle. This search is postulated to be more efficient if the enzyme can diffuse along the DNA, but our understanding of this process is incomplete. A key distinction between mechanisms of diffusion is whether the protein maintains continuous contact (sliding) or whether it undergoes microscopic dissociation (hopping). We describe a simple chemical assay to detect the ability of a DNA modifying enzyme to hop and have applied it to human alkyladenine DNA glycosylase (AAG), a monomeric enzyme that initiates repair of alkylated and deaminated purine bases. Our results indicate that AAG uses hopping to effectively search both strands of a DNA duplex in a single binding encounter. This raised the possibility that AAG might be capable of circumnavigating blocks such as tightly bound proteins. We tested this hypothesis by binding an EcoRI endonuclease dimer between two sites of DNA damage and measuring the ability of AAG to act at both damaged sites in a single binding encounter. Remarkably, AAG bypasses this roadblock in ∼50{\%} of the binding events. We infer that AAG makes significant excursions from the surface of the DNA, allowing reorientation between strands and the bypass of a bound protein. This has important biological implications for the search for DNA damage because eukaryotic DNA is replete with proteins and only transiently accessible.",
author = "Mark Hedglin and O'Brien, {Patrick J.}",
year = "2010",
month = "4",
day = "16",
doi = "10.1021/cb1000185",
language = "English (US)",
volume = "5",
pages = "427--436",
journal = "ACS Chemical Biology",
issn = "1554-8929",
publisher = "American Chemical Society",
number = "4",

}

Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein. / Hedglin, Mark; O'Brien, Patrick J.

In: ACS chemical biology, Vol. 5, No. 4, 16.04.2010, p. 427-436.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein

AU - Hedglin, Mark

AU - O'Brien, Patrick J.

PY - 2010/4/16

Y1 - 2010/4/16

N2 - Spontaneous DNA damage occurs throughout the genome, requiring that DNA repair enzymes search each nucleotide every cell cycle. This search is postulated to be more efficient if the enzyme can diffuse along the DNA, but our understanding of this process is incomplete. A key distinction between mechanisms of diffusion is whether the protein maintains continuous contact (sliding) or whether it undergoes microscopic dissociation (hopping). We describe a simple chemical assay to detect the ability of a DNA modifying enzyme to hop and have applied it to human alkyladenine DNA glycosylase (AAG), a monomeric enzyme that initiates repair of alkylated and deaminated purine bases. Our results indicate that AAG uses hopping to effectively search both strands of a DNA duplex in a single binding encounter. This raised the possibility that AAG might be capable of circumnavigating blocks such as tightly bound proteins. We tested this hypothesis by binding an EcoRI endonuclease dimer between two sites of DNA damage and measuring the ability of AAG to act at both damaged sites in a single binding encounter. Remarkably, AAG bypasses this roadblock in ∼50% of the binding events. We infer that AAG makes significant excursions from the surface of the DNA, allowing reorientation between strands and the bypass of a bound protein. This has important biological implications for the search for DNA damage because eukaryotic DNA is replete with proteins and only transiently accessible.

AB - Spontaneous DNA damage occurs throughout the genome, requiring that DNA repair enzymes search each nucleotide every cell cycle. This search is postulated to be more efficient if the enzyme can diffuse along the DNA, but our understanding of this process is incomplete. A key distinction between mechanisms of diffusion is whether the protein maintains continuous contact (sliding) or whether it undergoes microscopic dissociation (hopping). We describe a simple chemical assay to detect the ability of a DNA modifying enzyme to hop and have applied it to human alkyladenine DNA glycosylase (AAG), a monomeric enzyme that initiates repair of alkylated and deaminated purine bases. Our results indicate that AAG uses hopping to effectively search both strands of a DNA duplex in a single binding encounter. This raised the possibility that AAG might be capable of circumnavigating blocks such as tightly bound proteins. We tested this hypothesis by binding an EcoRI endonuclease dimer between two sites of DNA damage and measuring the ability of AAG to act at both damaged sites in a single binding encounter. Remarkably, AAG bypasses this roadblock in ∼50% of the binding events. We infer that AAG makes significant excursions from the surface of the DNA, allowing reorientation between strands and the bypass of a bound protein. This has important biological implications for the search for DNA damage because eukaryotic DNA is replete with proteins and only transiently accessible.

UR - http://www.scopus.com/inward/record.url?scp=77951113170&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77951113170&partnerID=8YFLogxK

U2 - 10.1021/cb1000185

DO - 10.1021/cb1000185

M3 - Article

C2 - 20201599

AN - SCOPUS:77951113170

VL - 5

SP - 427

EP - 436

JO - ACS Chemical Biology

JF - ACS Chemical Biology

SN - 1554-8929

IS - 4

ER -