Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex

Antiviral Activity of the G-Quadruplex Ligand TMPyP4 against Herpes Simplex Virus-1

(2021) Sara Artusi et al.   Viruses-Basel

RNA G-quadruplexes (rG4s): genomics and biological functions

(2021) Kaixin Lyu et al.   NUCLEIC ACIDS RESEARCH

Identifying G-Quadruplex-DNA-Disrupting Small Molecules

(2021) Jérémie Mitteaux et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unlocking G-Quadruplexes as Antiviral Targets

(2021) Ardavan Abiri et al.   PHARMACOLOGICAL REVIEWS

G2-quadruplex in the 3’UTR of IE180 regulates Pseudorabies Virus replication by enhancing gene expression

(2020) Ya-Shu Zhang et al.   RNA Biology

Small-molecule G-quadruplex stabilizers reveal a novel pathway of autophagy regulation in neurons

(2020) Jose F Moruno-Manchon et al.   eLife

Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths

(2020) Yashu Zhang et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back

(2020) Prakash Kharel et al.   NUCLEIC ACIDS RESEARCH

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA

(2019) Michael P. O'Hagan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure and Properties of Double-Sandwich Complexes at the Graphene Surface: A Theoretical Study

(2019) Vijay Madhav Miriyala et al.   Journal of Physical Chemistry C

The diverse structural landscape of quadruplexes

(2019) Helen L. Lightfoot et al.   FEBS LETTERS

Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition

(2019) Wenting Liu et al.   NUCLEIC ACIDS RESEARCH

G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy

(2018) Rafael del Villar-Guerra et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy

(2018) Emanuela Ruggiero et al.   NUCLEIC ACIDS RESEARCH

Unfolding Hidden Barriers by Active Enhanced Sampling

(2018) Jing Zhang et al.   PHYSICAL REVIEW LETTERS

Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria

(2018) Zbigniew Pietras et al.   Nature Communications

G-Quadruplex: A Regulator of Gene Expression and Its Chemical Targeting

(2018) Tian Tian et al.   Chem

Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36

(2018) Michael C. Chen et al.   NATURE

Novel Amphiphilic G-Quadruplex Binding Synthetic Derivative of TMPyP4 and Its Effect on Cancer Cell Proliferation and Apoptosis Induction

(2018) Ushasri Chilakamarthi et al.   BIOCHEMISTRY

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

(2018) Sunny Y. Yang et al.   Nature Communications

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

(2017) Federica Moraca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G-Quadruplexes: Prediction, Characterization, and Biological Application

(2017) Chun Kit Kwok et al.   TRENDS IN BIOTECHNOLOGY

ALS/FTD-Associated C9ORF72 Repeat RNA Promotes Phase Transitions In Vitro and in Cells

(2017) Marta M. Fay et al.   Cell Reports

Quadruplex nucleic acids as targets for anticancer therapeutics

(2017) Stephen Neidle   Nature Reviews Chemistry

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Quadruplex Nucleic Acids as Novel Therapeutic Targets

(2016) Stephen Neidle   JOURNAL OF MEDICINAL CHEMISTRY

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

(2016) Chun Kit Kwok et al.   NATURE METHODS

RNA G-quadruplex formation in defined sequence in living cells detected by bimolecular fluorescence complementation

(2016) Hong-he Liu et al.   Chemical Science

Molecular recognition of parallel quadruplex [d-(TTGGGGT)]4 by mitoxantrone: binding with 1 : 4 stoichiometry leads to telomerase inhibition

(2016) Tarikere Palakshan Pradeep et al.   RSC Advances

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

(2015) Susanta Haldar et al.   Journal of Chemical Theory and Computation

Ewald Summation for Molecular Simulations

(2015) Brad A. Wells et al.   Journal of Chemical Theory and Computation

High-throughput sequencing of DNA G-quadruplex structures in the human genome

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

G-quadruplexes and their regulatory roles in biology

(2015) Daniela Rhodes et al.   NUCLEIC ACIDS RESEARCH

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

(2015) Stephan A Ohnmacht et al.   Scientific Reports

Folding and Unfolding Pathways of the Human Telomeric G-Quadruplex

(2014) Robert D. Gray et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanistic insight into ligand binding to G-quadruplex DNA

(2014) Francesco Saverio Di Leva et al.   NUCLEIC ACIDS RESEARCH

Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3

(2013) Wan Jun Chung et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

TMPyP4 Porphyrin Distorts RNA G-quadruplex Structures of the Disease-associated r(GGGGCC)nRepeat of theC9orf72Gene and Blocks Interaction of RNA-binding Proteins

(2013) Bita Zamiri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations

(2013) Susanta Haldar et al.   Journal of Physical Chemistry C

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

(2013) Vu H. Le et al.   PLoS One

Formation of a Unique Cluster of G-Quadruplex Structures in the HIV-1 nef Coding Region: Implications for Antiviral Activity

(2013) Rosalba Perrone et al.   PLoS One

The G4 Genome

(2013) Nancy Maizels et al.   PLoS Genetics

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

(2012) G. Saladino et al.   Journal of Chemical Theory and Computation

Structural Basis for Telomeric G-Quadruplex Targeting by Naphthalene Diimide Ligands

(2012) Gavin W. Collie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The porphyrin TmPyP4 unfolds the extremely stable G-quadruplex in MT3-MMP mRNA and alleviates its repressive effect to enhance translation in eukaryotic cells

(2012) Mark J. Morris et al.   NUCLEIC ACIDS RESEARCH

Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation

(2012) Nicolas Beaume et al.   NUCLEIC ACIDS RESEARCH

5'-UTR RNA G-quadruplexes: translation regulation and targeting

(2012) A. Bugaut et al.   NUCLEIC ACIDS RESEARCH

Telomeres are favoured targets of a persistent DNA damage response in ageing and stress-induced senescence

(2012) Graeme Hewitt et al.   Nature Communications

Methods for investigating G-quadruplex DNA/ligand interactions

(2011) Pierre Murat et al.   CHEMICAL SOCIETY REVIEWS

Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets

(2011) Célia Fonseca Guerra et al.   CHEMISTRY-A EUROPEAN JOURNAL

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

DNA secondary structures and epigenetic determinants of cancer genome evolution

(2011) Subhajyoti De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Disordering of Human Telomeric G-Quadruplex with Novel Antiproliferative Anthrathiophenedione

(2011) Dmitry Kaluzhny et al.   PLoS One

A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex

(2010) Gavin W. Collie et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Shedding Light on the Interaction between TMPyP4 and Human Telomeric Quadruplexes

(2009) Luigi Martino et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Small Molecule That Disrupts G-Quadruplex DNA Structure and Enhances Gene Expression

(2009) Zoë A. E. Waller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The quadruplex r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA

(2009) N. Ofer et al.   NUCLEIC ACIDS RESEARCH

G-quadruplex structures: in vivo evidence and function

(2009) Hans J. Lipps et al.   TRENDS IN CELL BIOLOGY

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A hitchhiker's guide to G-quadruplex ligands

(2007) David Monchaud et al.   ORGANIC & BIOMOLECULAR CHEMISTRY