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Abyar F, Novak I. Investigation on the electronic structures of thiamine and related compounds: Free base or salt? J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2
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Eichler DR, Hamann HA, Harte KA, Papadantonakis GA. Hydration effects on the photoionization energy of 2′-deoxyguanosine 5′-phosphate and activation barriers for guanine methylation by carcinogenic methane diazonium ions. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Dracínský M, Pohl R. Determination of the Nucleic Acid Adducts Structure at the Nucleoside/Nucleotide Level by NMR Spectroscopy. Chem Res Toxicol 2016; 28:155-65. [PMID: 25584790 DOI: 10.1021/tx5004535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All living organisms are exposed to xenobiotics from the environment. The exposure can lead to the formation of covalent adducts of xenobiotics or their metabolites with nucleic acids (NAs).The knowledge of NA adduct structure provides valuable information n the mechanism of carcinogenesis on a molecular level. While NMR spectroscopy is extremely successful in structural analysis of many classes of molecules ranging from small inorganic and organic molecules to large biomacromolecules, the structural analysis of NA adducts by NMR spectroscopy is accompanied by some challenges. First, the structural diversity of the adducts is very large; the electrophilic species generated from the metabolism of xenobiotics can attack various atoms of the nucleobases, and new rings are frequently formed. The second challenge in the DNA adducts structure determination is the low sensitivity of NMR spectroscopy and low amount of the adducts isolated from in vivo experiments. Recent developments of NMR hardware and experimental methods have led, however, to unprecedented sensitivity. This contribution reviews NMR techniques that are commonly applied in the determination of nucleic acid adducts structure at the nucleoside/nucleotide level. These NMR techniques and the large structural heterogeneity of NA adducts are demonstrated on recent examples (mostly published after 2000) of NA adducts structure determined by NMR. Most of the examples report 2′-deoxyribonucles(t)ide derivatives, but RNA adducts are also briefly discussed. The influence of the formation of NA adducts on nucleoside conformation (particularly syn/anti orientation of the base) is also demonstrated on recent examples.
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Angelé-Martínez C, Goodman C, Brumaghim J. Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences. Metallomics 2014; 6:1358-81. [DOI: 10.1039/c4mt00057a] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.
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Affiliation(s)
| | - Craig Goodman
- Department of Chemistry
- Clemson University
- Clemson, USA
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Weber JM, Marcum J, Nielsen SB. UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation Channels, Time Scales, and Electronic Spectra. PHOTOPHYSICS OF IONIC BIOCHROMOPHORES 2013. [DOI: 10.1007/978-3-642-40190-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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6
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Rosenberg E, Kumar R. New methods for functionalizing biologically important molecules using triosmium metal clusters. Dalton Trans 2012; 41:714-22. [DOI: 10.1039/c1dt11173f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Selvam L, Chen FF, Wang F. Methylation of zebularine investigated using density functional theory calculations. J Comput Chem 2011; 32:2077-83. [PMID: 21541952 DOI: 10.1002/jcc.21785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 12/01/2010] [Accepted: 02/10/2011] [Indexed: 11/09/2022]
Abstract
Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1-(β-D-ribofuranosyl)-2-pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1-(β-D-ribofuranosyl)-5-methyl-2-pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital-based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine.
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Affiliation(s)
- Lalitha Selvam
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, Hawthorn, Melbourne, Victoria 3122 Australia
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8
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Cauët E, Valiev M, Weare JH. Vertical ionization potentials of nucleobases in a fully solvated DNA environment. J Phys Chem B 2010; 114:5886-94. [PMID: 20394358 DOI: 10.1021/jp9120723] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.; et al. J. Am. Chem. Soc. 2009, 131, 6460). In a first step, a high level of theory, CCSD(T)/aug-cc-pVDZ, was used to calculate the vertical IP of each of the four single bases isolated in the QM region while the remaining DNA fragment, counterions, and water solvent molecules were included in the MM region. The calculated vertical IPs show a large positive shift of 3.2-3.3 eV compared to the corresponding gas-phase values. This shift is similar for all four DNA bases. The origin of the large increase in vertical IPs of nucleobases is found to be the long-range electrostatic interactions with the solvation structure outside the DNA helix. Thermal fluctuations in the fluid can result in IP changes of roughly 1 eV on a picosecond time scale. IPs of pi-stacked and H-bonded clusters of DNA bases were also calculated using the same QM/MM model but with a lower level of theory, B3LYP/6-31G(d=0.2). An IP shift of 4.02 eV relative to the gas phase is found for a four-base-pair B-DNA duplex configuration. The primary goal of this work was to estimate the influence of long-range solvation interactions on the ionization properties of DNA bases rather than provide highly precise IP evaluations. The QM/MM model presented in this work provides an attractive method to treat the difficult problem of incorporating a detailed long-range structural model of physiological conditions into investigations of the electronic processes in DNA.
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Affiliation(s)
- Emilie Cauët
- Chemistry and Biochemistry Department, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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Yokojima S, Yoshiki N, Yanoi W, Okada A. Solvent effects on ionization potentials of guanine runs and chemically modified guanine in duplex DNA: effect of electrostatic interaction and its reduction due to solvent. J Phys Chem B 2010; 113:16384-92. [PMID: 19947608 PMCID: PMC2825092 DOI: 10.1021/jp9054582] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used.
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Affiliation(s)
- Satoshi Yokojima
- Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, 332-0012 Japan
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10
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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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11
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Ramos MMD, Correia HMG. Modelling the effect of structure and base sequence on DNA molecular electronics. NANOTECHNOLOGY 2008; 19:375202. [PMID: 21832544 DOI: 10.1088/0957-4484/19/37/375202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA.
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Affiliation(s)
- M M D Ramos
- Departamento de Física, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Ekanayake KS, Lebreton PR. Model transition states for methane diazonium ion methylation of guanine runs in oligomeric DNA. J Comput Chem 2007; 28:2352-65. [PMID: 17476668 DOI: 10.1002/jcc.20754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The DNA reaction pattern of the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, was examined at N7 and O(6) sites in guanine runs occurring in oligonucleotides and model oligonucleotides. Density functional B3LYP/6-31G*, and SCF 3-21G and STO-3G energies of model transition states were calculated in the gas phase and in the CPCM reaction field. For nucleotides containing two, three, and four stacked guanines with counterions in the gas phase, O(6) reactivity is greater than N7 reactivity. In the reaction field, N7 reactivity is 9.0 to 9.8 times greater than O(6) reactivity. For a double-stranded oligonucleotide containing two stacked guanines with counterions in the reaction field, the N7 and O(6) reactivities of the 3'-guanine are 3.9 times greater than the corresponding sites in the 5'-guanine. For double-stranded oligonucleotides with three or four stacked guanines and counterions, the reactivities of the interior guanines are higher than corresponding reactivities of guanines at the ends. These reaction patterns agree with most of the available experimental data. Activation energy decomposition analysis for gas-phase reactions in a double-stranded dinucleotide containing two stacked guanines with counterions indicates that selectivity at O(6) is almost entirely due to electrostatic forces. Selectivity at N7 also has a large electrostatic interaction. However, the orbital interaction also contributes significantly to the gas-phase selectivity, accounting for 32% of the total interaction energy difference between the 3'- and 5'-guanine reactions. In aqueous solution, the relative orbital contribution to N7 selectivity is likely to be larger.
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14
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Berashevich JA, Chakraborty T. Energy contribution of the solvent to the charge migration in DNA. J Chem Phys 2007; 126:035104. [PMID: 17249903 DOI: 10.1063/1.2428304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The authors have investigated the interactions of the reaction centers, participating in the charge transfer reaction within the DNA molecule with the phosphate backbones and the solvent molecules, and have estimated the contribution of these interactions into the charge migration in DNA. They have determined the unequal shift of the energy surfaces of the initial and final transition states of the transfer reaction along the energy axis and the dependence of the magnitude of the energy shift on the nature of the reaction centers and the surrounding environment. The nonuniform distribution of the negative charge in the DNA phosphate backbones results in an increase of the positive shift of the energy surface of the DNA base pairs in the center of the structure, where the maximum density of the negative charge is concentrated. Localization of the positive charge on the guanine and the adenine in the DNA base pairs in the oxidized state results in a dependence of the free energy of reaction in the solvent on the pair sequences and their arrangement in the DNA chain. As an example, for the G-C/A-T configuration the positive charges are localized on the same strand that results in a decrease of the free energy of reaction in the solvent for charge migration from G-C to A-T pair by 0.125 eV.
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Affiliation(s)
- Julia A Berashevich
- Department of Physics and Astronomy, The University of Manitoba, Winnipeg R3T 2N2, Canada
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Markovitsi D, Onidas D, Talbot F, Marguet S, Gustavsson T, Lazzarotto E. UVB/UVC induced processes in model DNA helices studied by time-resolved spectroscopy: Pitfalls and tricks. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2006.05.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Starikov EB, Fujita T, Watanabe H, Sengoku Y, Tanaka S, Wenzel W. Effects of molecular motion on charge transfer/transport through DNA duplexes with and without base pair mismatch. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020600835673] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Marguet S, Markovitsi D, Talbot F. One- and Two-Photon Ionization of DNA Single and Double Helices Studied by Laser Flash Photolysis at 266 nm. J Phys Chem B 2006; 110:11037-9. [PMID: 16771360 DOI: 10.1021/jp062578m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ionization of the DNA single and double helices (dA)20, (dT)20, (dAdT)10(dAdT)10 and (dA)20(dT)20, induced by nanosecond pulses at 266 nm, is studied by time-resolved absorption spectroscopy. The variation of the hydrated electron concentration with the absorbed laser intensity shows that, in addition to two-photon ionization, one-photon ionization takes place for (dAdT)10(dAdT)10, (dA)20(dT)20 and (dA)20 but not for (dT)20. The spectra of all adenine-containing oligomers at the microsecond time-scale correspond to the adenine deprotonated radical formed in concentrations comparable to that of the hydrated electron. The quantum yield for one-photon ionization of the oligomers (ca. 10(-3)) is higher by at least 1 order of magnitude than that of dAMP, showing clearly that organization of the bases in single and double helices leads to an important lowering of the ionization potential. The propensity of (dAdT)10(dAdT)10, containing alternating adenine-thymine sequences, to undergo one-photon ionization is lower than that of (dA)20(dT)20 and (dA)20, containing adenine runs. Pairing of the (dA)20 with the complementary strand leads to a decrease of quantum yield for one photon ionization by about a factor of 2.
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Okamoto A. Synthesis of Highly Functional Nucleic Acids and Their Application to DNA Technology. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2005. [DOI: 10.1246/bcsj.78.2083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yang X, Wang XB, Vorpagel ER, Wang LS. Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy. Proc Natl Acad Sci U S A 2004; 101:17588-92. [PMID: 15591345 PMCID: PMC539719 DOI: 10.1073/pnas.0405157101] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Indexed: 11/18/2022] Open
Abstract
Photodetachment photoelectron spectroscopy is used to probe the electronic structure of mono-, di-, and trinucleotide anions in the gas phase. A weak and well defined threshold band was observed in the photoelectron spectrum of 2'-deoxyguanosine 5'-monophosphate at a much lower ionization energy than the other three mononucleotides. Density function theory calculations revealed that this unique spectral feature is caused by electron-detachment from a pi orbital of the guanine base on 2'-deoxyguanosine 5'-monophosphate, whereas the lowest ionization channel for the other three mononucleotides takes place from the phosphate group. This low-energy feature was shown to be a "fingerprint" in all the spectra of dinucleotides and trinucleotides that contain the guanine base. The current experiment provides direct spectroscopic evidence that the guanine base is the site with the lowest ionization potential in oligonucleotides and DNA and is consistent with the fact that guanine is most susceptible to oxidation to give the guanine cation in DNA damage.
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Affiliation(s)
- Xin Yang
- Department of Physics, Washington State University, 2710 University Drive, Richland, WA 99352, USA
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Yokojima S, Yanoi W, Yoshiki N, Kurita N, Tanaka S, Nakatani K, Okada A. Solvent Effects on the Suppression of Oxidative Decomposition of Guanines by Phenyl Group Attachment in Deoxyribonucleic Acid (DNA). J Phys Chem B 2004. [DOI: 10.1021/jp037845s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Satoshi Yokojima
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Wataru Yanoi
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Norifumi Yoshiki
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Noriyuki Kurita
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Shigenori Tanaka
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Kazuhiko Nakatani
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
| | - Akira Okada
- Japan Science and Technology Corporation (JST), 4-1-8 Honcho, Kawaguchi 332-0012, Japan, Institute of Materials Science, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba 305-8573, Japan, Department of Knowledge-Based, Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, Advanced Materials and Devices Laboratory, Toshiba R&D Center, Kawasaki 212-8582, Japan, Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University,
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Fukuzumi S, Nishimine M, Ohkubo K, Tkachenko NV, Lemmetyinen H. Driving Force Dependence of Photoinduced Electron Transfer Dynamics of Intercalated Molecules in DNA. J Phys Chem B 2003. [DOI: 10.1021/jp035023p] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, CREST, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan, and The Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland
| | - Mari Nishimine
- Department of Material and Life Science, Graduate School of Engineering, CREST, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan, and The Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland
| | - Kei Ohkubo
- Department of Material and Life Science, Graduate School of Engineering, CREST, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan, and The Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland
| | - Nikolai V. Tkachenko
- Department of Material and Life Science, Graduate School of Engineering, CREST, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan, and The Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland
| | - Helge Lemmetyinen
- Department of Material and Life Science, Graduate School of Engineering, CREST, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan, and The Institute of Materials Chemistry, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland
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Freccero M, Gandolfi R, Sarzi-Amadè M. Selectivity of purine alkylation by a quinone methide. Kinetic or thermodynamic control? J Org Chem 2003; 68:6411-23. [PMID: 12895079 DOI: 10.1021/jo0346252] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alkylation reaction of 9-methyladenine and 9-methylguanine (as prototype substrates of deoxy-adenosine and -guanosine), by the parent o-quinone methide (o-QM), has been investigated in the gas phase and in aqueous solution, using density functional theory at the B3LYP/6-311+G(d,p) level. The effect of the medium on the reactivity, and on the stability of the resulting adducts, has been investigated by using the C-PCM solvation model to assess which adduct arises from the kinetically favorable path, or from an equilibrating process. The calculations indicate that the most nucleophilic site of the methyl-substituted nucleobases in the gas phase is the guanine oxygen atom (O(6)) (DeltaG()(gas) = 5.6 kcal mol(-)(1)), followed by the adenine N1 (DeltaG)(gas) = 10.3 kcal mol(-)(1)), while other centers exhibit a substantially lower nucleophilicity. The bulk effect of water as a solvent is the dramatic reduction of the nucleophilicity of both 9-methyladenine N1 (DeltaG)(solv) = 14.5 kcal mol(-)(1)) and 9-methylguanine O(6) (DeltaG)(solv) = 17.0 kcal mol(-)(1)). As a result there is a reversal of the nucleophilicity order of the purine bases. While O(6) and N7 nucleophilic centers of 9-methylguanine compete almost on the same footing, the reactivity gap between N1 and N7 of 9-methyladenine in solution is highly reduced. Regarding product stability, calculations predict that only two of the adducts of o-QM with 9-methyladenine, those at NH(2) and N1 positions, are lower in energy than reactants, both in the gas phase and in water. However, the adduct at N1 can easily dissociate in water. The adducts arising from the covalent modification of 9-methylguanine are largely more stable than reactants in the gas phase, but their stability is markedly reduced in water. In particular, the oxygen alkylation adduct becomes slightly unstable in water (DeltaG(solv) = +1.4 kcal mol(-)(1)), and the N7 alkylation product remains only moderately more stable than free reactants (DeltaG(solv) = -2.8 kcal mol(-)(1)). Our data show that site alkylations at the adenine N1 and the guanine O(6) and N7 in water are the result of kinetically controlled processes and that the selective modification of the exo-amino groups of guanine N2 and adenine N6 are generated by thermodynamic equilibrations. The ability of o-QM to form several metastable adducts with purine nucleobases (at guanine N7 and O(2), and adenine N1) in water suggests that the above adducts may act as o-QM carriers.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, Viale Taramelli 10, 27100 Pavia, Italy.
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Yoshioka Y, Kawai H, Sato T, Yamaguchi K, Saito I. Ab initio molecular orbital study on the G-selectivity of GGG triplet in copper(I)-mediated one-electron oxidation. J Am Chem Soc 2003; 125:1968-74. [PMID: 12580624 DOI: 10.1021/ja028039m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The G-selectivity for Cu(I)-mediated one-electron oxidation of 5'-TG(1)G(2)G(3)-3' and 5'-CG(1)G(2)G(3)-3' has been examined by ab initio molecular orbital calculations. It was confirmed that G(1) is selectively damaged by Cu(I) ion for both 5'-TG(1)G(2)G(3)-3' and 5'-CG(1)G(2)G(3)-3', being good agreement with experimental results. The Cu(I)-mediated G(1)-selectivity is primarily due to the stability of the Cu(I)-coordinated complex, [-XG(1)G(2)G(3)-,-Cu(I)(H(2)O)(3)](+). The Cu(I) ion coordinates selectively to N7 of G(2) of 5'-G(1)G(2)G(3)-3' rather than N7 of G(1). The G(2)-selective coordination induces the G(1)-selective trap of a hole that is created by one-electron oxidation and migrates to GGG triplet. Therefore, the radical cation of G(1) is selectively created in both 5'-TG(1)G(2)G(3)-3' and 5'-CG(1)G(2)G(3)-3', giving the G(1)-selective damage of 5'-G(1)G(2)G(3)-3'.
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Affiliation(s)
- Yasunori Yoshioka
- Chemistry Department for Materials, Faculty of Engineering, Mie University, Tsu, Mie 514-8507, Japan.
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Li X, Cai Z, Sevilla MD. Energetics of the Radical Ions of the AT and AU Base Pairs: A Density Functional Theory (DFT) Study. J Phys Chem A 2002. [DOI: 10.1021/jp021322n] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xifeng Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Zhongli Cai
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - M. D. Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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