(Q27670953)

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A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

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8 February 2020

A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex (English)

1 reference

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8 February 2020

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8 February 2020

Susan S Wallace

3

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8 February 2020

Sylvie Doublié

4

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8 February 2020

author name string

Stéphanie Duclos

2

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8 February 2020

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18 July 2011

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8 February 2020

Journal of Molecular Biology

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8 February 2020

412

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8 February 2020

22-34

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8 February 2020

1

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8 February 2020

Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues

1 reference

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20 March 2017

Crystal Structure of a Replicative DNA Polymerase Bound to the Oxidized Guanine Lesion Guanidinohydantoin ,

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Kinetics of Mismatch Formation opposite Lesions by the Replicative DNA Polymerase from Bacteriophage RB69

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Structure of the replicating complex of a pol alpha family DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Structure of a B-DNA dodecamer: conformation and dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Features and development of Coot

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Version 1.2 of the Crystallography and NMR system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

A novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIII

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

DNA polymerase proofreading: Multiple roles maintain genome stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

20 March 2017

Defining the structure of irregular nucleic acids: conventions and principles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

7 April 2017

Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

7 April 2017

Use of 2-aminopurine fluorescence to study the role of the beta hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Acyclic and dideoxy terminator preferences denote divergent sugar recognition by archaeon and Taq DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

The proofreading pathway of bacteriophage T4 DNA polymerase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Regulation of DNA polymerase exonucleolytic proofreading activity: studies of bacteriophage T4 "antimutator" DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 3' --> 5' exonuclease activities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Sequence dependence for bypass of thymine glycols in DNA by DNA polymerase I

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Thymine glycol lesions terminate chain elongation by DNA polymerase I in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Cocrystal structure of an editing complex of Klenow fragment with DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Oxidative damage to DNA: relation to species metabolic rate and life span

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

How DNA travels between the separate polymerase and 3'-5'-exonuclease sites of DNA polymerase I (Klenow fragment).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Excision repair of thymine glycols, urea residues, and apurinic sites in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

Synthesis of the diastereomers of thymidine glycol, determination of concentrations and rates of interconversion of their cis-trans epimers at equilibrium and demonstration of differential alkali lability within DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

29 September 2017

DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

2 June 2018

Processing of model single-strand breaks in phi X-174 RF transfecting DNA by Escherichia coli.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

2 June 2018

Oxidative damage in DNA. Lack of mutagenicity by thymine glycol lesions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

19 June 2018

Different behaviors in vivo of mutations in the beta hairpin loop of the DNA polymerases of the closely related phages T4 and RB69.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

27 November 2018

Interconversion of the cis-5R,6S- and trans-5R,6R-thymine glycol lesions in duplex DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

27 November 2018

Excision of products of oxidative DNA base damage by human NTH1 protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

27 November 2018

Thymine ring saturation and fragmentation products: lesion bypass, misinsertion and implications for mutagenesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167065

27 November 2018

Mutational and pH studies of the 3' --> 5' exonuclease activity of bacteriophage T4 DNA polymerase

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Template length, sequence context, and 3'-5' exonuclease activity modulate replicative bypass of thymine glycol lesions in vitro

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Processing of X-ray diffraction data collected in oscillation mode

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of specific DNA base damages in the X-ray-induced inactivation of bacteriophage PM2

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Functional effects of cis-thymine glycol lesions on DNA synthesis in vitro

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modeling and molecular mechanical studies of the cis-thymine glycol radiation damage lesion in DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Possible role for thymine glycol in the selective inhibition of DNA synthesis on oxidized DNA templates

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Using 2-Aminopurine Fluorescence and Mutational Analysis to Demonstrate an Active Role of Bacteriophage T4 DNA Polymerase in Strand Separation Required for 3′ → 5′-Exonuclease Activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/21781974

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.JMB.2011.07.007

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

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8 February 2020

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21781974%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21781974%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

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