J Sponer

Summary

Affiliation: Academy of Sciences of the Czech Republic
Country: Czech Republic

Publications

  1. ncbi Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 14:613-28. 1997
  2. ncbi Nonplanar DNA base pairs
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    J Biomol Struct Dyn 13:827-33. 1996
  3. ncbi Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 17:1087-96. 2000
  4. ncbi Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejskova 3, 182 23 Prague, Czech Republic
    Biopolymers 61:3-31. 2001
  5. ncbi 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
    J Sponer
    J Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolejskova 3, CZ 182 23 Prague, Czech Republic
    J Biol Inorg Chem 4:537-45. 1999
  6. ncbi 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
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 17:61-77. 1999
  7. pmc Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Biophys J 73:76-87. 1997
  8. ncbi Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 13:695-706. 1996
  9. ncbi Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture
    J E Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic
    Inorg Chem 40:3269-78. 2001
  10. ncbi Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    J Biomol Struct Dyn 14:117-35. 1996

Collaborators

Detail Information

Publications14

  1. ncbi Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 14:613-28. 1997
    ..The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base...
  2. ncbi Nonplanar DNA base pairs
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    J Biomol Struct Dyn 13:827-33. 1996
    ..Currently used empirical potentials are not accurate enough to properly cover the interactions associated with amino-group and base-pair nonplanarity...
  3. ncbi Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 17:1087-96. 2000
    ..This indeed can occur in biopolymers and may have an effect on the local DNA architecture. Nevertheless, nucleobases have no intrinsic propensity to form cation-pi interactions...
  4. ncbi Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejskova 3, 182 23 Prague, Czech Republic
    Biopolymers 61:3-31. 2001
    ..In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed...
  5. ncbi 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
    J Sponer
    J Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic, Dolejskova 3, CZ 182 23 Prague, Czech Republic
    J Biol Inorg Chem 4:537-45. 1999
    ..All structures have been optimized within the Hartree-Fock approximation, while interaction energies were evaluated with the inclusion of electron correlation...
  6. ncbi 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
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 17:61-77. 1999
    ..The results demonstrate specific differences among the cations and provide a set of reference structures and energies for verification and/or parametrization of empirical potentials and other theoretical methods...
  7. pmc Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Biophys J 73:76-87. 1997
    ..This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation...
  8. ncbi Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
    J Biomol Struct Dyn 13:695-706. 1996
    ..CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs...
  9. ncbi Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture
    J E Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic
    Inorg Chem 40:3269-78. 2001
    ....
  10. ncbi Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    J Biomol Struct Dyn 14:117-35. 1996
    ..In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry...
  11. ncbi Sequence-dependent elastic properties of DNA
    F Lankas
    J Heyrovsky Institute of Physical Chemistry, Dolejskova 3, Praha 8, 18200, Czech Republic
    J Mol Biol 299:695-709. 2000
    ..The present work shows that large-scale molecular dynamics simulations represent a unique source of data to study various aspects of DNA elasticity including its sequence-dependence...
  12. pmc A measure of bending in nucleic acids structures applied to A-tract DNA
    F Lankas
    Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
    Nucleic Acids Res 38:3414-22. 2010
    ..The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers...
  13. ncbi The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms
    J V Burda
    Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
    J Biol Inorg Chem 5:178-88. 2000
    ..The surprisingly large interaction energy for the latter structure is due to the strong H-bond between the NH3 ligand group of the metal adduct and the N6 nitrogen atom of the base...
  14. ncbi Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
    N Spackova
    Institute of Biophysics, Academy of Sciences of the Czech Republic, and National Centre for Biomolecular Research, Kralovopolska 135, 612 65 Brno, Czech Republic
    J Am Chem Soc 123:3295-307. 2001
    ..The trajectories provide a largely converged characterization of the structural dynamics of these four-stranded G-DNA molecules...