Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. (Q41788842)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15811914%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

title

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA (English)

1 reference

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10 January 2020

4

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10 January 2020

Marie Öhman

series ordinal

3

1 reference

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10 January 2020

author name string

Katarina Hart

series ordinal

1

1 reference

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10 January 2020

Boel Nyström

series ordinal

2

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10 January 2020

language of work or name

English

0 references

publication date

5 April 2005

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10 January 2020

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10 January 2020

volume

11

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10 January 2020

page(s)

609-618

1 reference

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10 January 2020

issue

5

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

10 January 2020

cites work

1 reference

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Opening mechanism of G.T/U pairs in DNA and RNA duplexes: a combined study of imino proton exchange and molecular dynamics simulation

6 June 2018

1 reference

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Control of human potassium channel inactivation by editing of a small mRNA hairpin

6 June 2018

1 reference

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

6 June 2018

1 reference

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Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

6 June 2018

1 reference

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ADAR2 A-->I editing: site selectivity and editing efficiency are separate events

6 June 2018

1 reference

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An ADAR that edits transcripts encoding ion channel subunits functions as a dimer.

6 June 2018

1 reference

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Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA

6 June 2018

1 reference

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

6 June 2018

1 reference

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

6 June 2018

1 reference

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

6 June 2018

1 reference

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Adenosine to inosine editing by ADAR2 requires formation of a ternary complex on the GluR-B R/G site

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

RNA editing by adenosine deaminases that act on RNA

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

AdoMet-dependent methylation, DNA methyltransferases and base flipping

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Conformational changes that occur during an RNA-editing adenosine deamination reaction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Imino proton exchange and base-pair kinetics in RNA duplexes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Substrate recognition by ADAR1 and ADAR2

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Analysis of the RNA-editing reaction of ADAR2 with structural and fluorescent analogues of the GluR-B R/G editing site.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Regulation of serotonin-2C receptor G-protein coupling by RNA editing

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Analysis of Xenopus dsRNA adenosine deaminase cDNAs reveals similarities to DNA methyltransferases

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

HhaI methyltransferase flips its target base out of the DNA helix

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Control of kinetic properties of AMPA receptor channels by nuclear RNA editing

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Substrate specificity of the dsRNA unwinding/modifying activity

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

RNA editing in brain controls a determinant of ion flow in glutamate-gated channels

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

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

6 June 2018

1 reference

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

18 August 2018

1 reference

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The trapping of a spontaneously "flipped-out" base from double helical nucleic acids by host-guest complexation with beta-cyclodextrin: the intrinsic base-flipping rate constant for DNA and RNA.

18 August 2018

1 reference

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370749

Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities

2 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15811914

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15811914

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.7147805

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15811914%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15811914%20AND%20SRC:MED&resulttype=core&format=json

10 January 2020

1 reference