Thematic Collection on Chemistry and Biology of DNA Damage

This Thematic Collection accompanies the review article entitled “An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals”. The organic chemistry of DNA damage is fundamentally important to diverse fields including medicinal chemistry, toxicology, and biotechnology. The Review entitled “An Overview of Chemical Processes That Damage Cellular DNA: Spontaneous Hydrolysis, Alkylation, and Reactions with Radicals” provides an overview of the common types of chemical reactions that lead to DNA damage under physiological conditions, while the additional Articles provide a complementary view of the methodologies involved in DNA damage analysis, the use of DNA adducts as biomarkers for the exposure to environmental toxins and mutagens, the importance of DNA repair processes, and the mechanisms by which specific drugs and mutagens carry out DNA alkylation and oxidation. Interested readers are directed to the 20th Anniversary Issue of Chemical Research in Toxicology that contains a number of relevant Reviews by leaders in the field of DNA damage chemistry and biology.”

-Kent S. Gates, Guest Editor University of Missouri–Columbia

Methodologies Involved in DNA Damage Analysis

Mutagenicity of the 1-Nitropyrene-DNA Adduct N-(Deoxyguanosin-8-yl)-1-aminopyrene in Mammalian Cells
Danielle L. Watt, Christopher D. Utzat, Pablo Hilario and Ashis K. Basu
DOI: 10.1021/tx700131e

GC/MS Methods To Quantify the 2-Deoxypentos-4-ulose and 3′-Phosphoglycolate Pathways of 4′ Oxidation of 2-Deoxyribose in DNA: Application to DNA Damage Produced by γ Radiation and Bleomycin
Bingzi Chen, Xinfeng Zhou, Koli Taghizadeh, Jingyang Chen, JoAnne Stubbe and Peter C. Dedon
DOI: 10.1021/tx700164y

Fluorescence Probing of Aminofluorene-Induced Conformational Heterogeneity in DNA Duplexes
Nidhi Jain, Yana K. Reshetnyak, Lan Gao, M. Paul Chiarelli and Bongsup P. Cho
DOI: 10.1021/tx7003536

Site-Specific Synthesis and Characterization of Oligonucleotides Containing an N⁶-(2-Deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine Lesion, the Ring-Opened Product from N7-Methylation of Deoxyguanosine
Plamen P. Christov, Kyle L. Brown, Ivan D. Kozekov, Michael P. Stone, Thomas M. Harris and Carmelo J. Rizzo
DOI: 10.1021/tx800352a

Proteomic Analysis of DNA-Protein Cross-Linking by Antitumor Nitrogen Mustards
Rachel L. Loeber, Erin D. Michaelson-Richie, Simona G. Codreanu, Daniel C. Liebler, Colin R. Campbell and Natalia Y. Tretyakova
DOI: 10.1021/tx900078y

Chemical Decomposition of 5-Aza-2′-deoxycytidine (Decitabine): Kinetic Analyses and Identification of Products by NMR, HPLC, and Mass Spectrometry
Daniel K. Rogstad, Jason L. Herring, Jacob A. Theruvathu, Artur Burdzy, Christopher C. Perry, Jonathan W. Neidigh and Lawrence C. Sowers
DOI: 10.1021/tx900131u

Tandem Mass Spectrometry-Based Detection of C4′-Oxidized Abasic Sites at Specific Positions in DNA Fragments
Goutam Chowdhury and F. Peter Guengerich
DOI: 10.1021/tx900115z

DNA Adducts as Biomarkers for Environmental Toxin and Mutagen Exposure

Analysis of DNA Adducts Formed in Vivo in Rats and Mice from 1,2-Dibromoethane, 1,2-Dichloroethane, Dibromomethane, and Dichloromethane Using HPLC/Accelerator Mass Spectrometry and Relevance to Risk Estimates
Kengo Watanabe, Rosa G. Liberman, Paul L. Skipper, Steven R. Tannenbaum and F. Peter Guengerich
DOI: 10.1021/tx700125p

Advanced Glycation End Products of DNA: Quantification of N²-(1-Carboxyethyl)-2′-deoxyguanosine in Biological Samples by Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry
Timothy Synold, Bixin Xi, Gerald E. Wuenschell, Daniel Tamae, James L. Figarola, Samuel Rahbar and John Termini
DOI: 10.1021/tx800224y

Development of a Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry Method for Analysis of Stable 4-Hydroxyequilenin-DNA Adducts in Human Breast Cancer Cells
Zhican Wang, Praneeth Edirisinghe, Johann Sohn, Zhihui Qin, Nicholas E. Geacintov, Gregory R. J. Thatcher and Judy L. Bolton
DOI: 10.1021/tx900063g

Importance of DNA Repair Processes

The Influence of Repair Pathways on the Cytotoxicity and Mutagenicity Induced by the Pyridyloxobutylation Pathway of Tobacco-Specific Nitrosamines
Li Li, Joana Perdigao, Anthony E. Pegg, Yanbin Lao, Stephen S. Hecht, Bruce R. Lindgren, Joyce T. Reardon, Aziz Sancar, Elizabeth V. Wattenberg and Lisa A. Peterson
DOI: 10.1021/tx9001572

In Vitro Replication and Repair Studies of Tandem Lesions Containing Neighboring Thymidine Glycol and 8-Oxo-7,8-dihydro-2′-deoxyguanosine
Yong Jiang, Yuesong Wang and Yinsheng Wang
DOI: 10.1021/tx8003449

Mechanisms of DNA Alkylation and Oxidation

Chemical Properties of the Leinamycin-Guanine Adduct in DNA
Tony Nooner, Sanjay Dutta, and Kent S. Gates
DOI: 10.1021/tx049964k

Enzyme-Activated, Hypoxia-Selective DNA Damage by 3-Amino-2-quinoxalinecarbonitrile 1,4-Di-N-oxide
Goutam Chowdhury, Delshanee Kotandeniya, J. Scott Daniels, Charles L. Barnes and Kent S. Gates
DOI: 10.1021/tx049836w

Aldo-Keto Reductase- and Cytochrome P450-Dependent Formation of Benzo[α]pyrene-Derived DNA Adducts in Human Bronchoalveolar Cells
Qian Ruan, Stacy L. Gelhaus, Trevor M. Penning, Ronald G. Harvey and Ian A. Blair
DOI: 10.1021/tx060180b

Identification of Adducts Formed in the Reaction of α-Acetoxy-N-nitrosopyrrolidine with Deoxyribonucleosides and DNA
Mingyao Wang, Yanbin Lao, Guang Cheng, Yongli Shi, Peter W. Villalta and Stephen S. Hecht
DOI: 10.1021/tx600332p

Site Specific N⁶-(2-Hydroxy-3,4-epoxybut-1-yl)adenine Oligodeoxynucleotide Adducts of 1,2,3,4-Diepoxybutane: Synthesis and Stability at Physiological pH
Sergey Antsypovich, Danaè Quirk-Dorr, Crystal Pitts and Natalia Tretyakova
DOI: 10.1021/tx060178k

Quantitative Correlation of Drug Bioactivation and Deoxyadenosine Alkylation by Acylfulvene
James F. Neels, Jiachang Gong, Xiang Yu and Shana J. Sturla
DOI: 10.1021/tx7001756

γ-Radiolysis and Hydroxyl Radical Produce Interstrand Cross-Links in DNA Involving Thymidine
Hui Ding and Marc M. Greenberg
DOI: 10.1021/tx7002307

Chemical–Biological Fingerprinting: Probing the Properties of DNA Lesions Formed by Peroxynitrite
Sarah Delaney, James C. Delaney and John M. Essigmann
DOI: 10.1021/tx700273u

Characterization of Oxaliplatin-DNA Adduct Formation in DNA and Differentiation of Cancer Cell Drug Sensitivity at Microdose Concentrations
Sang Soo Hah, Rhoda A. Sumbad, Ralph W. de Vere White, Kenneth W. Turteltaub and Paul T. Henderson
DOI: 10.1021/tx700376a

Formation of DNA-Protein Cross-Links Between γ-Hydroxypropanodeoxyguanosine and EcoRI
Laurie A. VanderVeen, Thomas M. Harris, Linda Jen-Jacobson and Lawrence J. Marnett
DOI: 10.1021/tx800092g

Mechanistic Aspects of the Formation of Guanidinohydantoin from Spiroiminodihydantoin under Acidic Conditions
Yu Ye, Barbara H. Munk, James G. Muller, Alexander Cogbill, Cynthia J. Burrows and H. Bernhard Schlegel
DOI: 10.1021/tx800402y

The Impact of NAT2 Acetylator Genotype on Mutagenesis and DNA Adducts from 2-Amino-9H-pyrido[2,3-b]indole
Robert J. Turesky, Jean Bendaly, Isil Yasa, Mark A. Doll and David W. Hein
DOI: 10.1021/tx800473w

Inherent Stereospecificity in the Reaction of Aflatoxin B₁ 8,9-Epoxide with Deoxyguanosine and Efficiency of DNA Catalysis
Kyle L. Brown, Urban Bren, Michael P. Stone and F. Peter Guengerich
DOI: 10.1021/tx900002g

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