(Q34627550)

3 August 2017

title

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

1 reference

3 August 2017

Benjamin Bouvier

1

1 reference

3 August 2017

Helmut Grubmüller

series ordinal

2

1 reference

3 August 2017

language of work or name

English

0 references

publication date

11 May 2007

1 reference

3 August 2017

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3 August 2017

volume

93

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3 August 2017

issue

3

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3 August 2017

page(s)

770-786

1 reference

DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion

3 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Computational approaches for investigating base flipping in oligonucleotides

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

DNA base flipping by a base pair-mimic nucleoside

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the 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=1913169

DNA bending by M.EcoKI methyltransferase is coupled to nucleotide 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=1913169

Bacteriophage T4 alpha-glucosyltransferase: a novel interaction with gp45 and aspects of the catalytic mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

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=1913169

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling 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=1913169

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Role of base flipping in specific recognition of damaged DNA by repair enzymes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Escaping free-energy minima

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or 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=1913169

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Imino proton exchange and base-pair kinetics in RNA 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=1913169

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=1913169

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions 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=1913169

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=1913169

HhaI methyltransferase flips its target base out of the DNA 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=1913169

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=1913169

Energetic coupling between DNA bending and base pair opening

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Defining the structure of irregular nucleic acids: conventions and principles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Base pair opening pathways 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=1913169

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=1913169

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=1913169

Structural basis for broad DNA-specificity in integron recombination

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

A selective, noncovalent assay for base flipping in DNA.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Base flipping in nucleotide excision repair

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1913169

High base pair opening rates in tracts of GC base pairs

26 October 2018

1 reference

12 December 2020

Specificity in Protein–DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI

1 reference

12 December 2020

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

1 reference

12 December 2020

Definitions and nomenclature of nucleic acid structure parameters

1 reference

12 December 2020

Disruption of the target G-C base-pair by the HhaI methyltransferase

1 reference

12 December 2020

The opening of a single base without perturbations of neighboring nucleotides: a study on crystal B-DNA duplex d(CGCGAATTCGCG)2

1 reference

12 December 2020

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.091751

Identifiers

DOI

1 reference

3 August 2017

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3 August 2017

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