4.7 Article

Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

Related references

Note: Only part of the references are listed.
Article Chemistry, Multidisciplinary

Conformational Dynamics of Strand Register Shifts in DNA G-Quadruplexes

J. Tassilo Gruen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Biochemistry & Molecular Biology

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

Justin A. Lemkul

NUCLEIC ACIDS RESEARCH (2020)

Article Chemistry, Physical

Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations

Barira Islam et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Review Cell Biology

The regulation and functions of DNA and RNA G-quadruplexes

Dhaval Varshney et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

Jaba Mitra et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Chemistry, Multidisciplinary

Identification of Intermediates in Peroxidase Catalytic Cycle of a DNAzyme Possessing Heme

Ryosuke Shinomiya et al.

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN (2019)

Review Chemistry, Organic

Binding and Beyond: What Else Can G-Quadruplex Ligands Do?

Michael P. O'Hagan et al.

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY (2019)

Review Chemistry, Multidisciplinary

Applications of guanine quartets in nanotechnology and chemical biology

Loic Stefan et al.

NATURE REVIEWS CHEMISTRY (2019)

Review Biochemistry & Molecular Biology

Nucleic acid enzymes based on functionalized nucleosides

Marcel Hollenstein

CURRENT OPINION IN CHEMICAL BIOLOGY (2019)

Review Chemistry, Multidisciplinary

DNA Quadruple Helices in Nanotechnology

Jean-Louis Mergny et al.

CHEMICAL REVIEWS (2019)

Article Biochemistry & Molecular Biology

G-quadruplexes Sequester Free Heme in Living Cells

Lucas T. Gray et al.

CELL CHEMICAL BIOLOGY (2019)

Review Chemistry, Multidisciplinary

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Jiri Sponer et al.

CHEMICAL REVIEWS (2018)

Article Chemistry, Multidisciplinary

Insight into How Telomeric G-Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin

Tingting Ai et al.

CHEMISTRY-AN ASIAN JOURNAL (2018)

Article Chemistry, Multidisciplinary

Destabilization of DNA G-Quadruplexes by Chemical Environment Changes during Tumor Progression Facilitates Transcription

Hisae Tateishi-Karimata et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Review Clinical Neurology

C9orf72-mediated ALS and FTD: multiple pathways to disease

Rubika Balendra et al.

NATURE REVIEWS NEUROLOGY (2018)

Article Biochemistry & Molecular Biology

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Marek Havrila et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Encoding canonical DNA quadruplex structure

Scarlett A. Dvorkin et al.

SCIENCE ADVANCES (2018)

Review Chemistry, Physical

DNAzymes: Selected for Applications

Devon Morrison et al.

SMALL METHODS (2018)

Article Chemistry, Physical

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

Marek Havrila et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Review Cell Biology

DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

Robert Hansel-Hertsch et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Chemistry, Multidisciplinary

Hemin-Graphene Derivatives with Increased Peroxidase Activities Restrain Protein Tyrosine Nitration

Huan Xu et al.

CHEMISTRY-A EUROPEAN JOURNAL (2017)

Article Chemistry, Multidisciplinary

A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme

Yuehua Guo et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Article Biochemistry & Molecular Biology

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

Jiri Sponer et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2017)

Article Chemistry, Multidisciplinary

The Effect of Adenine Repeats on G-quadruplex/hemin Peroxidase Mimicking DNAzyme Activity

Jielin Chen et al.

CHEMISTRY-A EUROPEAN JOURNAL (2017)

Article Chemistry, Multidisciplinary

Activity Enhancement of G-Quadruplex/Hemin DNAzyme by Flanking d(CCC)

Tianjun Chang et al.

CHEMISTRY-A EUROPEAN JOURNAL (2016)

Article Chemistry, Medicinal

Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Kelly Mulholland et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Chemistry, Medicinal

Quadruplex Nucleic Acids as Novel Therapeutic Targets

Stephen Neidle

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Biochemistry & Molecular Biology

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

Mikayel Aznauryan et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Folding and misfolding pathways of G-quadruplex DNA

Adrien Marchand et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Re-evaluation of G-quadruplex propensity with G4Hunter

Amina Bedrat et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Pharmacology & Pharmacy

Emerging Role of G-quadruplex DNA as Target in Anticancer Therapy

Graziella Cimino-Reale et al.

CURRENT PHARMACEUTICAL DESIGN (2016)

Article Chemistry, Multidisciplinary

Involvement of Long-Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G-Quadruplex

Irene Bessi et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Chemistry, Multidisciplinary

Characterization of the Interaction between Heme and a Parallel G-Quadruplex DNA Formed from d(TTAGGGT)

Haruna Shimizu et al.

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN (2015)

Article Chemistry, Multidisciplinary

Small molecule binding to a G-hairpin and a G-triplex: a new insight into anticancer drug design targeting G-rich regions

Arivazhagan Rajendran et al.

CHEMICAL COMMUNICATIONS (2015)

Article Chemistry, Inorganic & Nuclear

Cobalt(III)porphyrin to target G-quadruplex DNA

Laurent Sabater et al.

DALTON TRANSACTIONS (2015)

Review Biochemistry & Molecular Biology

G4-associated human diseases

Nancy Maizels

EMBO REPORTS (2015)

Article Chemistry, Physical

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Marie Zgarbova et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Chad W. Hopkins et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

All-Atomic Simulations on Human Telomeric G-Quadruplex DNA Binding with Thioflavin T

Di Luo et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Biotechnology & Applied Microbiology

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

Vicki S. Chambers et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemistry & Molecular Biology

Heme activation by DNA: isoguanine pentaplexes, but not quadruplexes, bind heme and enhance its oxidative activity

Nisreen Shumayrikh et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

G-quadruplexes and their regulatory roles in biology

Daniela Rhodes et al.

NUCLEIC ACIDS RESEARCH (2015)

Editorial Material Biochemistry & Molecular Biology

A pilgrim's guide to G-quadruplex nucleic acid folding

Valerie Gabelica

BIOCHIMIE (2014)

Article Chemistry, Medicinal

G-Quadruplex Structures and Their Interaction Diversity with Ligands

Sulin Zhang et al.

CHEMMEDCHEM (2014)

Article Biochemistry & Molecular Biology

Folding and Unfolding Pathways of the Human Telomeric G-Quadruplex

Robert D. Gray et al.

JOURNAL OF MOLECULAR BIOLOGY (2014)

Article Computer Science, Interdisciplinary Applications

SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations

Scott Le Grand et al.

COMPUTER PHYSICS COMMUNICATIONS (2013)

Article Chemistry, Physical

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Marie Zgarbova et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Multidisciplinary

Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations

Jiri Sponer et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Biochemical Research Methods

DNA quadruplex folding formalism - A tutorial on quadruplex topologies

Andreas Ioannis Karsisiotis et al.

METHODS (2013)

Article Biochemistry & Molecular Biology

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Petr Stadlbauer et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Chemistry, Multidisciplinary

Graphene-Supported Hemin as a Highly Active Biomimetic Oxidation Catalyst

Teng Xue et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)

Article Chemistry, Inorganic & Nuclear

Interaction between the Heme and a G-Quartet in a Heme-DNA Complex

Kaori Saito et al.

INORGANIC CHEMISTRY (2012)

Article Chemistry, Multidisciplinary

Quantum Mechanically Derived AMBER-Compatible Heme Parameters for Various States of the Cytochrome P450 Catalytic Cycle

Kiumars Shahrokh et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)

Article Chemistry, Medicinal

Molecular Basis of Structure-Activity Relationships between Salphen Metal Complexes and Human Telomeric DNA Quadruplexes

Nancy H. Campbell et al.

JOURNAL OF MEDICINAL CHEMISTRY (2012)

Article Chemistry, Multidisciplinary

Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene

Marko Trajkovski et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemistry & Molecular Biology

Interaction of human telomeric DNA with N-methyl mesoporphyrin IX

John M. Nicoludis et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Chemistry, Multidisciplinary

Kinetic and Thermodynamic Control of G-Quadruplex Folding

Yong Xue et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2011)

Article Chemistry, Analytical

Structure-function study of peroxidase-like G-quadruplex-hemin complexes

De-Ming Kong et al.

ANALYST (2010)

Article Chemistry, Analytical

Positive Effects of ATP on G-Quadruplex-Hemin DNAzyme-Mediated Reactions

De-Ming Kong et al.

ANALYTICAL CHEMISTRY (2010)

Review Biochemistry & Molecular Biology

The structures of quadruplex nucleic acids and their drug complexes

Stephen Neidle

CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

The formation pathway of tetramolecular G-quadruplexes

Caroline Bardin et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation

Anne De Cian et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Chemistry, Multidisciplinary

Geometric formalism for DNA quadruplex folding

Mateus Webba da Silva

CHEMISTRY-A EUROPEAN JOURNAL (2007)

Article Multidisciplinary Sciences

Crystal structure of parallel quadruplexes from human telomeric DNA

GN Parkinson et al.

NATURE (2002)

Article Chemistry, Multidisciplinary

The peroxidase activity of a hemin-DNA oligonucleotide complex: Free radical damage to specific guanine bases of the DNA

P Travascio et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)