Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics

No abstract is available for this paper.

• Publication year

  2001

• Venue

  Biopolymers

• Publication date

  Unknown publication date

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1002/1097-0282(2001)61:1<61::AID-BIP10047>3.0.CO;2-1PMID 11891629
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density

  2001cited by this paper
• Solution structure by NMR and molecular dynamics of a duplex containing a guanine opposite a N-(2-deoxy-beta-D-erythro-pentofuranosyl)formamide lesion.

  2000cited by this paper
• The peculiar role of cytosine in nucleoside conformational behaviour: Hydrogen bond donor capacity of nucleic bases

  2000cited by this paper
• Ground-State Properties of Nucleic Acid Constituents Studied by Density Functional Calculations. 3. Role of Sugar Puckering and Base Orientation on the Energetics and Geometry of 2‘-Deoxyribonucleosides and Ribonucleosides

  2000cited by this paper
• All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

  2000cited by this paper
• New insights into the structure of abasic DNA from molecular dynamics simulations

  2000cited by this paper
• Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study

  2000cited by this paper
• Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.

  1999cited by this paper
• Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA.

  1999cited by this paper
• Ground State Properties of the Nucleic Acid Constituents Studied by Density Functional Calculations. I. Conformational Features of Ribose, Dimethyl Phosphate, Uridine, Cytidine, 5‘-Methyl Phosphate−Uridine, and 3‘-Methyl Phosphate−Uridine

  1999cited by this paper
• Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics

  1999cited by this paper
• Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.

  1999cited by this paper
• Ab Initio Quantum Mechanical Study of the Structures and Energies for the Pseudorotation of 5‘-Dehydroxy Analogues of 2‘-Deoxyribose and Ribose Sugars

  1999cited by this paper
• Crystal structure of a DNA Holliday junction

  1999cited by this paper
• HXeSH, the First Example of a Xenon-Sulfur Bond

  1998cited by this paper
• Sequence-dependent dynamics of TATA-Box binding sites.

  1998cited by this paper
• Conformational Properties of the Deoxyribose and Ribose Moieties of Nucleic Acids: A Quantum Mechanical Study

  1998cited by this paper
• Conformations of the sugar-phosphate backbone in helical DNA crystal structures.

  1997cited by this paper
• Influence of water and sodium on the energetics of dimethylphosphate and its implications for DNA structure

  1997cited by this paper
• Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents

  1996cited by this paper
• How do the energetics of the stereoelectronic gauche and anomeric effects modulate the conformation of nucleos(t)ides?

  1996cited by this paper
• A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein

  1996cited by this paper
• DNA structural forms

  1996cited by this paper
• Conformational transitions in potential and free energy space for furanoses and 2'-deoxynucleosides

  1993cited by this paper
• Crystal structure of a yeast TBP/TATA-box complex

  1993cited by this paper
• The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.

  1992cited by this paper
• Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.

  1991cited by this paper
• Interaction of TFIID in the minor groove of the TATA element.

  1991cited by this paper
• TFIID binds in the minor groove of the TATA box.

  1991cited by this paper
• Atoms in molecules : a quantum theory

  1990cited by this paper
• Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences.

  1989cited by this paper
• Crystal structure of trp represser/operator complex at atomic resolution

  1988cited by this paper
• Three-dimensional structure of the ribonuclease T1 2'-GMP complex at 1.9-A resolution.

  1988cited by this paper
• Crystal structure of trp represser/operator complex at atomic resolution

  1988cited by this paper
• Empirical energy functions for energy minimization and dynamics of nucleic acids

  1986cited by this paper
• AB INITIO Molecular Orbital Theory

  1986cited by this paper
• Deceptive convergence in Møller-Plesset perturbation energies

  1986cited by this paper
• The calculation of higher-order energies in the many-body perturbation theory series

  1985cited by this paper
• Conformational studies of nucleic acids. II. The conformational energetics of commonly occurring nucleosides.

  1985cited by this paper
• On the convergence of the Møller-Plesset perturbation series

  1985cited by this paper
• How flexible is the furanose ring? 2. An updated potential energy estimate

  1982cited by this paper
• CONFORMATIONS OF NUCLEOSIDES AND NUCLEOTIDES

  1978cited by this paper
• Extreme conformational flexibility of the furanose ring in DNA and RNA

  1978cited by this paper
• Conformational studies on guanosine nucleotides and polynucleotides. The effect of the base on the glycosyl and backbone conformations

  1973cited by this paper
• Molecular orbital calculations on the conformation of nucleic acids and their constituents

  1973cited by this paper
• Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants.

  1973cited by this paper
• Syn–Anti effects on the spatial configuration of polynucleotide chains

  1973cited by this paper
• Nucleotides: Rigid or flexible?

  1973cited by this paper
• A model conformational study of nucleic acid phosphate ester bonds. The torsional potential of dimethyl phosphate monoanion.

  1973cited by this paper
• Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond model

  1972cited by this paper
• Molecular orbital calculations on the conformation of nucleic acids and their constituents. IV. Conformations about the exocyclic C(4')-C(5') bond.

  1972cited by this paper
• Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides

  1972cited by this paper
• Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.

  1972cited by this paper
• Nucleoside conformation and non-bonded interactions.

  1971cited by this paper
• Molecular orbital calculations on the conformation of nucleic acids and their constituents. I. Conformational energies of beta-nucleosides with C(3')-and C(2')-endo sugars.

  1971cited by this paper
• Molecular orbital calculations on the conformation of nucleic acids and their constituents. II. Conformational energies of nucleosides with C(3')-and C(2')-exo sugars.

  1971cited by this paper
• Stereochemistry of nucleic acids and polynucleotides. II. Allowed conformations of the monomer unit for different ribose puckerings.

  1970cited by this paper
• Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base‐sugar units

  1969cited by this paper
• Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono‐, di‐, tri‐, tetraphosphates, nucleic acids and polynucleotides

  1969cited by this paper
• Molecular orbital calculations on the preferred conformation of nucleosides

  1968cited by this paper
• Nucleoside conformations: an analysis of steric barriers to rotation about the glycosidic bond.

  1967cited by this paper

• Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies.

  2024cites this paper
• The structure of DNA fragments: Quantum-chemical modelling.

  2023cites this paper
• The building blocks of DNA and RNA

  2022cites this paper
• The dataset of covalent bond lengths resulting from the first-principle calculations

  2019cites this paper
• Polarizable force field for RNA based on the classical drude oscillator

  2018cites this paper
• Atomic charges for conformationally rich molecules obtained through a modified principal component regression.

  2018cites this paper
• Threocytidines: Insight into the Conformational Preferences of Artificial Threose Nucleic Acid (TNA) Building Blocks in B3LYP Studies.

  2018cites this paper
• Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation

  2017cites this paper
• Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition.

  2017cites this paper
• Different Conformations of 2'-Deoxycytidine in the Gas and Solid Phases: Competition between Intra- and Intermolecular Hydrogen Bonds.

  2016cites this paper
• Additive CHARMM force field for naturally occurring modified ribonucleotides

  2016cites this paper
• Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability.

  2016cites this paper
• Cell–Substrate Interactions

  2015cites this paper
• Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

  2015cites this paper
• Current status of protein force fields for molecular dynamics simulations.

  2015cites this paper
• Effects of Explicit and Implicit Solvent Models on the Hydrolysis Cleavage of N-Glycosidic Bond in 8-Oxo-7,8-dihydro-2 '-deoxyguanosine

  2014cites this paper
• Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

  2014cites this paper
• Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin.

  2014cites this paper
• Coarse-grained DNA model capable of simulating ribose flexibility

  2014cites this paper
• The “sugar” coarse-grained DNA model

  2014influential citation
• Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation.

  2013cites this paper
• Modeling the conformational preference of the carbon-bonded covalent adduct formed upon exposure of 2'-deoxyguanosine to ochratoxin A.

  2013cites this paper
• Conformational analysis of furanoside-containing mono- and oligosaccharides.

  2013cites this paper
• Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.

  2013cites this paper
• The conformation of a ribose derivative in aqueous solution: a neutron-scattering and molecular dynamics study.

  2013cites this paper
• Molecular structure and character of bonding of mono and divalent metal cations (Li+, Na+, K+, Mg2+, Ca2+, Zn2+, and Cu+) with guanosine: AIM and NBO analysis

  2012cites this paper
• 7.9 Biophysics of Nuclear Organization and Dynamics

  2012cites this paper
• The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.

  2012cites this paper
• Structural flexibility of DNA-like conformers of canonical 2'-deoxyribonucleosides.

  2012cites this paper
• Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity.

  2012cites this paper
• Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

  2011cites this paper
• Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA.

  2011cites this paper
• Intramolecular CH…O Hydrogen Bonds in the AI and BI DNA-like Conformers of Canonical Nucleosides and their Watson-Crick Pairs. Quantum Chemical and AIM Analysis

  2011cites this paper
• Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA

  2011cites this paper
• Selection of G-quadruplex folding topology with LNA-modified human telomeric sequences in K+ solution.

  2011cites this paper
• DNA Structure: Alphabet Soup for the Cellular Soul

  2011cites this paper
• Two Polymorphic Residues Account for the Differences in DNA Binding and Transcriptional Activation by NF-κB Proteins Encoded by Naturally Occurring Alleles in Nematostella vectensis

  2011cites this paper
• Modeling the dissociative hydrolysis of the natural DNA nucleosides.

  2010cites this paper
• Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

  2010cites this paper
• Conformational flexibility of c8-phenoxyl-2'-deoxyguanosine nucleotide adducts.

  2010cites this paper
• Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA.

  2009cites this paper
• Conformational sampling and energetics of drug-like molecules.

  2009cites this paper
• A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

  2009cites this paper
• CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

  2009cites this paper
• Внутрішньомолекулярні водневі зв''язки СН. . . о у біологічно важливих конформерах канонічних 2''-дезоксирибонуклеозидів: результати квантово-механічного топологічного аналізу електронної густини

  2009cites this paper
• Ab initio determination of the flexibility of 2′‐aminoribonucleosides and 2′‐aminoarabinonucleosides inserted in duplexes

  2008cites this paper
• The Building-Blocks of DNA and RNA

  2008cites this paper
• Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

  2008cites this paper
• Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes.

  2008cites this paper
• Analyzing the flexibility of RNA structures by constraint counting.

  2008cites this paper
• Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.

  2008cites this paper
• Comprehensive conformational analysis of the nucleoside analogue 2'-beta-deoxy-6-azacytidine by DFT and MP2 calculations.

  2007cites this paper
• The whole of intramolecular H-bonding in the isolated DNA nucleoside thymidine. AIM electron density topological study

  2007cites this paper
• Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

  2007cites this paper
• The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response

  2006cites this paper
• Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes.

  2006cites this paper
• Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

  2005cites this paper
• The structure of a mixed LNA/DNA:RNA duplex is driven by conformational coupling between LNA and deoxyribose residues as determined from 13C relaxation measurements.

  2005cites this paper
• Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides.

  2005cites this paper
• Insight into enzymatic C-F bond formation from QM and QM/MM calculations.

  2005cites this paper
• Empirical force fields for biological macromolecules: Overview and issues

  2004cites this paper
• Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

  2003cites this paper
• Computer simulation studies of the fidelity of DNA polymerases

  2003cites this paper
• Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study.

  2002cites this paper
• Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

  2002cites this paper
• Toxicology and Applied Pharmacology Insights

  year unknowncites this paper