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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0 references

1 reference

3

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3 November 2019

Jirí Sponer

5

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3 November 2019

author name string

Stefl R

1

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3 November 2019

Spacková N

2

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3 November 2019

Koca J

4

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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

14

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based on heuristic

inferred from page(s)

published in

Biophysical Journal

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3 November 2019

volume

80

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3 November 2019

issue

1

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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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

The development of telomerase inhibitors: the G-quartet approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Sodium and chlorine ions as part of the DNA solvation shell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Structural equilibrium of DNA represented with different force fields

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Calculations of nucleic acid conformations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Kinetics of sodium ion binding to DNA quadruplexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Overcoming potassium-mediated triplex inhibition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

The cohering telomeres of Oxytricha

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Structures for polyinosinic acid and polyguanylic acid

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Quadruplex structure of Oxytricha telomeric DNA oligonucleotides

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

Crystal structure of four-stranded Oxytricha telomeric DNA

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301247

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

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976028-6

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

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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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