251
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Hobza P, Sponer J. Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev 1999; 99:3247-76. [PMID: 11749516 DOI: 10.1021/cr9800255] [Citation(s) in RCA: 813] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- P Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Prague 8, Czech Republic
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252
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Ryjáček F, Kratochvı́l M, Hobza P. Adenine⋯2,4-difluorotoluene (modified base) pair: potential and free-energy surfaces. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)01013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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253
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Yuriev E, Scott D, Hanna MM. Effects of 5-[S-(2,4-dinitrophenyl)-thio]-2'-deoxyuridine analog incorporation on the structure and stability of DNA hybrids: implications for the design of nucleic acid probes. J Mol Recognit 1999; 12:337-45. [PMID: 10611643 DOI: 10.1002/(sici)1099-1352(199911/12)12:6<337::aid-jmr475>3.0.co;2-m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Labeled nucleic acid probes are used as diagnostic tools by detecting changes in gene expression upon hybridization to target RNAs or DNAs that are related to specific disease genes. 5-[S-(2, 4-Dinitrophenyl)-thio]-2'-deoxyuridine analog represents an excellent nucleic acid label, containing the DNP group which functions both as a probe and as a precursor for the introduction of a variety of fluorescent groups. This study describes thermal denaturation hybridization experiments with oligonucleotides containing the 5-[S-(2,4-dinitrophenyl)-thio]-2'-deoxyuridine analog. Using molecular modeling techniques, the effects of this analog on the hybrid structure and stability were examined, including (i) analog conformation, (ii) hydrogen bonding, (iii) stacking interactions and (iv) hybrid helical geometry. This analog does not prohibitively affect the hybrid thermal stability and incorporation of the analog does not compromise the structural integrity of the double helix. In particular, the sequence-dependence of the analog effects and the dependence on the modification site relative to the end(s) of the helix were investigated. Findings described here should provide guidelines in the rational design of nucleic acid probes.
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Affiliation(s)
- E Yuriev
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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254
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255
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An ab initio study of DNA base pair hydrogen bonding: a comparison of plane-wave versus Gaussian-type function methods. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00898-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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256
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Yoshioka Y, Kitagawa Y, Takano Y, Yamaguchi K, Nakamura T, Saito I. Experimental and Theoretical Studies on the Selectivity of GGG Triplets toward One-Electron Oxidation in B-Form DNA. J Am Chem Soc 1999. [DOI: 10.1021/ja991032t] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasunori Yoshioka
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
| | - Yasutaka Kitagawa
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
| | - Yu Takano
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
| | - Kizashi Yamaguchi
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
| | - Takashi Nakamura
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
| | - Isao Saito
- Contribution from the Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan, and CREST, Japan Science and Technology Corporation, Chiyoda-ku, Tokyo 102-0081, Japan
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257
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Sponer J, Burda JV, Leszczynksi J, Hobza P. 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 Biomol Struct Dyn 1999; 17:61-77. [PMID: 10496422 DOI: 10.1080/07391102.1999.10508341] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The structures and energies of the thioguanine-cytosine Watson-Crick (thioGC WC) base pair interacting with hydrated IIa (Mg2+, Ca2+, Ba2+) and IIb group (Zn2+, Cd2+, Hg2+) cations have been studied using ab initio techniques. Furthermore, complexes between guanine and thioguanine with hydrated cations have been characterized assuming various structures of the hydration shells. The complexes of the thioGC WC base pair with hydrated cations have similar properties as the previously studied GC WC base pair. There is substantial polarization stabilization of the base pairing due to cation binding which amounts to 7 - 11 kcal/mol. Soft Cd2+ and Hg2+ cations have a uniquely strong interaction with the thiogroup and induce substantial nonplanarity of the pairing. The thiogroup tends to reduce the number of water molecules in the first hydration shell of the cation. All complexes were optimized within the Hartree-Fock (HF) approximation while their energetics has been evaluated using the second-order Moller-Plesset perturbational method (MP2). All interaction energy evaluations and a substantial portion of the optimizations of the hydrated cation-(thio)guanine complexes have been repeated using Becke-3LYP Density Functional Theory method. All three approximations used (HF, Becke-3LYP, and MP2) give qualitatively the same results for the present cationic complexes. 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.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
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258
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259
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Barsky D, Kool ET, Colvin ME. Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity. J Biomol Struct Dyn 1999; 16:1119-34. [PMID: 10447197 DOI: 10.1080/07391102.1999.10508321] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although DNA polymerase fidelity has been mainly ascribed to Watson-Crick hydrogen bonds, two nonpolar isosteres for thymine (T) and adenine (A)--difluorotoluene (F) and benzimidazole (Z) --effectively mimic their natural counterparts in polymerization experiments with pol I (KF exo-) [JC Morales and ET Kool. Nature Struct Biol, 5, 950-954, 1998]. By ab initio quantum chemical gas phase methods (HF/6-31G* and MP2/6-31G**) and a solvent phase method (CPCM-HF/6-31G**), we find that the A-F interaction energy is 1/3 the A-T interaction energy in the gas phase and unstable in the solvent phase. The F-Z and T-Z interactions are very weak and T-Z is quite unstable in the solvent. Electrostatic solvation energy calculations on F, Z and toluene yield that Z is two times, and F and toluene are five times, less hydrophilic than the natural bases. Of the new "base-pairs" (F-Z, T-Z, and F-A), only F-A formed an A-T-like arrangement in unconstrained optimizations. F-Z and T-Z do not freely form planar arrangements, and constrained optimizations show that large amounts of energy are required to make these pairs fit the exact A-T geometry, suggesting that the polymerase does not require all bases to conform to the exact A-T geometry. We discuss a model for polymerase/nucleotide binding energies and investigate the forces and conformational range involved in the polymerase geometrical selection.
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Affiliation(s)
- D Barsky
- Biology and Biotechnology Research Program, Lawrence Livermore National Lab, Livermore, CA 94550, USA.
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260
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261
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Kajikawa Y, Azuma N, Tajima K. Crystallographic and ESR studies of π–π stacked binuclear copper(II) complexes of 1,3-bis(quinoline-2-carboxamido) and 1,3-bis(isoquinoline-3-carboxamido)propane. Inorganica Chim Acta 1999. [DOI: 10.1016/s0020-1693(99)00051-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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262
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Alderfer JL, Danilov VI, Poltev VI, Slyusarchuk ON. A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives: Monte Carlo simulation. J Biomol Struct Dyn 1999; 16:1107-17. [PMID: 10333180 DOI: 10.1080/07391102.1999.10508319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy preference is determined by water-water interaction. For other dimers conformational energy is the most important factor, or both the factors are of nearly equal importance. The introduction of the methyl group into the 5-position of uracil ring most noticeably influences the conformational energy and leads to the decrease of its stabilizing contribution to the total interaction energy. The introduction of halogen atoms increases the relative content of anti-syn and syn-anti conformations of DNPs as compared to the parent ones due to the formation of an energetically more favorable water structure around these conformations. A correlation is observed between the Monte Carlo results for the halogenated DNPs and their experimental photoproduct distribution. The data obtained demonstrates a sequence dependence in the photochemistry of the halogenated dinucleoside monophosphates.
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Affiliation(s)
- J L Alderfer
- Roswell Park Cancer Institute, Molecular & Cellular Biophysics Department, Buffalo, NY 14263, USA.
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263
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Šponer J, Sabat M, Burda JV, Leszczynski J, Hobza P. Interaction of the Adenine−Thymine Watson−Crick and Adenine−Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) Metal Cations: Absence of the Base Pair Stabilization by Metal-Induced Polarization Effects. J Phys Chem B 1999. [DOI: 10.1021/jp983744w] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Michal Sabat
- 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, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Jaroslav V. Burda
- 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, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Jerzy Leszczynski
- 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, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
| | - Pavel Hobza
- 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, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemical Physics, Faculty of Mathematics and Physics, Charles University, 121 16 Prague, Czech Republic, and Department of Chemistry, and Computational Center for
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264
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Mizutani M, Kubo I, Jitsukawa K, Masuda H, Einaga H. Nucleobase Stacking Evidenced on Ternary Metal (Palladium(II), Copper(II)) Complexes with Nucleobase Amino Acids and Aromatic Diimines. Inorg Chem 1999; 38:420-421. [PMID: 11673941 DOI: 10.1021/ic980438o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mamoru Mizutani
- Department of Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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265
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Florián J, Šponer J, Warshel A. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study. J Phys Chem B 1999. [DOI: 10.1021/jp983699s] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Florián
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
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266
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Computational Approaches to the Studies of the Interactions of Nucleic Acid Bases. COMPUTATIONAL MOLECULAR BIOLOGY 1999. [DOI: 10.1016/s1380-7323(99)80078-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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267
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Application of Molecular Orbital Theory to the Elucidation of Radical Processes Induced by Radiation Damage to DNA. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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268
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Saito I, Nakamura T, Nakatani K, Yoshioka Y, Yamaguchi K, Sugiyama H. Mapping of the Hot Spots for DNA Damage by One-Electron Oxidation: Efficacy of GG Doublets and GGG Triplets as a Trap in Long-Range Hole Migration. J Am Chem Soc 1998. [DOI: 10.1021/ja981888i] [Citation(s) in RCA: 278] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isao Saito
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
| | - Takashi Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
| | - Kazuhiko Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
| | - Yasunori Yoshioka
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
| | - Kizashi Yamaguchi
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
| | - Hiroshi Sugiyama
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering Kyoto University, Kyoto 606, Japan CREST, Japan Science and Technology Corporation Department of Chemistry Graduate School of Science, Osaka University, Toyonaka, Osaka 560, Japan Institute for Medical and Dental Engineering Tokyo Medical & Dental University, Tokyo 101, Japan
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269
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Pingale SS, Gadre SR, Bartolotti LJ. Electrostatic Insights into the Molecular Hydration Process: A Case Study of Crown Ethers. J Phys Chem A 1998. [DOI: 10.1021/jp982444b] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Libero J. Bartolotti
- North Carolina Supercomputing Center, 3021 Cornwallis Road, Research Triangle Park, North Carolina 27709
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270
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NOBELI I, PRICE SL, WHEATLEY RJ. Use of molecular overlap to predict intermolecular repulsion in N ··· H—O hydrogen bonds. Mol Phys 1998. [DOI: 10.1080/00268979809483187] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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271
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Dretschkow T, Lampner D, Wandlowski T. Structural transitions in 2,2′-bipyridine adlayers on Au(111)—an in-situ STM study 1This paper is dedicated to MJE, who contributed to the manuscript in a special way. 1. J Electroanal Chem (Lausanne) 1998. [DOI: 10.1016/s0022-0728(98)00325-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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272
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Šponer J, Šponer J, Čejka J, Wichterlová B. Theoretical Model of the n-Propylbenzene Formation in the Benzene Isopropylation over Zeolites. An Anti-Markovnikov-Type Proton Addition Promoted by the Steric Effect of MFI and MEL Zeolite Channels. J Phys Chem B 1998. [DOI: 10.1021/jp980637t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judit Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Jiří Čejka
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Blanka Wichterlová
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
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273
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Sundholm D, Sundberg MR, Uggla R. Intermolecular Interactions in p-Chlorobenzoic Acid Dimers. J Phys Chem A 1998. [DOI: 10.1021/jp9813589] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dage Sundholm
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Markku R. Sundberg
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Rolf Uggla
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
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274
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Rak J, Voityuk AA, Rösch N. Splitting of Cyclobutane-Type Uracil Dimer Cation Radicals. Hartree−Fock, MP2, and Density Functional Studies. J Phys Chem A 1998. [DOI: 10.1021/jp981665e] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janusz Rak
- Lehrstuhl für Theoretische Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Alexander A. Voityuk
- Lehrstuhl für Theoretische Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Notker Rösch
- Lehrstuhl für Theoretische Chemie, Technische Universität München, D-85747 Garching, Germany
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275
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Kratochvíl M, Engkvist O, Šponer J, Jungwirth P, Hobza P. Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies. J Phys Chem A 1998. [DOI: 10.1021/jp9816418] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Martin Kratochvíl
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague, Czech Republic
| | - Ola Engkvist
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague, Czech Republic
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague, Czech Republic
| | - Pavel Jungwirth
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague, Czech Republic
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague, Czech Republic
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276
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Bertran J, Oliva A, Rodríguez-Santiago L, Sodupe M. Single versus Double Proton-Transfer Reactions in Watson−Crick Base Pair Radical Cations. A Theoretical Study. J Am Chem Soc 1998. [DOI: 10.1021/ja9804417] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Bertran
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Antonio Oliva
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Luis Rodríguez-Santiago
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Mariona Sodupe
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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277
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Dretschkow T, Wandlowski T. In-situ scanning tunneling microscopy study of uracil on Au(100). Electrochim Acta 1998. [DOI: 10.1016/s0013-4686(98)00040-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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278
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Subramanian V, Sivanesan D, Ramasami T. The role of solvent on the base stacking properties of the stacked cytosine dimer. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)00458-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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279
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Hobza P, Šponer J. Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)00238-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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280
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Suzuki M, Amano N, Kakinuma J, Tateno M. Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. J Mol Biol 1997; 274:421-35. [PMID: 9405150 DOI: 10.1006/jmbi.1997.1406] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The roll-twist-slide correlation in the DNA crystal structures that are collected in the Nucleic Acid Data Base is analyzed in order to obtain a general understanding of the effects of the nucleotide sequence on the 3D structure of a dinucleotide step. It is concluded that the differences between the pyrimidine bases and the purine bases in terms of their physical shapes are the major factors that determine the stereochemical characteristics of the steps through base to backbone and base to base interactions. The characteristics are further modulated by the differences between the A:T and G:C base-pairs, which can be explained by enhancement of the purine-pyrimidine asymmetry in the A:T base-pair.
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Affiliation(s)
- M Suzuki
- AIST-NIBHT, CREST Centre of Structural Biology, Tsukuba, Higashi 1-1, 305, Japan
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281
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Šponer J, Leszczynski J, Hobza P. Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties. J Phys Chem A 1997. [DOI: 10.1021/jp9720404] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- J. 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, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - J. Leszczynski
- 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, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - P. Hobza
- 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, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
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282
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Burda JV, Šponer J, Leszczynski J, Hobza P. Interaction of DNA Base Pairs with Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction. J Phys Chem B 1997. [DOI: 10.1021/jp963753+] [Citation(s) in RCA: 204] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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283
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Johnson RC, Power TD, Holt JS, Immaraporn B, Monat JE, Sissoko AA, Yanik MM, Zagorodny AV, Cybulski SM. Reply to Comment on “Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases”. J Phys Chem B 1997. [DOI: 10.1021/jp970919d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. C. Johnson
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - T. D. Power
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - J. S. Holt
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - B. Immaraporn
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - J. E. Monat
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - A. A. Sissoko
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - M. M. Yanik
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - A. V. Zagorodny
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - S. M. Cybulski
- Department of Chemistry, Miami University, Oxford, Ohio 45056
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284
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Hobza P, Šponer J, Leszczynski J. Comment on “Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases”. J Phys Chem B 1997. [DOI: 10.1021/jp970622f] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague 8, Czech Republic, and Department of Chemistry, Jackson State University, Jakson, Mississippi 39217
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague 8, Czech Republic, and Department of Chemistry, Jackson State University, Jakson, Mississippi 39217
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague 8, Czech Republic, and Department of Chemistry, Jackson State University, Jakson, Mississippi 39217
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285
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Danilov VI, Slyusarchuk ON, Poltev VI, Alderfer JL. Protein-nucleic acid recognition: simulation of base and "model" amino acids complexes in DMSO by the Monte Carlo method. J Biomol Struct Dyn 1997; 15:347-55. [PMID: 9399160 DOI: 10.1080/07391102.1997.10508197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH+), acetic acid in neutral (AcOH) and deprotonated (AcO-) forms, G-AcO-, C-AcOH, and CH(+)-AcO- complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetically favorable. The G-AcO- complex formation is comparable with the formation of G-C base pair in energetically favorability. In this case the acetate anion can replace C in the G-C base pair. The formation of the C-AcOH complex is much less favorable than the formation of the G-C pair. However proton transfer from AcOH to C leads to the formation of the CH(+)-AcO- complex, which is the most favorable of all complexes studied. Here the acetic acid can replace G in a G-C base pair. The formation of G-AcO- and CH(+)-AcO- specific complexes detected in DMSO with the help of experiment and theory is a competitive process with respect to the formation of G-C base pairs, and can be considered the primary step in the real mechanism of protein-nucleic acid recognition.
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Affiliation(s)
- V I Danilov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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286
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McCarthy W, Plokhotnichenko AM, Radchenko ED, Smets J, Smith DMA, Stepanian SG, Adamowicz L. H-Bonded and Stacked Dimers of Pyrimidine and p-Benzoquinone. A Combined Matrix Isolation Infrared and Theoretical ab Initio Study. J Phys Chem A 1997. [DOI: 10.1021/jp971444t] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. McCarthy
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - A. M. Plokhotnichenko
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - E. D. Radchenko
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - J. Smets
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - D. M. A. Smith
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - S. G. Stepanian
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - L. Adamowicz
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, Institute for Low Temperature Physics and Engineering National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine, and Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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287
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Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL. The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 1997; 15:69-80. [PMID: 9283981 DOI: 10.1080/07391102.1997.10508947] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.
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Affiliation(s)
- V I Danilov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
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288
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Hobza P, Kabel�? M, ?poner J, Mejzl�k P, Vondr�?ek J. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19970715)18:9<1136::aid-jcc3>3.0.co;2-s] [Citation(s) in RCA: 243] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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289
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Alhambra C, Luque FJ, Gago F, Orozco M. Ab Initio Study of Stacking Interactions in A- and B-DNA. J Phys Chem B 1997. [DOI: 10.1021/jp962626a] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristóbal Alhambra
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Francisco J. Luque
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Federico Gago
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
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290
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Sponer J, Burda JV, Mejzlík P, Leszczynski J, Hobza P. Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study. J Biomol Struct Dyn 1997; 14:613-28. [PMID: 9130083 DOI: 10.1080/07391102.1997.10508161] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
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291
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292
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On the role of the basis set and electron correlation in the description of stacking interactions. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0097-8485(96)00035-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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293
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Hobza P. Chapter 7. Accurate ab initio calculations on large van der Waals clusters. ACTA ACUST UNITED AC 1997. [DOI: 10.1039/pc093257] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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294
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MP2 and CCSD(T) calculations on Hbonded and stacked formamide…formamide and formamidine…formamidine dimers. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)80025-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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295
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2,4-diselenouracil tautomers: structures, energies, and a comparison with uracil and 2,4-dithiouracil. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)80037-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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296
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Johnson RC, Power TD, Holt JS, Immaraporn B, Monat JE, Sissoko AA, Yanik MM, Zagorodny AV, Cybulski SM. Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp962161o] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. C. Johnson
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - T. D. Power
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - J. S. Holt
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - B. Immaraporn
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - J. E. Monat
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - A. A. Sissoko
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - M. M. Yanik
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - A. V. Zagorodny
- Department of Chemistry, Miami University, Oxford, Ohio 45056
| | - S. M. Cybulski
- Department of Chemistry, Miami University, Oxford, Ohio 45056
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297
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298
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Sponer J, Leszczynski J, Hobza P. Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dyn 1996; 14:117-35. [PMID: 8877568 DOI: 10.1080/07391102.1996.10508935] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. 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.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. J.S.-
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299
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Burda JV, Šponer J, Hobza P. Ab Initio Study of the Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+). ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952941h] [Citation(s) in RCA: 191] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaroslav V. Burda
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
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