(Q34186247)

31 July 2017

title

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations (English)

1 reference

31 July 2017

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Jaroslav Koca

4

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Jirí Sponer

object named as

Jirí Sponer

6

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Thomas E. Cheatham, III

5

object named as

Thomas E Cheatham

1 reference

31 July 2017

Eva Fadrná

1

1 reference

31 July 2017

Nad'a Spacková

2

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31 July 2017

Richard Stefl

3

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31 July 2017

language of work or name

English

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publication date

1 July 2004

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31 July 2017

number of pages

16

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inferred from page(s)

published in

Biophysical Journal

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31 July 2017

volume

87

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31 July 2017

issue

1

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31 July 2017

page(s)

227-242

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Simulation and modeling of nucleic acid structure, dynamics and interactions

31 July 2017

cites work

1 reference

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Theoretical methods for the simulation of nucleic acids.

5 July 2018

1 reference

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Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

5 July 2018

1 reference

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The structure of telomeric DNA.

5 July 2018

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Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

5 July 2018

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Identification of non-telomeric G4-DNA binding proteins in human, E. coli, yeast, and Arabidopsis.

5 July 2018

1 reference

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Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix

5 July 2018

1 reference

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The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Crystal structure of the potassium form of an Oxytricha nova G-quadruplex

5 July 2018

1 reference

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Molecular dynamics applied to nucleic acids

5 July 2018

1 reference

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Simulations of nucleic acids and their complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Crystal structure of parallel quadruplexes from human telomeric 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=1304345

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

A G-quadruplex-interactive potent small-molecule inhibitor of telomerase exhibiting in vitro and in vivo antitumor activity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Beyond nucleic acid base pairs: from triads to heptads

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Development and current status of the CHARMM force field for nucleic acids.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

G-quadruplexes as therapeutic targets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

A-Tract bending: insights into experimental structures by computational models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex 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=1304345

Nucleic acids: theory and computer simulation, Y2K.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Effect of loop sequence and size on DNA aptamer stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4))

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

NMR-Based model of a telomerase-inhibiting compound bound to G-quadruplex 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=1304345

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald 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=1304345

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Molecular modelling of protein-carbohydrate interactions. Understanding the specificities of two legume lectins towards oligosaccharides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Classical electrostatics in biology and chemistry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Monovalent cation-induced structure of telomeric DNA: the G-quartet model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Quadruplex structure of Oxytricha telomeric DNA oligonucleotides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Crystal structure of four-stranded Oxytricha telomeric 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=1304345

Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Hairpin and parallel quartet structures for telomeric sequences.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Conformational heterogeneity observed in simulations of a pyrene-substituted 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=1304345

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304345

Structure and stability of human telomeric sequence

28 October 2018

1 reference

12 December 2020

Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G4TnG4)

1 reference

12 December 2020

Simulation of the structure and dynamics of nonhelical RNA motifs

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

Accelerated assembly of G-quadruplex structures by a small molecule

1 reference

12 December 2020

A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations

1 reference

12 December 2020

Theoretical Studies of d(A:T)-Based Parallel-Stranded DNA Duplexes

1 reference

12 December 2020

10.1529/BIOPHYSJ.103.034751

Identifiers

DOI

1 reference

31 July 2017

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31 July 2017

1 reference