prof. RNDr. Jiří Šponer, DrSc.

2017

• GAJARSKY, M; ZIVKOVIC, ML; STADLBAUER, P; PAGANO, B; FIALA, R; AMATO, J; TOMASKA, L; SPONER, J; PLAVEC, J; TRANTIREK, L, 2017:Structure of a Stable G-Hairpin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 (10), p. 3591 - 3594.
• HAVRILA, M; STADLBAUER, P; ISLAM, B; OTYEPKA, M; SPONER, J, 2017:Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13 (8), p. 3911 - 3926.
• XU, JF; TSANAKOPOULOU, M; MAGNANI, CJ; SZABLA, R; SPONER, JE; SPONER, J; GORA, RW; SUTHERLAND, JD, 2017:A prebiotically plausible synthesis of pyrimidine beta-ribonucleosides and their phosphate derivatives involving photoanomerization. NATURE CHEMISTRY 9 (4), p. 303 - 309.

2016

• CIVIS, S; SZABLA, R; SZYJA, BM; SMYKOWSKI, D; IVANEK, O; KNIZEK, A; KUBELIK, P; SPONER, J; FERUS, M; SPONER, JE, 2016:TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. SCIENTIFIC REPORTS 6
• DRSATA, T; ZGARBOVA, M; JURECKA, P; SPONER, J; LANKAS, F, 2016:On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. BIOPHYSICAL JOURNAL 110 (4), p. 874 - 876.
• GKIONIS, K; KRUSE, H; SPONER, J, 2016: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 12 (4), p. 2000 - 2016.
• KREPL, M; CLERY, A; BLATTER, M; ALLAIN, FHT; SPONER, J, 2016:Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. NUCLEIC ACIDS RESEARCH 44 (13), p. 6452 - 6470.
• SPONER, JE; SPONER, J; NOVAKOVA, O; BRABEC, V; SEDO, O; ZDRAHAL, Z; COSTANZO, G; PINO, S; SALADINO, R; DI MAURO, E, 2016:Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. CHEMISTRY-A EUROPEAN JOURNAL 22 (11), p. 3572 - 3586.
• SPONER, JE; SZABLA, R; GORA, RW; SAITTA, AM; PIETRUCCI, F; SAIJA, F; DI MAURO, E; SALADINO, R; FERUS, M; CIVIS, S; SPONER, J, 2016: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 18 (30), p. 20047 - 20066.
• SZABLA, R; GORA, RW; SPONER, J, 2016:Ultrafast excited-state dynamics of isocytosine. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 (30), p. 20208 - 20218.

2015

• FERUS, M; NESVORNY, D; SPONER, J; KUBELIK, P; MICHALCIKOVA, R; SHESTIVSKA, V; SPONER, JE; CIVIS, S, 2015:High-energy chemistry of formamide: A unified mechanism of nucleobase formation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112 (3), p. 657 - 662.
• ISLAM, B; STADLBAUER, P; KREPL, M; KOCA, J; NEIDLE, S; HAIDER, S; SPONER, J, 2015:Extended molecular dynamics of a c-kit promoter quadruplex. NUCLEIC ACIDS RESEARCH 43 (18), p. 8673 - 8693.
• OHNMACHT, SA; MARCHETTI, C; GUNARATNAM, M; BESSER, RJ; HAIDER, SM; DI VITA, G; LOWE, HL; MELLINAS-GOMEZ, M; DIOCOU, S; ROBSON, M; SPONER, J; ISLAM, B; PEDLEY, RB; HARTLEY, JA; NEIDLE, S, 2015:A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer. SCIENTIFIC REPORTS 5
• STADLBAUER, P; KUHROVA, P; BANAS, P; KOCA, J; BUSSI, G; TRANTIREK, L; OTYEPKA, M; SPONER, J, 2015:Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. NUCLEIC ACIDS RESEARCH 43 (20), p. 9626 - 9644.
• SZABLA, R; CAMPOS, J; SPONER, JE; SPONER, J; GORA, RW; SUTHERLAND, JD, 2015:Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine. CHEMICAL SCIENCE 6 (3), p. 2035 - 2043.

2014

• CIVIS, S; FERUS, M; SPONER, JE; SPONER, J; KAVAN, L; ZUKALOVA, M, 2014:Room temperature spontaneous conversion of OCS to CO2 on the anatase TiO2 surface. CHEMICAL COMMUNICATIONS 50 (57), p. 7712 - 7715.
• DRSATA, T; SPACKOVA, N; JURECKA, P; ZGARBOVA, M; SPONER, J; LANKAS, F, 2014:Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. NUCLEIC ACIDS RESEARCH 42 (11), p. 7383 - 7394.
• GKIONIS, K; KRUSE, H; PLATTS, JA; MLADEK, A; KOCA, J; SPONER, J, 2014: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 (3), p. 1326 - 1340.
• KUEHROVA, P; OTYEPKA, M; SPONER, J; BANAS, P, 2014:Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (1), p. 401 - 411.
• MLADEK, A; BANAS, P; JURECKA, P; OTYEPKA, M; ZGARBOVA, M; SPONER, J, 2014: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 (1), p. 463 - 480.
• MLYNSKY, V; BANAS, P; SPONER, J; VAN DER KAMP, MW; MULHOLLAND, AJ; OTYEPKA, M, 2014:Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (4), p. 1608 - 1622.
• SZABLA, R; GORA, RW; SPONER, J; SPONER, JE, 2014:Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases. CHEMISTRY-A EUROPEAN JOURNAL 20 (9), p. 2515 - 2521.
• SZABLA, R; SPONER, JE; SPONER, J; SOBOLEWSKI, AL; GORA, RW, 2014:Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 (33), p. 17617 - 17626.

2013

• HAVRILA, M; REBLOVA, K; ZIRBEL, CL; LEONTIS, NB; SPONER, J, 2013: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 (46), p. 14302 - 14319.
• PINO, S; COSTANZO, G; GIORGI, A; SPONER, J; SPONER, JE; DI MAURO, E, 2013:Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP. ENTROPY 15 (12), p. 5362 - 5383.
• SPONER, J; MLADEK, A; SPACKOVA, N; CANG, XH; CHEATHAM, TE; GRIMME, S, 2013:Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 (26), p. 9785 - 9796.
• SPONER, J; SPONER, JE; MLADEK, A; BANAS, P; JURECKA, P; OTYEPKA, M, 2013:How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. METHODS 64 (1), p. 3 - 11.
• SPONER, J; SPONER, JE; MLADEK, A; JURECKA, P; BANAS, P; OTYEPKA, M, 2013:Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. BIOPOLYMERS 99 (12), p. 978 - 988.
• STADLBAUER, P; KREPL, M; CHEATHAM, TE; KOCA, J; SPONER, J, 2013:Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. NUCLEIC ACIDS RESEARCH 41 (14), p. 7128 - 7143.
• SZABLA, R; TUNA, D; GORA, RW; SPONER, J; SOBOLEWSKI, AL; DOMCKE, W, 2013:Photochemistry of 2-Aminooxazole, a Hypothetical Prebiotic Precursor of RNA Nucleotides. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 4 (16), p. 2785 - 2788.

2012

• BANAS, P; MLADEK, A; OTYEPKA, M; ZGARBOVA, M; JURECKA, P; SVOZIL, D; LANKAS, F; SPONER, J, 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 (7), p. 2448 - 2460.
• FERUS, M; CIVIS, S; MLADEK, A; SPONER, J; JUHA, L; SPONER, JE, 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 (51), p. 20788 - 20796.
• SPONER, J; CANG, XH; CHEATHAM, TE, 2012:Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. METHODS 57 (1), p. 25 - 39.
• SPONER, J; MLADEK, A; SPONER, JE; SVOZIL, D; ZGARBOVA, M; BANAS, P; JURECKA, P; OTYEPKA, M, 2012: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 (44), p. 15257 - 15277.
• SPONER, JE; SPONER, J, 2012: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 (1), p. 109 - 110.

2010

• DITZLER, MA; OTYEPKA, M; SPONER, J; WALTER, NG, 2010:Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. ACCOUNTS OF CHEMICAL RESEARCH 43 (1), p. 40 - 47.
• REBLOVA, K; RAZGA, F; LI, W; GAO, HX; FRANK, J; SPONER, J, 2010:Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. NUCLEIC ACIDS RESEARCH 38 (4), p. 1325 - 1340.

Pracoviště 1:	Masarykova univerzita - CEITEC MU
Pracoviště 2:	Masarykova univerzita Kamenice 753/5, Brno, 625 00