(Q33568290)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

title

Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Pavel Hobza

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Sarah A Harris

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

author name string

Jan Rezác

series ordinal

1

1 reference

PubMed publication ID

20074515

28 July 2017

language of work or name

English

0 references

publication date

1 January 2010

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

number of pages

10

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

volume

98

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

page(s)

101-110

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

16 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Local and global effects of strong DNA bending induced during molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Microscopic mechanics of hairpin DNA translocation through synthetic nanopores

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Molecular force balance measurements reveal that double-stranded DNA unbinds under force in rate-dependent pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

A consensus view of protein dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Structure and energy of a DNA dodecamer under tensile load

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Alpha/gamma transitions in the B-DNA backbone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Force spectroscopy of single DNA and RNA molecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Temperature dependence of unbinding forces between complementary DNA strands

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Cooperativity in drug-DNA recognition: a molecular dynamics study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Force-induced melting of the DNA double helix. 2. Effect of solution conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Force-induced melting of the DNA double helix 1. Thermodynamic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Replication by a single DNA polymerase of a stretched single-stranded DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Model energy landscapes and the force-induced dissociation of ligand-receptor bonds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Mechanical stability of single DNA molecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Dynamic force spectroscopy of single DNA molecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Polymerization and mechanical properties of single RecA-DNA filaments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Sequence-dependent mechanics of single DNA molecules.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Modelling extreme stretching of DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared withab initioquantum mechanics calculations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

On the nature of DNA-duplex stability.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Kinking occurs during molecular dynamics simulations of small DNA minicircles.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison w

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Single-molecule analysis of DNA uncoiling by a type II topoisomerase.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

Force and velocity measured for single molecules of RNA polymerase.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

DNA: an extensible molecule.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800961

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

31 October 2018

1 reference

12 December 2020

Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads

1 reference

12 December 2020

Modelling DNA stretching for physics and biology

1 reference

12 December 2020

Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids

1 reference

12 December 2020

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

12 December 2020

Force-induced melting of a short DNA double helix

1 reference

12 December 2020

Atomistic simulation of the DNA helix-coil transition

1 reference

12 December 2020

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

1 reference

12 December 2020

10.1016/J.BPJ.2009.08.062

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20074515%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

PubMed publication ID

20074515

1 reference