(Q34513794)

2 August 2017

title

On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics (English)

1 reference

2 August 2017

Elisa Fadda

1

1 reference

2 August 2017

Régis Pomès

series ordinal

2

1 reference

2 August 2017

language of work or name

English

0 references

publication date

28 September 2010

1 reference

2 August 2017

published in

Nucleic Acids Research

1 reference

2 August 2017

volume

39

1 reference

2 August 2017

issue

2

1 reference

2 August 2017

page(s)

767-780

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Creative Commons Attribution-NonCommercial 2.5 Generic

2 August 2017

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils

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Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation

7 July 2018

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Molecular dynamics simulations of nucleic acid-protein complexes.

7 July 2018

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Extrahelical damaged base recognition by DNA glycosylase enzymes

7 July 2018

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Apparent directional scanning for DNA repair

7 July 2018

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

7 July 2018

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DNA-uracil and human pathology

7 July 2018

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A molecular dynamics study of slow base flipping in DNA using conformational flooding

7 July 2018

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Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme

7 July 2018

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Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

7 July 2018

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Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

7 July 2018

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Incorporation of dUMP into DNA is a major source of spontaneous DNA damage, while excision of uracil is not required for cytotoxicity of fluoropyrimidines in mouse embryonic fibroblasts

7 July 2018

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Dynamic opening of DNA during the enzymatic search for a damaged base

7 July 2018

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Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Site-specific DNA damage recognition by enzyme-induced base flipping

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Competitive Na(+) and Rb(+) binding in the minor groove of DNA.

7 July 2018

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3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

7 July 2018

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A mechanistic perspective on the chemistry of DNA repair glycosylases

7 July 2018

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Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

7 July 2018

1 reference

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Alpha/gamma transitions in the B-DNA backbone

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Uracil in DNA--occurrence, consequences and repair

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

1H NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Micronutrient deficiencies. A major cause of DNA damage

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

DNA structure: cations in charge?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Two distinct modes of protein-induced bending in DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

DNA glycosylases in the base excision repair of DNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

BI-BII transitions in B-DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Hydrogen exchange and structural dynamics of proteins and nucleic acids

7 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

7 July 2018

12 December 2020

Influence of uracil defect on DNA structure: 1H NMR investigation at 500 MHz

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Effect of the methyl group on DNA bending and curvature: structure of d(GA4U4C)2 in solution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

DNA structure from A to Z.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

DNA binding and nucleotide flipping by the human DNA repair protein AGT.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3025553

High base pair opening rates in tracts of GC base pairs

27 October 2018

1 reference

12 December 2020

DNA fragmentation and cytotoxicity from increased cellular deoxyuridylate

1 reference

12 December 2020

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

1 reference

12 December 2020

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

12 December 2020

Structure of a B-DNA dodecamer. III. Geometry of hydration

1 reference

12 December 2020

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects

1 reference

12 December 2020

C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G

1 reference

12 December 2020

Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

1 reference

12 December 2020

Investigation of the influence of cytosine methylation on DNA flexibility

1 reference

12 December 2020

Sequence and conformational effects on imino proton exchange in A.T- and A.U-containing DNA and RNA duplexes

1 reference

12 December 2020

A single mode of DNA base-pair opening drives imino proton exchange

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKQ812

1 reference

2 August 2017

DBLP publication ID

journals/nar/FaddaP11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 August 2017

1 reference