(Q42029581)

15 October 2017

Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics (English)

1 reference

15 October 2017

7

1 reference

15 October 2017

Jeffrey N McKnight

6

0 references

author name string

Yu Ye

1

1 reference

15 October 2017

Mary R Stahley

2

1 reference

15 October 2017

Jianqing Xu

3

1 reference

15 October 2017

Joshua I Friedman

4

1 reference

15 October 2017

Yan Sun

5

1 reference

15 October 2017

Gregory D Bowman

8

1 reference

15 October 2017

James T Stivers

9

1 reference

15 October 2017

language of work or name

English

0 references

publication date

23 July 2012

1 reference

15 October 2017

1 reference

15 October 2017

51

1 reference

15 October 2017

30

1 reference

15 October 2017

6028-6038

1 reference

describes a project that uses

15 October 2017

ImageQuant

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3448002/fullTextXML

inferred from PubMed Central ID database lookup

cites work

Extranucleosomal DNA binding directs nucleosome sliding by Chd1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Benchmarking and analysis of protein docking performance in Rosetta v3.2.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Dynamics of nucleosome invasion by DNA binding proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Effect of the thymidylate synthase inhibitors on dUTP and TTP pool levels and the activities of DNA repair glycosylases on uracil and 5-fluorouracil in DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Dynamics of uracil and 5-fluorouracil in DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Structure of RCC1 chromatin factor bound to the nucleosome core particle

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Detection of damaged DNA bases by DNA glycosylase enzymes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Dynamics and function of compact nucleosome arrays

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Conformational analysis of nucleic acids revisited: Curves+

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Enzymatic capture of an extrahelical thymine in the search for uracil in DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Stopped-flow fluorescence resonance energy transfer for analysis of nucleosome dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Computational redesign of endonuclease DNA binding and cleavage specificity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Three-dimensional computation of atom depth in complex molecular structures.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Mapping nucleic acid structure by hydroxyl radical cleavage

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Rapid spontaneous accessibility of nucleosomal DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Nucleosomes facilitate their own invasion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

A mechanistic perspective on the chemistry of DNA repair glycosylases

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

DNA base excision repair of uracil residues in reconstituted nucleosome core particles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Consensus sequences for good and poor removal of uracil from double stranded DNA by uracil-DNA glycosylase

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Base-flipping mutations of uracil DNA glycosylase: substrate rescue using a pyrene nucleotide wedge

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Turning On uracil-DNA glycosylase using a pyrene nucleotide switch

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3448002

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

17 August 2018

1 reference

12 December 2020

Properties of a Recombinant Human Uracil-DNA Glycosylase from the UNG Gene and Evidence that UNG Encodes the Major Uracil-DNA Glycosylase

1 reference

12 December 2020

Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation

1 reference

12 December 2020

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

Nucleosome positioning determinants

1 reference

12 December 2020

Identifiers

DOI

10.1021/BI3006412

1 reference

15 October 2017

1 reference

15 October 2017

PubMed publication ID

22784353

1 reference