Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study (Q34711836)

4 August 2017

title

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study (English)

1 reference

4 August 2017

Feng Pan

1

1 reference

4 August 2017

Christopher Roland

series ordinal

2

1 reference

4 August 2017

Celeste Sagui

series ordinal

3

1 reference

4 August 2017

language of work or name

English

0 references

publication date

26 November 2014

1 reference

4 August 2017

published in

Nucleic Acids Research

1 reference

4 August 2017

volume

42

1 reference

4 August 2017

issue

22

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4 August 2017

page(s)

13981-13996

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Creative Commons Attribution 4.0 International

4 August 2017

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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7 July 2018

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A left-handed RNA double helix bound by the Z alpha domain of the RNA-editing enzyme ADAR1

7 July 2018

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

7 July 2018

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Charge density of divalent metal cations determines RNA stability

7 July 2018

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7 July 2018

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Molecular mechanisms for the B-Z transition in the example of poly[d(G-C) x d(G-C)] polymers. A critical review

7 July 2018

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Z-DNA-forming sequences generate large-scale deletions in mammalian cells

7 July 2018

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Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases

7 July 2018

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Determining the Mg2+ stoichiometry for folding an RNA metal ion core

7 July 2018

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7 July 2018

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Metal ions and RNA folding: a highly charged topic with a dynamic future

7 July 2018

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Spatial distribution of competing ions around DNA in solution.

7 July 2018

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The stretched intermediate model of B-Z DNA transition

7 July 2018

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Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation

7 July 2018

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Ion motions in molecular dynamics simulations on DNA.

7 July 2018

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DNA and its counterions: a molecular dynamics study

7 July 2018

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Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

7 July 2018

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High salt solution structure of a left-handed RNA double helix

7 July 2018

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Competitive Na(+) and Rb(+) binding in the minor groove of DNA.

7 July 2018

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7 July 2018

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A crystallographic study of the binding of 13 metal ions to two related RNA duplexes

7 July 2018

1 reference

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DNA helix: the importance of being GC-rich

7 July 2018

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Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.

7 July 2018

1 reference

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Z-DNA-binding proteins can act as potent effectors of gene expression in vivo

7 July 2018

1 reference

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Locating monovalent cations in the grooves of B-DNA

7 July 2018

1 reference

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Early events in RNA folding

7 July 2018

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1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Water and ion binding around RNA and DNA (C,G) oligomers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Left-handed Z-DNA: structure and function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Sequence-specific binding of counterions to B-DNA.

7 July 2018

1 reference

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The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

7 July 2018

1 reference

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Sodium and chlorine ions as part of the DNA solvation shell

7 July 2018

1 reference

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Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA

7 July 2018

1 reference

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DNA structure: cations in charge?

7 July 2018

1 reference

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Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

7 July 2018

1 reference

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Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

7 July 2018

1 reference

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The B-DNA dodecamer at high resolution reveals a spine of water on sodium

7 July 2018

1 reference

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Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions

7 July 2018

1 reference

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Structure and conformation of helical nucleic acids: analysis program (SCHNAaP).

7 July 2018

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Sequence-selective metal ion binding to DNA oligonucleotides.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

'Z-RNA'--a left-handed RNA double helix

7 July 2018

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The chemistry and biology of left-handed Z-DNA.

7 July 2018

1 reference

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Ribosome size distribution in extracts of potassium-depleted Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Locations of Z-DNA in polytene chromosomes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

7 July 2018

Left-handed DNA in vivo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Supercoiling of the DNA template during transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Raison d'être and structural model for the B-Z transition of poly d(G-C).poly d(G-C).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA.

7 July 2018

1 reference

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Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G

7 July 2018

1 reference

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Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes.

7 July 2018

1 reference

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Molecular structure of a left-handed double helical DNA fragment at atomic resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

7 July 2018

1 reference

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Anion binding to nucleic acids

7 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

A “Hydrat-Ion” Spine in a B-DNA Minor Groove

21 January 2018

1 reference

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The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

21 January 2018

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https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Ion atmosphere around nucleic acid.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena Ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure

21 January 2018

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Surface solvation for an ion in a water cluster.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Left-handed Z-DNA binding by the recA protein of Escherichia coli.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4267617

Structure and dynamics of hydrated ions

26 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Dependence of A-RNA simulations on the choice of the force field and salt strength

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1107

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

21 January 2018

1 reference

12 December 2020

Characterization of intermediate conformational states in the B in equilibrium Z transitions of poly(dG-dC).poly(dG-dC)

1 reference

12 December 2020

Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus

1 reference

12 December 2020

RNA double helices generated from crystal structures of double helical dinucleoside phosphates

1 reference

12 December 2020

Left-handed DNA and the synaptic pairing reaction promoted by Ustilago rec1 protein

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

Structural and functional defects in mammalian ribosomes after potassium deficiency

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12 December 2020

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

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12 December 2020

Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation

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12 December 2020

A-Z-RNA conformational changes effected by high pressure

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU1107

1 reference

4 August 2017

1 reference

4 August 2017

1 reference