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Markovitsi D. Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors. Photochem Photobiol 2024; 100:262-274. [PMID: 37365765 DOI: 10.1111/php.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.
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Affiliation(s)
- Dimitra Markovitsi
- CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, Orsay, France
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2
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Ling CCH, Chan WX, Siow JX, Loh ZH. Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment. J Phys Chem A 2024; 128:626-635. [PMID: 38207335 DOI: 10.1021/acs.jpca.3c08232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.
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Affiliation(s)
- Christine Chun Hui Ling
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Wei Xin Chan
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Jing Xuan Siow
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Zhi-Heng Loh
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
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3
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Balanikas E, Martinez-Fernandez L, Improta R, Podbevšek P, Baldacchino G, Markovitsi D. The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization. J Phys Chem Lett 2021; 12:8309-8313. [PMID: 34428044 DOI: 10.1021/acs.jpclett.1c01846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Guanine quadruplexes are four-stranded DNA/RNA structures composed of a guanine core (vertically stacked guanine tetrads) and peripheral groups (dangling ends and/or loops). Such a dual structural arrangement of the nucleobases favors their photoionization at energies significantly lower than the guanine ionization potential. This effect is important with respect to the oxidative DNA damage and for applications in the field of optoelectronics. Photoionization quantum yields, determined at 266 nm by nanosecond transient absorption spectroscopy, strongly depend on both the type and position of the peripheral nucleobases. The highest value (1.5 × 10-2) is found for the tetramolecular structure (AG4A)4 in which adenines are intermittently stacked on the adjacent guanine tetrads, as determined by nuclear magnetic resonance spectroscopy. Quantum chemistry calculations show that peripheral nucleobases interfere in a key step preceding electron ejection: charge separation, initiated by the population of charge transfer states during the relaxation of electronic excited states.
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Affiliation(s)
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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4
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D'Annibale V, Nardi AN, Amadei A, D'Abramo M. Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution. J Chem Theory Comput 2021; 17:1301-1307. [PMID: 33621084 PMCID: PMC8028051 DOI: 10.1021/acs.jctc.0c00728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we present the theoretical-computational modeling of the oxidation properties of four DNA nucleosides and nucleotides and a set of dinucleotides in solutions. Our estimates of the vertical ionization energies and reduction potentials, close to the corresponding experimental data, show that an accurate calculation of the molecular electronic properties in solutions requires a proper treatment of the effect of the environment. In particular, we found that the effect of the environment is to stabilize the oxidized state of the nucleobases resulting in a remarkable reduction-up to 6.6 eV-of the energy with respect to the gas phase. Our estimates of the aqueous and gas-phase vertical ionization energies, in good agreement with photoelectron spectroscopy experiments, also show that the effect on the reduction potential of the phosphate group and of the additional nucleotide in dinucleotides is rather limited.
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Affiliation(s)
| | | | - Andrea Amadei
- Department of Chemical Sciences and Technology, Tor Vergata University, Rome 00133, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
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5
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Balanikas E, Banyasz A, Douki T, Baldacchino G, Markovitsi D. Guanine Radicals Induced in DNA by Low-Energy Photoionization. Acc Chem Res 2020; 53:1511-1519. [PMID: 32786340 DOI: 10.1021/acs.accounts.0c00245] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanine (G) radicals are precursors to DNA oxidative damage, correlated with carcinogenesis and aging. During the past few years, we demonstrated clearly an intriguing effect: G radicals can be generated upon direct absorption of UV radiation with energy significantly lower than the G ionization potential. Using nanosecond transient absorption spectroscopy, we studied the primary species, ejected electrons and guanine radicals, which result from photoionization of various DNA systems in aqueous solution.The DNA propensity to undergo electron detachment at low photon energies greatly depends on its secondary structure. Undetected for monomers or unstacked oligomers, this propensity may be 1 order of magnitude higher for G-quadruplexes than for duplexes. The experimental results suggest nonvertical processes, associated with the relaxation of electronic excited states. Theoretical studies are required to validate the mechanism and determine the factors that come into play. Such a mechanism, which may be operative over a broad excitation wavelength range, explains the occurrence of oxidative damage observed upon UVB and UVA irradiation.Quantification of G radical populations and their time evolution questions some widespread views. It appears that G radicals may be generated with the same probability as pyrimidine dimers, which are considered to be the major lesions induced upon absorption of low-energy UV radiation by DNA. As most radical cations undergo deprotonation, the vast majority of the final reaction products is expected to stem from long-lived deprotonated radicals. Consequently, when G radical cations are involved, the widely used oxidation marker 8-oxodG is not representative of the oxidative damage.Beyond the biological consequences, photogeneration of electron holes in G-quadruplexes may inspire applications in nanoelectronics; although four-stranded structures are currently studied as molecular wires, their behavior as photoconductors has not been explored so far.In the present Account, after highlighting some key experimental issues, we first describe the photoionization process, and then, we focus on radicals. We use as show-cases new results obtained for genomic DNA and Oxytricha G-quadruplexes. Generation and reaction dynamics of G radicals in these systems provide a representative picture of the phenomena reported previously for duplexes and G-quadruplexes, respectively.
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Affiliation(s)
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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6
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Chakraborty R, Bose S, Ghosh D. Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study. J Comput Chem 2017; 38:2528-2537. [PMID: 28856705 DOI: 10.1002/jcc.24913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/11/2022]
Abstract
Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02-0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rahul Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Samik Bose
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debashree Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
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Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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Cadet J, Mouret S, Ravanat JL, Douki T. Photoinduced damage to cellular DNA: direct and photosensitized reactions. Photochem Photobiol 2012; 88:1048-65. [PMID: 22780837 DOI: 10.1111/j.1751-1097.2012.01200.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The survey focuses on recent aspects of photochemical reactions to cellular DNA that are implicated through the predominant formation of mostly bipyrimidine photoproducts in deleterious effects of human exposure to sunlight. Recent developments in analytical methods have allowed accurate and quantitative measurements of the main DNA photoproducts in cells and human skin. Highly mutagenic CC and CT bipyrimidine photoproducts, including cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) are generated in low yields with respect to TT and TC photoproducts. Another striking finding deals with the formation of Dewar valence isomers, the third class of bipyrimidine photoproducts that is accounted for by UVA-mediated isomerization of initially UVB generated 6-4PPs. Cyclobutadithymine (T<>T) has been unambiguously shown to be involved in the genotoxicity of UVA radiation. Thus, T<>T is formed in UVA-irradiated cellular DNA according to a direct excitation mechanism with a higher efficiency than oxidatively generated DNA damage that arises mostly through the Type II photosensitization mechanism. C<>C and C<>T are repaired at rates intermediate between those of T<>T and 6-4TT. Evidence has been also provided for the occurrence of photosensitized reactions mediated by exogenous agents that act either in an independent way or through photodynamic effects.
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Affiliation(s)
- Jean Cadet
- Laboratoire Lésions des Acides Nucléiques, SCIB-UMR-E n°3, CEA/UJF, Institut Nanosciences et Cryogénie, CEA/Grenoble, Grenoble Cedex, France
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9
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Abstract
Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.
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Affiliation(s)
- Miral Dizdaroglu
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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10
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Ariza-Mateos A, Prieto-Vega S, Díaz-Toledano R, Birk A, Szeto H, Mena I, Berzal-Herranz A, Gómez J. RNA self-cleavage activated by ultraviolet light-induced oxidation. Nucleic Acids Res 2011; 40:1748-66. [PMID: 21989404 PMCID: PMC3287179 DOI: 10.1093/nar/gkr822] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A novel UV-C-light-induced ribozyme activity was discovered within the highly structured 5'-genomic regions of both Hepatitis C Virus (HCV) and the related Classic Swine Fever Virus (CSFV). Cleavage is mediated by exposure to UV-C light but not by exogenous oxygen radicals. It is also very selective, occurring at base positions HCV C(79) and CSFV A(45) in some molecules and at the immediately adjacent 5'-positions HCV U(78) and CSFV U(44) in others. Among other reaction products, the majority of biochemically active products detected contained 3'-phosphate and 5'-phosphate-end groups at the newly generated termini, along with a much lower amount of 3'-hydroxyl end group. While preservation of an E-loop RNA structure in the vicinity of the cleavage site was a requisite for HCV RNA self-cleavage, this was not the case for CSFV RNA. The short size of the reactive domains (~33 nt), which are compatible with primitive RNA motifs, and the lack of sequence homology, indicate that as-yet unidentified UV-activated ribozymes are likely to be found throughout structured RNAs, thereby providing clues to whether early RNA self-cleavage events were mediated by photosensitive RNA structures.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', CSIC, Armilla, 18100 Granada, Spain
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Parker AW, Lin CY, George MW, Towrie M, Kuimova MK. Infrared characterization of the guanine radical cation: finger printing DNA damage. J Phys Chem B 2010; 114:3660-7. [PMID: 20175506 DOI: 10.1021/jp9106958] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidation of DNA represents a major pathway of genetic mutation. We have applied infrared spectroscopy in 77 K glass with supporting density functional theory (DFT) calculations (EDF1/6-31+G*) to provide an IR signature of the guanine radical cation G(+*), formed as a result of 193 nm photoionization of DNA. Deprotonation of this species to produce the neutral radical G(-H)(*) does not occur in 77 K glass. DFT calculations indicate that the formation of G(+*) within the double helix does not significantly perturb the geometry of the G/C pair, even though there is a significant movement of the N(1) proton away from G toward C. However, this is in stark contrast to drastic changes that are expected if full deprotonation of G/C occurs, producing the G(-H)(*)/C pair. These results are discussed in light of solution-phase time-resolved IR spectroscopic studies and demonstrate the power of IR to follow dynamics of DNA damage in natural environments.
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Affiliation(s)
- Anthony W Parker
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX, UK.
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12
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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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13
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The post-SCF quantum chemistry characteristics of the energetic heterogeneity of stacked guanine–guanine pairs found in B-DNA and A-DNA crystals. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Fukuzumi S, Miyao H, Ohkubo K, Suenobu T. Electron-transfer oxidation properties of DNA bases and DNA oligomers. J Phys Chem A 2007; 109:3285-94. [PMID: 16833661 DOI: 10.1021/jp0459763] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, SORST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan.
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15
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Yamaguchi H, Ohara H, Waker AJ. A model for the induction of DNA damages and their evolution into cell clonogenic inactivation. JOURNAL OF RADIATION RESEARCH 2006; 47:197-211. [PMID: 16819146 DOI: 10.1269/jrr.47.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The dependence of the initial production of DNA damages on radiation quality was examined by using a proposed new model on the basis of target theory. For the estimation of DNA damage-production by different radiation qualities, five possible modes of radiation action, including both direct and indirect effects, were assumed inside a target the molecular structure of which was defined to consist of 10 base-pairs of DNA surrounded by water molecules. The induction of DNA damage was modeled on the basis of comparisons between the primary ionization mean free path and the distance between pairs of ionized atoms, such distance being characteristic on the mode of radiation action. The OH radicals per average energy to produce an ion pair on the nanosecond time scale was estimated and used for indirect action. Assuming a relation between estimated yields of DNA damages and experimental inactivation cross sections for AT-cells, the present model enabled the quantitative reproduction of experimental results for AT-cell killing under aerobic or hypoxic conditions. The results suggest a higher order organization of DNA in a way that there will be at least two types of water environment, one filling half the space surrounding DNA with a depth of 3.7-4.3 nm and the other filling all space with a depth 4.6-4.9 nm.
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Affiliation(s)
- Hiroshi Yamaguchi
- International Space Radiation Laboratory National Institute of Radiological Sciences, Chiba, Japan.
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16
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Jones DB, Wang F, Winkler DA, Brunger MJ. Orbital based electronic structural signatures of the guanine keto G-7H/G-9H tautomer pair as studied using dual space analysis. Biophys Chem 2006; 121:105-20. [PMID: 16464529 DOI: 10.1016/j.bpc.2005.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 12/12/2005] [Accepted: 12/12/2005] [Indexed: 11/27/2022]
Abstract
Electronic structural signatures of the guanine-7H and guanine-9H tautomers have been investigated on an orbital by orbital basis using dual space analysis. A combination of density functional theory (B3LYP/TZVP), the statistical average of model orbital potentials (SAOP/TZ2P) method and outer valence Green's function theory (OVGF/TZVP) has been used to generate optimal tautomer geometries and accurate ionization energy spectra for the guanine tautomer pair. The present work found that the non-planar form for both of the guanine keto pair possesses lower energies than their corresponding planar counterparts, and that the canonical form of the guanine-7H tautomer has slightly lower total energy than guanine-9H. This latter result is in agreement with previous experimental and theoretical findings. In the planar guanine pair the geometric parameters and anisotropic molecular properties are compared, focusing on changes caused by the mobile proton transfer. It is demonstrated that the mobile proton only causes limited disturbance to isotropic properties, such as geometry and the energetics, of the guanine keto tautomer pair. The exception to this general statement is for related local changes such as the N((7))-C((8)) and C((8))-N((9)) bond length resonance between the single and double bonds, reflecting the nitrogen atom being bonded with the mobile proton in the tautomers. The mobile proton distorts the electron distribution of the tautomers, which leads to significant changes in the molecular anisotropic properties. The dipole moment of guanine-7H is altered by about a factor of three, from 2.23 to 7.05 D (guanine-9H), and the molecular electrostatic potentials also reflect significant electron charge distortion. The outer valence orbital momentum distributions, which were obtained using the plane wave impulse approximation (PWIA), have demonstrated quantitatively that the outer valence orbitals of the tautomer pair can be divided into three groups. That is orbitals 1a''-7a'' and 18a', which do not have visible alternations in the tautomeric process (which consist of either pi orbitals or are close to the inner valence shell); a second group comprising orbitals 19a'-22a', 25a', 26a', 28a', 29a' and 31a', which show small perturbations as a result of the mobile hydrogen locations; and group three, orbitals 23a', 24a', 27a', 30a' and 32a', which demonstrate significant changes due to the mobile proton transfer and are therefore considered as signature orbitals of the G-7H/G-9H keto tautomeric process.
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Affiliation(s)
- D B Jones
- School of Chemistry, Physics and Earth Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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17
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Abstract
Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.
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Affiliation(s)
- Esther M Conwell
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
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18
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Kuimova MK, Cowan AJ, Matousek P, Parker AW, Sun XZ, Towrie M, George MW. Monitoring the direct and indirect damage of DNA bases and polynucleotides by using time-resolved infrared spectroscopy. Proc Natl Acad Sci U S A 2006; 103:2150-3. [PMID: 16467159 PMCID: PMC1413690 DOI: 10.1073/pnas.0506860103] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleotide 5'-dGMP and polynucleotide poly(dGdC).poly(dGdC) have been irradiated by using a 200-fs, 200-nm laser pulses and spectrally characterized by using time-resolved infrared spectroscopy. Under the experimental conditions, 200-nm excitation generates both electronic excited states and radical cations through photoionization; the former decay rapidly to vibrationally hot ground state. By using infrared signatures we have been able to follow these processes, and at time scales of >1 ns we observe an infrared marker band at 1,702 cm(-1) within both 5'-dGMP and the polynucleotide assigned to a photoionized product of guanine. This transient has also been reproduced through indirect chemistry through the reaction with photogenerated carbonate radical with 5'-dGMP. The ability to use time-resolved infrared spectroscopy in this way paves the way for developing solution-phase studies to investigate both direct and indirect radiation chemistry of DNA.
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Affiliation(s)
- Marina K. Kuimova
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Alexander J. Cowan
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Pavel Matousek
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Anthony W. Parker
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
- To whom correspondence may be addressed. E-mail:
or
| | - Xue Zhong Sun
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Michael Towrie
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Michael W. George
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
- To whom correspondence may be addressed. E-mail:
or
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19
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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: 105] [Impact Index Per Article: 5.3] [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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20
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Angelov D, Beylot B, Spassky A. Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA. Biophys J 2004; 88:2766-78. [PMID: 15613625 PMCID: PMC1305372 DOI: 10.1529/biophysj.104.049015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxidative guanine lesions were analyzed, at the nucleotide level, within DNA exposed to nanosecond ultraviolet (266 nm) laser pulses of variable intensity (0.002-0.1 J/cm(2)). Experiments were carried out, at room temperature, in TE buffer (20 mM Tris-HCl, pH 7.5; 1 mM EDTA) containing 35 mM NaCl, on 5'-end radioactively labeled double-stranded and single-stranded oligomer DNA at a size of 33-37 nucleobases. Lesions were analyzed on polyacrylamide gel electrophoresis by taking advantage of the specific removal of 8-oxodG from DNA by the formamidopyrimidine DNA glycosylase (Fpg protein) and of the differential sensitivity of 8-oxodG and oxazolone to piperidine. The quantum yields of lesions at individual sites, determined from the normalized intensities of bands, were plotted against the irradiation energy levels. Simplified model fitting of the experimental data enabled to evaluate the spectroscopic parameters characterizing excitation and photoionization processes. Results show that the distribution of guanine residues, excited to the lowest triplet state or photoionized, is heterogeneous and depends on the primary and secondary DNA structure. These findings are generalized in terms of excitation energy and charge-migration mediated biphotonic ionization. On the basis of the changes in the yield of the guanyl radical resulting from local helical perturbations in the DNA pi-stack, it can be assessed that the distance range of migration is <6-8 bp.
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Affiliation(s)
- Dimitar Angelov
- UMR 8113 French National Center for Scientific Research, Institut Gustave Roussy, 94805 Villejuif, France
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21
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Kim JE, Choi S, Yoo JA, Chung MH. 8-Oxoguanine induces intramolecular DNA damage but free 8-oxoguanine protects intermolecular DNA from oxidative stress. FEBS Lett 2004; 556:104-10. [PMID: 14706835 DOI: 10.1016/s0014-5793(03)01385-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoguanine; 8-oxo-G), one of the major oxidative DNA adducts, is highly susceptible to further oxidation by radicals. We confirmed the higher reactivity of 8-oxo-G toward reactive oxygen (singlet oxygen and hydroxyl radical) or nitrogen (peroxynitrite) species as compared to unmodified base. In this study, we raised the question about the effect of this high reactivity toward radicals on intramolecular and intermolecular DNA damage. We found that the amount of intact nucleoside in oligodeoxynucleotide containing 8-oxo-G decreased more by various radicals at higher levels of 8-oxo-G incorporation, and that the oligodeoxynucleotide damage and plasmid cleavage by hydroxyl radical were inhibited in the presence of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG). We conclude that 8-oxo-G within DNA induces intramolecular DNA base damage, but that free 8-oxo-G protects intermolecular DNA from oxidative stress. These results suggest that 8-oxo-G within DNA must be rapidly released to protect DNA from overall oxidative damage.
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Affiliation(s)
- Ja-Eun Kim
- Department of Pharmacology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, 110-799, Seoul, South Korea
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22
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Shapkina T, Lappi S, Franzen S, Wollenzien P. Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome. Nucleic Acids Res 2004; 32:1518-26. [PMID: 14999094 PMCID: PMC390305 DOI: 10.1093/nar/gkh320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 02/10/2004] [Accepted: 02/10/2004] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) W m(-2), to determine strand breakage yields and the frequency and pattern of RNA-RNA cross- linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 x 10(-3) over the incident intensity range studied. The yield for RNA-RNA cross-linking was 3 x 10(-4) cross-links/photon at the intensity of 4.5 x 10(9) W m(-2), an approximately 4-fold higher yield per photon than obtained with a transilluminator. The cross-link yield/photon decreased at higher light intensities, probably due to intensity-dependent photoreversal. The pattern of cross-linking was similar to that observed with low intensity irradiation but with four additional long-range cross-links not previously seen in E.coli ribosomes. Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation.
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Affiliation(s)
- Tatjana Shapkina
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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23
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Senthilkumar K, Grozema FC, Guerra CF, Bickelhaupt FM, Siebbeles LDA. Mapping the sites for selective oxidation of guanines in DNA. J Am Chem Soc 2004; 125:13658-9. [PMID: 14599193 DOI: 10.1021/ja037027d] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effective energy of a positive charge when it is localized at a specific guanine nucleobase in DNA was calculated using density functional theory. The results demonstrate that the efficiency of a guanine to act as a hole-trap in DNA strongly depends on the nature of the flanking nucleobases. The presence of a pyrimidine base at the 3' position adjacent to a guanine significantly increases the localization energy of the positive charge. The calculated distributions of a positive charge in sequences of two or three adjacent guanines, flanked by other nucleobases, provide an explanation for experimental literature data on the site-selective oxidation of DNA.
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Affiliation(s)
- K Senthilkumar
- Radiation Chemistry Department, Interfaculty Reactor Institute, Delft University of Technology, Mekelweg 15, NL-2629 JB Delft, The Netherlands
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24
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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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25
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Effect of hydrogen bonding on the photo-oxidation of DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2002. [DOI: 10.1016/s1389-5567(02)00005-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Okamoto A, Tanabe K, Dohno C, Saito I. Modulation of remote DNA oxidation by hybridization with peptide nucleic acids (PNA). Bioorg Med Chem 2002; 10:713-8. [PMID: 11814860 DOI: 10.1016/s0968-0896(01)00320-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have examined the efficiency of DNA photooxidation in DNA/PNA duplex and DNA/(PNA)(2) triplex for the first time. DNA/PNA duplex was cleaved at GG steps by external riboflavin with high efficiency like specific GG cleavage in DNA/DNA duplex. However, the 5'G selectivity of the GG oxidation in DNA/PNA duplex was much lower than that observed in DNA/DNA duplex. Remote DNA oxidation of oxidant-tethered DNA/PNA duplex was considerably suppressed. In contrast, the formation of DNA/(PNA)(2) triplex by hybridization with two PNA strands completely inhibited the remote GG oxidation, indicating that PNA acts as an inhibition for remote oxidative DNA damage.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan
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27
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Schumm S, Prévost M, García-Fresnadillo D, Lentzen O, Moucheron C, Kirsch-De Mesmaeker A. Influence of the Sequence Dependent Ionization Potentials of Guanines on the Luminescence Quenching of Ru-Labeled Oligonucleotides: A Theoretical and Experimental Study. J Phys Chem B 2002. [DOI: 10.1021/jp013185k] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- S. Schumm
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
| | - M. Prévost
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
| | - D. García-Fresnadillo
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
| | - O. Lentzen
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
| | - C. Moucheron
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
| | - A. Kirsch-De Mesmaeker
- Organic Chemistry and Photochemistry, Université libre de Bruxelles, CP 160/08, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, Ingénierie Biomoléculaire, Université libre de Bruxelles, CP 165/64, 50 Avenue F.D. Roosevelt, B-1050 Brussels, Belgium, and Faculty of Chemistry, Universidad Complutense de Madrid, Avenida Complutense s/n, E−28040 Madrid, Spain
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29
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Peter O'Neill,*, Parker AW, Plumb MA, Siebbeles LDA. Guanine Modifications Following Ionization of DNA Occurs Predominantly via Intra- and Not Interstrand Charge Migration: An Experimental and Theoretical Study. J Phys Chem B 2001. [DOI: 10.1021/jp003514t] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter O'Neill,*
- MRC Radiation and Genome Stability Unit, Harwell, Oxfordshire OX11 ORD, U.K., Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 OQX, U.K., Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Anthony W. Parker
- MRC Radiation and Genome Stability Unit, Harwell, Oxfordshire OX11 ORD, U.K., Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 OQX, U.K., Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Mark A. Plumb
- MRC Radiation and Genome Stability Unit, Harwell, Oxfordshire OX11 ORD, U.K., Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 OQX, U.K., Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Laurens D. A. Siebbeles
- MRC Radiation and Genome Stability Unit, Harwell, Oxfordshire OX11 ORD, U.K., Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 OQX, U.K., Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
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30
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31
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Zhu Q, LeBreton PR. DNA Photoionization and Alkylation Patterns in the Interior of Guanine Runs. J Am Chem Soc 2000. [DOI: 10.1021/ja002523c] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Grozema FC, Berlin YA, Siebbeles LDA. Mechanism of Charge Migration through DNA: Molecular Wire Behavior, Single-Step Tunneling or Hopping? J Am Chem Soc 2000. [DOI: 10.1021/ja001497f] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ferdinand C. Grozema
- Contribution from the Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Yuri A. Berlin
- Contribution from the Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Laurens D. A. Siebbeles
- Contribution from the Radiation Chemistry Department, IRI, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
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33
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Stemp ED, Barton JK. The flash-quench technique in protein-DNA electron transfer: reduction of the guanine radical by ferrocytochrome c. Inorg Chem 2000; 39:3868-74. [PMID: 11196782 DOI: 10.1021/ic0000698] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electron transfer from a protein to oxidatively damaged DNA, specifically from ferrocytochrome c to the guanine radical, was examined using the flash-quench technique. Ru(phen)2dppz2+ (dppz = dipyridophenazine) was employed as the photosensitive intercalator, and ferricytochrome c (Fe3+ cyt c), as the oxidative quencher. Using transient absorption and time-resolved luminescence spectroscopies, we examined the electron-transfer reactions following photoexcitation of the ruthenium complex in the presence of poly(dA-dT) or poly(dG-dC). The luminescence-quenching titrations of excited Ru(phen)2dppz2+ by Fe3+ cyt c are nearly identical for the two DNA polymers. However, the spectral characteristics of the long-lived transient produced by the quenching depend strongly upon the DNA. For poly(dA-dT), the transient has a spectrum consistent with formation of a [Ru(phen)2dppz3+, Fe2+ cyt c] intermediate, indicating that the system regenerates itself via electron transfer from the protein to the Ru(III) metallointercalator for this polymer. For poly(dG-dC), however, the transient has the characteristics expected for an intermediate of Fe2+ cyt c and the neutral guanine radical. The characteristics of the transient formed with the GC polymer are consistent with rapid oxidation of guanine by the Ru(III) complex, followed by slow electron transfer from Fe2+ cyt c to the guanine radical. These experiments show that electron holes on DNA can be repaired by protein and demonstrate how the flash-quench technique can be used generally in studying electron transfer from proteins to guanine radicals in duplex DNA.
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Affiliation(s)
- E D Stemp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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34
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Ma JH, Lin WZ, Wang WF, Han ZH, Yao SD, Lin NY. Triplet state mechanism for electron transfer oxidation of DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2000; 57:76-81. [PMID: 11100840 DOI: 10.1016/s1011-1344(00)00081-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction of anthraquinone-2-sulfonate with nucleotides and DNA in acetonitrile and acetonitrile water solvent mixture have been studied using KrF laser photolysis aimed at elucidation of the reaction mechanism. Laser spectroscopy directly demonstrates that the initial species from interaction of anthraquinone-2-sulfonate with nucleotides are radical cations of nucleotides and radical anion of anthraquinone-2-sulfonate. In addition, formation of ion pair from interaction of any of nucleotides with anthraquinone-2-sulfonate is synchronous with decay of triplet anthraquinone-2-sulfonate, which has provided dynamic evidence for initiation of electron transfer from DNA bases to triplet anthraquinone-2-sulfonate. Moreover, direct observation of stabilized DNA guanyl radical cation from interaction of anthraquinone-2-sulfonate with DNA has provided initial evidence for selective cleavage of DNA at guanine moiety. The solvent-separated ion pairs in acetonitrile have evidently dissociated into free ions, thereby enabling independent study of the behavior of guanyl radical cations and radical anion of anthraquinone-2-sulfonate.
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Affiliation(s)
- J H Ma
- Laboratory of Radiation Chemistry, Shanghai Institute of Nuclear Research, Chinese Academy of Science, People's Republic of China
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Kerr CE, Eaton BE, Netzel TL. Synthesis of N,N-dialkylaniline-2'-deoxyuridine conjugates for DNA-mediated electron transfer studies. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:851-66. [PMID: 10893706 DOI: 10.1080/15257770008033027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Syntheses of two analogs of deoxyuridine with N,N-dialkylaniline chromophores are reported. 5-[3-(N-methylphenylamino)propanoyl]-2'-deoxyuridine (1) and 5-[2-(4-N,N-dimethylaminophenyl)ethyl)]-2'-deoxyuridine (2) are prepared by palladium-mediated coupling. Preparation of 2 was facilitated by in situ transient O4-trimethylsilyl protection during alkynylation which suppressed secondary cyclization of the coupling adduct.
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Affiliation(s)
- C E Kerr
- Georgia State University Chemistry Dept., Atlanta, GA 30303, USA
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36
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The study of far UV irradiation of 2-methoxycytosine in phosphate solution and its novel photoproduct. J Photochem Photobiol A Chem 2000. [DOI: 10.1016/s1010-6030(99)00248-8] [Citation(s) in RCA: 3] [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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37
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Bamatraf MMM, O'Neill P, Rao BSM. OH Radical-Induced Charge Migration in Oligodeoxynucleotides. J Phys Chem B 1999. [DOI: 10.1021/jp993036q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. M. M. Bamatraf
- Radiation and Genome Stability Unit, Medical Research Council, Harwell, Didcot, Oxfordshire, OX11 ORD, U.K., and Chemistry Department, University of Pune, Pune, 411 007, India
| | - P. O'Neill
- Radiation and Genome Stability Unit, Medical Research Council, Harwell, Didcot, Oxfordshire, OX11 ORD, U.K., and Chemistry Department, University of Pune, Pune, 411 007, India
| | - B. S. M. Rao
- Radiation and Genome Stability Unit, Medical Research Council, Harwell, Didcot, Oxfordshire, OX11 ORD, U.K., and Chemistry Department, University of Pune, Pune, 411 007, India
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38
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Kim NS, Zhu Q, LeBreton PR. Aqueous Ionization and Electron-Donating Properties of Dinucleotides: Sequence-Specific Electronic Effects on DNA Alkylation. J Am Chem Soc 1999. [DOI: 10.1021/ja992065b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nancy S. Kim
- Contribution from the Department of Chemistry, The University of Illinois at Chicago, Chicago, Illinois 60607-7061
| | - Qiqing Zhu
- Contribution from the Department of Chemistry, The University of Illinois at Chicago, Chicago, Illinois 60607-7061
| | - Pierre R. LeBreton
- Contribution from the Department of Chemistry, The University of Illinois at Chicago, Chicago, Illinois 60607-7061
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39
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Lewis FD, Liu X, Miller SE, Wasielewski MR. Electronic Interactions between π-Stacked DNA Base Pairs and Diphenylacetylene-4,4‘-dicarboxamide in Hairpin DNA. J Am Chem Soc 1999. [DOI: 10.1021/ja9924997] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Frederick D. Lewis
- Department of Chemistry, Northwestern University Evanston, Illinois 60208
| | - Xiaoyang Liu
- Department of Chemistry, Northwestern University Evanston, Illinois 60208
| | - Scott E. Miller
- Department of Chemistry, Northwestern University Evanston, Illinois 60208
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40
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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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41
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Núñez ME, Hall DB, Barton JK. Long-range oxidative damage to DNA: effects of distance and sequence. CHEMISTRY & BIOLOGY 1999; 6:85-97. [PMID: 10021416 DOI: 10.1016/s1074-5521(99)80005-2] [Citation(s) in RCA: 363] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Oxidative damage to DNA in vivo can lead to mutations and cancer. DNA damage and repair studies have not yet revealed whether permanent oxidative lesions are generated by charges migrating over long distances. Both photoexcited *Rh(III) and ground-state Ru(III) intercalators were previously shown to oxidize guanine bases from a remote site in oligonucleotide duplexes by DNA-mediated electron transfer. Here we examine much longer charge-transport distances and explore the sensitivity of the reaction to intervening sequences. RESULTS Oxidative damage was examined in a series of DNA duplexes containing a pendant intercalating photooxidant. These studies revealed a shallow dependence on distance and no dependence on the phasing orientation of the oxidant relative to the site of damage, 5'-GG-3'. The intervening DNA sequence has a significant effect on the yield of guanine oxidation, however. Oxidation through multiple 5'-TA-3' steps is substantially diminished compared to through other base steps. We observed intraduplex guanine oxidation by tethered *Rh(III) and Ru(III) over a distance of 200 A. The distribution of oxidized guanine varied as a function of temperature between 5 and 35 degrees C, with an increase in the proportion of long-range damage (> 100 A) occurring at higher temperatures. CONCLUSIONS Guanines are oxidized as a result of DNA-mediated charge transport over significant distances (e.g. 200 A). Although long-range charge transfer is dependent on distance, it appears to be modulated by intervening sequence and sequence-dependent dynamics. These discoveries hold important implications with respect to DNA damage in vivo.
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Affiliation(s)
- M E Núñez
- Division of Chemistry and Chemical Engineering, California Institute ofTechnology, Pasadena 91125, USA
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42
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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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43
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Gasper SM, Armitage B, Shui X, Hu GG, Yu C, Schuster GB, Williams LD. Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja981761t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susan M. Gasper
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Bruce Armitage
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Xiuqi Shui
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Gary G. Hu
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Changjun Yu
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Gary B. Schuster
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Loren Dean Williams
- Contribution from the School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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44
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Gasparutto D, Ravanat JL, Gérot O, Cadet J. Characterization and Chemical Stability of Photooxidized Oligonucleotides that Contain 2,2-Diamino-4-[(2-deoxy-β-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone. J Am Chem Soc 1998. [DOI: 10.1021/ja980674y] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Didier Gasparutto
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB, Laboratoire des Lésions des Acides Nucléiques, C.E.A/Grenoble, F-38054 Grenoble Cedex 9, France
| | - Jean-Luc Ravanat
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB, Laboratoire des Lésions des Acides Nucléiques, C.E.A/Grenoble, F-38054 Grenoble Cedex 9, France
| | - Olivier Gérot
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB, Laboratoire des Lésions des Acides Nucléiques, C.E.A/Grenoble, F-38054 Grenoble Cedex 9, France
| | - Jean Cadet
- Contribution from the Département de Recherche Fondamentale sur la Matière Condensée, SCIB, Laboratoire des Lésions des Acides Nucléiques, C.E.A/Grenoble, F-38054 Grenoble Cedex 9, France
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45
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Koizume S, Inoue H, Kamiya H, Ohtsuka E. Neighboring base damage induced by permanganate oxidation of 8-oxoguanine in DNA. Nucleic Acids Res 1998; 26:3599-607. [PMID: 9671825 PMCID: PMC147747 DOI: 10.1093/nar/26.15.3599] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We found that single-stranded DNA oligomers containing a 7, 8-dihydro-8-oxoguanine (8-oxo-G) residue have high reactivity toward KMnO4; the oxidation of 8-oxo-G induces damage to the neighboring nucleotide residues. This paper describes the novel reaction in detail, including experiments that demonstrate the mechanism involved in the induction of DNA damage. The results using DNAs of various base compositions indicated that damaged G, T and C (but not A) sites caused strand scissions after hot piperidine treatment and that the damage around the 8-oxo-G occurred at G sites in both single and double strands with high frequency. The latter substrates were less sensitive to damage. Further, kinetic studies of the KMnO4reaction of single-stranded oligomers suggested that thereactivity of the DNA bases at the site 5'-adjacent to the 8-oxo-G was in the order G >A >T, C. This preference correlates with the electron donating abilities of the bases. In addition, we found that the DNA damage at the G site, which was connected with the 8-oxo-G by a long abasic chain, was inhibited in the above order by the addition of dG, dA or dC. On the other hand, the damage reactions proceeded even after the addition of scavengers for active oxygen species. This study suggests the involvement of a redox process in the unique DNA damage initiated by the oxidation of the 8-oxo-G.
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Affiliation(s)
- S Koizume
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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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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47
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Kino K, Saito I, Sugiyama H. Product Analysis of GG-Specific Photooxidation of DNA via Electron Transfer: 2-Aminoimidazolone as a Major Guanine Oxidation Product. J Am Chem Soc 1998. [DOI: 10.1021/ja980763a] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Botchway SW, Chakrabarti S, Makrigiorgos GM. Novel Visible and Ultraviolet Light Photogeneration of Hydroxyl Radicals by 2-Methyl-4-nitro-quinoline-N-oxide (MNO) and 4, 4'-Dinitro-(2, 2') bipyridinyl-N, N'-dioxide (DBD). Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb09105.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Turro C, Hall DB, Chen W, Zuilhof H, Barton JK, Turro NJ. Solution Photoreactivity of Phenanthrenequinone Diimine Complexes of Rhodium and Correlations with DNA Photocleavage and Photooxidation. J Phys Chem A 1998. [DOI: 10.1021/jp981013q] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudia Turro
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Daniel B. Hall
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Wei Chen
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Han Zuilhof
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Jacqueline K. Barton
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, New York, New York 10027, and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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50
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Burrows CJ, Muller JG. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem Rev 1998; 98:1109-1152. [PMID: 11848927 DOI: 10.1021/cr960421s] [Citation(s) in RCA: 1389] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850
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