201
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hOGG1 Ser326Cys polymorphism and risk of hepatocellular carcinoma among East Asians: a meta-analysis. PLoS One 2013; 8:e60178. [PMID: 23577090 PMCID: PMC3618171 DOI: 10.1371/journal.pone.0060178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/21/2013] [Indexed: 01/30/2023] Open
Abstract
Background The hOGG1 gene encodes a DNA glycosylase enzyme responsible for DNA repair. The Ser326Cys polymorphism in this gene may influence its repair ability and thus plays a role in carcinogenesis. Several case-control studies have been conducted on this polymorphism and its relationship with the risk of hepatocellular carcinoma (HCC) among East Asians. However, their results are inconsistent. Methods We performed a meta-analysis of published case-control studies assessing the association of the hOGG1 Ser326Cys polymorphism with HCC risk among East Asians. PubMed, EMBASE, SCI, BIOSIS, CNKI and WanFang databases were searched. A random-effect model was used to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs). Analyses were conducted for additive, dominant and recessive genetic models. Results Eight studies were identified involving 2369 cases and 2442 controls assessing the association of the hOGG1 Ser326Cys polymorphism with HCC risk among East Asians. Applying a dominant genetic model, only in the Chinese population, the Cys allele was significantly associated with increased risk of HCC (OR 1.56, 95% CI 1.12–2.17). However, two studies influenced this finding according to sensitivity analysis. Furthermore, considerable heterogeneity and bias existed among Chinese studies. Conclusion There is limited evidence to support that the hOGG1 Ser326Cys polymorphism is associated with HCC risk among East Asians. Well-designed and large-sized studies are required to determine this relationship.
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202
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Haruna KI, Iida H, Nishimoto SI, Tanabe K. Stepwise regulation of hole transport in DNA by control of triplex formation. Bioorg Med Chem 2013; 21:2682-6. [PMID: 23587656 DOI: 10.1016/j.bmc.2013.03.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/19/2013] [Accepted: 03/21/2013] [Indexed: 10/27/2022]
Abstract
A functionality for regulating hole transport efficiency is a prerequisite for the utilization of DNA duplexes as nanodevices. Herein, we report the regulation of hole transport in anthraquinone-tethered DNA with dual triplex forming sites. Long-range photooxidation experiments showed that hole transport was effectively suppressed by the formation of triplex at low temperature, while it was recovered by dissociation to the duplex at higher temperature. Variation of temperature induced the formation and dissociation of the third strand at each triplex region individually, leading to the stepwise regulation of hole transport in DNA.
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Affiliation(s)
- Ken-ichi Haruna
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
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203
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Barnett RN, Joseph J, Landman U, Schuster GB. Oxidative Thymine Mutation in DNA: Water-Wire-Mediated Proton-Coupled Electron Transfer. J Am Chem Soc 2013; 135:3904-14. [DOI: 10.1021/ja311282k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Robert N. Barnett
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Joshy Joseph
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Uzi Landman
- School of Physics, Georgia Institute of Technology, Atlanta,
Georgia 30332-0430, United States
| | - Gary B. Schuster
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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204
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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205
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Osakada Y, Kawai K, Majima T. Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
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206
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Patel C, Garrec J, Dupont C, Dumont E. What Singles Out the G[8–5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations. Biochemistry 2013; 52:425-31. [DOI: 10.1021/bi301198h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Chandan Patel
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Céline Dupont
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Elise Dumont
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
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207
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Dupont C, Patel C, Ravanat JL, Dumont E. Addressing the competitive formation of tandem DNA lesions by a nucleobase peroxyl radical: a DFT-D screening. Org Biomol Chem 2013; 11:3038-45. [DOI: 10.1039/c3ob40280k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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208
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Wang X, Wang X, Cui S, Wang Y, Chen G, Guo Z. Specific recognition of DNA depurination by a luminescent terbium(iii) complex. Chem Sci 2013. [DOI: 10.1039/c3sc51781k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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209
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Ariafard A, Ghohe NM, Abbasi KK, Canty AJ, Yates BF. Theoretical investigation into the mechanism of 3'-dGMP oxidation by [Pt(IV)Cl4(dach)]. Inorg Chem 2012; 52:707-17. [PMID: 23270414 DOI: 10.1021/ic3018425] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism for the oxidation of 3'-dGMP by [PtCl(4)(dach)] (dach = diaminocyclohexane) in the presence of [PtCl(2)(dach)] has been investigated using density functional theory. We find that the initial complexation, i.e., the formation of [PtCl(3)(dach)(3'-dGMP)], is greatly assisted by the reaction of the encounter pair [PtCl(2)(dach)···3'-dGMP] with [PtCl(4)(dach)], leading to migration of an axial chlorine ligand from platinum(IV) to platinum(II). A dinuclear platinum(II)/platinum(IV) intermediate could not be found, but the reaction is predicted to pass through a platinum(III)/platinum(III) transition structure. A cyclization process, i.e., C8-O bond formation, from [PtCl(3)(dach)(3'-dGMP)] occurs through an intriguing phosphate-water-assisted deprotonation reaction, analogous to the opposite of a proton shuttle mechanism. Followed by this, the guanine moiety is oxidized via dissociation of the Pt(IV)-Cl(ax) bond, and the cyclic ether product is finally formed after deprotonation. We have provided rationalizations, including molecular orbital explanations, for the key steps in the process. Our results help to explain the effect of [PtCl(4)(dach)] on the complexation step and the effect of a strong hydroxide base on the cyclization reaction. The overall reaction cycle is intricate and involves autocatalysis by a platinum(II) species.
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Affiliation(s)
- Alireza Ariafard
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran, Iran.
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210
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Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res 2012; 23:129-41. [PMID: 23093720 PMCID: PMC3530673 DOI: 10.1101/gr.136739.111] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.
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Affiliation(s)
- Eric E Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA.
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211
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Pluhařová E, Ončák M, Seidel R, Schroeder C, Schroeder W, Winter B, Bradforth SE, Jungwirth P, Slavíček P. Transforming Anion Instability into Stability: Contrasting Photoionization of Three Protonation Forms of the Phosphate Ion upon Moving into Water. J Phys Chem B 2012; 116:13254-64. [DOI: 10.1021/jp306348b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eva Pluhařová
- Institute
of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department of Physical Chemistry, Institute of Chemical Technology, Technická
5, 16628 Prague 6, Czech Republic
| | - Milan Ončák
- Department of Physical Chemistry, Institute of Chemical Technology, Technická
5, 16628 Prague 6, Czech Republic
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| | - Christi Schroeder
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| | - William Schroeder
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| | - Pavel Jungwirth
- Institute
of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, Institute of Chemical Technology, Technická
5, 16628 Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 3,
18223 Prague 8, Czech Republic
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212
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Zhou C, Matsika S, Kotur M, Weinacht TC. Fragmentation Pathways in the Uracil Radical Cation. J Phys Chem A 2012; 116:9217-27. [DOI: 10.1021/jp209213e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Congyi Zhou
- Department
of Chemistry, Temple University, Philadelphia,
Pennsylvania 19122,
United States
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia,
Pennsylvania 19122,
United States
| | - Marija Kotur
- Department
of Physics, Stony Brook University, Stony
Brook, New York 11794,
United States
| | - Thomas C. Weinacht
- Department
of Physics, Stony Brook University, Stony
Brook, New York 11794,
United States
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213
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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: 209] [Impact Index Per Article: 17.4] [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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214
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Kellie JL, Wetmore SD. Mechanistic and conformational flexibility of the covalent linkage formed during β-lyase activity on an AP-site: application to hOgg1. J Phys Chem B 2012; 116:10786-97. [PMID: 22877319 DOI: 10.1021/jp306344g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The β/δ-lyase activity of bifunctional glycosylases on damaged nucleotides in DNA involves the formation of a covalent linkage between the protein (lysine or N-terminal proline) and DNA (C1' of the damaged nucleotide). In the present study, the conformational and mechanistic flexibility of the cross-link is examined. Repair of 8-oxoguanine damage by hOgg1 is considered as a representative system, and the glycosylase through β-lyase steps are investigated using density functional theory. (PCM/SMD)-M06-2X/6-311+G(2df,2p)//PCM-B3LYP/6-31G(d) energetics were determined for eight unique mechanisms differing in the conformation of the imine linkage (E/Z), the proton (pro-S/R) abstracted during elimination, and whether the ring-opening step is base catalyzed. This initial study used a model system limited to the damaged nucleoside 3'-monophosphate and a model nucleophile to investigate this series of complex reaction steps. The great flexibility exhibited by the linkage and clustered β-elimination energetics indicate sterics will play a large role in predicting the preferred lyase mechanism for a given enzyme. The stationary points identified herein can be overlaid into a protein structure to assist in generating initial guesses for large model systems. By comparing the characterized geometries and enzyme active sites, methods for catalysis of the various chemical steps can be identified, and these possibilities are discussed in detail for hOgg1. Interestingly, the most stable structure on the potential energy surface occurs before elimination of the 3'-phosphate. Hydrolysis of the protein-DNA cross-link at this point would yield an AP-site, which provides support for the recently observed monofunctional activity of hOgg1.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
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215
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Ariafard A, Tabatabaie ES, Aghmasheh S, Najaflo S, Yates BF. Density functional theory studies on the oxidation of 5'-dGMP and 5'-dAMP by a platinum(IV) complex. Inorg Chem 2012; 51:8002-13. [PMID: 22809133 DOI: 10.1021/ic300038m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Density functional theory has been used to investigate the oxidation of a guanine nucleotide by platinum(IV), a process that can be important in the degradation of DNA. For the first time, we have provided a comprehensive mechanism for all of the steps in this process. A number of intermediates are predicted to occur but with short lifetimes that would make them difficult to observe experimentally. A key step in the mechanism is electron transfer from guanine to platinum(IV), and we show that this is driven by the loss of a chloride ligand from the platinum complex after nucleophilic attack of 5'-phosphate to C8 of guanine. We have investigated several different initial platinum(IV) guanine adducts and shown that the adduct formed from replacement of an axial chlorine ligand in the platinum(IV) complex undergoes oxidation more easily. We have studied adenine versus guanine adducts, and our results show that oxidation of the former is more difficult because of disruption of the aromatic π system that occurs during the process. Finally, our results show that the acidic hydrolysis step to form the final oxidized product occurs readily via an initial protonation of N7 of the guanine.
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Affiliation(s)
- Alireza Ariafard
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran, Iran.
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216
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Khodade VS, Dharmaraja AT, Chakrapani H. Synthesis, reactive oxygen species generation and copper-mediated nuclease activity profiles of 2-aryl-3-amino-1,4-naphthoquinones. Bioorg Med Chem Lett 2012; 22:3766-9. [DOI: 10.1016/j.bmcl.2012.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 03/16/2012] [Accepted: 04/03/2012] [Indexed: 01/08/2023]
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217
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Sathyaraj G, Kiruthika M, Weyhermüller T, Nair BU. Ruthenium(II) [3 + 2 + 1] mixed ligand complexes: substituent effect on photolability, photooxidation of bases, photocytotoxicity and photonuclease activity. Dalton Trans 2012; 41:8460-71. [PMID: 22652837 DOI: 10.1039/c2dt30260h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Mixed ligand complexes of ruthenium(II), [Ru(itpy)(bpy)Cl]ClO(4)1, [Ru(itpy)(phen)Cl]ClO(4)2, [Ru(bitpy)(bpy)Cl]ClO(4)3 and [Ru(bitpy)(phen)Cl]ClO(4)4 have been synthesized and characterized. Complex 3 has also been characterized crystallographically. These complexes exhibit photolability of the Ru-Cl bond. Upon irradiation at 440 nm in the presence of nucleosides and nucleotides the complexes exchange chloride for the nucleoside or nucleotide. The photolability of the Ru-Cl bond depends on the nature of the substituent in the tridentate tpy ligand. Photolysis of the complexes in the presence of a nucleoside or nucleotide also produces 8-oxoguanine due to the oxidation of guanine by the excited states of the complexes. These four complexes exhibit photonuclease properties and bring about the cleavage of plasmid DNA when irradiated at 440 nm. These complexes have been found to be toxic towards NIH 3T3 cells under photolytic conditions.
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Affiliation(s)
- Gopal Sathyaraj
- Chemical Laboratory, Central Leather Research Institute, CSIR, Adyar, Chennai, 600020, India
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218
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Kawai K, Hayashi M, Majima T. Hole transfer in LNA and 5-Me-2'-deoxyzebularine-modified DNA. J Am Chem Soc 2012; 134:9406-9. [PMID: 22591000 DOI: 10.1021/ja302641e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the measurement of hole-transfer rate constants (k(ht)) in locked nucleic acid (LNA) and 5-Me-2'-deoxyzebularine (B)-modified DNA. LNA modification, which makes DNA more rigid, caused a decrease of more than 2 orders of magnitude in k(ht), whereas B modification, which increases DNA flexibility, increased k(ht) by more than 20-fold. The present results clearly showed that hole-transfer efficiency in DNA can be increased by increasing DNA flexibility.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan.
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219
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Zhang Y, Wang M, Li H, Zhang H, Shi Y, Wei F, Liu D, Liu K, Chen D. Accumulation of nuclear and mitochondrial DNA damage in the frontal cortex cells of patients with HIV-associated neurocognitive disorders. Brain Res 2012; 1458:1-11. [PMID: 22554480 DOI: 10.1016/j.brainres.2012.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 03/28/2012] [Accepted: 04/02/2012] [Indexed: 12/31/2022]
Abstract
Oxidative stress has been suggested to play a key role in the neuropathogenesis of HIV infection. HIV proteins (gp120, Tat) and proinflammatory cytokines can trigger the production of reactive oxygen species (ROS), resulting in DNA and RNA lesions. Among all the lesions induced by ROS, one of the most abundant lesions in DNA and RNA is 8-hydroxydeoxyguanosine (8-oxoG). Here, we studied accumulated DNA oxidative damage induced by ROS in the central nervous system (CNS) in tissue from neuro-AIDS patients. The frontal cortex of autopsy tissue from HIV-1 infected patients was adopted for analysis for HIV-1 subtype, nuclear and mitochondrial DNA lesions by immunofluorescence staining, qPCR and sequencing of PCR cloning. This study provides evidence that HIV infection in the CNS leads to nuclear and mitochondrial genomic DNA damage in the brain. High level of nuclear and mtDNA 8-oxoG damage were identified in the cortex autopsy tissue of HAND patients. Increased accumulation of mtDNA mutations and depletion occurs in brain tissue in a subset of HAND cases, and is significantly different from that observed in control cases. These findings suggest that higher level of ROS in the CNS of HAND patients would contribute to the HIV induced neuro-inflammation and apoptosis of neuronal and glial cells.
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Affiliation(s)
- Yulin Zhang
- Department of Medicine, Beijing You An Hospital, Capital Medical University, Beijing 100069, China
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220
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Abe Y, Nakagawa O, Yamaguchi R, Sasaki S. Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site. Bioorg Med Chem 2012; 20:3470-9. [PMID: 22560836 DOI: 10.1016/j.bmc.2012.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 01/27/2023]
Abstract
DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase-polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson-Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3'-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson-Crick type are formed at the AP site.
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Affiliation(s)
- Yukiko Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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222
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Golan A, Bravaya KB, Kudirka R, Kostko O, Leone SR, Krylov AI, Ahmed M. Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds. Nat Chem 2012; 4:323-9. [DOI: 10.1038/nchem.1298] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/07/2012] [Indexed: 01/26/2023]
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223
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Kawai K, Hayashi M, Majima T. HOMO energy gap dependence of hole-transfer kinetics in DNA. J Am Chem Soc 2012; 134:4806-11. [PMID: 22335550 DOI: 10.1021/ja2109213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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224
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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225
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Cadet J, Loft S, Olinski R, Evans MD, Bialkowski K, Richard Wagner J, Dedon PC, Møller P, Greenberg MM, Cooke MS. Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids. Free Radic Res 2012; 46:367-81. [PMID: 22263561 DOI: 10.3109/10715762.2012.659248] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A broad scientific community is involved in investigations aimed at delineating the mechanisms of formation and cellular processing of oxidatively generated damage to nucleic acids. Perhaps as a consequence of this breadth of research expertise, there are nomenclature problems for several of the oxidized bases including 8-oxo-7,8-dihydroguanine (8-oxoGua), a ubiquitous marker of almost every type of oxidative stress in cells. Efforts to standardize the nomenclature and abbreviations of the main DNA degradation products that arise from oxidative pathways are reported. Information is also provided on the main oxidative radicals, non-radical oxygen species, one-electron agents and enzymes involved in DNA degradation pathways as well in their targets and reactivity. A brief classification of oxidatively generated damage to DNA that may involve single modifications, tandem base modifications, intrastrand and interstrand cross-links together with DNA-protein cross-links and base adducts arising from the addition of lipid peroxides breakdown products is also included.
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Affiliation(s)
- Jean Cadet
- Direction des Sciences de Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, Grenoble Cedex 9, France.
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226
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Joseph J, Schuster GB. Oxidatively generated damage to DNA at 5-methylcytosine mispairs. Photochem Photobiol Sci 2012; 11:998-1003. [PMID: 22327601 DOI: 10.1039/c2pp05379a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Oxidatively generated damage to DNA has been implicated as causing mutations that lead to aging and disease. The one-electron oxidation of normal DNA leads to formation of a nucleobase radical cation that hops through the DNA until it is trapped irreversibly, primarily by reaction at guanine. It has been observed that 5-methylcytosine (C(m)) is a mutational "hot-spot". However, C(m) in a Watson-Crick base pair with G is not especially susceptible to oxidatively induced damage. Radical cation hopping is inhibited in duplexes that contain C-A or C-T mispairs, but no reaction is detected at cytosine. In contrast, we find that the one-electron oxidation of DNA that contains C(m)-A or C(m)-T mispairs results primarily in reaction at C(m) even in the presence of GG steps. The reaction at C(m) is attributed to proton coupled electron transfer, which provides a relatively low activation barrier path for reaction at 5-methylcytosine. This enhanced reactivity of C(m) in mispairs may contribute to the formation of mutational hot spots at C(m).
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Affiliation(s)
- Joshy Joseph
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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227
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Garrec J, Patel C, Rothlisberger U, Dumont E. Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations. J Am Chem Soc 2012; 134:2111-9. [DOI: 10.1021/ja2084042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Chandan Patel
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
| | - Ursula Rothlisberger
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Elise Dumont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
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228
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Cerón-Carrasco JP, Jacquemin D. Interplay between hydroxyl radical attack and H-bond stability in guanine–cytosine. RSC Adv 2012. [DOI: 10.1039/c2ra22389a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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229
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Molecular effects of chemotherapeutic drugs and their modulation by antioxidants in the testis. Eur J Pharmacol 2012; 674:207-16. [DOI: 10.1016/j.ejphar.2011.11.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 11/08/2011] [Accepted: 11/15/2011] [Indexed: 11/23/2022]
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230
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Barhoumi A, Halas NJ. Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy. J Phys Chem Lett 2011; 2:3118-3123. [PMID: 24427449 PMCID: PMC3888867 DOI: 10.1021/jz201423b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.
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Affiliation(s)
- Aoune Barhoumi
- Department of Chemistry, Rice University, Houston, TX 77005 (USA)
| | - Naomi J. Halas
- Department of Chemistry, Rice University, Houston, TX 77005 (USA)
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005 (USA)
- Department of Bioengineering, Rice University, Houston, TX 77005 (USA)
- Corresponding Author PHONE: (713) 348-5611; Fax: (+1)713-348-5686
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231
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Dupont C, Patel C, Dumont E. Improved DFT description of intrastrand cross-link formation by inclusion of London dispersion corrections. J Phys Chem B 2011; 115:15138-44. [PMID: 22049920 DOI: 10.1021/jp209074q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The formation of covalent linkages between two vicinal nucleotides has been proved experimentally to constitute a particularly deleterious class of DNA lesions. These tandem lesions by essence present a competitive chemistry. The density functional theory with dispersion (DFT-D) method is shown to dramatically improve the theoretical description of the formation of a prototypical intrastrand cross-link, when compared to pure or hybrid GGA functionals which strongly deviate from the π-π self-stacking mode, as dinucleotides are artificially stabilized by the formation of unrealistic intramolecular hydrogen bonds (HBs). Inclusion of London dispersion correction restores a more realistic picture of the reactant structure and also of geometries and energies along the reaction profile. This paves the way toward a robust insilico screening of intrastrand cross-link DNA defects.
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Affiliation(s)
- Céline Dupont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon, Lyon, France
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232
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Yang X, Fang C, Mei H, Chang T, Cao Z, Shangguan D. Characterization of G-quadruplex/hemin peroxidase: substrate specificity and inactivation kinetics. Chemistry 2011; 17:14475-84. [PMID: 22106035 DOI: 10.1002/chem.201101941] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Indexed: 02/05/2023]
Abstract
Recently, G-quadruplex/hemin (G4/hemin) complexes have been found to exhibit peroxidase activity, and this feature has been extensively exploited for colorimetric detection of various targets. To further understand and characterize this important DNAzyme, its substrate specificity, inactivation mechanism, and kinetics have been examined by comparison with horseradish peroxidase (HRP). G4/hemin DNAzyme exhibits broader substrate specificity and much higher inactivation rate than HRP because of the exposure of the catalytic hemin center. The inactivation of G4/hemin DNAzyme is mainly attributed to the degradation of hemin by H(2)O(2) rather than the destruction of G4. Both the inactivation rate and catalytic oxidation rate of G4/hemin DNAzyme depend on the concentration of H(2)O(2), which suggests that active intermediates formed by G4/hemin and H(2)O(2) are the branch point of catalysis and inactivation. Reducing substrates greatly inhibit the inactivation of G4/hemin DNAzyme by rapidly reacting with the active intermediates. A possible catalytic and inactivation process of G4/hemin has been proposed. These results imply a potential cause for the hemin-mediated cellular injury and provide insightful information for the future application of G4/hemin DNAzyme.
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Affiliation(s)
- Xiaojuan Yang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, PR China
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233
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Transient spectroscopy of dipyridophenazine metal complexes which undergo photo-induced electron transfer with DNA. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.04.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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234
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Bonin J, Robert M. Photoinduced Proton-Coupled Electron Transfers in Biorelevant Phenolic Systems. Photochem Photobiol 2011; 87:1190-203. [DOI: 10.1111/j.1751-1097.2011.00996.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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235
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Lippert AR, Van de Bittner GC, Chang CJ. Boronate oxidation as a bioorthogonal reaction approach for studying the chemistry of hydrogen peroxide in living systems. Acc Chem Res 2011; 44:793-804. [PMID: 21834525 PMCID: PMC3178007 DOI: 10.1021/ar200126t] [Citation(s) in RCA: 593] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reactive oxygen species (ROS), such as hydrogen peroxide, are important products of oxygen metabolism that, when misregulated, can accumulate and cause oxidative stress inside cells. Accordingly, organisms have evolved molecular systems, including antioxidant metalloenzymes (such as superoxide dismutase and catalase) and an array of thiol-based redox couples, to neutralize this threat to the cell when it occurs. On the other hand, emerging evidence shows that the controlled generation of ROS, particularly H(2)O(2), is necessary to maintain cellular fitness. The identification of NADPH oxidase enzymes, which generate specific ROS and reside in virtually all cell types throughout the body, is a prime example. Indeed, a growing body of work shows that H(2)O(2) and other ROS have essential functions in healthy physiological signaling pathways. The signal-stress dichotomy of H(2)O(2) serves as a source of motivation for disentangling its beneficial from its detrimental effects on living systems. Molecular imaging of this oxygen metabolite with reaction-based probes is a powerful approach for real-time, noninvasive monitoring of H(2)O(2) chemistry in biological specimens, but two key challenges to studying H(2)O(2) in this way are chemoselectivity and bioorthogonality of probe molecules. Chemoselectivity is problematic because traditional methods for ROS detection suffer from nonspecific reactivity with other ROS. Moreover, some methods require enzymatic additives not compatible with live-cell or live-animal specimens. Additionally, bioorthogonality requires that the reactions must not compete with or disturb intrinsic cellular chemistry; this requirement is particularly critical with thiol- or metal-based couples mediating the major redox events within the cell. Chemoselective bioorthogonal reactions, such as alkyne-azide cycloadditions and related click reactions, the Staudinger-Bertozzi ligation, and the transformations used in various reaction-based molecular probes, have found widespread application in the modification, labeling, and detection of biological molecules and processes. In this Account, we summarize H(2)O(2) studies from our laboratory using the H(2)O(2)-mediated oxidation of aryl boronates to phenols as a bioorthogonal approach to detect fluxes of this important ROS in living systems. We have installed this versatile switch onto organic and inorganic scaffolds to serve as "turn-on" probes for visible and near-infrared (NIR) fluorescence, ratiometric fluorescence, time-gated lanthanide luminescence, and in vivo bioluminescence detection of H(2)O(2) in living cells and animals. Further chemical and genetic manipulations target these probes to specific organelles and other subcellular locales and can also allow them to be trapped intracellularly, enhancing their sensitivity. These novel chemical tools have revealed fundamental new biological insights into the production, localization, trafficking, and in vivo roles of H(2)O(2) in a wide variety of living systems, including immune, cancer, stem, and neural cell models.
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Affiliation(s)
- Alexander R. Lippert
- Department of Chemistry, University of California, Berkeley, California, 94720, USA
| | | | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, 94720, USA
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236
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Kawai K, Matsutani E, Maruyama A, Majima T. Probing the Charge-Transfer Dynamics in DNA at the Single-Molecule Level. J Am Chem Soc 2011; 133:15568-77. [DOI: 10.1021/ja206325m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Eri Matsutani
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Atsushi Maruyama
- Institute for Materials Chemistry and Engineering, Kyushu University, Motooka 744-CE11, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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237
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Leavens FMV, Churchill CDM, Wang S, Wetmore SD. Evaluating how discrete water molecules affect protein-DNA π-π and π(+)-π stacking and T-shaped interactions: the case of histidine-adenine dimers. J Phys Chem B 2011; 115:10990-1003. [PMID: 21809837 DOI: 10.1021/jp205424z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Changes in the magnitude of (M06-2X/6-31+G(d,p)) π-π stacking and T-shaped (nucleobase-edge and amino acid-edge) interactions between (neutral or protonated) histidine (His) and adenine (A) dimers upon microsolvation with up to four discrete water molecules were determined. A variety of histidine-water interactions were considered including conventional (N-H···O, N···H-O, C-H···O) hydrogen bonding and nonconventional (X-H···π (neutral His) or lone-pair···π (protonated His)) contacts. Overall, the effects of discrete His-H(2)O interactions on the neutral histidine-adenine π-π contacts are negligible (<3 kJ mol(-1) or 15%) regardless of the type of water binding, the number of water molecules bound, or the His-A dimer (stacked or (amino acid- or nucleobase-edge) T-shaped) configuration. This suggests that previously reported gas-phase binding strengths for a variety of neutral amino acid-nucleobase dimers are likely relevant for a wide variety of (microsolvated) environments. In contrast, the presence of water decreases the histidine-adenine π(+)-π interaction by up to 15 kJ mol(-1) (or 30%) for all water binding modes and orientations, as well as different stacked and T-shaped His(+)-A dimers. Regardless of the larger effect of discrete histidine-water interactions on the magnitude of the π(+)-π compared with π-π interactions, the π(+)-π binding strengths remain substantially larger than the corresponding π-π contacts. These findings emphasize the distinct nature of π(+)-π and π-π interactions and suggest that π(+)-π contacts can provide significant stabilization in biological systems relative to π-π contacts under many different environmental conditions.
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Affiliation(s)
- Fern M V Leavens
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4
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238
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Age-associated neurodegeneration and oxidative damage to lipids, proteins and DNA. Mol Aspects Med 2011; 32:305-15. [DOI: 10.1016/j.mam.2011.10.010] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/11/2011] [Indexed: 01/08/2023]
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239
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Ghosh D, Isayev O, Slipchenko LV, Krylov AI. Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk. J Phys Chem A 2011; 115:6028-38. [PMID: 21500795 PMCID: PMC3116069 DOI: 10.1021/jp110438c] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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240
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Electrocatalytic activity of [Ru(bpy)3]2+ toward guanine oxidation upon incorporation of surfactants and SWCNTs. J APPL ELECTROCHEM 2011. [DOI: 10.1007/s10800-011-0297-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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241
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Genereux JC, Wuerth SM, Barton JK. Single-step charge transport through DNA over long distances. J Am Chem Soc 2011; 133:3863-8. [PMID: 21348520 DOI: 10.1021/ja107033v] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.
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Affiliation(s)
- Joseph C Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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242
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Wenninger M, Fazio D, Megerle U, Trindler C, Schiesser S, Riedle E, Carell T. Flavin-Induced DNA Photooxidation and Charge Movement Probed by Ultrafast Transient Absorption Spectroscopy. Chembiochem 2011; 12:703-6. [DOI: 10.1002/cbic.201000730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Indexed: 02/03/2023]
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243
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Yamada H, Kitauchi Y, Tanabe K, Ito T, Nishimoto SI. Anthraquinone-sensitized photooxidation of 5-methylcytosine in DNA leading to piperidine-induced efficient strand cleavage. Chemistry 2011; 17:2225-35. [PMID: 21294186 DOI: 10.1002/chem.201001884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Indexed: 11/10/2022]
Abstract
One-electron photooxidations of 5-methyl-2'-deoxycytidine (d(m)C) and 5-trideuteriomethyl-2'-deoxycytidine ([D(3)]d(m)C) by sensitization with anthraquinone (AQ) derivatives were investigated. Photoirradiation of an aerated aqueous solution containing d(m)C and anthraquinone 2-sulfonate (AQS) afforded 5-formyl-2'-deoxycytidine (d(f)C) and 5-hydroxymethyl-2'-deoxycytidine (d(hm)C) in good yield through an initial one-electron oxidation process. The deuterium isotope effect on the AQS-sensitized photooxidation of d(m)C suggests that the rate-determining step in the photosensitized oxidation of d(m)C involves internal transfer of the C5-hydrogen atom of a d(m)C-tetroxide intermediate to produce d(f)C and d(hm)C. In the case of a 5-methylcytosine ((m)C)-containing duplex DNA with an AQ chromophore that is incorporated into the backbone of the DNA strand so as to be immobilized at a specific position, (m)C underwent efficient direct one-electron oxidation by the photoexcited AQ, which resulted in an exclusive DNA strand cleavage at the target (m)C site upon hot piperidine treatment. In accordance with the suppression of the strand cleavage at 5-trideuterio-methylcytosine observed in a similar AQ photosensitization, it is suggested that deprotonation at the C5-methyl group of an intermediate (m)C radical cation may occur as a key elementary reaction in the photooxidative strand cleavage at the (m)C site. Incorporation of an AQ sensitizer into the interior of a strand of the duplex enhanced the one-electron photooxidation of (m)C, presumably because of an increased intersystem crossing efficiency that may lead to efficient piperidine-induced strand cleavage at an (m)C site in a DNA duplex.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering Research Unit, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan.
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244
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Kanvah S, Schuster GB. Effect of positively charged backbone groups on radical cation migration and reaction in duplex DNA. CAN J CHEM 2011. [DOI: 10.1139/v10-145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A series of DNA oligomers were prepared that contain guanidinium linkages (positively charged) positioned selectively in place of and among the normal negatively charged phosphodiester backbone groups of duplex DNA. One-electron oxidation of these DNA oligomers by UV irradiation of a covalently linked anthraquinone group generates a radical cation (electron “hole”) that migrates by hopping through the DNA and is trapped at reactive sites, GG steps, to form mutated bases that are detected by strand cleavage after subsequent piperidine treatment of the irradiated DNA. Analysis of the strand cleavage pattern reveals that guanidinium substitution in these oligomers does not measurably affect the charge migration rate but it does inhibit reaction at nearby guanines.
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Affiliation(s)
- Sriram Kanvah
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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245
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Kawai K, Kodera H, Majima T. Photocatalytic formation of I-I bonds using DNA which enables detection of single nucleotide polymorphisms. J Am Chem Soc 2011; 132:14216-20. [PMID: 20860356 DOI: 10.1021/ja105850d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
By decreasing the HOMO energy gap between the base-pairs to increase the charge conductivity of DNA, the positive charge photochemically generated in DNA can be made to migrate along the π-way of DNA over long distances to form a long-lived charge-separated state. By fine-tuning the kinetics of the charge-transfer reactions, we designed a functionalized DNA system in which absorbed photon energy is converted into chemical energy to form I-I covalent bonds, where more than 100 I(2) molecules were produced per functionalized DNA. Utilizing the fact that charge-transfer kinetics through DNA is sensitive to the presence of a single mismatch that causes the perturbation of the π-stacks, single nucleotide polymorphisms (SNPs) in genomic sequences were detected by measuring the photon energy conversion efficiency in DNA by a conventional starch iodine method.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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246
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Tanabe K, Yamada H, Nishimoto SI. Preparation of Functionalized Oligodeoxynucleotides and Photochemical One-electron Oxidation of 5-Methylcytosine in DNA. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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247
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Lee SF, Pervaiz S. Assessment of Oxidative Stress-Induced DNA Damage by Immunoflourescent Analysis of 8-OxodG. Methods Cell Biol 2011; 103:99-113. [DOI: 10.1016/b978-0-12-385493-3.00005-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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248
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Warren JJ, Tronic TA, Mayer JM. Thermochemistry of proton-coupled electron transfer reagents and its implications. Chem Rev 2010; 110:6961-7001. [PMID: 20925411 PMCID: PMC3006073 DOI: 10.1021/cr100085k] [Citation(s) in RCA: 1193] [Impact Index Per Article: 85.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jeffrey J. Warren
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - Tristan A. Tronic
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - James M. Mayer
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
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249
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Kumar A, Sevilla MD. Proton-coupled electron transfer in DNA on formation of radiation-produced ion radicals. Chem Rev 2010; 110:7002-23. [PMID: 20443634 PMCID: PMC2947616 DOI: 10.1021/cr100023g] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
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250
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Bravaya KB, Kostko O, Dolgikh S, Landau A, Ahmed M, Krylov AI. Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra. J Phys Chem A 2010; 114:12305-17. [DOI: 10.1021/jp1063726] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oleg Kostko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stanislav Dolgikh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Musahid Ahmed
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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