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

Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G-Quadruplex DNA Structure

(2012) Parisa Akhshi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study

(2012) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

NMR spectroscopy of G-quadruplexes

(2012) Michael Adrian et al.   METHODS

Axis of ageing: telomeres, p53 and mitochondria

(2012) Ergün Sahin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1

(2012) Carla Bazzicalupi et al.   NUCLEIC ACIDS RESEARCH

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

(2012) D. Wei et al.   NUCLEIC ACIDS RESEARCH

An In Silico Study of the Differential Effect of Oxidation on Two Biologically Relevant G-Quadruplexes: Possible Implications in Oncogene Expression

(2012) William J. D. Stebbeds et al.   PLoS One

Frontiers in Molecular Dynamics Simulations of DNA

(2011) Alberto Pérez et al.   ACCOUNTS OF CHEMICAL RESEARCH

Surface area accessibility and the preferred topology of telomeric DNA quadruplex–ligand complexes

(2011) Shozeb M. Haider et al.   BIOCHIMIE

A structural analysis of G-quadruplex/ligand interactions

(2011) Shozeb M. Haider et al.   BIOCHIMIE

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Structural Basis of Telomeric RNA Quadruplex−Acridine Ligand Recognition

(2011) Gavin W. Collie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis

(2011) Xiaohui Cang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of Human Telomeric DNA in Crowded Solution

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

Mass spectrometry of G-quadruplex DNA: Formation, recognition, property, conversion, and conformation

(2011) Gu Yuan et al.   MASS SPECTROMETRY REVIEWS

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

Comprehensive survey and geometric classification of base triples in RNA structures

(2011) Amal S. Abu Almakarem et al.   NUCLEIC ACIDS RESEARCH

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

Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

(2010) Wiktor Zierkiewicz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The structures of quadruplex nucleic acids and their drug complexes

(2009) Stephen Neidle   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Classification and energetics of the base-phosphate interactions in RNA

(2009) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

Quadruplex DNA crystal structures and drug design

(2008) Stephen Neidle et al.   BIOCHIMIE

Molecular Dynamics and Principal Components Analysis of Human Telomeric Quadruplex Multimers

(2008) Shozeb Haider et al.   BIOPHYSICAL JOURNAL

Topology Conservation and Loop Flexibility in Quadruplex–Drug Recognition: Crystal Structures of Inter- and Intramolecular Telomeric DNA Quadruplex–Drug Complexes

(2008) Gary N. Parkinson et al.   JOURNAL OF MOLECULAR BIOLOGY

Energetics of the Human Tel-22 Quadruplex−Telomestatin Interaction: A Molecular Dynamics Study

(2008) Saurabh Agrawal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2008) Bruno Pagano et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular dynamics of a κB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation

(2008) Cameron Mura et al.   NUCLEIC ACIDS RESEARCH

Stability and kinetics of G-quadruplex structures

(2008) A. N. Lane et al.   NUCLEIC ACIDS RESEARCH