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

The G-Triplex DNA

(2013) Vittorio Limongelli et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Spin-Crossing in an Organometallic Pt–Benzene Complex

(2013) Jaroslav Granatier et al.   Journal of Chemical Theory and Computation

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

(2013) Barira Islam et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment

(2012) Eunae Kim et al.   Journal of Chemical Theory and Computation

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Energetic Basis of Human Telomeric DNA Folding into G-Quadruplex Structures

(2012) Matjaž Bončina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Kinetics and Folding Pathways of Intramolecular G-Quadruplex Nucleic Acids

(2012) Amy Y. Q. Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Populated Intermediates in the Thermal Unfolding of the Human Telomeric Quadruplex

(2012) Robert D. Gray et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Isothermal folding of G-quadruplexes

(2012) Robert D. Gray et al.   METHODS

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

(2012) Jiří Šponer et al.   METHODS

Strand directionality affects cation binding and movement within tetramolecular G-quadruplexes

(2012) Primož Šket et al.   NUCLEIC ACIDS RESEARCH

The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages

(2012) George R. Clark et al.   NUCLEIC ACIDS RESEARCH

Intramolecular folding in three tandem guanine repeats of human telomeric DNA

(2011) Deepak Koirala et al.   CHEMICAL COMMUNICATIONS

Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+

(2011) Changwon Yang et al.   JOURNAL OF CHEMICAL PHYSICS

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

Structure of Human Telomeric DNA in Crowded Solution

(2011) Brahim Heddi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Roman V. Reshetnikov et al.   NUCLEIC ACIDS RESEARCH

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

(2011) Xiaohui Cang et al.   NUCLEIC ACIDS RESEARCH

Multiple Routes to Characterize the Folding of a Small DNA Hairpin

(2010) Guillem Portella et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure, location and interactions of G-quadruplexes

(2010) Julian L. Huppert   FEBS Journal

Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations

(2010) Roman Reshetnikov et al.   Journal of Chemical Theory and Computation

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

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex Structures

(2010) Tomoko Mashimo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tetramolecular DNA Quadruplexes in Solution: Insights into Structural Diversity and Cation Movement

(2010) Primož Šket et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry

(2010) F. Rosu et al.   NUCLEIC ACIDS RESEARCH

The structures of quadruplex nucleic acids and their drug complexes

(2009) Stephen Neidle   CURRENT OPINION IN STRUCTURAL BIOLOGY

Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer

(2009) Stephen Neidle   FEBS Journal

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

Energetics and Kinetics of a Conformational Switch in G-Quadruplex DNA†

(2009) Robert D. Gray et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2009) Zhenjiang Zhang et al.   NUCLEIC ACIDS RESEARCH

Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study

(2008) Hui Li et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Polymorphism of human telomeric quadruplex structures

(2008) Jixun Dai et al.   BIOCHIMIE

Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions

(2008) Yong Qin et al.   BIOCHIMIE

Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes

(2008) Julian Leon Huppert   CHEMICAL SOCIETY REVIEWS

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

Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures

(2008) Robert D. Gray et al.   NUCLEIC ACIDS RESEARCH

Targeting telomeres and telomerase

(2007) Anne De Cian et al.   BIOCHIMIE