An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation (Q39902156)

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English	An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation	scientific article

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scholarly article

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Europe PubMed Central

PMC publication ID

15 September 2017

An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation (English)

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Europe PubMed Central

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15 September 2017

Jonathan B. Chaires

4

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24779348%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

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Huy T Le

1

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1 June 2020

William L Dean

2

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1 June 2020

Robert Buscaglia

3

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1 June 2020

John O Trent

5

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1 June 2020

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8 May 2014

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15 September 2017

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16

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Journal of Physical Chemistry B

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1 June 2020

118

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1 June 2020

20

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1 June 2020

5390-5405

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1 June 2020

Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection

1 reference

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22 September 2017

G-quadruplexes incorporating modified constituents: a review

1 reference

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22 September 2017

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.

1 reference

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22 September 2017

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation

1 reference

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22 September 2017

Structure and stability of higher-order human telomeric quadruplexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

1 reference

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22 September 2017

G-quadruplex-induced instability during leading-strand replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

The stability of intramolecular DNA G-quadruplexes compared with other macromolecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models

1 reference

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22 September 2017

Linkage of cation binding and folding in human telomeric quadruplex DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of Human Telomeric DNA in Crowded Solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structural insights into G-quadruplexes: towards new anticancer drugs

1 reference

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22 September 2017

Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Human telomeric G-quadruplex: thermodynamic and kinetic studies of telomeric quadruplex stability.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Energetics and kinetics of a conformational switch in G-quadruplex DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of the Human Telomere in K + Solution: A Stable Basket-Type G-Quadruplex with Only Two G-Tetrad Layers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Stability and kinetics of G-quadruplex structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Polymorphism of human telomeric quadruplex structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

G-quadruplexes: targets in anticancer drug design.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Hydrodynamic modeling: the solution conformation of macromolecules and their complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Quadruplex DNA: sequence, topology and structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Prevalence of quadruplexes in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Telomerase inhibition as cancer therapy.

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22 September 2017

The design of G-quadruplex ligands as telomerase inhibitors

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Crystal structure of parallel quadruplexes from human telomeric DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Calculation of hydrodynamic properties of small nucleic acids from their atomic structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

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

1 reference

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22 September 2017

Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems

1 reference

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22 September 2017

G-quadruplexes as therapeutic targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

22 September 2017

Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase

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22 September 2017

Telomerase inhibitors

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22 September 2017

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

1 reference

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22 September 2017

G-quadruplex DNA: a potential target for anti-cancer drug design

1 reference

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22 September 2017

Normal human chromosomes have long G-rich telomeric overhangs at one end

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22 September 2017

A survey of telomerase activity in human cancer

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22 September 2017

Divalent transition metal cations counteract potassium-induced quadruplex assembly of oligo(dG) sequences

1 reference

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22 September 2017

Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex

1 reference

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22 September 2017

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22 September 2017

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

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22 September 2017

Not all G-quadruplexes are created equally: an investigation of the structural polymorphism of the c-Myc G-quadruplex-forming sequence and its interaction with the porphyrin TMPyP4

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17 June 2018

Small-molecule-induced DNA damage identifies alternative DNA structures in human genes

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17 June 2018

The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions.

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17 June 2018

Molecular modeling and simulation of G-quadruplexes and quadruplex-ligand complexes

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17 June 2018

G-quadruplex nucleic acids as therapeutic targets

1 reference

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17 June 2018

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

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17 June 2018

G-quadruplexes in promoters throughout the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

17 June 2018

Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

20 August 2018

An integrated molecular dynamics (MD) and experimental study of higher order human telomeric quadruplexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

20 August 2018

The tail of the telomere

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

20 August 2018

Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species.

1 reference

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20 August 2018

Normal modes and essential dynamics.

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20 August 2018

Hydration regulates the thermodynamic stability of DNA structures under molecular crowding conditions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

20 August 2018

Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles

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20 August 2018

Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation.

1 reference

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20 August 2018

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.

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20 August 2018

Stability and Cations Coordination of DNA and RNA 14-Mer G-Quadruplexes: A Multiscale Computational Approach

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2 December 2018

Targeting telomeres and telomerase

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032189

2 December 2018

Hydration in drug design. 2. Influence of local site surface shape on water binding

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12 December 2020

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Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking

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https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

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Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Equilibrium centrifugation of nonideal systems. Donnan effect in self-associating systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins

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https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural transition of d(G4T4G4) from antiparallel to parallel G-quartet induced by divalent cations

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics simulations to provide new insights into the asymmetrical ammonium ion movement inside of the [d(G3T4G4)]2 G-quadruplex DNA structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A thermodynamic signature for drug-DNA binding mode

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3' sequence of d(AG3(TTAG3)3)

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Frictional coefficients of multisubunit structures. I. Theory

1 reference

https://pubmed.ncbi.nlm.nih.gov/24779348

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1021/JP502213Y

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1 June 2020

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Europe PubMed Central

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1 June 2020

PubMed publication ID

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Europe PubMed Central

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1 June 2020

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