DSDNA
Structure and Dynamics of Nucleic Acids
Publications Overview of the Department of Structure and Dynamics of Nucleic Acids
2013
2012
- (2012), On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134, 20788-20796 [AIS=2.799, IF=9.907 H]
- (2012), How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid: ribonucleic acid duplex, NUCLEIC ACIDS RESEARCH 40, 7573-7583 [AIS=3.007, IF=8.026 H]
- (2012), Structure and mechanical properties of the ribosomal L1 stalk three-way junction, NUCLEIC ACIDS RESEARCH 40, 6290-6303 [AIS=3.007, IF=8.026 H]
- (2012), Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment, CHEMISTRY-A EUROPEAN JOURNAL 18, 12372-12387 [AIS=1.532, IF=5.925 H]
- (2012), A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8, 3232-3242 [AIS=1.718, IF=5.215 H]
- (2012), Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8, 2448-2460 [AIS=1.716, IF=5.215 H]
- (2012), Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8, 2506-2520 [AIS=1.716, IF=5.215 H]
- (2012), Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study, JOURNAL OF PHYSICAL CHEMISTRY B 116, 12721-12734 [AIS=1.161, IF=3.696 H]
- (2012), Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8, 335-347 [AIS=1.764, IF=5.138 VH]
- (2012), Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration, JOURNAL OF PHYSICAL CHEMISTRY B 116, 9899-9916 [AIS=1.161, IF=3.696 VH]
- (2012), Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction Route, JOURNAL OF PHYSICAL CHEMISTRY A 116, 720-726 [AIS=0.855, IF=2.732 VH]
2011
- (2011), Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133, 14270-14279 [AIS=, IF=]
- (2011), NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133, 13790-13793 [AIS=2.799, IF=9.907 H]
- (2011), Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process, NUCLEIC ACIDS RESEARCH 39, 9789-9802 [AIS=3.012, IF=7.836 V]
- (2011), Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways, CHEMISTRY-A EUROPEAN JOURNAL 17, 847-854 [AIS=1.594, IF=5.382 VH]
- (2011), A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis, JOURNAL OF PHYSICAL CHEMISTRY B 115, 13897-13910 [AIS=1.331, IF=3.603 VH]
- (2011), QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms, JOURNAL OF PHYSICAL CHEMISTRY B 115, 13911-13924 [AIS=1.331, IF=3.603 VH]
- (2011), 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, JOURNAL OF PHYSICAL CHEMISTRY A 115, 11277-11292 [AIS=0.855, IF=2.732 VH]
- (2011), On the Geometry and Electronic Structure of the As-DNA Backbone, JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2, 389-392 [AIS=0, IF=0 VH]
- (2011), Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes, NUCLEIC ACIDS RESEARCH 39, 4499-4512 [AIS=3.012, IF=7.836 H]
- (2011), Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7, 2886-2902 [AIS=1.764, IF=5.138 H]
- (2011), Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7, 2963-2980 [AIS=1.764, IF=5.138 H]
- (2011), Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13, 10869-10871 [AIS=1.329, IF=3.454 H]
- (2011), On the Stabilization of Ribose by Silicate Minerals, ASTROBIOLOGY 11, 115-121 [AIS=1.204, IF=3.257 H]
2010
- (2010), A measure of bending in nucleic acids structures applied to A-tract DNA, NUCLEIC ACIDS RESEARCH 38, 3414-3422 [AIS=3, IF=7.48 H]
- (2010), A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA, NUCLEIC ACIDS RESEARCH 38, 299-313 [AIS=3, IF=7.48 H]
- (2010), Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM, NUCLEIC ACIDS RESEARCH 38, 1325-1340 [AIS=3, IF=7.48 H]
- (2010), Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme, JOURNAL OF PHYSICAL CHEMISTRY B 114, 6642-6652 [AIS=1.396, IF=3.471 H]
- (2010), On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets-Quantum Chemical Insights into RNA Structural Biology, JOURNAL OF PHYSICAL CHEMISTRY B 114, 3307-3320 [AIS=1.396, IF=3.471 H]
- (2010), Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations, JOURNAL OF PHYSICAL CHEMISTRY B 114, 10581-10593 [AIS=1.396, IF=3.471 VH]
- (2010), An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 910-929 [AIS=1.731, IF=4.804 VH]
- (2010), Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 3817-3835 [AIS=1.746, IF=4.804 VH]
- (2010), Quantum Chemical Studies of Nucleic Acids Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?, JOURNAL OF PHYSICAL CHEMISTRY B 114, 15723-15741 [AIS=1.399, IF=3.471 VH]
- (2010), Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In, ACCOUNTS OF CHEMICAL RESEARCH 43, 40-47 [AIS=6.383, IF=18.203 VH]
- (2010), Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome, NUCLEIC ACIDS RESEARCH 38, 6247-6264 [AIS=3.001, IF=7.479 VH]
- (2010), Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues, CHEMISTRY-A EUROPEAN JOURNAL 16, 3057-3065 [AIS=1.593, IF=5.382 VH]
- (2010), Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 3836-3849 [AIS=1.746, IF=4.804 H]
- (2010), Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 3003-3014 [AIS=1.746, IF=4.804 H]
- (2010), Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12, 3522-3534 [AIS=1.3, IF=4.12 VH]
- (2010), Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12, 10476-10493 [AIS=1.298, IF=4.116 H]
- (2010), Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?, JOURNAL OF PHYSICAL CHEMISTRY B 114, 1191-1203 [AIS=1.396, IF=3.471 H]
- (2010), Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics, JOURNAL OF PHYSICAL CHEMISTRY B 114, 8701-8712 [AIS=1.396, IF=3.471 H]
2009
- (2009), Classification and energetics of the base-phosphate interactions in RNA, NUCLEIC ACIDS RESEARCH 37, 4898-4918 [AIS=3, IF=7.48 H]
- (2009), Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion, NUCLEIC ACIDS RESEARCH 37, 7321-7331 [AIS=3, IF=7.48 H]
- (2009), Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme, RNA-A PUBLICATION OF THE RNA SOCIETY 15, 560-575 [AIS=2.81, IF=5.2 H]
- (2009), Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5, 2088-2100 [AIS=1.731, IF=4.804 H]
- (2009), Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations, BIOPHYSICAL JOURNAL 97, 2004-2013 [AIS=1.917, IF=4.39 H]
- (2009), Dependence of A-RNA simulations on the choice of the force field and salt strength, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 11, 10701-10711 [AIS=1.3, IF=4.12 VH]
- (2009), Interactions of the "Piano-stool" [Ruthenium(II)(eta(6)-arene)(en)Cl](+) Complexes With Water and Nucleobases; A initio and DFT Study, JOURNAL OF COMPUTATIONAL CHEMISTRY 30, 1758-1770 [AIS=2.215, IF=3.769 H]
- (2009), Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM, METHODS 49, 202-216 [AIS=1.702, IF=3.763 H]
- (2009), Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin-Spin Couplings, JOURNAL OF PHYSICAL CHEMISTRY B 113, 1182-1191 [AIS=1.396, IF=3.471 H]
- (2009), Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations, JOURNAL OF PHYSICAL CHEMISTRY B 113, 1743-1755 [AIS=1.396, IF=3.471 VH]
- (2009), Structural Interpretation of J Coupling Constants in Guanosine and Deoxyguanosine: Modeling the Effects of Sugar Pucker, Backbone Conformation, and Base Pairing, JOURNAL OF PHYSICAL CHEMISTRY A 113, 8379-8386 [AIS=0.882, IF=2.899 H]
- (2009), Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5, 1524-1544 [AIS=1.731, IF=4.804 VH]
- (2009), Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 '-OH Group of Ribose, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5, 1166-1179 [AIS=1.731, IF=4.804 VH]
- (2009), Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5, 2514-2530 [AIS=1.731, IF=4.804 VH]
2008
- (2008), Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose, CHEMISTRY-A EUROPEAN JOURNAL 14, 9990-9998 [AIS=1.593, IF=5.382 VH]
- (2008), General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility, JOURNAL OF PHYSICAL CHEMISTRY B 112, 11177-11187 [AIS=1.396, IF=3.471 VH]
- (2008), Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids, JOURNAL OF PHYSICAL CHEMISTRY B 112, 8188-8197 [AIS=1.396, IF=3.471 H]
- (2008), Tautomeric equilibrium, stability, and hydrogen bonding in 2 '-deoxyguanosine monophosphate complexed with Mg2+, JOURNAL OF PHYSICAL CHEMISTRY B 112, 150-157 [AIS=1.396, IF=3.471 H]
- (2008), Effect of local sugar and base geometry on C-13 and N-15 magnetic shielding anisotropy in DNA nucleosides, JOURNAL OF BIOMOLECULAR NMR 42, 209-223 [AIS=0.764, IF=2.659 H]
- (2008), Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by Charmm explicit solvent molecular dynamics, BIOPOLYMERS 89, 732-746 [AIS=0.871, IF=2.605 H]
- (2008), Nature and magnitude of aromatic stacking of nucleic acid bases, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 10, 2595-2610 [AIS=1.3, IF=4.12 H]
2007
- (2007), Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA, NUCLEIC ACIDS RESEARCH 35, 4007-4017 [AIS=3, IF=7.48 VH]
- (2007), The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis, NUCLEIC ACIDS RESEARCH 35, 1933-1946 [AIS=3, IF=7.48 H]
- (2007), Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics, BIOPHYSICAL JOURNAL 93, 3932-3949 [AIS=1.917, IF=4.39 VH]
- (2007), Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers, BIOPHYSICAL JOURNAL 92, 3817-3829 [AIS=1.917, IF=4.39 H]
- (2007), Molecular dynamics simulations and their application to four-stranded DNA, METHODS 43, 278-290 [AIS=1.702, IF=3.763 VH]
- (2007), Leading RNA tertiary interactions: Structures, energies, and water insertion of a-minor and p-interactions. A quantum chemical view, JOURNAL OF PHYSICAL CHEMISTRY B 111, 9153-9164 [AIS=1.396, IF=3.471 VH]
- (2007), Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: The cis- and trans-Watson-Crick/sugar edge base pair family, JOURNAL OF PHYSICAL CHEMISTRY B 111, 10813-10824 [AIS=1.396, IF=3.471 H]
- (2007), Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA, JOURNAL OF PHYSICAL CHEMISTRY B 111, 870-879 [AIS=1.396, IF=3.471 H]
- (2007), Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair, BIOCHEMISTRY 46, 11263-11278 [AIS=1.315, IF=3.226 H]
- (2007), Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme, BIOPOLYMERS 85, 392-406 [AIS=0.871, IF=2.605 H]
- (2007), Molecular dynamics simulations of RNA: An in silico single molecule approach, BIOPOLYMERS 85, 169-184 [AIS=0.871, IF=2.605 H]
2006
- (2006), Trapped water molecules are essential to structural dynamics and function of a ribozyme, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103, 13380-13385 [AIS=4.86, IF=9.43 H]
- (2006), Indirect NMR spin-spin coupling constants (3)J(P, C) and (2)J(P, H) across the P-O center dot center dot center dot H-C link can be used for structure determination of nucleic acids, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128, 6823-6828 [AIS=2.701, IF=8.58 H]
- (2006), Structural and evolutionary classification of G/U wobble basepairs in the ribosome, NUCLEIC ACIDS RESEARCH 34, 1326-1341 [AIS=3, IF=7.48 H]
- (2006), RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics, STRUCTURE 14, 825-835 [AIS=3.13, IF=5.9 VH]
- (2006), Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids, JOURNAL OF PHYSICAL CHEMISTRY B 110, 22894-22902 [AIS=1.396, IF=3.471 H]
- (2006), Mechanism of action of anticancer titanocene derivatives: An insight from quantum chemical calculations, JOURNAL OF PHYSICAL CHEMISTRY B 110, 19632-19636 [AIS=1.396, IF=3.471 VH]
- (2006), Copper cation interactions with biologically essential types of ligands: A computational DFT study, JOURNAL OF PHYSICAL CHEMISTRY A 110, 4795-4809 [AIS=0.882, IF=2.899 H]
- (2006), Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations, BIOPOLYMERS 82, 504-520 [AIS=0.871, IF=2.605 VH]
- (2006), Molecular dynamics simulations of sarcin-ricin rRNA motif, NUCLEIC ACIDS RESEARCH 34, 697-708 [AIS=3, IF=7.48 VH]
- (2006), Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps, CHEMISTRY-A EUROPEAN JOURNAL 12, 2854-2865 [AIS=1.593, IF=5.382 VH]
- (2006), Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme, BIOPHYSICAL JOURNAL 91, 626-638 [AIS=1.917, IF=4.39 VH]
- (2006), Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 8, 1985-1993 [AIS=1.3, IF=4.12 H]
2005
- (2005), Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 127, 14663-14667 [AIS=2.701, IF=8.58 H]
- (2005), Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations, JOURNAL OF MOLECULAR BIOLOGY 351, 731-748 [AIS=2.051, IF=3.871 H]
- (2005), Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs, JOURNAL OF PHYSICAL CHEMISTRY B 109, 11399-11410 [AIS=1.396, IF=3.471 VH]
- (2005), Sugar edge/sugar edge base pairs in RNA: Stabilities and structures from quantum chemical calculations, JOURNAL OF PHYSICAL CHEMISTRY B 109, 18680-18689 [AIS=1.396, IF=3.471 VH]
- (2005), Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family, JOURNAL OF PHYSICAL CHEMISTRY A 109, 2292-2301 [AIS=0.882, IF=2.899 VH]
- (2005), Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence, BIOPHYSICAL CHEMISTRY 118, 31-41 [AIS=0.685, IF=2.276 H]
- (2005), Are the hydrogen bonds of RNA (A center dot U) stronger than those of DNA (A center dot T)? A quantum mechanics study, CHEMISTRY-A EUROPEAN JOURNAL 11, 5062-5066 [AIS=1.593, IF=5.382 H]
- (2005), Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases, BIOPHYSICAL JOURNAL 88, 3466-3485 [AIS=1.917, IF=4.39 VH]
2004
- (2004), Metal-mediated deamination of cytosine: Experiment and DFT calculations, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 43, 5396-5399 [AIS=3.296, IF=11.829 VH]
- (2004), DNA deformability at the base pair level, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 4124-4125 [AIS=2.701, IF=8.58 H]
- (2004), Theoretical study of the guanine -> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 14642-14650 [AIS=2.701, IF=8.58 VH]
- (2004), Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex, BIOPHYSICAL JOURNAL 87, 3397-3412 [AIS=1.917, IF=4.39 H]
- (2004), Ribosomal RNA kink-turn motif - A flexible molecular hinge, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 22, 183-193 [AIS=0.32, IF=1.124 VH]
- (2004), Accurate interaction energies of hydrogen-bonded nucleic acid base pairs, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 10142-10151 [AIS=2.701, IF=8.58 VH]
- (2004), Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 663-672 [AIS=2.701, IF=8.58 H]
- (2004), Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations, BIOPHYSICAL JOURNAL 87, 227-242 [AIS=1.917, IF=4.39 VH]
- (2004), Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 6, 2772-2780 [AIS=1.3, IF=4.12 VH]
- (2004), Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field, JOURNAL OF PHYSICAL CHEMISTRY B 108, 5466-5471 [AIS=1.396, IF=3.471 H]
2003
- (2003), Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets, NUCLEIC ACIDS RESEARCH 31, 6942-6952 [AIS=3, IF=7.48 H]
- (2003), DNA basepair step deformability inferred from molecular dynamics simulations, BIOPHYSICAL JOURNAL 85, 2872-2883 [AIS=1.917, IF=4.39 H]
- (2003), Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates, BIOPHYSICAL JOURNAL 85, 1787-1804 [AIS=1.917, IF=4.39 H]
- (2003), Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs, JOURNAL OF MOLECULAR BIOLOGY 330, 967-978 [AIS=2.051, IF=3.871 VH]
- (2003), Outer-shell and inner-shell coordination of phosphate group to hydrated metal ions (Mg2+, Cu,2+Zn2+, Cd2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects, JOURNAL OF PHYSICAL CHEMISTRY B 107, 1913-1923 [AIS=1.396, IF=3.471 H]
- (2003), The influence of N-7 guanine modifications on the strength of Watson-Crick base pairing and guanine N-1 acidity: Comparison of gas-phase and condensed-phase trends, JOURNAL OF PHYSICAL CHEMISTRY B 107, 5349-5356 [AIS=1.396, IF=3.471 H]
- (2003), Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5 '-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA, JOURNAL OF PHYSICAL CHEMISTRY B 107, 8669-8681 [AIS=1.396, IF=3.471 H]
- (2003), Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4 ',6-diamidino-2-phenylindole and DNA duplexes in solution, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 125, 1759-1769 [AIS=2.701, IF=8.58 H]
- (2003), Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E, BIOPHYSICAL JOURNAL 84, 3564-3582 [AIS=1.917, IF=4.39 VH]
- (2003), Molecular interactions of nucleic acid bases. A review of quantum-chemical studies, COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS 68, 2231-2282 [AIS=0.208, IF=0.856 VH]
2002
- (2002), The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA, JOURNAL OF BIOLOGICAL CHEMISTRY 277, 28491-28497 [AIS=2.223, IF=5.328 H]
- (2002), Loss of Hoogsteen pairing ability upon N1 adenine platinum binding, INORGANIC CHEMISTRY 41, 2855-2863 [AIS=1.018, IF=4.657 H]
- (2002), Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG), EUROPEAN JOURNAL OF BIOCHEMISTRY 269, 2868-2877 [AIS=1.219, IF=3.042 H]
- (2002), Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts, BIOPHYSICAL JOURNAL 82, 2592-2609 [AIS=1.917, IF=4.39 H]
2001
- (2001), Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 123, 3295-3307 [AIS=2.701, IF=8.58 H]
- (2001), Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture, INORGANIC CHEMISTRY 40, 3269-3278 [AIS=1.018, IF=4.657 H]
- (2001), Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine, BIOPHYSICAL JOURNAL 80, 455-468 [AIS=1.917, IF=4.39 H]
- (2001), Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding, JOURNAL OF MOLECULAR BIOLOGY 313, 1073-1091 [AIS=2.051, IF=3.871 VH]
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2000
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