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Corbella M, Voityuk AA, Curutchet C. How abasic sites impact hole transfer dynamics in GC-rich DNA sequences. Phys Chem Chem Phys 2018; 20:23123-23131. [DOI: 10.1039/c8cp03572e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hole transfer dynamics through GC-rich DNA duplexes containing abasic sites is strongly modulated by the nature of the unpaired nucleobase.
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Affiliation(s)
- Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Alexander A. Voityuk
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
- 08010 Barcelona
- Spain
- Institut de Química Computacional i Catàlisi and Departament de Química
- Universitat de Girona
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTC-UB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
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52
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Wang SR, Song YY, Wei L, Liu CX, Fu BS, Wang JQ, Yang XR, Liu YN, Liu SM, Tian T, Zhou X. Cucurbit[7]uril-Driven Host-Guest Chemistry for Reversible Intervention of 5-Formylcytosine-Targeted Biochemical Reactions. J Am Chem Soc 2017; 139:16903-16912. [PMID: 29091409 DOI: 10.1021/jacs.7b09635] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
5-Formylcytosine (5fC) is identified as one of the key players in active DNA demethylation and also as an epigenetic mark in mammals, thus representing a novel attractive target to chemical intervention. The current study represents an attempt to develop a reversible 5fC-targeted intervention tool. A supramolecular aldehyde reactive probe was therefore introduced for selective conversion of the 5fC to 5fC-AD nucleotide. Using various methods, we demonstrate that cucurbit[7]uril (CB7) selectively targets the 5fC-AD nucleotide in DNA, however, the binding of CB7 to 5fC-AD does not affect the hydrogen bonding properties of natural nucleobases in duplex DNA. Importantly, CB7-driven host-guest chemistry has been applied for reversible intervention of a variety of 5fC-targeted biochemical reactions, including restriction endonuclease digestion, DNA polymerase elongation, and polymerase chain reaction. On the basis of the current study, the macrocyclic CB7 creates obstructions that, through steric hindrance, prevent the enzyme from binding to the substrate, whereas the CB7/5fC-AD host-guest interactions can be reversed by treatment with adamantanamine. Moreover, fragment- and site-specific identification of 5fC modification in DNA has been accomplished without sequence restrictions. These findings thus show promising potential of host-guest chemistry for DNA/RNA epigenetics.
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Affiliation(s)
- Shao-Ru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Yan-Yan Song
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Lai Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Chao-Xing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Jia-Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Xi-Ran Yang
- College of Chemical Engineering and Technology, Wuhan University of Science and Technology , Wuhan 430081, Hubei, China
| | - Yi-Nong Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Si-Min Liu
- College of Chemical Engineering and Technology, Wuhan University of Science and Technology , Wuhan 430081, Hubei, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan 430072, Hubei, China
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53
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Nickoloff JA, Jones D, Lee SH, Williamson EA, Hromas R. Drugging the Cancers Addicted to DNA Repair. J Natl Cancer Inst 2017; 109:3832892. [PMID: 28521333 PMCID: PMC5436301 DOI: 10.1093/jnci/djx059] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/10/2017] [Indexed: 12/29/2022] Open
Abstract
Defects in DNA repair can result in oncogenic genomic instability. Cancers occurring from DNA repair defects were once thought to be limited to rare inherited mutations (such as BRCA1 or 2). It now appears that a clinically significant fraction of cancers have acquired DNA repair defects. DNA repair pathways operate in related networks, and cancers arising from loss of one DNA repair component typically become addicted to other repair pathways to survive and proliferate. Drug inhibition of the rescue repair pathway prevents the repair-deficient cancer cell from replicating, causing apoptosis (termed synthetic lethality). However, the selective pressure of inhibiting the rescue repair pathway can generate further mutations that confer resistance to the synthetic lethal drugs. Many such drugs currently in clinical use inhibit PARP1, a repair component to which cancers arising from inherited BRCA1 or 2 mutations become addicted. It is now clear that drugs inducing synthetic lethality may also be therapeutic in cancers with acquired DNA repair defects, which would markedly broaden their applicability beyond treatment of cancers with inherited DNA repair defects. Here we review how each DNA repair pathway can be attacked therapeutically and evaluate DNA repair components as potential drug targets to induce synthetic lethality. Clinical use of drugs targeting DNA repair will markedly increase when functional and genetic loss of repair components are consistently identified. In addition, future therapies will exploit artificial synthetic lethality, where complementary DNA repair pathways are targeted simultaneously in cancers without DNA repair defects.
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Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Dennie Jones
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
| | - Suk-Hee Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
| | - Robert Hromas
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
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54
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Admiraal SJ, O'Brien PJ. Reactivity and Cross-Linking of 5'-Terminal Abasic Sites within DNA. Chem Res Toxicol 2017; 30:1317-1326. [PMID: 28485930 DOI: 10.1021/acs.chemrestox.7b00057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nicking of the DNA strand immediately upstream of an internal abasic (AP) site produces 5'-terminal abasic (dRp) DNA. Both the intact and the nicked abasic species are reactive intermediates along the DNA base excision repair (BER) pathway and can be derailed by side reactions. Aberrant accumulation of the 5'-terminal abasic intermediate has been proposed to lead to cell death, so we explored its reactivity and compared it to the reactivity of the better-characterized internal abasic intermediate. We find that the 5'-terminal abasic group cross-links with the exocyclic amine of a nucleotide on the opposing strand to form an interstrand DNA-DNA cross-link (ICL). This cross-linking reaction has the same kinetic constants and follows the same pH dependence as the corresponding cross-linking reaction of intact abasic DNA, despite the changes in charge and flexibility engendered by the nick. However, the ICL that traps nicked abasic DNA has a shorter lifetime at physiological pH than the otherwise analogous ICL of intact abasic DNA due to the reversibility of the cross-linking reaction coupled with faster breakdown of the 5'-terminal abasic species via β-elimination. Unlike internal abasic DNA, 5'-terminal abasic DNA can also react with exocyclic amines of unpaired nucleotides at the 3'-end of the nick, thereby bridging the nick by connecting DNA strands of the same orientation. The discovery and characterization of cross-links between 5'-terminal abasic sites and exocyclic amines of both opposing and adjacent nucleotides add to our knowledge of DNA damage with the potential to disrupt DNA transactions.
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Affiliation(s)
- Suzanne J Admiraal
- Department of Biological Chemistry, University of Michigan Medical School , 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-5606, United States
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan Medical School , 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-5606, United States
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55
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Olmon ED, Delaney S. Differential Ability of Five DNA Glycosylases to Recognize and Repair Damage on Nucleosomal DNA. ACS Chem Biol 2017; 12:692-701. [PMID: 28085251 DOI: 10.1021/acschembio.6b00921] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Damage to genomic DNA leads to mutagenesis and disease. Repair of single base damage is initiated by DNA glycosylases, the first enzymes in the base excision repair pathway. Although eukaryotic packaging of chromosomal DNA in nucleosomes is known to decrease DNA glycosylase efficiency, the impact on individual glycosylases is unclear. Here, we present a model system in which we examine the repair of site-specific base damage in well-characterized nucleosome core particles by five different DNA glycosylases. We find that DNA glycosylase efficiency on nucleosome substrates depends not only on the geometric orientation of the damaged base but also on its identity, as well as on the size, structure, and mechanism of the glycosylase. We show via molecular modeling that inhibition of glycosylase activity is largely due to steric obstruction by the nucleosome core.
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Affiliation(s)
- Eric D. Olmon
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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56
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Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 771:99-127. [PMID: 28342455 DOI: 10.1016/j.mrrev.2017.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 02/07/2023]
Abstract
Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.
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57
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Llamas EM, Tome JPC, Rodrigues JMM, Torres T, Madder A. Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking. Org Biomol Chem 2017. [DOI: 10.1039/c7ob01269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.
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Affiliation(s)
- Eva M. Llamas
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
- Departamento de Química Orgánica
| | - João P. C. Tome
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - João M. M. Rodrigues
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Imdea-Nanoscience
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
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58
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Xu W, Kool D, O'Flaherty DK, Keating AM, Sacre L, Egli M, Noronha A, Wilds CJ, Zhao L. O 6-2'-Deoxyguanosine-butylene-O 6-2'-deoxyguanosine DNA Interstrand Cross-Links Are Replication-Blocking and Mutagenic DNA Lesions. Chem Res Toxicol 2016; 29:1872-1882. [PMID: 27768841 DOI: 10.1021/acs.chemrestox.6b00278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA interstrand cross-links (ICLs) are cytotoxic DNA lesions derived from reactions of DNA with a number of anti-cancer reagents as well as endogenous bifunctional electrophiles. Deciphering the DNA repair mechanisms of ICLs is important for understanding the toxicity of DNA cross-linking agents and for developing effective chemotherapies. Previous research has focused on ICLs cross-linked with the N7 and N2 atoms of guanine as well as those formed at the N6 atom of adenine; however, little is known about the mutagenicity of O6-dG-derived ICLs. Although less abundant, O6-alkylated guanine DNA lesions are chemically stable and highly mutagenic. Here, O6-2'-deoxyguanosine-butylene-O6-2'-deoxyguanosine (O6-dG-C4-O6-dG) is designed as a chemically stable ICL, which can be induced by the action of bifunctional alkylating agents. We investigate the DNA replication-blocking and mutagenic properties of O6-dG-C4-O6-dG ICLs during an important step in ICL repair, translesion DNA synthesis (TLS). The model replicative DNA polymerase (pol) Sulfolobus solfataricus P2 DNA polymerase B1 (Dpo1) is able to incorporate a correct nucleotide opposite the cross-linked template guanine of ICLs with low efficiency and fidelity but cannot extend beyond the ICLs. Translesion synthesis by human pol κ is completely inhibited by O6-dG-C4-O6-dG ICLs. Moderate bypass activities are observed for human pol η and S. solfataricus P2 DNA polymerase IV (Dpo4). Among the pols tested, pol η exhibits the highest bypass activity; however, 70% of the bypass products are mutagenic containing substitutions or deletions. The increase in the size of unhooked repair intermediates elevates the frequency of deletion mutation. Lastly, the importance of pol η in O6-dG-derived ICL bypass is demonstrated using whole cell extracts of Xeroderma pigmentosum variant patient cells and those complemented with pol η. Together, this study provides the first set of biochemical evidence for the mutagenicity of O6-dG-derived ICLs.
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Affiliation(s)
| | | | - Derek K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | | | - Lauralicia Sacre
- Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Anne Noronha
- Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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59
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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60
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Xu W, Ouellette A, Ghosh S, O'Neill TC, Greenberg MM, Zhao L. Mutagenic Bypass of an Oxidized Abasic Lesion-Induced DNA Interstrand Cross-Link Analogue by Human Translesion Synthesis DNA Polymerases. Biochemistry 2015; 54:7409-22. [PMID: 26626537 DOI: 10.1021/acs.biochem.5b01027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5'-(2-Phosphoryl-1,4-dioxobutane) (DOB) is an oxidized abasic site that is produced by several antitumor agents and γ-radiolysis. DOB reacts reversibly with a dA opposite the 3'-adjacent nucleotide to form DNA interstrand cross-links (ICLs), genotoxic DNA lesions that can block DNA replication and transcription. Translesion synthesis (TLS) is an important step in several ICL repair pathways to bypass unhooked intermediates generated by endonucleolytic incision. The instability of DOB-ICLs has made it difficult to learn about their TLS-mediated repair capability and mutagenic potential. We recently developed a method for chemically synthesizing oligonucleotides containing a modified DOB-ICL analogue. Herein, we examined the capabilities of several highly relevant eukaryotic TLS DNA polymerases (pols), including human pol η, pol κ, pol ι, pol ν, REV1, and yeast pol ζ, to bypass this DOB-ICL analogue. The prelesion, translesion, and postlesion replication efficiency and fidelity were examined. Pol η showed moderate bypass activity when encountering the DOB-ICL, giving major products one or two nucleotides beyond the cross-linked template nucleotide. In contrast, DNA synthesis by the other pols was stalled at the position before the cross-linked nucleotide. Steady-state kinetic data and liquid chromatography-mass spectrometry sequencing of primer extension products by pol η unambiguously revealed that pol η-mediated bypass is highly error-prone. Together, our study provides the first set of in vitro evidence that the DOB-ICL is a replication-blocking and highly miscoding lesion. Compared to several other TLS pols examined, pol η is likely to contribute to the TLS-mediated repair of the DOB-ICL in vivo.
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Affiliation(s)
| | | | - Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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61
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Kou Y, Koag MC, Lee S. N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA. J Am Chem Soc 2015; 137:14067-70. [PMID: 26517568 DOI: 10.1021/jacs.5b10172] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polβ-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polβ-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.
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Affiliation(s)
- Yi Kou
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Myong-Chul Koag
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Seongmin Lee
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
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62
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Abstract
How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.
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63
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Ghosh S, Greenberg MM. Correlation of Thermal Stability and Structural Distortion of DNA Interstrand Cross-Links Produced from Oxidized Abasic Sites with Their Selective Formation and Repair. Biochemistry 2015; 54:6274-83. [PMID: 26426430 DOI: 10.1021/acs.biochem.5b00860] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C4'-oxidized (C4-AP) and C5'-oxidized abasic sites (DOB) that are produced following abstraction of a hydrogen atom from the DNA backbone reversibly form cross-links selectively with dA opposite a 3'-adjacent nucleotide, despite the comparable proximity of an opposing dA. A previous report on UvrABC incision of DNA substrates containing stabilized analogues of the ICLs derived from C4-AP and DOB also indicated that the latter is repaired more readily by nucleotide excision repair [Ghosh, S., and Greenberg, M. M. (2014) Biochemistry 53, 5958-5965]. The source for selective cross-link formation was probed by comparing the reactivity of ICL analogues of C4-AP and DOB that mimic the preferred and disfavored cross-links with that of reagents that indirectly detect distortion by reacting with the nucleobases. The disfavored C4-AP and DOB analogues were each more reactive than the corresponding preferred cross-link substrates, suggesting that the latter are more stable, which is consistent with selective ICL formation. In addition, the preferred DOB analogue is more reactive than the respective C4-AP ICL, which is consistent with its more efficient incision by UvrABC. The conclusions drawn from the chemical probing experiments are corroborated by UV melting studies. The preferred ICLs exhibit melting temperatures higher than those of the corresponding disfavored isomers. These studies suggest that oxidized abasic sites form reversible interstrand cross-links with dA opposite the 3'-adjacent thymidine because these products are more stable and the thermodynamic preference is reflected in the transition states for their formation.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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64
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Weng L, Greenberg MM. Rapid Histone-Catalyzed DNA Lesion Excision and Accompanying Protein Modification in Nucleosomes and Nucleosome Core Particles. J Am Chem Soc 2015; 137:11022-31. [PMID: 26290445 DOI: 10.1021/jacs.5b05478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
C5'-Hydrogen atoms are frequently abstracted during DNA oxidation. The oxidized abasic lesion 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) is an electrophilic product of the C5'-radical. DOB is a potent irreversible inhibitor of DNA polymerase β, and forms interstrand cross-links in free DNA. We examined the reactivity of DOB within nucleosomes and nucleosome core particles (NCPs), the monomeric component of chromatin. Depending upon the position at which DOB is generated within a NCP, it is excised from nucleosomal DNA at a rate 275-1500-fold faster than that in free DNA. The half-life of DOB (7.0-16.8 min) in NCPs is shorter than any other abasic lesion. DOB's lifetime in NCPs is also significantly shorter than the estimated lifetime of an abasic site within a cell, suggesting that the observed chemistry would occur intracellularly. Histones also catalyze DOB excision when the lesion is present in the DNA linker region of a nucleosome. Schiff-base formation between DOB and histone proteins is detected in nucleosomes and NCPs, resulting in pyrrolone formation at the lysine residues. The lysines modified by DOB are often post-translationally modified. Consequently, the histone modifications described herein could affect the regulation of gene expression and may provide a chemical basis for the cytotoxicity of the DNA damaging agents that produce this lesion.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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65
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Zhao F, Wang B, Zhang X, Tian H, Wang W, Ru S. Induction of DNA base damage and strand breaks in peripheral erythrocytes and the underlying mechanism in goldfish (Carassius auratus) exposed to monocrotophos. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:613-624. [PMID: 25666866 DOI: 10.1007/s10695-015-0032-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
Using goldfish (Carassius auratus) as the model animal, the present study revealed the types of the DNA damage induced by monocrotophos, a highly toxic organophosphorus pesticide, and explored the mechanism underlying the DNA-damaging effect of this pesticide. Results of the alkaline comet assay showed that global DNA damage (including single- and double-strand breaks and alkali-labile sites) in peripheral erythrocytes of goldfish, measured as olive tail moment, was significantly increased by exposure to 0.01, 0.10, and 1.00 mg/L monocrotophos for 24, 48, 96, and 168 h. In particular, alkali-labile sites rather than single- or double-strand breaks, distinguished by the alkaline, pH 12.1, and neutral comet assays, were mainly induced by monocrotophos at 48 h. Oxidative damage in DNA bases and telomeric DNA was investigated by using the alkaline comet assay combined with endonuclease III or formamidopyrimidine DNA glycosylase and with fluorescence in situ hybridization, respectively. Further, glutathione peroxidase activity significantly decreased at 24 h but increased at 96 and 168 h, and malondialdehyde concentrations significantly increased at 48 h but gradually decreased at 96 and 168 h, which indicated an over-production of reactive oxygen species (ROS) at short exposure durations, but effective scavenging at long exposure durations in the peripheral blood tissues. Accordingly, our results suggest that DNA damage induced by monocrotophos in fish blood cells is possibly due to the inhibition of ROS scavenging and resulted accumulation of ROS.
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Affiliation(s)
- Fei Zhao
- Marine Life Science College, Ocean University of China, 5 Yushan Road, Qingdao, 266003, Shandong Province, People's Republic of China
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Zhao F, Wang B, Zhang X, Tian H, Wang W, Ru S. Induction of DNA base damage and strand breaks in peripheral erythrocytes and the underlying mechanism in goldfish (Carassius auratus) exposed to monocrotophos. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:613-624. [PMID: 25666866 DOI: 10.1007/s10695-015-0032-2/figures/8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/03/2015] [Indexed: 05/25/2023]
Abstract
Using goldfish (Carassius auratus) as the model animal, the present study revealed the types of the DNA damage induced by monocrotophos, a highly toxic organophosphorus pesticide, and explored the mechanism underlying the DNA-damaging effect of this pesticide. Results of the alkaline comet assay showed that global DNA damage (including single- and double-strand breaks and alkali-labile sites) in peripheral erythrocytes of goldfish, measured as olive tail moment, was significantly increased by exposure to 0.01, 0.10, and 1.00 mg/L monocrotophos for 24, 48, 96, and 168 h. In particular, alkali-labile sites rather than single- or double-strand breaks, distinguished by the alkaline, pH 12.1, and neutral comet assays, were mainly induced by monocrotophos at 48 h. Oxidative damage in DNA bases and telomeric DNA was investigated by using the alkaline comet assay combined with endonuclease III or formamidopyrimidine DNA glycosylase and with fluorescence in situ hybridization, respectively. Further, glutathione peroxidase activity significantly decreased at 24 h but increased at 96 and 168 h, and malondialdehyde concentrations significantly increased at 48 h but gradually decreased at 96 and 168 h, which indicated an over-production of reactive oxygen species (ROS) at short exposure durations, but effective scavenging at long exposure durations in the peripheral blood tissues. Accordingly, our results suggest that DNA damage induced by monocrotophos in fish blood cells is possibly due to the inhibition of ROS scavenging and resulted accumulation of ROS.
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Affiliation(s)
- Fei Zhao
- Marine Life Science College, Ocean University of China, 5 Yushan Road, Qingdao, 266003, Shandong Province, People's Republic of China
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Kalaitzakis D, Kouridaki A, Noutsias D, Montagnon T, Vassilikogiannakis G. Methylene Blue as a Photosensitizer and Redox Agent: Synthesis of 5-Hydroxy-1H-pyrrol-2(5H)-ones from Furans. Angew Chem Int Ed Engl 2015; 54:6283-7. [DOI: 10.1002/anie.201500744] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/09/2015] [Indexed: 11/11/2022]
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Kalaitzakis D, Kouridaki A, Noutsias D, Montagnon T, Vassilikogiannakis G. Methylene Blue as a Photosensitizer and Redox Agent: Synthesis of 5-Hydroxy-1H-pyrrol-2(5H)-ones from Furans. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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69
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Weng L, Zhou C, Greenberg MM. Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis. ACS Chem Biol 2015; 10:622-30. [PMID: 25475712 PMCID: PMC4336632 DOI: 10.1021/cb500737y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The
histone proteins in nucleosome core particles are known to
catalyze DNA cleavage at abasic and oxidized abasic sites, which are
produced by antitumor antibiotics and as a consequence of other modalities
of DNA damage. The lysine rich histone tails whose post-translational
modifications regulate genetic expression in cells are mainly responsible
for this chemistry. Cleavage at a C4′-oxidized abasic site
(C4-AP) concomitantly results in modification of lysine residues in
histone tails. Using LC-MS/MS, we demonstrate here that that Lys8,
-12, -16, and -20 of histone H4 were modified when C4-AP was incorporated
at a hot spot (superhelical location 1.5) for DNA damage within a
nucleosome core particle. A new DNA–protein cross-linking method
that provides a more quantitative analysis of individual amino acid
reactivity is also described. DNA–protein cross-links were
produced by an irreversible reaction between a nucleic acid electrophile
that was produced following oxidatively induced rearrangement of a
phenyl selenide derivative of thymidine (3) and nucleophilic
residues within proteins. In addition to providing high yields of
DNA–protein cross-links, kinetic analysis of the cross-linking
reaction yielded rate constants that enabled ranking the contributions
by individual or groups of amino acids. Cross-linking from 3 at superhelical location 1.5 revealed the following order of reactivity
for the nucleophilic amino acids in the histone H4 tail: His18 >
Lys16
> Lys20 ≈ Lys8, Lys12 > Lys5. Cross-linking via 3 will be generally useful for investigating DNA–protein
interactions.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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70
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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71
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Song Q, Cannistraro VJ, Taylor JS. Synergistic modulation of cyclobutane pyrimidine dimer photoproduct formation and deamination at a TmCG site over a full helical DNA turn in a nucleosome core particle. Nucleic Acids Res 2014; 42:13122-33. [PMID: 25389265 PMCID: PMC4245940 DOI: 10.1093/nar/gku1049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Sunlight-induced C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C or 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by DNA polymerase η and defines a probable mechanism for the origin of UV-induced C to T mutations. We have now determined the photoproduct formation and deamination rates for 10 consecutive T=mCG CPDs over a full helical turn at the dyad axis of a nucleosome and find that whereas photoproduct formation and deamination is greatly inhibited for the CPDs closest to the histone surface, it is greatly enhanced for the outermost CPDs. Replacing the G in a T=mCG CPD with A greatly decreased the deamination rate. These results show that rotational position and flanking sequence in a nucleosome can significantly and synergistically modulate CPD formation and deamination that contribute to C to T mutations associated with skin cancer induction and may have influenced the evolution of the human genome.
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Affiliation(s)
- Qian Song
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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Ghosh S, Greenberg MM. Nucleotide excision repair of chemically stabilized analogues of DNA interstrand cross-links produced from oxidized abasic sites. Biochemistry 2014; 53:5958-65. [PMID: 25208227 PMCID: PMC4172206 DOI: 10.1021/bi500914d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nucleotide excision repair is a primary pathway in cells for coping with DNA interstrand cross-links (ICLs). Recently, C4'-oxidized (C4-AP) and C5'-oxidized abasic sites (DOB) that are produced following hydrogen atom abstraction from the DNA backbone were found to produce ICLs. Because some of the ICLs derived from C4-AP and DOB are too unstable to characterize in biochemical processes, chemically stable analogues were synthesized [Ghosh, S., and Greenberg, M. M. (2014) J. Org. Chem. 79, 5948-5957]. UvrABC incision of DNA substrates containing stabilized analogues of the ICLs derived from C4-AP and DOB was examined. The incision pattern for the ICL related to the C4'-oxidized abasic site was typical for UvrABC substrates. UvrABC cleaved both strands of the substrate containing the C4-AP ICL analogue, but it was a poor substrate. UvrABC incised <30% of the C4-AP ICL analogue over an 8 h period, raising the possibility that this cross-link will be inefficiently repaired in cells. Furthermore, double-strand breaks were not detected upon incision of an internally labeled hairpin substrate containing the C4-AP ICL analogue. UvrABC incised the stabilized analogue of the DOB ICL more efficiently (~20% in 1 h). Furthermore, the incision pattern was unique, and the cross-linked substrate was converted into a single product, a double-strand break. The template strand was exclusively incised on the template strand on the 3'-side of the cross-linked dA. Although the outcomes of the interaction between UvrABC and these two cross-linked substrates are different from one another, they provide additional examples of how seemingly simple lesions (C4-AP and DOB) can potentially exert significant deleterious effects on biochemical processes.
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Affiliation(s)
- Souradyuti Ghosh
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Koag MC, Kou Y, Ouzon-Shubeita H, Lee S. Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine. Nucleic Acids Res 2014; 42:8755-66. [PMID: 24966350 PMCID: PMC4117778 DOI: 10.1093/nar/gku554] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
N7-Methyl-2′-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2′-fluorine-mediated transition-state destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2′-fluoro-m7dG (Fm7dG), by human DNA polymerase β (polβ) and solved three X-ray structures of polβ in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows polβ catalysis ∼300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson–Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the polβ-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by polβ. In addition, the polβ-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7-methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that polβ catalysis across m7dG is slow, yet highly accurate.
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Affiliation(s)
- Myong-Chul Koag
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Kou
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hala Ouzon-Shubeita
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Seongmin Lee
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
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Cadet J, Wagner JR. Oxidatively generated base damage to cellular DNA by hydroxyl radical and one-electron oxidants: similarities and differences. Arch Biochem Biophys 2014; 557:47-54. [PMID: 24820329 DOI: 10.1016/j.abb.2014.05.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 01/05/2023]
Abstract
Hydroxyl radical (OH) and one-electron oxidants that may be endogenously formed through oxidative metabolism, phagocytosis, inflammation and pathological conditions constitute the main sources of oxidatively generated damage to cellular DNA. It is worth mentioning that exposure of cells to exogenous physical agents (UV light, high intensity UV laser, ionizing radiation) and chemicals may also induce oxidatively generated damage to DNA. Emphasis is placed in this short review article on the mechanistic aspects of OH and one-electron oxidant-mediated formation of single and more complex damage (tandem lesions, intra- and interstrand cross-links, DNA-protein cross-links) in cellular DNA arising from one radical hit. This concerns DNA modifications that have been accurately measured using suitable analytical methods such as high performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Evidence is provided that OH and one-electron oxidants after generating neutral radicals and base radical cations respectively may partly induce common degradation pathways. In addition, selective oxidative reactions giving rise to specific degradation products of OH and one-electron oxidation reactions that can be used as representative biomarkers of these oxidants have been identified.
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Affiliation(s)
- Jean Cadet
- Institut Nanosciences et Cryogénie, CEA/Grenoble, F-38054 Grenoble Cedex 9, France; Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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