Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics. (Q33887108)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28634300%20AND%20SRC:MED&resulttype=core&format=json

23 March 2020

title

Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics (English)

1 reference

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23 March 2020

author

Alberto Marin-Gonzalez

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23 March 2020

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23 March 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28634300%20AND%20SRC:MED&resulttype=core&format=json

23 March 2020

Fernando Moreno-Herrero

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23 March 2020

author name string

Alberto Marin-Gonzalez

1 reference

29 July 2017

J G Vilhena

1 reference

29 July 2017

Fernando Moreno-Herrero

1 reference

29 July 2017

language of work or name

English

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publication date

20 June 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28634300%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

23 March 2020

published in

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23 March 2020

volume

114

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23 March 2020

issue

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23 March 2020

page(s)

7049-7054

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Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers.

23 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

On the absence of intrahelical DNA dynamics on the μs to ms timescale

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Blind predictions of DNA and RNA tweezers experiments with force and torque

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Exploring polymorphisms in B-DNA helical conformations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Recent advances in magnetic tweezers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Frontiers in Molecular Dynamics Simulations of DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Cytosine methylation alters DNA mechanical properties

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Conformational analysis of nucleic acids revisited: Curves+

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Twist-stretch coupling and phase transition during DNA supercoiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Recent advances in optical tweezers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Giant proteins that move DNA: bullies of the genomic playground.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

DNA overwinds when stretched

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Single-molecule measurements of the persistence length of double-stranded RNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Crystal structure of a Rad51 filament

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Structural transitions and elasticity from torque measurements on DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Ten years of tension: single-molecule DNA mechanics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Salt dependence of the elasticity and overstretching transition of single DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

A crystallographic map of the transition from B-DNA to A-DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Ionic effects on the elasticity of single DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Entropic elasticity of lambda-phage DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5502642

Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Dynamics of B-DNA on the microsecond time scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Strain softening in stretched DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Modeling DNA Dynamics under Steady Deforming Forces and Torques

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Sequence-dependent elastic properties of DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Decreased resistance to bacterial infection and granulocyte defects in IAP-deficient mice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

Simulations of RNA Interactions with Monovalent Ions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1705642114

DNA stretching and compression: large-scale simulations of double helical structures

21 January 2018

1 reference

PubMed

12 December 2020

Recombination Hotspots and Single-Stranded DNA Binding Proteins Couple DNA Translocation to DNA Unwinding by the AddAB Helicase-Nuclease

1 reference

PubMed

12 December 2020

1 reference

12 December 2020

1 reference

12 December 2020

DNA Twist Stability Changes with Magnesium(2+) Concentration

1 reference

PubMed

12 December 2020

Identifiers

DOI

10.1073/PNAS.1705642114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28634300%20AND%20SRC:MED&resulttype=core&format=json

23 March 2020

0 references

1 reference

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23 March 2020

1 reference

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