The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

Could hydrolysis of arsenic substituted DNA be prevented? Protection arises from stacking interactions

(2012) Jing Wang et al.   CHEMICAL COMMUNICATIONS

Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment

(2012) Judith M. Fonville et al.   CHEMISTRY-A EUROPEAN JOURNAL

DFT Study of B-like Conformations of Deoxydinucleoside Monophosphates Containing Gua and/or Cyt and their Complexes with Na+Cation

(2012) Valery I. Poltev et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Dependence of Deformability of Geometries and Characteristics of Intramolecular Hydrogen Bonds in Canonical 2′-Deoxyribonucleotides on DNA Conformations

(2012) Gennady V. Palamarchuk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

(2012) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

(2012) Pavel Banáš 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

Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form

(2012) Jiande Gu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural and Functional Consequences of Phosphate–Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP

(2012) Yu Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

(2012) Ivana Beššeová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

(2012) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex

(2012) Margriet Ovaere et al.   NUCLEIC ACIDS RESEARCH

Toward an Alternative Biology

(2012) G. F. Joyce   SCIENCE

Synthetic Genetic Polymers Capable of Heredity and Evolution

(2012) V. B. Pinheiro et al.   SCIENCE

Charged Nucleobases and Their Potential for RNA Catalysis

(2011) Jennifer L. Wilcox et al.   ACCOUNTS OF CHEMICAL RESEARCH

Frontiers in Molecular Dynamics Simulations of DNA

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

Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions

(2011) Narayanan Veeraraghavan et al.   BIOCHEMISTRY

Working the kinks out of nucleosomal DNA

(2011) Wilma K Olson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

(2011) Arnošt Mládek et al.   Journal of Chemical Theory and Computation

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

(2011) Ilyas Yildirim et al.   Journal of Chemical Theory and Computation

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

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

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Calculating the Response of NMR Shielding Tensor σ(31P) and2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+Cation

(2011) Ladislav Benda et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

(2011) Marie Zgarbová et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Conformational Flexibility of C8-Phenoxylguanine Adducts in Deoxydinucleoside Monophosphates

(2011) Andrea L. Millen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single Strand Break in DNA Coupled to the O—P Bond Cleavage. A Computational Study

(2011) Janusz Rak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

(2011) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Geometry and Electronic Structure of the As-DNA Backbone

(2011) Arnošt Mládek et al.   Journal of Physical Chemistry Letters

Impact of Arsenic/Phosphorus Substitution on the Intrinsic Conformational Properties of the Phosphodiester Backbone of DNA Investigated Using ab Initio Quantum Mechanical Calculations

(2011) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The chemical origins of life and its early evolution: an introduction

(2011) D. M. J. Lilley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The chemical versatility of RNA

(2011) D. A. Hiller et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA

(2011) Arnošt Mládek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA

(2011) Cassandra D. M. Churchill et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

HDV-like self-cleaving ribozymes

(2011) Chiu-Ho T. Webb et al.   RNA Biology

DFT study of DNA sequence dependence at the level of dinucleoside monophosphates

(2011) V.I. Poltev et al.   Computational and Theoretical Chemistry

Polarization effects in molecular interactions

(2011) F. Javier Luque et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

(2010) Jui-Hui Chen et al.   BIOCHEMISTRY

Nonparametric Clustering for Studying RNA Conformations

(2010) X. Le Faucheur et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

(2010) Ilyas Yildirim et al.   Journal of Chemical Theory and Computation

Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

(2010) Arnošt Mládek 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

Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts

(2010) Andrea L. Millen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?

(2010) Jiří Šponer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation States of the Key Active Site Residues and Structural Dynamics of theglmSRiboswitch As Revealed by Molecular Dynamics

(2010) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

(2010) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations

(2010) Jana Přecechtělová et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex

(2010) Xiang-Jun Lu et al.   NUCLEIC ACIDS RESEARCH

Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

(2010) Jiande Gu et al.   NUCLEIC ACIDS RESEARCH

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

(2010) F. Wolfe-Simon et al.   SCIENCE

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

(2009) Mark A. Ditzler et al.   ACCOUNTS OF CHEMICAL RESEARCH

Modulating RNA structure and catalysis: lessons from small cleaving ribozymes

(2009) Cedric Reymond et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Important effects of neighbouring nucleotides on electron induced DNA single-strand breaks

(2009) Pierre-François Loos et al.   CHEMICAL PHYSICS LETTERS

Scaled MP3 Non-Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data

(2009) Michal Pitoňák et al.   CHEMPHYSCHEM

Nuance in the double-helix and its role in protein–DNA recognition

(2009) Remo Rohs et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational study of the molecular mechanisms of caffeine action: Caffeine complexes with adenosine receptors

(2009) V. I. Poltev et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Intramolecular Basis Set Superposition Error Effects on the Planarity of DNA and RNA Nucleobases

(2009) David Asturiol et al.   Journal of Chemical Theory and Computation

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

Studies on the torsions of nucleic acids using ABEEMσπ/MM method

(2009) Fang-Fang Wang et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Structural Interpretation ofJCoupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing

(2009) Zuzana Vokáčová et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, BI, and BIIForms of Duplex DNA

(2009) Alexander D. MacKerell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin−Spin Couplings

(2009) Zuzana Vokáčová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme

(2009) Robert C. Spitale et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Direct Raman Measurement of an Elevated Base pKain the Active Site of a Small Ribozyme in a Precatalytic Conformation

(2009) Man Guo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   METHODS

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

(2009) Lu Liu et al.   Nature Chemical Biology

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

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme

(2009) M. A. Ditzler et al.   RNA

Widespread Occurrence of Self-Cleaving Ribozymes

(2009) C.-H. T. Webb et al.   SCIENCE

Effect of local sugar and base geometry on 13C and 15N magnetic shielding anisotropy in DNA nucleosides

(2008) Eva Brumovská et al.   JOURNAL OF BIOMOLECULAR NMR

Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy

(2008) Tait Takatani et al.   JOURNAL OF CHEMICAL PHYSICS

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

(2008) David Asturiol et al.   JOURNAL OF CHEMICAL PHYSICS

Enthalpy difference between conformations of normal alkanes: Intramolecular basis set superposition error (BSSE) in the case of n-butane and n-hexane

(2008) Roman M. Balabin   JOURNAL OF CHEMICAL PHYSICS

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

(2008) Yan Zhao et al.   Journal of Chemical Theory and Computation

Force field parameters for rotation around χ torsion axis in nucleic acids

(2008) Hirotaka Ode et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

(2008) Daniel Svozil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

(2008) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis

(2008) Kwangho Nam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The UA_handle: a versatile submotif in stable RNA architectures†

(2008) Luc Jaeger et al.   NUCLEIC ACIDS RESEARCH

DNA conformations and their sequence preferences

(2008) Daniel Svozil et al.   NUCLEIC ACIDS RESEARCH

Nature and magnitude of aromatic stacking of nucleic acid bases

(2008) Jiří Šponer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

(2008) K. Nam et al.   RNA

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

(2008) J. S. Richardson et al.   RNA

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide

(2007) Haydée Valdés et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY