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Abstract
Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo, Prague, Czech Republic
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2
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GALETICH I, STAPANIAN SG, SHELKOVSKY V, KOSEVICH M, ADAMOWICZ L. Mass spectrometric andab initiostudy of the interaction between 9-methylguanine and amino acid amide group. Mol Phys 2002. [DOI: 10.1080/00268970210149740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Galetich I, Stepanian SG, Shelkovsky V, Kosevich M, Blagoi, Adamowicz L. Structures and Interaction Energies of Nucleic Acid Base−Amino Acid Complexes. Methylcytosines−Acrylamide Model. J Phys Chem B 1999. [DOI: 10.1021/jp990990e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- I. Galetich
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
| | - S. G. Stepanian
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
| | - V. Shelkovsky
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
| | - M. Kosevich
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
| | - Blagoi
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
| | - L. Adamowicz
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Institute for Low-Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, Kharkov 310164, Ukraine
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Gorb L, Podolyan Y, Leszczynski J. A theoretical investigation of tautomeric equilibria and proton transfer in isolated and monohydrated cytosine and isocytosine molecules. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(99)00139-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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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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6
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Galetich I, Kosevich M, Shelkovsky V, Stepanian S, Blagoi Y, Adamowicz L. Structure and energy of nucleic acid base–amino acid complexes: 1. 1-methyl-uracil-acrylamide. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00756-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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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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Kosevich MV, Shelkovsky VS, Stepanian SG. Dependence of the biological activity and mass spectrometric pattern on the structure peculiarities of the molecule of alkylating drug thiotepa. Biophys Chem 1996; 57:123-31. [PMID: 17023335 DOI: 10.1016/0301-4622(95)00053-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/1994] [Revised: 02/28/1995] [Accepted: 02/28/1995] [Indexed: 11/25/2022]
Abstract
Structural and electronic parameters of the chemotherapeutic alkylating drug thiotepa obtained by MNDO and MINDO/3 quantum mechanical calculations are used to explain some physical, chemical and biological properties of this compound. On the basis of the revealed difference between the preferential conformations of the thiotepa molecule in crystal and vacuum, a conclusion is made concerning the precautions in the choice of the appropriate molecular geometry in the search of structure-activity correlations. The theoretical data are also applied to the explanation of some peculiarities of soft ionization mass spectra of thiotepa, in particular its sensitivity to high field effects and the absence of protonation. The modeling of some reactions of thiotepa directly in the conditions of field ionization mass spectrometric experiment is discussed.
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Affiliation(s)
- M V Kosevich
- B. Verkin Institute for Low Temperature Physics and Engineering of the Academy of Sciences of Ukraine, Lenin Ave. 47, Kharkov 310164, Ukraine
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Zielenkiewicz W, Zielenkiewicz A, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases. VIII. Enthalpies of hydration of 6-alkyluracils. J SOLUTION CHEM 1993. [DOI: 10.1007/bf00647721] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Sukhodub LF, Teplitsky AB. Associate hydrations and energies of nucleotide bases as revealed by low-temperature field ionization mass-spectrometric data. J Biomol Struct Dyn 1991; 8:889-907. [PMID: 2059345 DOI: 10.1080/07391102.1991.10507851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The formation of water clusters, polyhydrates of nucleotide bases and their associates during simultaneous condensation of water and base molecules in vacuo onto a surface of a needle emitter cooled to 170 K was studied by field ionization mass spectrometry. It was found that different emitter temperatures are characterized by a specific distribution of intensities of cluster currents, depending on the number of water molecules in clusters. These distributions correlate with structural peculiarities and the relative energetics of formation of water clusters, polyhydrates of nucleotide bases and their associates at low temperature. The features observed in mass spectra for clusters m9Ade (H2O)5, m1Ura (H2O)4 and m9Ade m1Ura (H2O)2 are treated as a result of formation of energetically favorable structures stabilized by H-bonded bridges of water molecules. The relative association constants and formation enthalpies of the noncomplementary pairs Ade Cyt, Gua Ura and the associates which model the aminoacid-base complexes m1Ura Gln and m1.3(2)Thy Gln were determined from the temperature dependencies of the intensities of mass spectra peaks in the range 290-320 K.
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Affiliation(s)
- L F Sukhodub
- Applied Physics Division, Ukrainian Academy of Sciences, Sumy, USSR
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Zielenkiewicz A, Zielenkiewicz W, Sukhodub LF, Glukhova OT, Teplitsky AB, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases V. Enthalpies of hydration of N-methylated adenines. J SOLUTION CHEM 1984. [DOI: 10.1007/bf00647691] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Poltev VI, Grokhlina TI, Malenkov GG. Hydration of nucleic acid bases studied using novel atom-atom potential functions. J Biomol Struct Dyn 1984; 2:413-29. [PMID: 6400943 DOI: 10.1080/07391102.1984.10507576] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contains terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases - uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecular interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interactions play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by "bridges" formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.
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Affiliation(s)
- V I Poltev
- Institute of Biological Physics, USSR Academy of Sciences, Moscow Region
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Sukhodub LF, Shelkovski VS, Wierzchowski KL. Mass-spectrometric investigations on hydration of nucleic acid components in vacuum. II. N-methylated adenines. Biophys Chem 1984; 19:191-200. [PMID: 6722272 DOI: 10.1016/0301-4622(84)87001-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Association reactions between water and N-methylated adenines (M), occurring under field-ionization conditions in a mass spectrometer at the tungsten point emitter surface, were studied at a number of temperatures. The origin of the peaks observed in the mass spectra at m/e ratios corresponding to MH+ was assigned to M X H2O monohydrates , of those corresponding to (MH X H2O)+ and (MH2)2+ to double hydrates M(H2O)3. Measurements of the relative peak intensities allowed calculation of apparent equilibrium constants, Kass, for successive hydration steps, and hence the respective van't Hoff enthalpies of hydration. Both the equilibrium and the energy parameters obtained support the available quantum-mechanical single-layer hydration schemes of adenine and of its N-methylated derivatives.
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