Mechanistic insight into ligand binding to G-quadruplex DNA (Q33635614)

28 July 2017

Mechanistic insight into ligand binding to G-quadruplex DNA (English)

1 reference

Francesco Saverio Di Leva

28 July 2017

1 reference

1 reference

G-quadruplex DNA

3 January 2024

Francesco Saverio Di Leva

1

0 references

Vittorio Limongelli

Vittorio Limongelli

5

0 references

Ettore Novellino

Ettore Novellino

2

0 references

Michele Parrinello

4

Michele Parrinello

1 reference

28 July 2017

Andrea Cavalli

3

1 reference

PubMed ID

24753420

28 July 2017

language of work or name

English

0 references

publication date

21 April 2014

1 reference

28 July 2017

Nucleic Acids Research

1 reference

28 July 2017

42

1 reference

28 July 2017

9

1 reference

28 July 2017

5447-5455

1 reference

Creative Commons Attribution 3.0 Unported

28 July 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Exploring the chemical space of G-quadruplex binders: discovery of a novel chemotype targeting 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=4027208

Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

G-quadruplex structures are stable and detectable in human genomic DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Funnel metadynamics as accurate binding free-energy method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Quantitative visualization of DNA G-quadruplex structures in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A model of smart G-quadruplex ligand

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A dual-site simultaneous binding mode in the interaction between parallel-stranded G-quadruplex [d(TGGGGT)]4 and cyanine dye 2,2'-diethyl-9-methyl-selenacarbocyanine bromide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

DNA secondary structures: stability and function of G-quadruplex structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Sampling protein motion and solvent effect during ligand binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

N-cyclic bay-substituted perylene G-quadruplex ligands have selective antiproliferative effects on cancer cells and induce telomere damage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Selective Binding of Distamycin A Derivative to G-Quadruplex Structure [d(TGGGGT)](4).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Making sense of G-quadruplex and i-motif functions in oncogene promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Alternative lengthening of telomeres: models, mechanisms and implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A thermodynamic approach to the affinity optimization of drug candidates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

G-quadruplex nucleic acids as therapeutic targets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Targeting DNA quadruplexes with distamycin A and its derivatives: an ITC and NMR study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A hitchhiker's guide to G-quadruplex ligands

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Protection of telomeres through independent control of ATM and ATR by TRF2 and POT1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Telomere uncapping by the G-quadruplex ligand RHPS4 inhibits clonogenic tumour cell growth in vitro and in vivo consistent with a cancer stem cell targeting mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A semiempirical free energy force field with charge-based desolvation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

G-quadruplexes in promoters throughout the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

The G-quadruplex ligand telomestatin inhibits POT1 binding to telomeric sequences in vitro and induces GFP-POT1 dissociation from telomeres in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Automatic atom type and bond type perception in molecular mechanical calculations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Scalable molecular dynamics with NAMD

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Shelterin: the protein complex that shapes and safeguards human telomeres

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Prevalence of quadruplexes in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Helix formation by guanylic acid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Escaping free-energy minima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Switching and signaling at the telomere

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Specific association of human telomerase activity with immortal cells and cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Structure of a B-DNA dodecamer: conformation and dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Inhibition of telomerase by G-quartet DNA structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

Structure and function of telomeres

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4027208

G-quadruplex ligand RHPS4 potentiates the antitumor activity of camptothecins in preclinical models of solid tumors.

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular g-quadruplex

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Stabilizing parallel G-quadruplex DNA by a new class of ligands: two non-planar alkaloids through interaction in lateral grooves

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Targeting telomeres and telomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Tandem Application of Virtual Screening and NMR Experiments in the Discovery of Brand New DNA Quadruplex Groove Binders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Shooting for Selective Druglike G-Quadruplex Binders: Evidence for Telomeric DNA Damage and Tumor Cell Death

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU247

Telomerase inhibition with a novel G-quadruplex-interactive agent, telomestatin: in vitro and in vivo studies in acute leukemia

21 January 2018

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

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

1 reference

12 December 2020

Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU247

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

PubMed ID

24753420