Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. (Q28346246)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11159416%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

title

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine (English)

1 reference

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molecular dynamics simulation

3 November 2019

main subject

biophysics

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1 reference

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3 November 2019

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3 November 2019

Stefl R

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3 November 2019

Spacková N

series ordinal

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3 November 2019

Koca J

series ordinal

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3 November 2019

language of work or name

English

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publication date

1 January 2001

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3 November 2019

number of pages

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

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3 November 2019

volume

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3 November 2019

issue

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3 November 2019

page(s)

455-468

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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))

3 November 2019

cites work

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

20 March 2017

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Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA

20 March 2017

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

20 March 2017

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

20 March 2017

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The high-resolution crystal structure of a parallel-stranded guanine tetraplex

20 March 2017

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Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat

20 March 2017

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

20 March 2017

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A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes

20 March 2017

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An A-type double helix of DNA having B-type puckering of the deoxyribose rings.

7 April 2017

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The development of telomerase inhibitors: the G-quartet approach

29 September 2017

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Sodium and chlorine ions as part of the DNA solvation shell

29 September 2017

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6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation

29 September 2017

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Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

29 September 2017

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

29 September 2017

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

29 September 2017

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Structural equilibrium of DNA represented with different force fields

29 September 2017

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Calculations of nucleic acid conformations

29 September 2017

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Kinetics of sodium ion binding to DNA quadruplexes

29 September 2017

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Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA

29 September 2017

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Triplex formation at the rat neu gene utilizing imidazole and 2'-deoxy-6-thioguanosine base substitutions

29 September 2017

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Structural properties of the [d(G3T4G3)]2 quadruplex: evidence for sequential syn-syn deoxyguanosines

29 September 2017

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Overcoming potassium-mediated triplex inhibition

29 September 2017

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Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova

29 September 2017

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All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3' terminus

29 September 2017

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The cohering telomeres of Oxytricha

29 September 2017

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

29 September 2017

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Retinoblastoma susceptibility genes contain 5' sequences with a high propensity to form guanine-tetrad structures

29 September 2017

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Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method

29 September 2017

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

2 June 2018

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Allosteric Interactions between DNA Strands and Monovalent Cations in DNA Quadruplex Assembly: Thermodynamic Evidence for Three Linked Association Pathways

2 June 2018

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Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

2 June 2018

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Structures for polyinosinic acid and polyguanylic acid

2 June 2018

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Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs

2 June 2018

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Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops

2 June 2018

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Quadruplex DNA formation in a region of the tRNA gene supF associated with hydrogen peroxide mediated mutations

2 June 2018

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Quadruplex structure of Oxytricha telomeric DNA oligonucleotides

2 June 2018

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Crystal structure of four-stranded Oxytricha telomeric DNA

2 June 2018

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Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

2 June 2018

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Solution structure of a parallel-stranded tetraplex formed by d(TG4T) in the presence of sodium ions by nuclear magnetic resonance spectroscopy

27 November 2018

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G-strings at chromosome ends

7 January 2021

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

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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Accelerated assembly of G-quadruplex structures by a small molecule

7 January 2021

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Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations

7 January 2021

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Comparison of simple potential functions for simulating liquid water

7 January 2021

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7 January 2021

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Incorporation of 2'-deoxy-6-thioguanosine into G-rich oligodeoxyribonucleotides inhibits G-tetrad formation and facilitates triplex formation

7 January 2021

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Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships

7 January 2021

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7 January 2021

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Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences Among Cations, and Flexibility of the Cation Hydration Shell

7 January 2021

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7 January 2021

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Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties

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7 January 2021

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11159416%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11159416%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

PubMed publication ID

11159416

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11159416%20AND%20SRC:MED&resulttype=core&format=json