Publications

Computational Studies of DNA and RNA - Šponer and Lankaš, Eds.
This ca 650 pages book will by published by Springer in August 2006 and covers all basic areas of computational studies of nucleic acids, with chapters written by the leading experts in the field. The book contains undergrad info and several chapters are devoted to experimental techniques.

 

2018

  • Cassone, G.; Sponer, J.; Sponer, J. E.; Pietrucci, F.; Saitta, A. M.; Saija, F., Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field. Chemical Communications 2018, in press, DOI: 10.1039/C1038CC00045J.
  • Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R. A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P., et al., RNA Structural Dynamics as Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews 2017, in press, DOI:10.1021/acs.chemrev.1027b00427.
  • Figiel, M.; Krepl, M.; Park, S.; Poznański, J.; Skowronek, K.; Gołąb, A.; Ha, T.; Šponer, J.; Nowotny, M., Mechanism of Polypurine Tract Primer Generation by HIV-1 Reverse Transcriptase. Journal of Biological Chemistry 2017, 293, 191-202.
  • Saladino, R.; Šponer, J. E.; Šponer, J.; Di Mauro, E., Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem 2018, 19, 22-25.
  • Zgarbová, M.; Jurečka, P.; Šponer, J.; Otyepka, M., A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker. Journal of Chemical Theory and Computation 2018, 14, 319-328.

 

2017

  • Mlynsky, V.; Kuhrova, P.; Jurecka, P.; Sponer, J.; Otyepka, M.; Banas, P., Mapping Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. Journal of Physical Chemistry B 2017, 121, 10828-10840.
  • Saladino, R.; Bizzarri, B. M.; Botta, L.; Šponer, J.; Šponer, J. E.; Georgelin, T.; Jaber, M.; Rigaud, B.; Kapralov, M.; Timoshenko, G. N., et al., Proton Irradiation: A Key to the Challenge of N-glycosidic Bond Formation in a Prebiotic Context. Scientific Reports 2017, 7, e14709.
  • Pokorna, P.; Krepl, M.; Kruse, H.; Sponer, J., MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-histidine Ligand and Mg2+. Journal of Chemical Theory and Computation 2017, 13, 5658–5670.
  • Cragnolini, T.; Chakraborty, D.; Šponer, J.; Derreumaux, P.; Pasquali, S.; Wales, D. J., Multifunctional Energy Landscape for a DNA G-quadruplex: An Evolved Molecular Switch. Journal of Chemical Physics 2017, 147, e152715.
  • Konté, N. D. d.; Krepl, M.; Damberger, F. F.; Ripin, N.; Duss, O.; Sponer, J.; Allain, F. H.-T., Aromatic Side-chain Conformational Switch on the Surface of the RNA Recognition Motif Enables RNA Discrimination. Nature Communications 2017, 8, e654.
  • Cassone, G.; Creazzo, F.; Giaquinta, P. V.; Sponer, J.; Saija, F., Ionic Diffusion and Oroton Transfer in Aqueous Solutions of Alkali Metal Salts. Physical Chemistry Chemical Physics 2017, 19, 20420-20429.
  • Costanzo, G.; Giorgi, A.; Scipioni, A.; Timperio, A. M.; Mancone, C.; Tripodi, M.; Kapralov, M.; Krasavin, E.; Kruse, H.; Šponer, J., et al., Nonenzymatic Oligomerization of 3′,5′-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA. Chembiochem 2017, 18, 1535-1543.
  • Cassone, G.; Pietrucci, F.; Saija, F.; Guyot, F.; Sponer, J.; Sponer, J. E.; Saitta, A. M., Novel Electrochemical Route to Cleaner Fuel Dimethyl Ether. Scientific Reports 2017, 7, e6901.
  • Havrila, M.; Stadlbauer, P.; Islam, B.; Otyepka, M.; Sponer, J., Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. Journal of Chemical Theory and Computation 2017, 13, 3911-3926.
  • Noureini, S. K.; Esmaeili, H.; Abachi, F.; Khiali, S.; Islam, B.; Kuta, M.; Saboury, A. A.; Hoffmann, M.; Sponer, J.; Parkinson, G., et al., Selectivity of Major Isoquinoline Alkaloids from Chelidonium Majus towards Telomeric G-quadruplex: A Study Using a Transition-FRET (t-FRET) Assay. Biochimica et Biophysica Acta (BBA) - General Subjects 2017, 1861, 2020-2030.
  • Krepl, M.; Blatter, M.; Cléry, A.; Damberger, F. F.; Allain, F. H. T.; Sponer, J., Structural Study of the Fox-1 RRM Protein Hydration Reveals a Role for Key Water Molecules in RRM-RNA Recognition Nucleic Acids Research 2017, 45, 8046-8063.
  • Szabla, R.; Kruse, H.; Sponer, J.; Gora, R. W., Water-chromophore Electron Transfer Determines the Photochemistry of Cytosine and Cytidine. Physical Chemistry Chemical Physics 2017, 19, 17531-17537.
  • Drsata, T.; Reblova, K.; Beššeová, I.; Sponer, J.; Lankas, F., rRNA C-loops: Mechanical Properties of a Recurrent Structural Motif. Journal of Chemical Theory and Computation 2017, 13, 3359-3371.
  • Islam, B.; Stadlbauer, P.; Gil Ley, A.; Pérez-Hernández, G.; Haider, S.; Neidle, S.; Bussi, G.; Banáš, P.; Otyepka, M.; Sponer, J., Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. Journal of Chemical Theory and Computation 2017, 13, 2458–2480.
  • Šponer, J.; Bussi, G.; Stadlbauer, P.; Kührová, P.; Banáš, P.; Islam, B.; Haider, S.; Neidle, S.; Otyepka, M., Folding of Guanine Quadruplex Molecules–funnel-like Mechanism or Kinetic Partitioning? An Overview from MD Simulation Studies. Biochimica et Biophysica Acta (BBA) - General Subjects 2017, 1861, 1246–1263.
  • Šponer, J. E.; Šponer, J.; Mauro, E. D., New Evolutionary Insights Into the Non-enzymatic Origin of RNA Oligomers. Wiley Interdisciplinary Reviews: RNA 2017, 8, e1400.
  • Šponer, J.; Krepl, M.; Banáš, P.; Kührová, P.; Zgarbová, M.; Jurečka, P.; Havrila, M.; Otyepka, M., How to Understand Atomistic Molecular Dynamics Simulations of RNA and Protein–RNA Complexes? Wiley Interdisciplinary Reviews: RNA 2017, 8, e1405.
  • Gresh, N.; Naseem-Khan, S.; Lagardère, L.; Piquemal, J.-P.; Sponer, J. E.; Sponer, J., Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential. Journal of Physical Chemistry B 2017, 121, 3997-4014.
  • Figiel, M.; Krepl, M.; Poznański, J.; Gołąb, A.; Šponer, J.; Nowotny, M., Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase. Nucleic Acids Research 2017, 45, 3341-3352.
  • Xu, J.; Tsanakopoulou, M.; Magnani, C. J.; Szabla, R.; Šponer, J. E.; Šponer, J.; Góra, R. W.; Sutherland, J. D., A Prebiotically Plausible Synthesis of Pyrimidine β-ribonucleosides and their Phosphate Derivatives Involving Photoanomerization. Nature Chemistry 2017, 9, 303-309.
  • Zgarbová, M.; Jurečka, P.; Banáš, P.; Havrila, M.; Šponer, J.; Otyepka, M., Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. The Journal of Physical Chemistry B 2017, 121, 2420-2433.
  • Gajarský, M.; Živković, M. L.; Stadlbauer, P.; Pagano, B.; Fiala, R.; Amato, J.; Tomáška, L.; Šponer, J.; Plavec, J.; Trantírek, L., Structure of a Stable G-Hairpin. Journal of the American Chemical Society 2017, 139, 3591-3594.
  • Zgarbová, M.; Jurečka, P.; Lankaš, F.; Cheatham, T. E.; Šponer, J.; Otyepka, M., Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. Journal Of Chemical Information And Modeling 2017, 57, 275-287.
  • Cassone, G.; Sponer, J.; Saija, F.; Di Mauro, E.; Marco Saitta, A.; Sponer, J. E., Stability of 2',3' and 3',5' Cyclic Nucleotides in Formamide and in Water: A Theoretical Insight into the Factors Controlling the Accumulation of Nucleic Acid Building Blocks in a Prebiotic Pool. Physical Chemistry Chemical Physics 2017, 19, 1817-1825.

 

2016

  • Krepl, M.; Cléry, A.; Blatter, M.; Allain, F. H. T.; Sponer, J., Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. Nucleic Acids Research 2016, 44, 6452-6470.
  • Galindo-Murillo, R.; Robertson, J. C.; Zgarbova, M.; Sponer, J.; Otyepka, M.; Jurecka, P.; Cheatham, T. E., Assessing the Current State of AMBER Force Field Modifications for DNA. Journal of Chemical Theory and Computation 2016, 12, 4114–4127.
  • Kuhrova, P.; Best, R.; Bottaro, S.; Bussi, G.; Sponer, J.; Otyepka, M.; Banas, P., Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. Journal of Chemical Theory and Computation 2016, 12, 4534–4548.
  • Bottaro, S.; Banáš, P.; Sponer, J.; Bussi, G., Free Energy Landscape of GAGA and UUCG RNA Tetraloops. Journal of Physical Chemistry Letters 2016, 7, 4032–4038.
  • Šponer, J. E.; Šponer, J.; Nováková, O.; Brabec, V.; Šedo, O.; Zdráhal, Z.; Costanzo, G.; Pino, S.; Saladino, R.; Di Mauro, E., Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry-A European Journal 2016, 22, 3572-3586.
  • Szabla, R.; Havrila, M.; Kruse, H.; Šponer, J., Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective. The Journal of Physical Chemistry B 2016, 120, 10635-10648.
  • Stadlbauer, P.; Mazzanti, L.; Cragnolini, T.; Wales, D. J.; Derreumaux, P.; Pasquali, S.; Šponer, J., Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. Journal of Chemical Theory and Computation 2016, 12, 6077-6097.
  • Dršata, T.; Zgarbová, M.; Jurečka, P.; Šponer, J.; Lankaš, F., On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophysical Journal 2016, 110, 874-876.
  • Civiš, S.; Szabla, R.; Szyja, B. M.; Smykowski, D.; Ivanek, O.; Knížek, A.; Kubelík, P.; Šponer, J.; Ferus, M.; Šponer, J. E., TiO2-catalyzed Synthesis of Sugars from Formaldehyde in Extraterrestrial Impacts on the Early Earth. Scientific Reports 2016, 6, e23199.
  • Islam, B.; Stadlbauer, P.; Neidle, S.; Haider, S.; Sponer, J., Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds? The Journal of Physical Chemistry B 2016, 120, 2899-2912.
  • Gkionis, K.; Kruse, H.; Šponer, J., Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. Journal of Chemical Theory and Computation 2016, 12, 2000-2016.
  • Rebič, M.; Laaksonen, A.; Šponer, J.; Uličný, J.; Mocci, F., Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models. Journal of Physical Chemistry B 2016, 120, 7380-7391.
  • Sponer, J. E.; Szabla, R.; Gora, R. W.; Saitta, A. M.; Pietrucci, F.; Saija, F.; Di Mauro, E.; Saladino, R.; Ferus, M.; Civis, S., et al., Prebiotic Synthesis of Nucleic Acids and their Building Blocks at the Atomic Level - Merging Models and Mechanisms from Advanced Computations and Experiments. Physical Chemistry Chemical Physics 2016, 18, 20047-20066.
  • Szabla, R.; Gora, R. W.; Sponer, J., Ultrafast Excited-state Dynamics of Isocytosine. Physical Chemistry Chemical Physics 2016, 18, 20208-20218.
  • Costanzo, G.; Pino, S.; Timperio, A. M.; Sponer, J. E.; Sponer, J.; Novakova, O.; Sedo, O.; Zdrahal, Z.; Di Mauro, E., Non-Enzymatic Oligomerization of 3 ', 5 ' Cyclic AMP. PLoS One 2016, 11, e0165723.
  • Zhang, X.; Xu, C.; Di Felice, R.; Sponer, J.; Islam, B.; Stadlbauer, P.; Ding, Y.; Mao, L.; Mao, Z.-W.; Qin, P. Z., Conformations of Human Telomeric G-quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry 2016, 55 (2), 360–372.
  • Szabla, R.; Gora, R. W.; Janicki, M.; Sponer, J., Photorelaxation of Imidazole and Adenine via Electron-driven Proton Transfer Along H2O Wires. Faraday Discussions 2016, 195, 237-251.
  • Šponer, J. E.; Šponer, J.; Di Mauro, E., Four Ways to Oligonucleotides Without Phosphoimidazolides. Journal of Molecular Evolution 2016, 82, 5-10.

 

2015

  • Havrila, M.; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, M.; Otyepka, M.; Šponer, J., Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. The Journal of Physical Chemistry B 2015, 119, 15176-15190.
  • Zgarbová, M.; Šponer, J.; Otyepka, M.; Cheatham, T. E.; Galindo-Murillo, R.; Jurečka, P., Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. Journal of Chemical Theory and Computation 2015, 11, 5723-5736.
  • Kruse, H.; Mladek, A.; Gkionis, K.; Hansen, A.; Grimme, S.; Sponer, J., Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit. Journal of Chemical Theory and Computation 2015, 11, 4972-4991.
  • Stadlbauer, P.; Kuhrova, P.; Banas, P.; Koca, J.; Bussi, G.; Trantirek, L.; Otyepka, M.; Sponer, J., Hairpins Participating in Folding of Human Telomeric Sequence Quadruplexes Studied by Standard and T-REMD Simulations. Nucleic Acids Research 2015, 43, (20), 9626-9644.
  • Islam, B.; Stadlbauer, P.; Krepl, M.; Koca, J.; Neidle, S.; Haider, S.; Sponer, J., Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Research 2015, 43 (18), 8673-8693.
  • Dubecky, M.; Walter, N. G.; Sponer, J.; Otyepka, M.; Banas, P., Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage. Biopolymers 2015, 103, 550-562.
  • Haldar, S.; Kuhrova, P.; Banas, P.; Spiwok, V.; Sponer, J.; Hobza, P.; Otyepka, M., Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. Journal of Chemical Theory and Computation 2015, 11, 3866-3877.
  • Gresh, N.; Sponer, J. E.; Devereux, M.; Gkionis, K.; de Courcy, B.; Piquemal, J. P.; Sponer, J., Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. Journal of Physical Chemistry B 2015, 119, 9477-9495.
  • Ohnmacht, S. A.; Marchetti, C.; Gunaratnam, M.; Besser, R. J.; Haider, S. M.; Di Vita, G.; Lowe, H. L.; Mellinas-Gomez, M.; Diocou, S.; Robson, M.; Sponer, J.; Islam, B.; Pedley, RB.; Hartley, JA.; Neidle, S., A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. Scientific Reports 2015, 5, 11385, nestrankovano.
  • Ferus, M.; Knizek, A.; Sponer, J.; Sponer, J. E.; Civis, S., RADICAL SYNTHESIS OF NUCLEIC ACID BASES FROM FORMAMIDE IN IMPACT PLASMA. Chemicke Listy 2015, 109, 406-414.
  • Szabla, R.; Campos, J.; Sponer, J. E.; Sponer, J.; Gora, R. W.; Sutherland, J. D., Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine. Chemical Science 2015, 6, 2035-2043.
  • Sripathi, K. N.; Banas, P.; Reblova, K.; Sponer, J.; Otyepka, M.; Walter, N. G., Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Physical Chemistry Chemical Physics 2015, 17, 5887-5900.
  • Ferus, M.; Nesvorny, D.; Sponer, J.; Kubelik, P.; Michalcikova, R.; Shestivska, V.; Sponer, J. E.; Civis, S., High-energy chemistry of formamide: A unified mechanism of nucleobase formation. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, 657-662.
  • Sponer, J. E.; Sponer, J.; Giorgi, A.; Di Mauro, E.; Pino, S.; Costanzo, G., Untemplated Nonenzymatic Polymerization of 3 ',5 ' cGMP: A Plausible Route to 3 ',5 '-Linked Oligonucleotides in Primordia. Journal of Physical Chemistry B 2015, 119, 2979-2989.
  • Stadlbauer, P.; Sponer, J.; Costanzo, G.; Di Mauro, E.; Pino, S.; Sponer, J. E., Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides. Chemistry - A European Journal 2015, 21, 3596-3604.
  • Krepl, M.; Havrila, M.; Stadlbauer, P.; Banas, P.; Otyepka, M.; Pasulka, J.; Stefl, R.; Sponer, J., Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation 2015, 11, 1220-1243.
  • Mlynsky, V.; Kuhrova, P.; Zgarbova, M.; Jurecka, P.; Walter, N. G.; Otyepka, M.; Sponer, J.; Banas, P., Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations. Journal of Physical Chemistry B 2015, 119, 4220-4229.
  • Szabla, R.; Sponer, J.; Gora, R. W., Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of pi sigma* States in Chromophore-Water Clusters. Journal of Physical Chemistry Letters 2015, 6, 1467-1471.
  • Estarellas, C.; Otyepka, M.; Koca, J.; Banas, P.; Krepl, M.; Sponer, J., Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochimica Et Biophysica Acta-General Subjects 2015, 1850, 1072-1090.
  • Panecka, J.; Sponer, J.; Trylska, J., Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Biochimie 2015, 112C, 96-110.
  • Mlynsky, V.; Walter, N. G.; Sponer, J.; Otyepka, M.; Banas, P., The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations. Physical Chemistry Chemical Physics 2015, 17, 670-679.
  • Kruse, H.; Sponer, J., Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions. Physical Chemistry Chemical Physics 2015, 17, 1399-1410.

 

2014

  • Drsata, T.; Zgarbova, M.; Spackova, N.; Jurecka, P.; Sponer, J.; Lankas, F., Mechanical Model of DNA Allostery. Journal of Physical Chemistry Letters 2014, 5, 3831-3835.
  • Pasi, M.; Maddocks, J. H.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham, T.; Dans, P. D.; Jayaram, B.; Lankas, F.; Laughton, C.; Mitchell, J.; Osman, R.; Orozco, M.; Pérez, A.; Petkevičiūtė, D.; Spackova, N.; Sponer, J.; Zakrzewska, K.; Lavery, R., μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research 2014, 42, 12272-12283.
  • Szabla, R.; Sponer, J. E.; Sponer, J.; Sobolewski, A. L.; Gora, R. W., Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. Physical Chemistry Chemical Physics 2014, 16, 17617-17626.
  • Zgarbová, M.; Otyepka, M.; Šponer, J.; Lankaš, F.; Jurečka, P., Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. Journal of Chemical Theory and Computation 2014, 10, 3177-3189.
  • Szabla, R.; Gora, R. W.; Sponer, J.; Sponer, J. E., Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases. Chemistry-a European Journal 2014, 20, 2515-2521
  • Stadlbauer, P.; Trantirek, L.; Cheatham, T. E., III; Koca, J.; Sponer, J., Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie 2014, 105C, 22-35.
  • Panecka, J.; Havrila, M.; Reblova, K.; Sponer, J.; Trylska, J., Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study. Journal of Physical Chemistry B 2014, 118, 6687-6701.
  • S. Civiš, M. Ferus, J. E. Šponer, J. Šponer, L. Kavan, M. Zukalova: Room Temperature Spontaneous Conversion of OCS to CO2 on the Anatase TiO2 Surface. Chemical Communications, 2014, 50, 7712-7715.
  • T. Drsata, N. Spackova, P. Jurecka, M. Zgarbova, J. Sponer, F. Lankas: Mechanical properties of symmetric and asymmetric DNA A-tracts: Implications for looping and nucleosome positioning. Nucleic Acids Research, 2014, 42, 7383-7394.
  • K. Sripathi, W. Tay, M. Otyepka, P. Banas, J. Sponer, N.G. Walter, Disparate HDV Ribozyme Crystal Structures Represent Intermediates on a Rugged Free Energy. RNA, 2014, 20, 1112-1128.
  • J. Šponer, P. Banáš, P. Jurečka, M. Zgarbová, P. Kührová, M. Havrila, M. Krepl, P. Stadlbauer, M. Otyepka: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. Journal of Physical Chemistry Letters, 5, 2014, 1771-1782.
  • M. Ferus, R. Michalčíková, V. Shestivská, J. Šponer, J. E. Šponer, S. Civiš: High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation. Journal of Physical Chemistry A, 118, 2014, 719-736.
  • K. Gkionis, H. Kruse, J. A. Platts, A. Mladek, J. Koca, J. Sponer: Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. Journal of Chemical Theory and Computation, 10, 2014, 1326-1340.
  • P. Kührová, M. Otyepka, J. Šponer, P. Banáš: Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 10, 2014, 401-411.
  • A. Mládek, P. Banáš, P. Jurečka, M. Otyepka, M. Zgarbová, J. Šponer: Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. Journal of Chemical Theory and Computation, 10, 2014, 463-480.
  • V. Mlýnský, P. Banáš, J. Šponer, M. W. van der Kamp , A. J. Mulholland, M. Otyepka: Comparison of ab Initio, DFT, and semiempirical QM/MM approaches for description of catalytic mechanism of hairpi ribozyme. Journal of Chemical Theory and Computation, 10, 2014, 1608-1622.
  • H. Kruse, M. Havrila, J. Sponer: QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. Journal of Chemical Theory and Computation, 2014, 10, 2615-2629.

 

2013

  • M. Havrila, K. Reblova, C. L. Zirbel, N. B. Leontis, J. Sponer: lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop. Journal of Physical Chemistry B, 117, 2013, 14302-14319.
  • S. Pino, G. Constanzo, A. Giorgi, J. Sponer, J. E. Sponer, E. Di Mauro: Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP. Entropy, 15, 2013, 5362-5383.
  • R. Szabla, D. Tuna, R. W. Gora, J. Sponer, A. L. Sobolewski, W. Domcke: Photochemistry of 2-Aminooxazole, a Hypothetical Prebiotic Precursor of RNA Nucleotides. The Journal of Physical Chemistry Letters, 4, 2013, 2785-2788.
  • P. Stadlbauer, M. Krepl, T. E. Cheatham III, J. Koca, J. Sponer: Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Research, 42, 2013, 7128-7143.
  • J. E. Sponer, A. Mladek, J. Sponer: Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions. Physical Chemistry Chemical Physics, 15, 2013, 6235-6242.
  • R. Szabla, J. E. Sponer, J. Sponer, R. W. Gora: Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions. Physical Chemistry Chemical Physics, 15, 2013, 7812-7818.
  • A. Mladek, M. Krepl, D. Svozil, P. Cech, M. Otyepka, P. Banas, M. Zgarbova, P. Jurecka, J. Sponer: 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. Physical Chemistry Chemical Physics, 15, 2013, 7295-7310.
  • B. Islam, M. Sgobba, C. Laughton, M. Orozco, J. Sponer, S. Neidle, S. Haider: Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Research, 41, 2013, 2723-2735.
  • M. Krepl, M. Otyepka, P. Banas, J. Sponer: Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. Journal of Physical Chemistry B, 117, 2013, 1872-1879.
  • P. Kuhrova, P. Banas, R. B. Best, J. Sponer, M. Otyepka: Computer Folding of RNA Tetraloops? Are We There Yet?. Journal of Chemical Theory and Computation, 9, 2013, 2115-2125.
  • M. Zgarbova, F. J. Luque, J. Sponer, T. E. Cheatham III, M. Otyepka, P. Jurecka: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Journal of Chemical Theory and Computation, 9, 2013, 2339-2354.
  • M. Krepl, K. Reblova, J. Koca, J. Sponer: Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops. Journal of Physical Chemistry B, 117, 2013, 5540-5555.
  • J. Sponer, A. Mladek, N. Spackova, X. H. Cang, T. E. Cheatham III, S. Grimme: Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. Journal of the American Chemical Society, 135, 2013, 9785-9796.
  • J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, M. Otyepka: Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment. Biopolymers, 2013, 99, 978-988.
  • J. Sponer, J. E. Sponer, A. Mladek, P. Jurecka, P. Banas, M. Otyepka: How to understand Quantum Chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods, 2013, 64, 3-11.
  • T. Dršata, A. Pérez, M. Orozco, A.V. Morozov, J. Šponer and F. Lankaš: Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation 2013, 707-721.

 

2012

  • C.A. Morgado, D. Svozil, D.H. Turner, J. Sponer: Understanding the role of base stacking in nucleic acids. MD and QM analysis of  tandem GA base pairs in RNA duplexes. Physical Chemistry Chemical Physics, 14, 201, 12580-12591
  • J.E. Sponer, A. Mladek, J. Sponer, M. Fuentes-Cabrera: Formamide-Based Prebiotic Synthesis of Nucleobases: A Kinetically Accessible Reaction. Journal of Physical Chemistry A, 116, 2012, 720-726
  • J.E. Sponer, J. Sponer: Is formamide nature's choice to create life? Comment on the paper "Formamide and the origin of life" by Raffaele Saladino et al.  Physics of Life Reviews, 9, 2012, 109-110
  • J. Sponer, X. Cang, T.E. Cheatham, III: Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods, 57, 2012, 25-39.
  • M. Krepl, M. Zgarbova, P. Stadlbauer, M. Otyepka, P. Banas, J. Koca, T.E. Cheatham, III, P. Jurecka, J. Sponer: Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA Journal of Chemical Theory and Computation,  8, 2012, 2506-2520.
  • P. Banas, A. Mladek, M. Otyepka, M. Zgarbova, P. Jurecka, D. Svozil, F. Lankas, J. Sponer: 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, 2012, 2448-2460
  • K. Reblova, J. Sponer, F. Lankas: Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Research,40, 2012, 6290-6303
  • J. Sponer, C.A. Morgado, D. Svozil: Comment on "Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings. Journal of Physical Chemistry B, 116, 2012, 8331-8332.
  • M. Ovaere, J. Sponer, J.E. Sponer, P. Herdewijn, L.  Van Meervelt, L: How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid: ribonucleic acid duplex. Nucleic Acids Research,40, 2012, 7573-7583
  • I. Besseova, P. Banas, P.  Kuhrova, P.  Kosinova, M. Otyepka, J. Sponer: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. Journal of Physical Chemistry B116, 2012, 9899-9916
  • J.M.  Fonville, M. Swart, Z. Vokacova, V. Sychrovsky, J.E. Sponer, J. Sponer, C.W. Hilbers, F.M. Bickelhaupt, S.S. Wijmenga: Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment. Chemistry - A European Journal, 18, 2012,12372-12387
  • J. Sponer, A. Mladek, J.E. Sponer, D. Svozil, M. Zgarbova, P. Banas, P., Jurecka, M. Otyepka: The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Physical Chemistry Chemical Physics, 14, 2012, 15257-15277
  • P. Banas, P. Sklenovsky, J.E. Wedekind, J. Sponer, M. Otyepka: Molecular mechanism of preQ 1 riboswitch action: A molecular dynamics study. Journal of Physical Chemistry B, 116, 2012, 12721-12734.
  • J. Sponer, M. Otyepka, P. Banas, K. Reblova, NG. Walter: Molecular Dynamics Simulations of RNA molecules. In: Innovations in Biomolecular Modelling and Simulations, T. Schlick, Ed., Vol. 2, 2012, 129-154.
  • J. Sponer, J.E. Sponer, N.B. Leontis: Quantum chemical studies of recurrent interactions in RNA 3D motifs. In: RNA 3D Structure, Analysis and Prediction. Nucleic Acids and Molecular Biology 27, 2012, 239-279.
  • J. Sponer, M.K. Shukla, J. Leszczynski: Computational modelling of DNA and RNA fragments. In: Handbook of Computational Chemistry, Leszczynski J., Ed. 2012, 1258-1275.
  • J.V. Burda, J. Sponer, J. Leszczynski: Metal interactions with nucleobases, base pairs, and oligomer sequences. In: Handbook of Computational Chemistry, Leszczynski J., Ed. 2011, 1278-1308.
  • M. Zgarbova, F.J. Luque, J. Sponer, M. Otyepka, P. Jurecka:  Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. Journal of Chemical Theory and Computation 8, 2012, 3232-3242. 
  • M. Ferus, S. Civis, A. Mladek, J. Sponer, L. Juha, J. E. Sponer: 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 Americal Chemical Society, 134, 2013, 20788-20796.

 

2011

  • Mlýnsky, V. Banáš, P. Walter, NG. Šponer, J. Otyepka, M.: QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms. Journal of Physical Chemistry B, 115, 2011, 13911-13924.
  • X. Cang, J. Šponer, T.E. Cheatham, III: Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis. Journal of the American Chemical Society 133, 2011, 14270-14279.
  • M. Zgarbová, M. Otyepka, J. Šponer, A. Mládek, P. Banáš, T.E. Cheatham, III, P. Jurečka: 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, 2011, 2886-2902.
  • P. Sklenovský, P. Florová, P. Banáš, K. Réblová, F. Lankaš, M. Otyepka, J. Šponer: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. Journal of Chemical Theory and Computation 7, 2011, 2963-2980.
  • X. Cang, J. Šponer, T.E. Cheatham, III: Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Research 39, 2011, 4499-4512.
  • A. Mládek, J. Šponer, B.G. Sumpter, M. Fuentes-Cabrera, J.E. Šponer: On the Geometry and Electronic Structure of the As-DNA Backbone. Journal of Physical Chemistry Letters 2, 2011, 389-392.
  • A. Vazquez-Mayagoitia, S.R. Horton, B.G. Sumpter, J. Šponer, J.E. Šponer, M. Fuentes-Cabrera: On the Stabilization of Ribose by Silicate Minerals. Astrobiology 11, 2011, 115-121.
  • A. Mládek, J. Šponer, B.G. Sumpter, M. Fuentes-Cabrera, J.E. Šponer: Theoretical modeling on the kinetics of the arsenate-ester hydrolysis: implications to the stability of As-DNA. Physical Chemistry Chemical Physics 13, 2011, 10869-10871.
  • J.E. Šponer, J. Šponer, M. Fuentes-Cabrera: Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways. Chemistry - A European Journal 17, 2011, 847-854.
  • R. Fiala, N. Špačková, S. Foldynová-Trantírková, J. Šponer, V. Sklenář, L. Trantírek: NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA. Journal of the American Chemical Society 133, 2011, 13790–13793.
  • R.V. Reshetnikov, J. Šponer, O.I. Rassokhina, A.M. Kopylov, P.O. Tsvetkov, A.A. Makarov, A.V. Golovin: Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. Nucleic Acids Research, 2011, 39, 2011, 9789-9802
  • K. Réblová , J.E. Šponer, N. Špačková, I. Beššeová, J. Šponer: A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. Journal of Physical Chemistry B, 2011, 115, 2011, 13897-13910.
  • M. Zgarbová, P. Jurečka, P. Banáš, M. Otyepka, J.E. Šponer, N.B. Leontis, C.L. Zirbel, J. Šponer: 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, 2011, 11277-11292.
  • J.E. Šponer, J. Šponer, M. Fuentes-Cabrera: Prebiotic routes to nucleosides. A quantum chemical insight into the energetics of the multistep reaction pathways. Chemistry - A European Journal, 17, 2011, 847-854.

 

2010

  • M.A. Ditzler, M. Otyepka, J. Šponer, N.G. Walter: Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Accounts of Chemical Research, 43, 2010, 40-47.
  • R. Lavery, K. Zakrzewska, D.L. Beveridge, T.C. Bishop, D.A. Case, T.E. Cheatham, III, S. Dixit, B. Jayaram, F. Lankaš, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Špačková, J. Šponer: 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, 2010, 299-313.
  • D. Svozil, P. Hobza, J. Šponer: 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, 2010, 1191-1203.
  • K. Réblová, F. Rázga, W. Li, H. Gao, J. Frank, J. Šponer: Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Research 38, 2010, 1325-1340.
  • J.E. Šponer, Á. Vázquez-Mayagoitia, B.G. Sumpter, J. Leszczynski, J. Šponer, M. Otyepka, P. Banáš, M. Fuentes-Cabrera: Theoretical study on the intermolecular interactions of potentially primordial base pair analogues, Chemistry - A European Journal 16, 2010, 3057-3065.
  • F. Lankaš, N. Špačková, M. Moakher, P. Enkhbayar, J. Šponer: A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Research 38, 2010, 3414-3422.
  • K. Réblová, Z. Střelcová , P. Kulhánek , I. Beššeová, D.H. Mathews, K. Van Nostrand, I. Yildirim, D.H. Turner and J. Šponer: An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helixes 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. Journal of Chemical Theory and Computation 6, 2010, 910-929.
  • C.A. Morgado, P. Jurečka, D. Svozil, P. Hobza, J. Šponer: Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2 and force field descriptions. Physical Chemistry Chemical Physics 14, 2010, 3522-3534.
  • P. Sharma, J.E. Šponer, J. Šponer, S. Sharma, D. Bhatatcharyya, A. Mitra: On the Role of cis Hoogsteen:Sugar Edge Family of Base Pairs in Platforms and Triplets - Quantum Chemical Insights into RNA Structural Biology Ribozyme. Journal of Physical Chemistry B 114, 2010, 3307-3320.
  • V. Mlýnský, P. Banáš, D. Hollas, K. Réblová,, N.G. Walter, J. Šponer, M. Otyepka: 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, 2010, 6642-6652.
  • I. Beššeová, K. Réblová, N.B. Leontis, J. Šponer: Molecular Dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Research 38, 2010, 6247-6264.
  • P. Banáš, N.G. Walter, J. Šponer, M. Otyepka: Protonation States of the Key Active Site Residues and Structural Dynamics of glmS Riboswitch as Revealed by Molecular Dynamics. Journal of Physical Chemistry B 114, 2010, 8701-8712.
  • N. Špačková, K. Réblová, J. Šponer:  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, 2010, 10581-10593.
  • M. Zgarbová, M. Otyepka, J. Šponer, P. Hobza, P. Jurečka: 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, 2010, 10476-10493.
  • R. Reshetnikov, A. Golovin, V. Spiridonova, A. Kopylov, J. Šponer: 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, 2010, 3003-3014.
  • J. Šponer, J.E. Šponer, A. Petrov, N.B. Leontis: 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, 2010, 15723-15741.
  • P. Banáš, D. Hollas, M. Zgarbová, P. Jurečka, M. Orozco, T.E, Cheatham, III, J. Šponer, M. Otyepka: Performance of molecular mechanics force fields for RNA simulations. Stability of UUCG and GNRA hairpins. Journal of Chemical Theory and Computation, 6, 2010, 3836-3849.

 

2009

  • Z. Vokáčová, M. Budešínský, I. Rosenberg, B. Schneider, J. Šponer, V. Sychrovský: 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, 2009, 1182-1191.
  • A. Mládek, P. Sharma, A. Mitra, D. Bhattacharyya, J. Šponer, J.E. Šponer: Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations. Journal of Physical Chemistry B 113, 2009, 1743-1755.
  • M.A. Ditzler, J. Šponer, N.G. Walter: 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, 2009, 560-575.
  • J. Šponer, M. Zgarbová, P. Jurečka, K.E. Riley, J.E. Šponer, P. Hobza: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 '-OH Group of Ribose. Journal of Chemical Theory and Computation 5, 2009, 1166-1179.
  • C.A. Morgado, P. Jurečka, D. Svozil, P. Hobza, J. Šponer: 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, 2009, 1524-1544.
  • Z. Futera, J. Klenko, J.E. Šponer, J. Šponer, J.V. Burda: 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, 2009, 1758-1770.
  • Z. Vokáčová, F.M. Bickelhaupt, J. Šponer, V. Sychrovský: 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, 2009, 8379-8386.
  • I. Yildirim, H.A. Stern, J. Šponer, N. Špačková, D.H. Turner: 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, 2009, 2088-2100.
  • C.L. Zirbel, J.E. Šponer, J. Šponer, J. Stombaugh, N.B. Leontis: Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Research, 37, 2009, 4898-4918.
  • J. Curuksu, J. Šponer, M. Zacharias: The elbow flexibility of the kt38 RNA kink turn motif investigated by free energy molecular dynamics simulations. Biophysical Journal, 97, 2009, 2004-2013.
  • P. Banáš, P. Jurečka, N.G. Walter, J. Šponer, M. Otyepka:.Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM, Methods, 49, 2009, 202-216.
  • E. Fadrná, N. Špačková, J. Sarzynska, J. Koča, M. Orozco, T.E. Cheatham III, T. Kulinski, J. Šponer: Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. Journal of Chemical Theory and Computation, 5, 2009, 2514-2530.
  • I. Beššeová, M. Otyepka, K. Réblová, J. Šponer: Dependence of A-RNA simulations on the choice of the force field and salt strength Physical Chemistry Chemical Physics, 11, 2009, 10701-10711.
  • V. Sychrovský, S. Foldynová-Trantírková, N. Špačková, K. Robeyns, L. van Meervelt, W. Blankenfeldt, Z. Vokáčová, J. Šponer, L. Trantírek: 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, 2009, 7321-7331.

 

2008

  • J.E. Šponer, B. G. Sumpter, J. Leszczynski, J. Šponer, M. Fuentes-Cabrera: Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose. Chemistry - A European Journal 14, 2008, 9990-9998.
  • E. Brumovská, V. Sychrovský, Z. Vokáčová, J. Šponer, B. Schneider, L. Trantírek: Effect of local sugar and base geometry on C-13 and N-15 magnetic shielding anisotropy in DNA nucleosides. Journal of Biomolecular NMR 42, 2008, 209-223.
  • P. Banáš, L. Rulíšek, V. Hánošová, D. Svozil, N. G. Walter, J. Šponer, M. Otyepka: 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, 2008, 11177-11187.
  • J. Sarzynska , K. Réblová , J. Šponer, T. Kulinski: Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by Charmm explicit solvent molecular dynamics. Biopolymers 89, 2008, 732-746.
  • D. Svozil, J. E. Šponer, I. Marchan, A. Perez, T. E. Cheatham III, F. Forti, F. J. Luque, M. Orozco, J. Šponer: Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. Journal of Physical Chemistry B 112, 2008, 8188-8197.
  • J. Šponer, K. E. Riley, P. Hobza: Nature and magnitude of aromatic stacking of nucleic acid bases. Physical Chemistry Chemical Physics 10, 2008, 2595-2610.
  • D. Kosenkov, L. Gorb, O. V. Shishkin, J. Šponer, J. Leszczynski: Tautomeric equilibrium, stability, and hydrogen bonding in 2 '-deoxyguanosine monophosphate complexed with Mg2+. Journal of Physical Chemistry B 112, 2008, 150-157.

 

2007

  • M. Fuentes-Cabrera, B.G. Sumpter, J.E. Šponer, J. Šponer, L. Petit, J.C. Wells: 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, 2007, 870-879.
  • J. Sefcikova, M.V. Krasovska, N. Špačková, J. Šponer, N.G. Walter: Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers 85, 2007, 392-406.
  • J. Sefcikova, M.V. Krasovska, J. Šponer J, N.G. Walter: The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Research 35, 2007, 1933-1946.
  • Pérez, I. Marchán, D. Svozil, J. Šponer, T. E. Cheatham, III, C.A. Laughton, M. Orozco: Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of / Conformers. Biophysical Journal 92, 2007, 3817-3829.
  • F. Rázga, J. Koča, A. Mokdad, J. Šponer: Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research 35, 2007, 4007-4017.
  • J.E. Šponer, K. Réblová, A. Mokdad, V. Sychrovský, J. Leszczynski, J. Šponer: 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, 2007, 9153-9164.
  • J. Šponer, N. Špačková: Molecular dynamics simulations and their application to four-stranded DNA. Methods 43, 2007, 278-290.
  • K. Réblová, E. Fadrná, J. Sarzynska, T. Kulinski, P. Kulhánek, E. Ennifar, J. Koča, J. Šponer: Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophysical Journal 93, 2007, 3932-3949.
  • Z. Vokáčová J. Šponer, J.E. Šponer, V. Sychrovský: Theoretical Study of the Scalar Coupling Constants Across the Non-covalent Contacts in RNA Base Pairs, the cis- and trans- Watson-Crick/Sugar Edge Base bPair Family. Journal of Physical Chemistry B 111, 2007, 10813-10824.
  • S.R. Meneni, S.M. Shell, L. Gao, P. Jurečka, W. Lee, J. Šponer, Y. Zou, M.P. Chiarelli, B.P. Cho: Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair. Biochemistry 46, 2007, 11263-11278.
  • S.E. McDowell, N. Špačková, J. Šponer, N.G. Walter: Molecular Dynamics Simulations of RNA: An In Silico Single Molecule Approach. Biopolymers 85, 2007, 169-184.

 

2006

  • N. Špačková, T.E. Cheatham, III, J. Šponer: Molecular dynamics simulations of Nucleic Acids.In: Computational studies of RNA and DNA. J. Šponer, F. Lankaš, Eds., Computational studies of RNA and DNA. Dordrecht: Springer, 2006, pp. 301-326.
  • J. Šponer, P. Jurečka, P Hobza: Base stacking and base pairing. In: Computational studies of RNA and DNA. J. Šponer, F. Lankaš, Eds., Computational studies of RNA and DNA. Dordrecht: Springer, 2006, pp. 343-388.
  • J.E. Šponer, J.V. Burda, J. Leszczynki, J. Šponer: Interaction of metal cations with Nucleic Acids and their building units. In: Computational studies of RNA and DNA. J. Šponer, F. Lankaš, Eds., Computational studies of RNA and DNA. Dordrecht: Springer, 2006, pp. 389-410.
  • M.M Rhodes, K. Réblová, J. Šponer, N.G. Walter: Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proceedings of the National Academy of Sciences of the USA 103, 2006, 13380-13385.
  • J.E. Šponer, J. Leszczynski, J. Šponer: Mechanism of action of anticancer titanocene derivatives: An insight from quantum chemical calculations Journal of Physical Chemistry B 110, 2006, 19632-19636.
  • V. Sychrovský, Z. Vokáčová, J. Šponer, N. Špačková, B. Schneider: Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids. Journal of Physical Chemistry B 110, 2006, 22894-22902.
  • J. Šponer, P. Jurečka, I. Marchan, F. J. Luque, M. Orozco, P. Hobza: Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. Chemistry - A European Journal 12, 2006, 2854-2865.
  • N. Špačková, J. Šponer: Molecular Dynamics simulations of Sarcin Ricin rRNA motif. Nucleic Acids Research 34, 2006, 697-708.
  • M. Pavelka, M. Simanek, J. Sponer, J.V. Burda: Copper cations interactions with biologically essential types of ligands: a computational DFT study: Journal of Physical Chemistry A 110, 2006, 4795-4809.
  • A. Mokdad, M.V. Krasovska, J. Šponer, Neocles B. Leontis: Structural and evolutionary classification of G/U wobble in the ribosome. Nucleic Acids Research 34, 2006, 1326-1341.
  • F. Rázga, M. Zacharias, K. Réblová, J. Koča, J. Šponer: RNA Kink-turns as molecular elbows: hydration, cation-binding and large-scale dynamics. Structure 14, 2006, 825-835.
  • V. Sychrovský, J. Šponer, L. Trantírek, B. Schneider: Indirect NMR spin-spin coupling constants (3)J(P, C) and (2)J(P, H) across the P-O ... H-C link can be used for structure determination of nucleic acids. Journal of the American Chemical Society 128, 2006, 6823-6828.
  • P. Jurečka, J. Šponer, J.Černý, P. Hobza: 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, 2006, 1985-1993.
  • M. V. Krasovska, J. Sefcikova, K. Réblová ,B. Schneider, N. G. Walter, J. Šponer: Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme. Biophysical Journal 91, 2006, 626-638.
  • K. Réblová, F. Lankaš, F. Rázga, M. V. Krasovska, J. Koča, J. Šponer: Structure, dynamics and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82, 2006, 504-520.
  • J. V. Burda, J. Šponer, J. Leszczynski: Towards the elucidation of the activation of cisplatin in anticancer treatment. Computational Chemistry: Reviews of Current Trends, Chapter 6, 10, 2006, 265-321.

 

2005

  • J. Bertran, M. Sodupe, J. Šponer, J.E. Šponer: Metal cation - nucleic acids interactions. In: Electronic Encyclopedia of Computational Chemistry, Online Edition von Rague Schleyer P, Schaefer III HF, Schreiner PR, Jorgensen WL, Thiel W, Glen RC, editors. John Wiley & Sons, Ltd, Chichester, UK. Artikle online posting date: 15th March 2005. DOI: 10.1002/0470845015.cn0094
  • J.E. Šponer, N. Špačková, P. Kulhánek, J. Leszczynski, J. Šponer. 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, 2005, 2292-2301.
  • F. Rázga, J. Koča, J. Šponer, N.B. Leontis Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases. Biophysical Journal. 88, 2005 88: 3466-3485
  • J.E. Šponer, N. Špačková, J. Leszczynski, J. Šponer. Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. Journal of Physical Chemistry B 109, 2005, 11399-11410.
  • M.V. Krasovska, J. Sefcikova, N. Špačková, J. Šponer, N.G. Walter: 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, 2005, 731-748.
  • A. Pérez, J. Šponer, P. Jurečka, P. Hobza, F.J. Luque, M. Orozco: Are the hydrogen bonds of RNA (A.U) stronger than those of DNA (A.T)? A quantum mechanics study. Chemistry - A European Journal 11, 2005, 5062-5066.
  • J.E. Šponer, J. Leszczynski, V. Sychrovský, J. Šponer: The Sugar Edge/Sugar Edge base pairs in RNA. Stabilities and structures from quantum chemical calculations. Journal of Physical Chemistry B 109, 2005, 18680-18689.
  • Vladimír Sychrovský, Norbert Müller, Bohdan Schneider, Vilko Smrečki, Vladimir Špirko, Jiří Šponer, Lukáš Trantírek: Sugar Pucker Modulates the Cross-Correlated Relaxation Rates Across the Glycosidic Bond in DNA. Journal of the American Chemical Society 127, 2005, 14663-14667.
  • F. Barone, F. Lankaš, N. Špačková, J. Šponer, P. Karran, M. Bignami, F. Mazzei: Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence. Biophysical Chemistry 118, 2005, 31-41.

 

2004

  • N. Špačková, E. Cubero, J. Šponer, M. Orozco: Theoretical study of the guanine->6-thioguanine substitution in duplexes, triplexes, and tetraplexes. Journal of the American Chemical Society 126, 2004, 14642-14650
  • K. Réblová, N. Špačková, J. Koča, N. B. Leontis, J. Šponer: Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein komplex. Biophysical Journal 87, 2004, 3397-3412
  • E. Fadrná, N. Špačková, R. Štefl, J. Koča, T. E. Cheatham III, and J. Šponer: Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophysical Journal 87, 2004, 227-242
  • F. Rázga, N. Špačková, K. Réblová, J. Koča, N. B. Leontis, J. Šponer: Ribosomal RNA Kink-turn motif - a flexible molecular hinge. Journal of Biomolecular Structure and Dynamics 22, 2004, 183-194
  • J. E. Šponer, P. Sanz Miguel, L. Rodriguez-Santiago, A. Erxleben, M. Krumm, M. Sodupe, J. Šponer, B. Lippert, Metal mediated deamination of cytosine. Experiment and mechanistic insight from DFT calculations. Angewandte Chemie 43, 2004, 5396-5399.
  • J. Šponer, P. Jurečka, P. Hobza: Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. Journal of the American Chemical Society 126, 2004, 10142 - 10151
  • V. Sychrovský, J. Šponer, P. Hobza: 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, 2004, 663-672.
  • P. Jurečka, J. Šponer, P. Hobza: Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term and a comparison with the AMBER force field. Journal of Physical Chemistry B 108, 2004, 5466-5471
  • F. Lankaš, J. Šponer, J. Langowski, T.E. Cheatham III: DNA deformability at the base pair level. Journal of the American Chemical Society 126, 2004, 4124-4125
  • J. E. Šponer, V. Sychrovský, P. Hobza, J. Šponer: 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 2004, 2772-2780.

 

2003

  • K. Réblova, N. Špačková, J. E. Šponer, J. Koča, J. Šponer: Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets . Nucleic Acid Research 31, 2003, 6942-6952.
  • J. Šponer, P. Hobza: Molecular interactions of nucleic acid bases. A review of quantum-chemical studies. Collection of Czechoslovak Chemical Communications 68, 2003, 2231-2282
  • N. Špačková, T. E. Cheatham, III, F. Ryjáček, F. Lankaš, L. van Meervelt, P. Hobza and J. Šponer, Molecular dynamics simulations and thermodynamics analysis of DNA - drug complexes. Minor groove binding between 4?,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. Journal of the American Chemical Society 125, 2003, 1759-1769.
  • L. Rulíšek and J. Šponer: Outer-shell and inner-shell coordination of phosphate group to hydrated metal ions (Mg2+, Cu2+, Zn2+, Cd2+) in presence and absence of nucleobase. The role of non-electrostatic effects. Journal of Physical Chemistry B 106, 2003, 1913-1923.
  • K. Réblová, N. Špačková, R. Štefl, K. Csaszar, J. Koča, N.B. Leontis and J. Šponer: Non-Watson-Crick base pairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA Loop E. Biophysical Journal 84, 2003, 3564-3582.
  • J. V. Burda, J. Šponer, J. Hrabáková, M. Zeizinger, J. Leszczynski: The Influence of N7 Guanine Modifications on the Strength of Watson-Crick Base Pairing and Guanine N1 acidity: comparison of gas phase and condensed phase trends. Journal of Physical Chemistry B 107, 2003, 5349-5356.
  • J. Šponer, A. Mokdad, J. E. Šponer, N. Špačková, J. Leszczynski, N. B. Leontis:Unique tertiary and neighbor interactions determine conservation patterns of cis Watson-Crick A/G base pairs. Journal of Molecular Biology 330, 2003, 967-978.
  • R. Štefl, T.E. Cheatham, III, N. Špačková, E. Fadrná, I. Berger, J. Koča, J. Šponer: Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophysical Journal 85, 2003, 1787-1804
  • N. Gresh, J.E. Šponer, N. Špačková, J. Leszczynski, J. Šponer: Theoretical study of binding of hydrated cations Zn(II) and Mg(II) to guanosine 5' monophosphate. Towards polarizable molecular mechanics for DNA and RNA. Journal of Physical Chemistry B 107, 2003, 8669-8681.
  • F. Lankaš, J. Šponer, J. Langowski, T.E. Cheatham III: DNA base-pair step deformability inferred from molecular dynamics simulations. Biophysical Journal 85, 2003, 2872-2883.

 

2002

  • J. Sponer, J. Leszczynski, Pavel Hobza: Electronic properties, hydrogen bonding, stacking and cation-binding of DNA and RNA bases. Biopolymers 61, 2001, 3-36.
  • D. Reha , M. Kabelac, F. Ryjacek, J. Sponer, J.E. Sponer, M. Elstner; S. Suhai, P. Hobza: Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. Journal of the American Chemical Society 124, 2002, 3366-3376.
  • Lankas F, Cheatham TE, Spackova N, Hobza P, Langowski J, Sponer J Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophysical Journal 82, 2002, 2592-2609.
  • Schmidt KS, Reedijk J, Weisz K, Janke EMB, Sponer JE, Sponer J, Lippert B Loss of Hoogsteen pairing ability upon N1 adenine platinum binding Inorganic Chemistry 41, 2002, 2855-2863.
  • Warmlander S, Sponer JE, Sponer J, Leijon M: The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA. Journal of Biological Chemistry 277, 2002, 28491-28497.
  • Trygubenko SA, Bogdan TV, Rueda M, Orozco M, Luque FJ, Sponer J, Slavicek P, Hobza P: Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution - Part 1. Cytosine. Physical Chemistry Chemical Physics 4, 2002, 4192-4203.
  • P. Hobza and J. Sponer:Toward True DNA Base-Stacking Energies: MP2, CCSD(T), and Complete Basis Set Calculations. Journal of the American Chemical Society 124, 2002, 11802-11808.
  • K. Uytterhoeven, J. Šponer, L. Van Meervelt: Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). European Journal of Biochemistry 269, 2002, 2868-2877.

 

2001

  • R. Stefl, N. Spackova, I. Berger,J. Koca, J. Sponer: Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal 80, 2001, 455-468.
  • J.E. Sponer, Z. Sobalik, J. Leszczynski, B. Wichterlova: Effect of Metal Coordination on the Charge Distribution over the Cation Binding Sites of Zeolites. A Combined Experimental and Theoretical Study J. Phys. Chem. B 105, 2001, 8285-8290.
  • J.E. Sponer, J. Sponer, J. Cejka: Ab initio quantum-chemical study on the zeolite catalyzed transformation of para-xylene J. Mol. Struct. (THEOCHEM) 540, 2001, 145-152
  • N. Spackova, I. Berger, J. Sponer: Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed GCGC quartets. Journal of the American Chemical Society 123, 2001, 3295-3307.
  • J. Muňoz, J. Sponer, P. Hobza, M. Orozco, F. Javier Luque: Interactions of hydrated Mg2+ cation with bases, base pairs and nucleotides. Electron topology, Natural Bond Orbital, electrostatics, and vibrational study. Journal of Physical Chemistry B 105, 2001, 6051-6060.
  • J. E. Sponer, J. Leszczynski, F. Glahé, B. Lippert, J. Sponer: Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture. Inorganic Chemistry 40, 2001, 3269-3278.
  • U. Dornberger, N. Spackova, A. Walter, F.A. Gollmick, J. Sponer, H. Fritzsche: Solution structure of the dodecamer d(CATGGGCCCATG)2 is B-DNA. Experimental and molecular dynamics study. Journal of Biomolecular Structure and Dynamics 19, 2001, 159-174.
  • J.V. Burda, J. Sponer, J. Leszczynski: The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study. Physical Chemistry Chemical Physics 3, 2001, 4404-4411.
  • J. Sponer, J. Leszczynski, P. Hobza: Hydrogen bonding, stacking and cation binding of DNA bases Journal of Molecular Structure (THEOCHEM) 573, 2001, 43-53.
  • M. Zeizinger, J.V. Burda, J. Sponer, V. Kapsa, J. Leszczynski: A systematic ab initio study of the hydration of selected palladium square-planar complexes. A comparison with platinum analogues. Journal of Physical Chemistry A 105, 2001, 8086-8092.
  • K. Csaszar, N. Spackova, R. Stefl, J. Sponer, N. B. Leontis: Molecular dynamics of frameshifting pseudoknot from Beet Western Yellows Virus (BWYV): The role of non-Watson-Crick base pairing, ordered hydration, cation binding and base mutations on stability and unfolding. Journal of Molecular Biology 313, 2001, 1073-1091
  • J. E. Sponer, F. Glahe, J. Leszczynski, B. Lippert, J. Sponer, How nucleobases rotate when bonded to a metal ion: detailed view from an ab initio quantum chemical study of a cytosine complex of trans-a2PtII. Journal of Physical Chemistry B 105, 2001, 12171-12179.

 

2000

  • J. Sponer, I. Berger, N. Spackova, J. Leszczynski, P. Hobza: Aromatic base stacking in DNA: From ab initio calculations to molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics. Conversation 11, Vol. 2 Proceedings 1, 2000, 383-407.
  • J.V.Burda, J. Sponer, J. Leszczynski: The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms. Journal of Biological Inorganic Chemistry 5, 2000, 178-188.
  • M. Kratochvil, J. Sponer, P. Hobza: Global minimum of the adenine thymine base pair corresponds neither to Watson-Crick nor to Hoogsteen structures. Molecular dynamic/quenching/AMBER and post Hartree-Fock ab initio study. Journal of the American Chemical Society 122, 2000, 3495-3499.
  • J. Sponer, P. Hobza: Interaction energies of hydrogen bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals. Journal of Physical Chemistry A 104, 2000, 4592-4597.
  • F. Lankas, J. Sponer, P. Hobza, J. Langowski: Sequence-dependent elastic properties of DNA. Journal of Molecular Biology 299, 2000, 697-712.
  • Z. Sobalik, J.E. Sponer, B. Wichterlova, Experimental and Theoretical Description of Transition Metal Ion Structures in Zeolites Relevant to deNox Catalysis, Stud. Surf. Sci. Cat. 2000, 130, 1463.
  • P. Hobza, J. Sponer, E. Cubero, M. Orozco, F.J. Luque: C-H...O contacts in the adenine.uracil and uracil...uracil nucleic acid base pairs: Nonempirical ab initio study with inclusion of electron correlation effects. Journal of Physical Chemistry B 104, 2000, 6286-6292
  • M. Kabelac, M. Kratochvil, J. Sponer, P. Hobza: Structure, energetics, vibrational frequencies and charge transfer of base pairs, nucleoside pairs, nucleotide pairs and B-DNA pairs of trinucleotides. Ab initio HF-MINI-1 and empirical potential study. Journal of Biomolecular Structure and Dynamics 17, 2000, 1077-1086.
  • J. Sponer, J.E. Sponer, J. Leszczynski: Cation - pi and amino-acceptor interactions between hydrated metal cations and DNA bases. Quantum-chemical view. Journal of Biomolecular Structure and Dynamics 17, 2000, 1087-1096.
  • J.E. Sponer, J. Cejka, J. Dedecek, B. Wichterlova, Coordination and Properties of Cobalt in the Molecular Sieves CoAPO-5 and -11, Microporous Mesoporous Mater., 2000, 37, 117.
  • J. Sponer, M. Sabat, L. Gorb, J. Leszczynski, B. Lippert, P. Hobza: The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing Journal of Physical Chemistry B 104, 2000, 7535-7544.
  • J.V. Burda, P. Seizinger, J. Sponer, J. Leszczynski: Hydration of cis- and trans-platin. A pseudopotential treatment in the frame of G-3 type theory for platinum complexes. Journal of Chemical Physics 113, 2000, 2224-2232.
  • N. Spackova, I. Berger, J. Sponer: Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G.A Mismatch Pairs. Journal of the American Chemical Society 122, 2000, 7564-7572.
  • J. Sponer, P. Hobza, J. Leszczynski: Aromatic DNA base stacking and H-bonding. Computational Chemistry - Reviews of Current Trends. Vol. 5., Leszczynski, J. ed. World Scientific Publisher, Singapore, 2000, 171-210.
  • J. Cejka, N. Zilkova, J.E. Sponer, B. Wichterlova, Kinetic and Theoretical Study of the Effect of Molecular Sieve Structure on the Selectivity to Propylbenzenes in Alkylation of Benzene with Isopropyl Alcohol, Collect. Czech. Chem. Commun., 1998, 63, 1769.
  • J. Sponer, J. Florian, H.-L. Ng, J.E. Sponer, N. Spackova: Local conformational variations observed in B-DNA crystals do not improve base stacking. Computational analysis of base stacking in d(CATGGGCCCATG)2 B<->A intermediate crystal structure. Nucleic Acids Research 24, 2000, 4893-4902.

 

1999

  • J. Florian, J. Sponer, A. Warshel: Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: ab initio/Langevine dipole study. Journal of Physical Chemistry B 103, 1999, 884-892.
  • O.V. Shiskhin, J. Sponer, P. Hobza: Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs. Journal of Molecular Structure 477, 1999, 15-21.
  • J. Cejka, J.E. Sponer, N. Zilkova, B. Wichterlova, The Effect of Molecular Sieve Structure on Benzene Propylation Selectivity to iso-/n-Propylbenzenes. Catalytic and Theoretical Study, Proceedings of the 12th International Zeolite Conference, Materials Research Society: Warrandale, 1999, Vol. 2, p. 1419.
  • J Sponer, M. Sabat, J.V. Burda, J. Leszczynski, Pavel Hobza: Interaction of the Adenine-Thymine Watson-Crick and Adenine-Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group II a (Mg2+, Ca2+, Sr2+, Ba2+) and II b (Zn2+, Cd2+, Hg2+) Metal Cations. Absence of the Base Pair Stabilization by Metal-Induced Polarization Effects. Journal of Physical Chemistry B 103, 1999, 2528-2534.
  • N. Spackova, I. Berger, J. Sponer: Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex molecules. Journal of the American Chemical Society 121, 1999, 5519-5534.
  • J Sponer, P. Hobza, J. Leszczynski: Computational approaches to the studies of the interactions of nucleic acid bases. In: Computational Molecular Biology, Theoretical Computational Chemistry, Vol. 8, J. Leszczynski, Ed., Elsevier Science B.V. 1999, 85-117.
  • J. Sponer, J.V. Burda, J. Leszczynski, P. Hobza: Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences among Cations, and Flexibility of the Cation Hydration Shell. Journal of Biomolecular Structure and Dynamics, 17, 1999, 61-79.
  • J Sponer, M. Sabat, J.V. Burda, J. Leszczynski, P. Hobza, B. Lippert: Metal ions in non-complementary DNA base pairs. Ab initio study of Cu(I), Ag(I) and Au(I) complexes with the cytosine - adenine base pair. Journal of Biological Inorganic Chemistry 4, 1999, 537-545.
  • P. Hobza, J. Sponer: Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 99, 1999, 3247-3276.
  • D. Vlieghe, J. Sponer, L. Van Meervelt. Crystal structure of d(GGCCTTAAGG) complexed with DAPI reveals novel binding mode. Biochemistry 38, 1999, 16443-16451
  • N. Gresh, J. Sponer Complexes of pentahydrated Zn2+ with guanine, adenine, and the guanine-cytosine and adenine-thymine base-pairs. Structures and energies characterized by polarizable molecular mechanics and ab initio calculations. Journal of Physical Chemistry A 103, 1999, 11415-11427
  • J. Sponer, J. E. Sponer, L. Gorb, J. Leszczynski, B. Lippert: Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine. Theoretical and experimental views. Journal of Physical Chemistry A 103, 1999, 11406-11413

 

1998

  • P. Hobza, J. Sponer: Significant structural deformations of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree-Fock. Chemical Physics Letters 288, 1998, 7-14
  • N. Spackova, I. Berger, M. Egli, J. Sponer: Molecular dynamics of four-stranded intercalated hemiprotonated i-DNA. Stable trajectories on a nanosecond scale. Journal of the American Chemical Society 120, 1998, 6147-6151.
  • J. Sponer, J.V. Burda, M. Sabat, J. Leszczynski, P. Hobza: Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. Journal of Physical Chemistry A 102, 1998, 5951-5957.
  • B. Luisi, M. Orozco, J. Sponer, F.J. Luque, Z. Shakked: On the potential role of the amino nitrogen atom as a hydrogen acceptor in macromolecules. Journal of Molecular Biology 279, 1998, 1123-1136.
  • J. Sponer, M. Sabat, J.V. Burda, A. M. Doody, J. Leszczynski, P. Hobza: Stabilization of the purine purine pyrimidine DNA base triplets by divalent metal cations. Journal of Biomolecular Structure and Dynamics, 16, 1998, 139-144.
  • M. Kratochvil, O. Engkvist, J. Sponer, P. Jungwirth, P. Hobza: Uracil dimer: potential energy and free energy surfaces: ab initio beyond Hartree-Fock and empirical potential studies. Journal of Physical Chemistry A 102, 1998, 6921-6926.
  • J. Sponer, P. Hobza: DNA bases and base pairs: Ab initio calculations. Encyclopedia of Computational Chemistry, P.vR. Schleyer, Ed. 1998, 777-789.
  • N.U. Zhanpeisov, J. Sponer, J. Leszczynski: Reverse Watson-Crick isocytosine-cytosine and guanine-cytosine base pairs stabilized by the formation of the minor tautomers of bases. An ab initio study in gas phase and in a water cluster. Journal of Physical Chemistry A 102, 1998, 10374-10379.

 

1997

  • V. Spirko, J. Sponer, P. Hobza: Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. Journal of Chemical Physics 106, 1997, 1472-1479.
  • J. Sponer, P. Hobza: MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 267, 1997, 263-270.
  • J. Sponer, J.V. Burda, P. Mejzlík, J. Leszczynski, P. Hobza: Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: Ab initio quantum-chemical and empirical potential study. Journal of Biomolecular Structure and Dynamics, 14, 1997, 613-629.
  • P. Hobza, M. Kabelac, J. Sponer, P. Mejzlik, J. Vondrasek: Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases. Comparison with nonempirical beyond-Hartree-Fock results. Journal of Computational Chemistry 18, 1997, 1136-1150.
  • J. Sponer, H.A. Gabb, J. Leszczynski, P. Hobza: Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA. A quantum-chemical study. Biophysical Journal 73, 1997, 76-87.
  • J. Molnar, M. Kolonits, M. Hargittai, Molecular Structure of SbF3 and BiF3: an Electron Diffraction Study, J. Mol. Struct., 1997, 413, 441.
  • P. Hobza, J. Sponer, J.Leszczynski: Comment on "Electron-correlated" calculations of electric properties of nucleic acid "bases". Journal of Physical Chemistry B 101, 1997, 8038-8039.
  • J.V. Burda, J. Sponer, J.Leszczynski, P. Hobza: Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Nonempirical ab initio calculations on structures, energies, and nonadditivity of interactions. Journal of Physical Chemistry B 101, 1997, 9670-9677.
  • J. Sponer, J. Leszczynski, P. Hobza: Thioguanine and thiouracils: Hydrogen-bondng and stacking properties. Journal of Physical Chemistry A 101, 1997, 9489-9495.

 

1996

  • J. Sponer, J. Leszczynski, P. Hobza: Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. Journal of Physical Chemistry 100, 1996, 1965-1974.
  • J. Sponer, P. Hobza: DNA base amino groups and their role in molecular interactions: ab initio and preliminary density functional theory calculations. International Journal of Quantum Chemistry, 57, 1996, 959-970.
  • J. Sponer, J. Leszczynski, P. Hobza: Interactions of DNA bases and the structure of DNA. A nonempirical ab initio study with inclusion of electron correlation. In: Computational Chemistry - Reviews of Current Trends. Leszczynski, J. ed. World Scientific Publisher, Singapore, 1996, 185-218.
  • J. Sponer, J. Leszczynski, V. Vetterl, P. Hobza: Base stacking and hydrogen bonding in protonated cytosine dimer. The role of molecular ion-dipole and induction interactions. Journal of Biomolecular Structure and Dynamics. 13, 1996, 695-707.
  • J. Sponer, P. Hobza: Nonempirical ab initio calculations on DNA base pairs. Chemical Physics 204, 1996, 365-372.
  • J. Sponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base stacking. Nonempirical ab initio and empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs. Journal of Physical Chemistry 100, 1996, 5590-5596.
  • J. Molnar, R.J.M. Konings, M. Kolonits, M. Hargittai, Molecular Structure of CeI3 from Electron Diffraction and Vibrational Spectroscopy, J. Mol. Struct., 1996, 375, 223.
  • J. Molnar, R.J.M. Konings, A.S. Booij, M. Hargittai, Molecular Structure of SbI3 and BiI3 from Combined Electron Diffraction and Vibrational Spectroscopic Studies, Inorg. Chem., 1996, 35, 7639.
  • J. Sponer, J. Florian, J. Leszczynski, P. Hobza: Nonplanar DNA base pairs. Journal of Biomolecular Structure and Dynamics 13, 1996, 827-833.
  • J. Sponer, J. Leszczynski, P. Hobza: Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. Journal of Computational Chemistry 17, 1996, 841-850.
  • J.V. Burda, J. Sponer, P. Hobza: An ab initio study of the interaction of guanine and adenine with various monovalent and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+, Cu+, Ag+, Au+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+). Journal of Physical Chemistry 100, 1996, 7250-7255.
  • P. Hobza, F. Hubalek, M. Kabelac, P. Mejzlik, J. Sponer, J. Vondrasek. Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results. Chemical Physics Letters 257, 1996, 31-35.
  • J. Sponer, J. Leszczynski, P. Hobza: Hydrogen bonding and stacking of DNA bases. A review of ab initio quantum-chemical studies. Journal of Biomolecular Structure and Dynamics 14, 1996, 117-136.
  • P. Hobza, J. Sponer: Thermodynamics characteristics for the formation of H-bonded DNA base pairs. Chemical Physics Letters 261, 1996, 379-384.
  • O. Bludsky, J. Sponer, J. Leszczynski, V. Spirko, P. Hobza: amino groups in nucleic acid bases, aniline, aminopyridines and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion. Journal of Chemical Physics 105, 1996, 11042-11050.
  • P. Hobza, J. Sponer: MP2 and CCSD(T) calculations on H-bonded and stacked formamide...formamide and formamidine...formamidine dimers. Journal of Molecular Structure (THEOCHEM) 388, 1996, 115-120.
  • J. Leszczynski, J. Sponer: 2,4-Diselenouracil tautomers: structures, energies, and a comparison with uracil and 2,4-dithiouracil. Journal of Molecular Structure (THEOCHEM) 388, 1996, 237-244.

 

1995

  • P. Hobza, J. Sponer, M. Polasek: H-bonded and stacked DNA base pairs: cytosine dimer. Ab initio second order Moller-Plesset study. Journal of the American Chemical Society 117, 1995, 792-798.
  • P. Hobza, J. Sponer, T. Reschel: Density functional theory and molecular clusters. Journal of Computational Chemistry 16, 1995, 1315-1325.
  • J. Sponer, J. Leszczynski: Tautomerism of xanthine: The second order Moller-Plesset study. Structural Chemistry 6, 1995, 281-286.
  • J. Molnar, C.J. Marsden, M. Hargittai, Molecular Structure and Force Fields of Monomeric and Dimeric Magnesium Dichloride from Electron Diffraction and Quantum Chemical Calculations, J. Phys. Chem., 1995, 99, 9062.
  • J. Molnar, M. Hargittai, Prediction of the Shape of Lanthanide Trihalides, J. Phys. Chem., 1995, 99, 10780.

 

1989-1994

  • J. Sponer, J. Kypr: Characterization of the Base Stacking Interactions in DNA by Means of Lennard-Jones Empirical Potentials. General Physiology & Biophysics 8, 1989, 257 - 272
  • J. Sponer, J. Kypr: Base Pair Buckling Can Eliminate the Interstrand Purine Clash in the C-G Steps of B-DNA. Journal of Biomolecular Structure & Dynamics 7, 1990, 1211-1221
  • J. Sponer, C. Davadorzh, V. Mornstein: The Influence of Viscosity on the Ultrasonic Cavitation Threshold at Low MHz Region of Ultrasound. Studia biophysica 137, 1990, 81-89
  • J. Sponer: The Dependence of Ultrasonic Cavitation Threshold on Raised Ambient Pressure. Studia biophysica 137, 1990, 91-97
  • J. Sponer: The Dependence of Cavitation Threshold on Ultrasonic Frequency. Czechoslovak Journal of Physics B 40, 1990, 1123-1132
  • J. Sponer, J. Kypr: On the Use of Empirical Potentials in Studies of Base Stacking in DNA. In: Theoretical Biochemistry and Molecular Biophysics, vol. 1, DNA, eds. D. L. Beveridge, R. Lavery, Adenine Press, New York, 1991, 271-284
  • J. Sponer, J. Kypr: Different Intrastrand and Interstrand Contributions to Stacking Account for Roll Variations at the Alternating Purine-Pyrimidine Sequences in A-DNA and A-RNA. Journal o Molecular Biology 221, 1991, 761-764
  • J. Sponer: Theoretical Estimation of Ultrasonic Cavitation Threshold for Very Short Pulses of Ultrasound. Ultrasonics 29, 1991, 376-380.
  • J. Sponer, J. Kypr: Correlations among Roll, Rise, Cup and Stagger in DNA Structures Suggested by Empirical Potential Calculations. Journal of Biomolecular Structure and Dynamics 11, 1993, 27-41.
  • J. Sponer, J. Kypr: Theoretical Analysis of the Base Stacking in DNA. Choice of the Force Field and a Comparison with the Oligonucleotide Crystal Structures. Journal of Biomolecular Structure and Dynamics 11, 1993, 277-292.
  • J. Sponer, P. Hobza: Bifurcated Hydrogen Bonds in DNA Crystal Structures. An Ab Initio Quantum Chemical Study. Journal of the American Chemical Society 116, 1994, 709-714.
  • J. Sponer, P. Hobza: Sequence Dependent Intrinsic Deformability of DNA Base Amino Groups. An Ab Initio Quantum Chemical Analysis. Journal of Molecular Structure (THEOCHEM) 305, 1994, 35-40.
  • J. Sponer, J. Kypr: Close Mutual Contacts of the Amino Groups in DNA. International Journal of Biological Macromolecules. 16, 1994, 3-6.
  • J. Sponer, P. Hobza: Nonplanar geometries of DNA bases. Second order Moller-Plesset study. Journal of Physical Chemistry 98, 1994, 3161-3164.
  • J. Sponer, R. Burcl, P. Hobza: Interactions between Amino Groups in DNA. An Ab Initio Study and a Comparison with the Empirical Potentials. Journal of Biomolecular Structure and Dynamics 11, 1994, 1357-1376.
  • J. Sponer, J. Jursa, J. Kypr: Interactions between the Guanine Amino Group and the Adenine Six Membered Ring Stabilizes the Unusual Conformation of the CpA Step in B-DNA. Nucleosides & Nucleotides 13, 1994, 1669-1677.
  • J. Sponer, P. Hobza: G.C base pair in parallel-stranded DNA - a novel type of base pairing: An ab initio quantum chemical study. Journal of Biomolecular Structure and Dynamics 12, 1994, 671-680.
  • M. Hargittai, J. Molnar, T.M. Klap(tke, I.C. Tornieporth-Oetting, M. Kolonits, I. Hargittai, Iodine azide. Molecular Structure from Gas Phase Electron Diffraction, J. Phys. Chem., 1994, 98, 10095.