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1

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

Šponer, Jiří, Mládek, Arnošt, Šponer, Judit E., Svozil, Daniel, Zgarbová, Marie, Banáš, Pavel, Jurečka, Petr, Otyepka, Michal

Journal:

Physical Chemistry Chemical Physics

Année:

2012

Langue:

english

Fichier:

PDF, 2.78 MB

english, 2012

2

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G., Otyepka, Mich

Journal:

Chemical Reviews

Année:

2018

Langue:

english

Fichier:

PDF, 77.37 MB

english, 2018

3

DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations

Jiří Šponer, Pavel Hobza

Journal:

International Journal of Quantum Chemistry

Année:

1996

Langue:

english

Fichier:

PDF, 874 KB

english, 1996

4

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

Jiří Šponer, Jerzy Leszczynski, Pavel Hobza

Journal:

Année:

2001

Langue:

english

Fichier:

PDF, 628 KB

english, 2001

5

Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways

Dr. Judit E. Šponer, Prof. Jiří Šponer, Dr. Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Année:

2011

Langue:

english

Fichier:

PDF, 396 KB

english, 2011

6

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

Pavel Hobza, Jiří Šponer

Journal:

Chemical Physics Letters

Année:

1996

Langue:

english

Fichier:

PDF, 481 KB

english, 1996

7

Is formamide natureʼs choice to create life?: Comment on the paper “Formamide and the origin of life” by Raffaele Saladino et al.

Judit E. Šponer, Jiří Šponer

Journal:

Physics of Life Reviews

Année:

2012

Langue:

english

Fichier:

PDF, 71 KB

english, 2012

8

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations

Hobza, Pavel, Šponer, Jiří

Journal:

Chemical Reviews

Année:

1999

Langue:

english

Fichier:

PDF, 344 KB

english, 1999

9

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Šponer, Jiří, Šponer, Judit E., Mládek, Arnošt, Banáš, Pavel, Jurečka, Petr, Otyepka, Michal

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2013

10

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Mlýnský, Vojtěch, Banáš, Pavel, Šponer, Jiří, van der Kamp, Marc W., Mulholland, Adrian J., Otyepka, Michal

Journal:

Journal of Chemical Theory and Computation

Année:

2014

Langue:

english

Fichier:

PDF, 6.03 MB

english, 2014

11

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Gkionis, Konstantinos, Kruse, Holger, Platts, James A., Mládek, Arnošt, Koča, Jaroslav, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Année:

2014

Langue:

english

Fichier:

PDF, 2.79 MB

english, 2014

12

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Année:

2015

Langue:

english

Fichier:

PDF, 2.60 MB

english, 2015

13

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

Havrila, Marek, Zgarbová, Marie, Jurečka, Petr, Banáš, Pavel, Krepl, Miroslav, Otyepka, Michal, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Année:

2015

Langue:

english

Fichier:

PDF, 3.81 MB

english, 2015

14

Derivation of reliable geometries in QM calculations of DNA structures: explicit solvent QM/MM and restrained implicit solvent QM optimizations of G-quadruplexes.

Gkionis, Konstantinos, Kruse, Holger, Sponer, Jiri

Journal:

Journal of Chemical Theory and Computation

Année:

2016

Langue:

english

Fichier:

PDF, 6.77 MB

english, 2016

15

Cover Picture: Synthesis of Chiral Tertiary Alcohols by CuI-Catalyzed Enantioselective Addition of Organomagnesium Reagents to Ketones / Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario / Intermolecular Peptide Cross-

Rong, Jiawei, Pellegrini, Tilde, Harutyunyan, Syuzanna R., Šponer, Judit E., Šponer, Jiří, Nováková, Olga, Brabec, Viktor, Šedo, Ondrej, Zdráhal, Zbyněk, Costanzo, Giovanna, Pino, Samanta, Saladino, R

Journal:

Chemistry - A European Journal

Année:

2016

Fichier:

PDF, 447 KB

2016

16

Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases

Szabla, Rafał, Góra, Robert W., Šponer, Jiří, Šponer, Judit E.

Journal:

Chemistry - A European Journal

Année:

2014

Langue:

english

Fichier:

PDF, 691 KB

english, 2014

17

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

Szabla, Rafał, Havrila, Marek, Kruse, Holger, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Année:

2016

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2016

18

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

Gresh, Nohad, Naseem-Khan, Sehr, Lagardère, Louis, Piquemal, Jean-Philip, Sponer, Judit E., Sponer, Jiri

Journal:

Journal of Physical Chemistry B

Année:

2017

Langue:

english

Fichier:

PDF, 4.40 MB

english, 2017

19

Selectivity of major isoquinoline alkaloids from Chelidomium majus towards telomeric G-quadruplex: A study using a modified transition-FRET (t-FRET) assay

Noureini, Sakineh Kazemi, Esmaeili, Hosein, Abachi, Farzane, Khiali, Soraia, Islam, Barira, Kuta, Martyna, Saboury, Ali A., Hoffmann, Marcin, Sponer, Jiri, Parkinson, Gary, Haider, Shozeb

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Année:

2017

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2017

20

Novel electrochemical route to cleaner fuel dimethyl ether

Cassone, Giuseppe, Pietrucci, Fabio, Saija, Franz, Guyot, François, Sponer, Jiri, Sponer, Judit E., Saitta, A. Marco

Journal:

Scientific Reports

Année:

2017

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2017

21

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-histidine Ligand and Mg 2+ .

Pokorná, Pavlína, Krepl, Miroslav, Kruse, Holger, Sponer, Jiri

Journal:

Journal of Chemical Theory and Computation

Année:

2017

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2017

22

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Havrila, Marek, Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Mergny, Jean-Louis, Otyepka, Michal, Šponer, Jiří

Journal:

Nucleic Acids Research

Année:

2018

Langue:

english

Fichier:

PDF, 3.93 MB

english, 2018

23

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

Suddala, Krishna C., Price, Ian R., Dandpat, Shiba S., Janeček, Michal, Kührová, Petra, Šponer, Jiří, Banáš, Pavel, Ke, Ailong, Walter, Nils G.

Journal:

Nature Communications

Année:

2019

Langue:

english

Fichier:

PDF, 3.21 MB

english, 2019

24

Mechanismus der metallvermittelten Desaminierung von Cytosin – Experiment und DFT-Rechnungen

Judit E. Šponer, Pablo J. Sanz Miguel, Luis Rodríguez-Santiago, Andrea Erxleben, Michael Krumm, Mariona Sodupe, Jiří Šponer, Bernhard Lippert

Journal:

Angewandte Chemie

Année:

2004

Langue:

german

Fichier:

PDF, 169 KB

german, 2004

25

Metal-Mediated Deamination of Cytosine: Experiment and DFT Calculations

Judit E. Šponer, Pablo J. Sanz Miguel, Luis Rodríguez-Santiago, Andrea Erxleben, Michael Krumm, Mariona Sodupe, Jirí Šponer, Bernhard Lippert

Journal:

Angewandte Chemie International Edition

Année:

2004

Langue:

english

Fichier:

PDF, 168 KB

english, 2004

26

Molecular dynamics simulations of RNA: An in silico single molecule approach

S. Elizabeth McDowell, Nad'a Špačková, Jiří Šponer, Nils G. Walter

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 901 KB

english, 2007

27

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

Jana Sefcikova, Maryna V. Krasovska, Nad'a Špačková, Jiří Šponer, Nils G. Walter

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 770 KB

english, 2007

28

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

Joanna Sarzyńska, Kamila Réblová, Jiří Šponer, Tadeusz Kuliński

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2008

29

Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

Alberto Pérez, Jiri Sponer, Petr Jurecka, Pavel Hobza, F. Javier Luque, Modesto Orozco

Journal:

Chemistry - A European Journal

Année:

2005

Langue:

english

Fichier:

PDF, 89 KB

english, 2005

30

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

Jiří Šponer, Petr Jurečka, Ivan Marchan, F. Javier Luque, Modesto Orozco, Pavel Hobza

Journal:

Chemistry - A European Journal

Année:

2006

Langue:

english

Fichier:

PDF, 232 KB

english, 2006

31

Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose

Judit E. Šponer, Bobby G. Sumpter, Jerzy Leszczynski, Jiří Šponer, Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Année:

2008

Langue:

english

Fichier:

PDF, 454 KB

english, 2008

32

Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

Judit E. Šponer, Álvaro Vázquez-Mayagoitia, Bobby G. Sumpter, Jerzy Leszczynski, Jiří Šponer, Michal Otyepka, Pavel Banáš, Miguel Fuentes-Cabrera

Journal:

Chemistry - A European Journal

Année:

2010

Langue:

english

Fichier:

PDF, 413 KB

english, 2010

33

ChemInform Abstract: Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical ab initio Calculations

Pavel Hobza, Jiri Sponer

Journal:

Année:

2000

Fichier:

PDF, 26 KB

2000

34

Interactions of the “piano-stool” [ruthenium(II) (η6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Zdeněk Futera, Julia Klenko, Judit E. Šponer, Jiří Šponer, Jaroslav V. Burda

Journal:

Journal of Computational Chemistry

Année:

2009

Langue:

english

Fichier:

PDF, 505 KB

english, 2009

35

Density functional theory and molecular clusters

Pavel Hobza, Jiří šponer, Tomáš Reschel

Journal:

Journal of Computational Chemistry

Année:

1995

Langue:

english

Fichier:

PDF, 774 KB

english, 1995

36

Nonempirical ab initio calculations on DNA base pairs

Jiří Šponer, Pavel Hobza

Journal:

Chemical Physics

Année:

1996

Langue:

english

Fichier:

PDF, 827 KB

english, 1996

37

Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock

Pavel Hobza, Jiřı́ Šponer

Journal:

Chemical Physics Letters

Année:

1998

Langue:

english

Fichier:

PDF, 158 KB

english, 1998

38

Intramolecular flexibility of DNA bases in adenine–thymine and guanine–cytosine Watson–Crick base pairs

OlegV Shishkin, Jiŕı́ Šponer, Pavel Hobza

Journal:

Journal of Molecular Structure

Année:

1999

Langue:

english

Fichier:

PDF, 93 KB

english, 1999

39

Coordination and properties of cobalt in the molecular sieves CoAPO-5 and -11

Judit Šponer, Jiřı́ Čejka, Jiřı́ Dědeček, Blanka Wichterlová

Journal:

Microporous and Mesoporous Materials

Année:

2000

Langue:

english

Fichier:

PDF, 268 KB

english, 2000

40

Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)

Koen Uytterhoeven, Jiri Sponer, Luc Van Meervelt

Journal:

Année:

2002

Langue:

english

Fichier:

PDF, 458 KB

english, 2002

41

Tautomerism of xanthine: The second-order MØller-Plesset study

Jiři šponer, Jerzy Leszczyński

Journal:

Structural Chemistry

Année:

1995

Langue:

english

Fichier:

PDF, 389 KB

english, 1995

42

The use of interconnected β-tricalcium phosphate as bone substitute after curettage of benign bone tumours

Pavel Šponer, Karel Urban, Tomáš Kučera, Aleš Kohout, Jindra Brtková, Jiří Knížek

Journal:

European Journal of Orthopaedic Surgery & Traumatology

Année:

2011

Langue:

english

Fichier:

PDF, 308 KB

english, 2011

43

Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair

Jiří Šponer, Michal Sabat, Jaroslav V. Burda, Jerzy Leszczynski, Pavel Hobza, Bernhard Lippert

Journal:

JBIC Journal of Biological Inorganic Chemistry

Année:

1999

Langue:

english

Fichier:

PDF, 107 KB

english, 1999

44

Effect of local sugar and base geometry on13C and15N magnetic shielding anisotropy in DNA nucleosides

Eva Brumovská, Vladimír Sychrovský, Zuzana Vokáčová, Jiří Šponer, Bohdan Schneider, Lukáš Trantírek

Journal:

Journal of Biomolecular NMR

Année:

2008

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2008

45

Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

Flavia Barone, Filip Lankas, Nada Spackova, Jiri Sponer, Peter Karran, Margherita Bignami, Filomena Mazzei

Journal:

Biophysical Chemistry

Année:

2005

Langue:

english

Fichier:

PDF, 331 KB

english, 2005

46

Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases: N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views

Šponer, Jiří, Šponer, Judit E., Gorb, Leonid, Leszczynski, Jerzy, Lippert, Bernhard

Journal:

Journal of Physical Chemistry A

Année:

1999

Langue:

english

Fichier:

PDF, 270 KB

english, 1999

47

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

Beššeová, Ivana, Banáš, Pavel, Kührová, Petra, Košinová, Pavlína, Otyepka, Michal, Šponer, Jiří

Journal:

Journal of Physical Chemistry B

Année:

2012

Langue:

english

Fichier:

PDF, 17.32 MB

english, 2012

48

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Morgado, Claudio A., Svozil, Daniel, Turner, Douglas H., Šponer, Jiří

Journal:

Physical Chemistry Chemical Physics

Année:

2012

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2012

49

Sequence dependent intrinsic deformability of the DNA base amino groups. An ab initio quantum chemical analysis

Jiří Šponer, Pavel Hobza

Journal:

Journal of Molecular Structure: THEOCHEM

Année:

1994

Langue:

english

Fichier:

PDF, 543 KB

english, 1994

50

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Filip Rázga, Martin Zacharias, Kamila Réblová, Jaroslav Koča, Jiří Šponer

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 475 KB

english, 2006