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Rasmussen AM, Lind MC, Kim S, Schaefer HF. Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines. J Chem Theory Comput 2010; 6:930-9. [DOI: 10.1021/ct900478c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Rasmussen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Sunghwan Kim
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
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52
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López JC, Alonso JL, Peña I, Vaquero V. Hydrogen bonding and structure of uracil–water and thymine–water complexes. Phys Chem Chem Phys 2010; 12:14128-34. [DOI: 10.1039/c0cp00665c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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53
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Electron density analysis of tautomeric mechanisms of adenine, thymine and guanine and the pairs of thymine with adenine or guanine. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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54
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Vogt N, Dorofeeva OV, Sipachev VA, Rykov AN. Molecular Structure of 9H-Adenine Tautomer: Gas-Phase Electron Diffraction and Quantum-Chemical Studies. J Phys Chem A 2009; 113:13816-23. [DOI: 10.1021/jp905755u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalja Vogt
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Olga V. Dorofeeva
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Victor A. Sipachev
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
| | - Anatolii N. Rykov
- Chemieinformationssysteme, Universität Ulm, 89069 Ulm, Germany, and Department of Chemistry, Moscow State University, Moscow 119992, Russia
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55
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Wincel H. Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1900-1905. [PMID: 19665394 DOI: 10.1016/j.jasms.2009.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 06/28/2009] [Accepted: 06/29/2009] [Indexed: 05/28/2023]
Abstract
Thermochemical data, DeltaH(o)(n), DeltaS(o)(n), and DeltaG(o)(n), for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4-13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
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56
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Cerón-Carrasco JP, Requena A, Zúñiga J, Michaux C, Perpète EA, Jacquemin D. Intermolecular Proton Transfer in Microhydrated Guanine−Cytosine Base Pairs: a New Mechanism for Spontaneous Mutation in DNA. J Phys Chem A 2009; 113:10549-56. [DOI: 10.1021/jp906551f] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | | | | | - C. Michaux
- Laboratorie de Chimie Biologique Structurale, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles, 61, 5000 Namur, Belgium
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57
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Jaeger HM, Schaefer HF. Characterizing radiation-induced oxidation of DNA by way of the monohydrated guanine-cytosine radical cation. J Phys Chem B 2009; 113:8142-8. [PMID: 19445496 DOI: 10.1021/jp900444k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of one water molecule with the guanine-cytosine radical cation has been studied with ab initio and density functional methods in order to help elucidate the nature of oxidized aqueous DNA. The theoretical spin density of [GC]*(+) reveals that the radical center is localized on guanine. The adiabatic ionization potential lowers from 7.63 to 6.71 eV in concurrence with the formation of the Watson-Crick base pair and hydration by one water molecule. A natural bond orbital analysis of partial charges shows that approximately 80% of the positive charge persists on guanine upon hydration and formation of the Watson-Crick base pair with cytosine. Hydration energies were computed with second-order Z-averaged perturbation theory (ZAPT2) using the aug-cc-pVDZ basis set at 11 stationary points on the B3LYP/DZP++ potential energy surface. The hydration energy at the global minimum is 14.2 kcal mol(-1). The lowest energy structures correspond to hydration near the glycosidic bond sites. Structural changes in the Watson-Crick base pair are predominantly seen for monohydration in the groove regions of double-helix DNA.
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Affiliation(s)
- Heather M Jaeger
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2556, USA.
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58
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Cerón-Carrasco JP, Requena A, Michaux C, Perpète EA, Jacquemin D. Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair. J Phys Chem A 2009; 113:7892-8. [DOI: 10.1021/jp900782h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - C. Michaux
- Laboratorie de Chimie Biologique Structurale, Facultés Universitaires Notre-Dame de la Paix Rue de Bruxelles, 61. 5000 Namur, Belgium
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59
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Zelený T, Hobza P, Kabelác M. Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium. Phys Chem Chem Phys 2009; 11:3430-5. [PMID: 19421545 DOI: 10.1039/b819350a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The potential energy surfaces of guanine...cytosine complexes and microhydrated guanine...cytosine (one and two water molecules) were investigated by the molecular dynamics/quenching method (MD/Q), using the empirical potential Parm94 force field, implemented in the Amber program package. The calculations were conducted for all the possible combinations of the four most stable tautomers of guanine and three of cytosine (covering the canonical forms in both cases). The obtained structures were sorted by their structural motifs into three main groups: planar hydrogen-bonded; stacked; and T-shaped structures. The most stable structures found at the empirical potential energy surfaces were fully reoptimised at the second-order Møller-Plesset perturbation theory as well as using the density functional method with an empirical dispersion term (DFT-D). A combination of the canonical form of guanine and cytosine and canonical cytosine with a guanine tautomer where the hydrogen is switched from position N9 to N7 are energetically preferred in microsolvated systems as well as those without the presence of a solvent. The rising number of water molecules leads to smaller differences between the stability of the various combinations of the tautomers of bases in the base pairs. For some of the tautomer combinations (mainly the enol-enol combination), two water molecules are sufficient for the preference of stacked structures over the H-bonded ones. The interaction energies and geometries obtained by the second-order Møller-Plesset perturbation theory method and the much less computationally demanding DFT-D method are comparable, except for stacked complexes, where the interaction energies are overestimated on average by 3 kcal mol(-1) at the MP2 level.
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Affiliation(s)
- Tomás Zelený
- Department of Physical Chemistry, Faculty of Sciences, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic.
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60
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González-Vázquez J, González L, Samoylova E, Schultz T. Thymine relaxation after UV irradiation: the role of tautomerization and πσ* states. Phys Chem Chem Phys 2009; 11:3927-34. [DOI: 10.1039/b815602f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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61
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Chi LM, Lam SL. Nuclear magnetic resonance investigation of primer--template models: formation of a pyrimidine bulge upon misincorporation. Biochemistry 2008; 47:4469-76. [PMID: 18358004 DOI: 10.1021/bi8001456] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our previous studies have shown that misaligned structures can occur upon misincorporation of a dNTP opposite thymine templates. The formation of misaligned structures during DNA replication, if not repaired properly, can be bypassed and extended by low-fidelity polymerases and ultimately lead to mutations. In this study, the base pair structures at the replicating sites of a set of primer-template models which mimic the situation upon misincorporation of a dNTP opposite cytosine templates have been determined. High-resolution NMR structural results show that misaligned structures with a C-bulge can be formed upon incorporation of dCTP, dTTP, and dATP opposite 5'-GC, 5'-AC, and 5'-TC templates, respectively. The stabilities of misaligned structures depend on the types of terminal base pairs at the replicating sites. Together with the structural findings in thymine templates, we conclude that terminal G.C and C.G base pairs always contribute a larger stabilizing effect to the misaligned structures containing a pyrimidine bulge than terminal A.T and T.A base pairs. Misalignment and thus deletion mutation are more likely to occur if misincorporation of a nucleotide opposite a pyrimidine template can cause template slippage to form a terminal G.C or C.G base pair. Although misalignment also occurs when the newly formed terminal base pair is an A.T base pair or a T.A base pair, both misaligned and mismatched conformers coexist, which can lead to deletion and substitution mutations, respectively.
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Affiliation(s)
- Lai Man Chi
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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62
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Theoretical investigation (DFT and MP2) of the intermolecular proton transfer in the supersystems uracil-(H2O) n and uracil-(CH3OH) n (n = 1, 2). MONATSHEFTE FUR CHEMIE 2008. [DOI: 10.1007/s00706-007-0831-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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63
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Improta R. The excited states of π-stacked 9-methyladenine oligomers: a TD-DFT study in aqueous solution. Phys Chem Chem Phys 2008; 10:2656-64. [DOI: 10.1039/b718562f] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Crespo-Hernandez CE, Close DM, Gorb L, Leszczynski J. Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues. J Phys Chem B 2007; 111:5386-95. [PMID: 17447808 DOI: 10.1021/jp0684224] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.
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Affiliation(s)
- Carlos E Crespo-Hernandez
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
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