Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations (Q39733785)

14 September 2017

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations (English)

1 reference

14 September 2017

Richard Lavery

3

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author name string

Emmanuel Giudice

series ordinal

1

1 reference

14 September 2017

Péter Várnai

series ordinal

2

1 reference

14 September 2017

language of work or name

English

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publication date

1 March 2003

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14 September 2017

Nucleic Acids Research

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14 September 2017

31

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14 September 2017

5

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14 September 2017

1434-1443

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New insights into the structure of abasic DNA from molecular dynamics simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

A structural snapshot of base-pair opening in DNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Determination of the residence time of water molecules hydrating B'- DNA and B-DNA, by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

DNA curvature and deformation in protein-DNA complexes: a step in the right direction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

VMD: visual molecular dynamics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

HhaI methyltransferase flips its target base out of the DNA helix

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Dynamical theory of activated processes in globular proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Hydrogen exchange and structural dynamics of proteins and nucleic acids

14 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

14 September 2017

12 December 2020

Energetic coupling between DNA bending and base pair opening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Defining the structure of irregular nucleic acids: conventions and principles

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Base pair opening pathways in B-DNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Molecular dynamics study of the base pair opening process in the self-complementary octanucleotide d(CTGATCAG).

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Sequence dependence of base-pair opening in a DNA dodecamer containing the CACA/GTGT sequence motif

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=149832

Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA

20 August 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature

1 reference

12 December 2020

Reverse turns in blocked dipeptides are intrinsically unstable in water

1 reference

12 December 2020

Studies of base pair kinetics by NMR measurement of proton exchange

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

High base pair opening rates in tracts of GC base pairs

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

Identifiers

DOI

10.1093/NAR/GKG239

1 reference

14 September 2017

1 reference

14 September 2017

PubMed publication ID

12595551

1 reference