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Journal of Biomolecular Structure and Dynamics Volume 17, 1999 - Issue 1
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Original Articles

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

Jiří Šponer J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23, Prague, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Knálovopolská 135, 612 65, Brno, Czech Republic
,
Jaroslav V. Burda Department of Mathematics and Physics, Charles University, Ke Karlovu 2, Prague
,
Jerzy Leszczynski Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS, 39217, USA
&
Pavel Hobzal J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23, Prague, Czech Republic
Pages 61-77 | Received 05 Mar 1999, Published online: 21 May 2012

Citations (42)

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Debashree Bandyopadhyay & Dhananjay Bhattacharyya. (2003) Different Modes of Interaction Between Hydrated Magnesium Ion and DNA Functional Groups: Database Analysis and ab initio Studies. Journal of Biomolecular Structure and Dynamics 21:3, pages 447-458.
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Articles from other publishers (41)

Briana T. A. Boychuk & Stacey D. Wetmore. (2023) Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal–Nucleic Acid Complexes. Journal of Chemical Theory and Computation 19:15, pages 5273-5288.
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Zhaoxi Sun, Xiaohui Wang, John Z. H. Zhang & Qiaole He. (2019) Sulfur-substitution-induced base flipping in the DNA duplex. Physical Chemistry Chemical Physics 21:27, pages 14923-14940.
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Jaroslav V. Burda, Jiří Šponer & Filip Šebesta. 2017. Handbook of Computational Chemistry. Handbook of Computational Chemistry 1827 1874 .
Jaroslav V. Burda & Filip Šebesta. 2016. Handbook of Computational Chemistry. Handbook of Computational Chemistry 1 48 .
Sumirtha Balaratnam & Soumitra Basu. (2015) Divalent cation-aided identification of physico-chemical properties of metal ions that stabilize RNA g-quadruplexes. Biopolymers 103:7, pages 376-386.
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Jean-Yves Salpin, Violette Haldys, Sébastien Guillaumont, Jeanine Tortajada, Marcela Hurtado & Al Mokhtar Lamsabhi. (2014) Gas-Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple-Photon Dissociation Spectroscopy Study. ChemPhysChem 15:14, pages 2959-2971.
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Shozeb M Haider & Stephen Neidle. 2012. Innovations in Biomolecular Modeling and Simulations. Innovations in Biomolecular Modeling and Simulations 33 52 .
Jaroslav V Burda, Jiřı́ Šponer & Jerzy Leszczynski. 2012. Handbook of Computational Chemistry. Handbook of Computational Chemistry 1277 1308 .
Zdeněk Chval, Daniela Chvalová & Fabrice Leclerc. (2011) Modeling the RNA 2′OH Activation: Possible Roles of Metal Ion and Nucleobase as Catalysts in Self-Cleaving Ribozymes. The Journal of Physical Chemistry B 115:37, pages 10943-10956.
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Romina Oliva & Luigi Cavallo. (2009) Frequency and Effect of the Binding of Mg 2+ , Mn 2+ , and Co 2+ Ions on the Guanine Base in Watson−Crick and Reverse Watson−Crick Base Pairs . The Journal of Physical Chemistry B 113:47, pages 15670-15678.
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Giovanni Villani. (2009) Properties of the Thiobase Pairs Hydrogen Bridges: A Theoretical Study. The Journal of Physical Chemistry B 113:7, pages 2128-2134.
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Serge A. Krasnokutski, Yuxiu Lei, Jung Sup Lee & Dong-Sheng Yang. (2008) Pulsed-field ionization photoelectron and IR-UV resonant photoionization spectroscopy of Al-thymine. The Journal of Chemical Physics 129:12.
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Yu Zhang & Kaixun Huang. (2007) The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine–thymine base pair: A comparative study. Journal of Molecular Structure: THEOCHEM 822:1-3, pages 57-64.
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Martin Lepšík & Martin J. Field. (2007) Binding of Calcium and Other Metal Ions to the EF-Hand Loops of Calmodulin Studied by Quantum Chemical Calculations and Molecular Dynamics Simulations. The Journal of Physical Chemistry B 111:33, pages 10012-10022.
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Yu Zhang & Kaixun Huang. (2007) On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine–cytosine Watson–Crick and guanine–guanine reverse-Hoogsteen DNA base pairs. Journal of Molecular Structure: THEOCHEM 812:1-3, pages 51-62.
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Neethu Sundaresan & Cherumuttathu H. Suresh. (2007) A Base-Sugar−Phosphate Three-Layer ONIOM Model for Cation Binding:  Relative Binding Affinities of Alkali Metal Ions for Phosphate Anion in DNA. Journal of Chemical Theory and Computation 3:3, pages 1172-1182.
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Neethu Sundaresan, C. K. S. Pillai & Cherumuttathu H. Suresh. (2006) Role of Mg 2+ and Ca 2+ in DNA Bending:  Evidence from an ONIOM-Based QM-MM Study of a DNA Fragment . The Journal of Physical Chemistry A 110:28, pages 8826-8831.
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Sébastien Guillaumont, Jeanine Tortajada, Jean-Yves Salpin & Al Mokhtar Lamsabhi. (2005) Experimental and computational study of the gas-phase interactions between lead(II) ions and two pyrimidic nucleobases: Uracil and thymine. International Journal of Mass Spectrometry 243:3, pages 279-293.
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Partha Pratim Bera & Henry F. SchaeferIIIIII. (2005) (G–H) • –C and G–(C–H) • radicals derived from the guanine·cytosine base pair cause DNA subunit lesions . Proceedings of the National Academy of Sciences 102:19, pages 6698-6703.
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Anton S. Petrov, Gene Lamm & George R. Pack. (2005) Calculation of the binding free energy for magnesium-RNA interactions. Biopolymers 77:3, pages 137-154.
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Anton S. Petrov, Joni Funseth-Smotzer & George R. Pack. (2005) Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium. International Journal of Quantum Chemistry 102:5, pages 645-655.
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Nad'a Špačková, Elena Cubero, Jiří Šponer & Modesto Orozco. (2004) Theoretical Study of the Guanine → 6-Thioguanine Substitution in Duplexes, Triplexes, and Tetraplexes. Journal of the American Chemical Society 126:44, pages 14642-14650.
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Anton S. Petrov, George R. Pack & Gene Lamm. (2004) Calculations of Magnesium−Nucleic Acid Site Binding in Solution. The Journal of Physical Chemistry B 108:19, pages 6072-6081.
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Marc Noguera, Joan Bertran & Mariona Sodupe. (2003) A Quantum Chemical Study of Cu 2+ Interacting with Guanine−Cytosine Base Pair. Electrostatic and Oxidative Effects on Intermolecular Proton-Transfer Processes . The Journal of Physical Chemistry A 108:2, pages 333-341.
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Jiří Šponer & Pavel Hobza. (2003) Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies. Collection of Czechoslovak Chemical Communications 68:12, pages 2231-2282.
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Juan Bertran, Marc Noguera & Mariona Sodupe. 2003. Fundamental World of Quantum Chemistry. Fundamental World of Quantum Chemistry 1231 1255 .
Jordi Muñoz, J. L. Gelpí, Montserrat Soler-López, Juan A. Subirana, Modesto Orozco & F. Javier Luque. (2002) Can Divalent Metal Cations Stabilize the Triplex Motif? Theoretical Study of the Interaction of the Hydrated Mg 2+ Cation with the G−G·C Triplet . The Journal of Physical Chemistry B 106:34, pages 8849-8857.
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Kathrin S. SchmidtJan ReedijkKlaus WeiszEline M. Basilio JankeJudit E. SponerJiri SponerBernhard Lippert. (2002) Loss of Hoogsteen Pairing Ability upon N1 Adenine Platinum Binding. Inorganic Chemistry 41:11, pages 2855-2863.
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Anton S. Petrov, Gene Lamm & George R. Pack. (2002) Water-Mediated Magnesium-Guanine Interactions. The Journal of Physical Chemistry B 106:12, pages 3294-3300.
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Judit E. ŠponerFrank GlahéJerzy LeszczynskiBernhard LippertJiří Šponer. (2001) How Nucleobases Rotate When Bonded to a Metal Ion:  Detailed View from an Ab Initio Quantum Chemical Study of a Cytosine Complex of trans -a 2 Pt II . The Journal of Physical Chemistry B 105:48, pages 12171-12179.
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Michael Meyer, Christoph Schneider, Maria Brandl & Jürgen Sühnel. (2001) Cyclic Adenine-, Cytosine-, Thymine-, and Mixed Guanine−Cytosine-Base Tetrads in Nucleic Acids Viewed from a Quantum-Chemical and Force Field Perspective. The Journal of Physical Chemistry A 105:51, pages 11560-11573.
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Jiřı&#x; Šponer, Jerzy Leszczynski & Pavel Hobza. (2001) Hydrogen bonding, stacking and cation binding of DNA bases. Journal of Molecular Structure: THEOCHEM 573:1-3, pages 43-53.
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Michael Meyer, Maria Brandl & Jürgen Sühnel. (2001) Are Guanine Tetrads Stabilized by Bifurcated Hydrogen Bonds?. The Journal of Physical Chemistry A 105:35, pages 8223-8225.
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Jordi Muñoz, Jirí Sponer, Pavel Hobza, Modesto Orozco & F. Javier Luque. (2001) Interactions of Hydrated Mg 2+ Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study . The Journal of Physical Chemistry B 105:25, pages 6051-6060.
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A. Rakitin, P. Aich, C. Papadopoulos, Yu. Kobzar, A. S. Vedeneev, J. S. Lee & J. M. Xu. (2001) Metallic Conduction through Engineered DNA: DNA Nanoelectronic Building Blocks. Physical Review Letters 86:16, pages 3670-3673.
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Michael Meyer, Thomas Steinke, Maria Brandl & J�rgen S�hnel. (2001) Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. Journal of Computational Chemistry 22:1, pages 109-124.
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Richard Štefl, Nad’a Špačková, Imre Berger, Jaroslav Koča & Jiří Šponer. (2001) Molecular Dynamics of DNA Quadruplex Molecules Containing Inosine, 6-Thioguanine and 6-Thiopurine. Biophysical Journal 80:1, pages 455-468.
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Ji?� ?poner, Jerzy Leszczynski & Pavel Hobza. (2001) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61:1, pages 3-31.
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Jiří Šponer & Pavel Hobza. (2000) Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals. The Journal of Physical Chemistry A 104:19, pages 4592-4597.
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Jiří Šponer, Judit E. Šponer, Leonid Gorb, Jerzy Leszczynski & Bernhard Lippert. (1999) Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases:  N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views. The Journal of Physical Chemistry A 103:51, pages 11406-11413.
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Nohad Gresh & Jırí Šponer. (1999) Complexes of Pentahydrated Zn 2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations . The Journal of Physical Chemistry B 103:51, pages 11415-11427.
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