1
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Lin JC, Oludare A, Jung H. Connecting dots between nucleotide biosynthesis and DNA lesion repair/bypass in cancer. Biosci Rep 2024; 44:BSR20231382. [PMID: 39189649 PMCID: PMC11427732 DOI: 10.1042/bsr20231382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/01/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Purine and pyrimidine nucleotides are crucial building blocks for the survival of cells, and there are layers of pathways to make sure a stable supply of them including de novo nucleotide biosynthesis. Fast-growing cells including cancer cells have high demand for nucleotide, and they highly utilize the nucleotide biosynthesis pathways. Due to the nature of the fast-growing cells, they tend to make more errors in replication compared with the normal cells. Naturally, DNA repair and DNA lesion bypass are heavily employed in cancer cells to ensure fidelity and completion of the replication without stalling. There have been a lot of drugs targeting cancer that mimic the chemical structures of the nucleobase, nucleoside, and nucleotides, and the resistance toward those drugs is a serious problem. Herein, we have reviewed some of the representative nucleotide analog anticancer agents such as 5-fluorouracil, specifically their mechanism of action and resistance is discussed. Also, we have chosen several enzymes in nucleotide biosynthesis, DNA repair, and DNA lesion bypass, and we have discussed the known and potential roles of these enzymes in maintaining genomic fidelity and cancer chemotherapy.
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Affiliation(s)
- Jackson C Lin
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
| | - Ayobami Oludare
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
| | - Hunmin Jung
- The Division of Medicinal Chemistry, School of Pharmacy, The University of Connecticut, Storrs, Connecticut 06269, U.S.A
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2
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Mäkinen JJ, Rosenqvist P, Virta P, Metsä-Ketelä M, Belogurov GA. Probing the nucleobase selectivity of RNA polymerases with dual-coding substrates. J Biol Chem 2024; 300:107755. [PMID: 39260691 DOI: 10.1016/j.jbc.2024.107755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/13/2024] Open
Abstract
Formycin A (FOR) and pyrazofurin A (PYR) are nucleoside analogs with antiviral and antitumor properties. They are known to interfere with nucleic acid metabolism, but their direct effect on transcription is less understood. We explored how RNA polymerases (RNAPs) from bacteria, mitochondria, and viruses utilize FOR, PYR, and oxidized purine nucleotides. All tested polymerases incorporated FOR in place of adenine and PYR in place of uridine. FOR also exhibited surprising dual-coding behavior, functioning as a cytosine substitute, particularly for viral RNAP. In contrast, 8-oxoadenine and 8-oxoguanine were incorporated in place of uridine in addition to their canonical Watson-Crick codings. Our data suggest that the interconversion of canonical anti and alternative syn conformers underlies dual-coding abilities of FOR and oxidized purines. Structurally distinct RNAPs displayed varying abilities to utilize syn conformers during transcription. By examining base pairings that led to substrate incorporation and the entire spectrum of geometrically compatible pairings, we have gained new insights into the nucleobase selection processes employed by structurally diverse RNAPs. These insights may pave the way for advancements in antiviral therapies.
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Affiliation(s)
- Janne J Mäkinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
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3
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Averill JR, Lin JC, Jung J, Jung H. Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer. Nucleic Acids Res 2024; 52:4295-4312. [PMID: 38416579 PMCID: PMC11077093 DOI: 10.1093/nar/gkae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 03/01/2024] Open
Abstract
5-Fluorouracil (5-FU) is the first-line chemotherapeutic agent in colorectal cancer, and resistance to 5-FU easily emerges. One of the mechanisms of drug action and resistance of 5-FU is through DNA incorporation. Our quantitative reverse-transcription PCR data showed that one of the translesion synthesis (TLS) DNA polymerases, DNA polymerase η (polη), was upregulated within 72 h upon 5-FU administration at 1 and 10 μM, indicating that polη is one of the first responding polymerases, and the only TLS polymerase, upon the 5-FU treatment to incorporate 5-FU into DNA. Our kinetic studies revealed that 5-fluoro-2'-deoxyuridine triphosphate (5FdUTP) was incorporated across dA 41 and 28 times more efficiently than across dG and across inosine, respectively, by polη indicating that the mutagenicity of 5-FU incorporation is higher in the presence of inosine and that DNA lesions could lead to more mutagenic incorporation of 5-FU. Our polη crystal structures complexed with DNA and 5FdUTP revealed that dA:5FdUTP base pair is like dA:dTTP in the active site of polη, while 5FdUTP adopted 4-enol tautomer in the base pairs with dG and HX increasing the insertion efficiency compared to dG:dTTP for the incorrect insertions. These studies confirm that polη engages in the DNA incorporation and bypass of 5-FU.
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Affiliation(s)
- Jameson R Averill
- Division of Medicinal Chemistry, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Jackson C Lin
- Division of Medicinal Chemistry, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - John Jung
- Division of Medicinal Chemistry, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Hunmin Jung
- Division of Medicinal Chemistry, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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4
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Kruchinin AA, Kamzeeva PN, Zharkov DO, Aralov AV, Makarova AV. 8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals? Int J Mol Sci 2024; 25:1342. [PMID: 38279342 PMCID: PMC10816367 DOI: 10.3390/ijms25021342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.
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Affiliation(s)
- Alexander A. Kruchinin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
| | - Polina N. Kamzeeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alena V. Makarova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
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5
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Tian LF, Gao H, Yang S, Liu YP, Li M, Xu W, Yan XX. Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis. Int J Biol Macromol 2023; 253:126770. [PMID: 37683741 DOI: 10.1016/j.ijbiomac.2023.126770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Translesion synthesis (TLS) is a kind of DNA repair that maintains the stability of the genome and ensures the normal growth of life in cells under emergencies. Y-family DNA polymerases, as a kind of error-prone DNA polymerase, mainly perform TLS. Previous studies have suggested that the occurrence of tumors is associated with the overexpression of human DNA polymerase of the Y family. And the combination of Y-family DNA polymerase inhibitors is promising for cancer therapy. Here we report the functional and structural characterization of a member of the Y-family DNA polymerases, TTEDbh. We determine TTEDbh is an extreme TLS polymerase that can cross oxidative damage sites, and further identify the amino acids and novel structures that are critical for DNA binding, synthesis, fidelity, and oxidative damage bypass. Moreover, previously unnoticed structural elements with important functions have been discovered and analyzed. These studies provide a more experimental basis for further elucidating the molecular mechanisms of DNA polymerase in the Y family. It could also shed light on the design of drugs to target tumors.
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Affiliation(s)
- Li-Fei Tian
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongwei Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyu Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Ping Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingzhou Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Balint E, Unk I. For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases. Int J Mol Sci 2023; 25:363. [PMID: 38203535 PMCID: PMC10779026 DOI: 10.3390/ijms25010363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
DNA polymerases constitute a versatile group of enzymes that not only perform the essential task of genome duplication but also participate in various genome maintenance pathways, such as base and nucleotide excision repair, non-homologous end-joining, homologous recombination, and translesion synthesis. Polymerases catalyze DNA synthesis via the stepwise addition of deoxynucleoside monophosphates to the 3' primer end in a partially double-stranded DNA. They require divalent metal cations coordinated by active site residues of the polymerase. Mg2+ is considered the likely physiological activator because of its high cellular concentration and ability to activate DNA polymerases universally. Mn2+ can also activate the known DNA polymerases, but in most cases, it causes a significant decrease in fidelity and/or processivity. Hence, Mn2+ has been considered mutagenic and irrelevant during normal cellular function. Intriguingly, a growing body of evidence indicates that Mn2+ can positively influence some DNA polymerases by conferring translesion synthesis activity or altering the substrate specificity. Here, we review the relevant literature focusing on the impact of Mn2+ on the biochemical activity of a selected set of polymerases, namely, Polβ, Polλ, and Polµ, of the X family, as well as Polι and Polη of the Y family of polymerases, where congruous data implicate the physiological relevance of Mn2+ in the cellular function of these enzymes.
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Affiliation(s)
| | - Ildiko Unk
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, H-6726 Szeged, Hungary;
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7
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Eichman BF. Repair and tolerance of DNA damage at the replication fork: A structural perspective. Curr Opin Struct Biol 2023; 81:102618. [PMID: 37269798 PMCID: PMC10525001 DOI: 10.1016/j.sbi.2023.102618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/05/2023]
Abstract
The replication machinery frequently encounters DNA damage and other structural impediments that inhibit progression of the replication fork. Replication-coupled processes that remove or bypass the barrier and restart stalled forks are essential for completion of replication and for maintenance of genome stability. Errors in replication-repair pathways lead to mutations and aberrant genetic rearrangements and are associated with human diseases. This review highlights recent structures of enzymes involved in three replication-repair pathways: translesion synthesis, template switching and fork reversal, and interstrand crosslink repair.
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Affiliation(s)
- Brandt F Eichman
- Vanderbilt University, Department of Biological Sciences and Department of Biochemistry, 5270A MRBIII, 465 21st Ave S, Nashville, TN 37232 USA.
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8
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Osifová Z, Šála M, Dračínský M. Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives. ACS OMEGA 2023; 8:25538-25548. [PMID: 37483191 PMCID: PMC10357537 DOI: 10.1021/acsomega.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for life on Earth. Canonical nucleobases form base pairs according to two main geometries: Watson-Crick pairing, which enables the static functions of nucleic acids, such as the storing of genetic information; and Hoogsteen pairing, which facilitates the dynamic functions of these biomacromolecules. This precisely tuned system can be affected by oxidation or substitution of nucleobases, leading to changes in their hydrogen-bonding patterns. This paper presents an investigation into the intermolecular interactions of various 8-substituted purine derivatives with their hydrogen-bonding partners. The systems were analyzed using nuclear magnetic resonance spectroscopy and density functional theory calculations. Our results demonstrate that the stability of hydrogen-bonded complexes, or base pairs, depends primarily on the number of intermolecular H-bonds and their donor-acceptor alternation. No strong preferences for a particular geometry, either Watson-Crick or Hoogsteen, were found.
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Affiliation(s)
- Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
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9
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Gu S, Szymanski ES, Rangadurai AK, Shi H, Liu B, Manghrani A, Al-Hashimi HM. Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs. Nat Chem Biol 2023; 19:900-910. [PMID: 37095237 DOI: 10.1038/s41589-023-01306-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/08/2023] [Indexed: 04/26/2023]
Abstract
Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. Here, we show that DNA dynamics determine the frequency of misincorporating the A•G mismatch, and altered dynamics explain the high frequency of 8-oxoguanine (8OG) A•8OG misincorporation. NMR measurements revealed that Aanti•Ganti (population (pop.) of >91%) transiently forms sparsely populated and short-lived Aanti+•Gsyn (pop. of ~2% and kex = kforward + kreverse of ~137 s-1) and Asyn•Ganti (pop. of ~6% and kex of ~2,200 s-1) Hoogsteen conformations. 8OG redistributed the ensemble, rendering Aanti•8OGsyn the dominant state. A kinetic model in which Aanti+•Gsyn is misincorporated quantitatively predicted the dA•dGTP misincorporation kinetics by human polymerase β, the pH dependence of misincorporation and the impact of the 8OG lesion. Thus, 8OG increases replicative errors relative to G because oxidation of guanine redistributes the ensemble in favor of the mutagenic Aanti•8OGsyn Hoogsteen state, which exists transiently and in low abundance in the A•G mismatch.
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Affiliation(s)
- Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Base4, Durham, NC, USA
| | - Atul K Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Hospital for Sick Children, Toronto, Ontario, Canada
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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10
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Tew DJ, Hebert JM, Schmier BJ. Discovery and properties of a monoclonal antibody targeting 8-oxoA, an oxidized adenine lesion in DNA and RNA. Redox Biol 2023; 62:102658. [PMID: 36989571 PMCID: PMC10074937 DOI: 10.1016/j.redox.2023.102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/17/2023] Open
Abstract
8-oxoA, a major oxidation product of adenosine, is a mispairing, mutagenic lesion that arises in DNA and RNA when •OH radicals or one-electron oxidants attack the C8 adenine atom or polymerases misincorporate 8-oxo(d)ATP. The danger of 8-oxoA is underscored by the existence of dedicated cellular repair machinery that explicitly excise it from DNA, the attenuation of translation induced by 8-oxoA-mRNA or damaged ribosomes, and its potency as a TLR7 agonist. Here we present the discovery, purification, and biochemical characterization of a new mouse IgGk1 monoclonal antibody (6E4) that specifically targets 8-oxoA. Utilizing an AchE-based competitive ELISA assay, we demonstrate the selectivity of 6E4 for 8-oxoA over a plethora of canonical and chemically modified nucleosides including 8-oxoG, A, m6A, 2-oxoA, and 5-hoU. We further show the ability of 6E4 to exclusively recognize 8-oxoA in nucleoside triphosphates (8-oxoATP) and DNA/RNA oligonucleotides containing a single 8-oxoA. 6E4 also binds 8-oxoA in duplex DNA/RNA antigens where the lesion is either paired correctly or base mismatched. Our findings define the 8-oxoAde nucleobase as the critical epitope and indicate mAb 6E4 is ideally suited for a broad range of immunological applications in nucleic acid detection and quality control.
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11
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Servius HW, Pidugu LS, Sherman ME, Drohat AC. Rapid excision of oxidized adenine by human thymine DNA glycosylase. J Biol Chem 2022; 299:102756. [PMID: 36460098 PMCID: PMC9800633 DOI: 10.1016/j.jbc.2022.102756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Oxidation of DNA bases generates mutagenic and cytotoxic lesions that are implicated in cancer and other diseases. Oxidative base lesions, including 7,8-dihydro-8-oxoguanine, are typically removed through base excision repair. In addition, oxidized deoxynucleotides such as 8-oxo-dGTP are depleted by sanitizing enzymes to preclude DNA incorporation. While pathways that counter threats posed by 7,8-dihydro-8-oxoguanine are well characterized, mechanisms protecting against the major adenine oxidation product, 7,8-dihydro-8-oxoadenine (oxoA), are poorly understood. Human DNA polymerases incorporate dGTP or dCTP opposite oxoA, producing mispairs that can cause A→C or A→G mutations. oxoA also perturbs the activity of enzymes acting on DNA and causes interstrand crosslinks. To inform mechanisms for oxoA repair, we characterized oxoA excision by human thymine DNA glycosylase (TDG), an enzyme known to remove modified pyrimidines, including deaminated and oxidized forms of cytosine and 5-methylcystosine. Strikingly, TDG excises oxoA from G⋅oxoA, A⋅oxoA, or C⋅oxoA pairs much more rapidly than it acts on the established pyrimidine substrates, whereas it exhibits comparable activity for T⋅oxoA and pyrimidine substrates. The oxoA activity depends strongly on base pairing and is 370-fold higher for G⋅oxoA versus T⋅oxoA pairs. The intrinsically disordered regions of TDG contribute minimally to oxoA excision, whereas two conserved residues (N140 and N191) are catalytically essential. Escherichia coli mismatch-specific uracil DNA-glycosylase lacks significant oxoA activity, exhibiting excision rates 4 to 5 orders of magnitude below that of its ortholog, TDG. Our results reveal oxoA as an unexpectedly efficient purine substrate for TDG and underscore the large evolutionary divergence of TDG and mismatch-specific uracil DNA-glycosylase.
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12
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Li C, Xue Y, Ba X, Wang R. The Role of 8-oxoG Repair Systems in Tumorigenesis and Cancer Therapy. Cells 2022; 11:cells11233798. [PMID: 36497058 PMCID: PMC9735852 DOI: 10.3390/cells11233798] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Tumorigenesis is highly correlated with the accumulation of mutations. The abundant and extensive DNA oxidation product, 8-Oxoguanine (8-oxoG), can cause mutations if it is not repaired by 8-oxoG repair systems. Therefore, the accumulation of 8-oxoG plays an essential role in tumorigenesis. To avoid the accumulation of 8-oxoG in the genome, base excision repair (BER), initiated by 8-oxoguanine DNA glycosylase1 (OGG1), is responsible for the removal of genomic 8-oxoG. It has been proven that 8-oxoG levels are significantly elevated in cancer cells compared with cells of normal tissues, and the induction of DNA damage by some antitumor drugs involves direct or indirect interference with BER, especially through inducing the production and accumulation of reactive oxygen species (ROS), which can lead to tumor cell death. In addition, the absence of the core components of BER can result in embryonic or early post-natal lethality in mice. Therefore, targeting 8-oxoG repair systems with inhibitors is a promising avenue for tumor therapy. In this study, we summarize the impact of 8-oxoG accumulation on tumorigenesis and the current status of cancer therapy approaches exploiting 8-oxoG repair enzyme targeting, as well as possible synergistic lethality strategies involving exogenous ROS-inducing agents.
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Affiliation(s)
- Chunshuang Li
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Yaoyao Xue
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
- Correspondence: (X.B.); (R.W.)
| | - Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (X.B.); (R.W.)
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13
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Wu J, Zhang M, Song L, Tan Y, Taniguchi Y, Hipolito CJ, Zhang Y, Yin Y. Implications of N7-hydrogen and C8-keto on the base pairing, mutagenic potential and repair of 8-oxo-2'-deoxy-adenosine: Investigation by nucleotide analogues. Bioorg Chem 2022; 127:106029. [PMID: 35858520 DOI: 10.1016/j.bioorg.2022.106029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 11/02/2022]
Abstract
Oxidative lesions, such as 8-oxo-dG and 8-oxo-dA, are continuously generated from exposure to reactive oxygen species. While 8-oxo-dG has been extensively studied, 8-oxo-dA has not received as much attention until recently. Herein, we report the synthesis of duplex DNAs incorporating dA, 8-oxo-dA, 7-deaza-dA, 8-Br-dA, and 8-Br-7-deaza-dA, which have different substitutions at 7- and 8-position, for the investigation into the implications of N7-hydrogen and C8-keto on the base pairing preference, mutagenic potential and repair of 8-oxo-dA. Base pairing study suggested that the polar N7-hydrogen and C8-keto of 8-oxo-dA, rather than the syn-preference, might be essential for 8-oxo-dA to form a stable base pair with dG. Insertion and extension studies using KF-exo- and human DNA polymerase β indicated that the efficient dGTP insertion opposite 8-oxo-dA and extension past 8-oxo-dA:dG are contingent upon not only the stable base pair with dG, but also the flexibility of the active site in polymerase. The N7-hydrogen in 8-oxo-dA or C7-hydrogen in 7-deaza-dA and 8-Br-7-deaza-dA was suggested to be important for the recognition by hOGG1, although the excision efficiencies of 7-deaza-dA and 8-Br-7-deaza-dA were much lower than 8-oxo-dA. This study provides an insight into the structure-function relationship of 8-oxo-dA by nucleotide analogues.
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Affiliation(s)
- Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mengmeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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14
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Jung H, Rayala NK, Lee S. Effects of N7-Alkylguanine Conformation and Metal Cofactors on the Translesion Synthesis by Human DNA Polymerase η. Chem Res Toxicol 2022; 35:512-521. [PMID: 35239327 DOI: 10.1021/acs.chemrestox.1c00416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-enzymatic alkylation on DNA often generates N7-alkyl-2'-deoxyguanosine (N7alkylG) adducts as major lesions. N7alkylG adducts significantly block replicative DNA polymerases and can be bypassed by translesion synthesis (TLS) polymerases such as polymerase η (polη). To gain insights into the bypass of N7alkylG by TLS polymerases, we conducted kinetic and structural studies of polη catalyzing across N7BnG, a genotoxic lesion generated by the carcinogenic N-nitrosobenzylmethylamine. The presence of templating N7BnG in the polη catalytic site decreased the replication fidelity by ∼9-fold, highlighting the promutagenicity of N7BnG. The catalytic efficiency for dCTP incorporation opposite N7BnG decreased ∼22-fold and ∼7-fold compared to the incorporation opposite undamaged guanine in the presence of Mg2+ and Mn2+, respectively. A crystal structure of the complexes grown with polη, templating N7BnG, incoming dCTP, and Mg2+ ions showed the lack of the incoming nucleotide and metal cofactors in the polη catalytic site. Interestingly, the templating N7BnG adopted a syn conformation, which has not been observed in the published N7alkylG structures. The preferential formation of syn-N7BnG conformation at the templating site may deter the binding of an incoming dCTP, causing the inefficient bypass by polη. In contrast, the use of Mn2+ in place of Mg2+ in co-crystallization yielded a ternary complex displaying an anti-N7BnG:dCTP base pair and catalytic metal ions, which would be a close mimic of a catalytically competent state. We conclude that certain bulky N7-alkylG lesions can slow TLS polymerase-mediated bypass by adopting a catalytically unfavorable syn conformation in the replicating base pair site.
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Affiliation(s)
- Hunmin Jung
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Naveen Kumar Rayala
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
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15
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Aralov AV, Gubina N, Cabrero C, Tsvetkov VB, Turaev AV, Fedeles BI, Croy RG, Isaakova EA, Melnik D, Dukova S, Ryazantsev DY, Khrulev AA, Varizhuk AM, González C, Zatsepin TS, Essigmann JM. 7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli. Nucleic Acids Res 2022; 50:3056-3069. [PMID: 35234900 PMCID: PMC8989528 DOI: 10.1093/nar/gkac148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/09/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
This work investigated the structural and biological properties of DNA containing 7,8-dihydro-8-oxo-1,N6-ethenoadenine (oxo-ϵA), a non-natural synthetic base that combines structural features of two naturally occurring DNA lesions (7,8-dihydro-8-oxoadenine and 1,N6-ethenoadenine). UV-, CD-, NMR spectroscopies and molecular modeling of DNA duplexes revealed that oxo-ϵA adopts the non-canonical syn conformation (χ = 65º) and fits very well among surrounding residues without inducing major distortions in local helical architecture. The adduct remarkably mimics the natural base thymine. When considered as an adenine-derived DNA lesion, oxo-ϵA was >99% mutagenic in living cells, causing predominantly A→T transversion mutations in Escherichia coli. The adduct in a single-stranded vector was not repaired by base excision repair enzymes (MutM and MutY glycosylases) or the AlkB dioxygenase and did not detectably affect the efficacy of DNA replication in vivo. When the biological and structural data are viewed together, it is likely that the nearly exclusive syn conformation and thymine mimicry of oxo-ϵA defines the selectivity of base pairing in vitro and in vivo, resulting in lesion pairing with A during replication. The base pairing properties of oxo-ϵA, its strong fluorescence and its invisibility to enzymatic repair systems in vivo are features that are sought in novel DNA-based probes and modulators of gene expression.
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Affiliation(s)
- Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Nina Gubina
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute of Theoretical and Experimental Biophysics RAS, Pushchino 142290, Russia
| | - Cristina Cabrero
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - Anton V Turaev
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Bogdan I Fedeles
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G Croy
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | - Denis Melnik
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Svetlana Dukova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Dmitriy Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Alexei A Khrulev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid 28006, Spain
| | - Timofei S Zatsepin
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia.,Chemistry Department, Lomonosov Moscow State University, Moscow 119992, Russia
| | - John M Essigmann
- Department of Biological Engineering, Department of Chemistry and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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Suzuki T, Takeuchi M, Ozawa-Tamura A. Reactions of 3′,5′-di-O-acetyl-2′-deoxyguansoine and 3′,5′-di-O-acetyl-2′-deoxyadenosine to UV light in the presence of uric acid. Genes Environ 2022; 44:4. [PMID: 35063039 PMCID: PMC8781611 DOI: 10.1186/s41021-022-00234-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Introduction
Recently, it was revealed that uric acid is a photosensitizer of reactions of nucleosides on irradiation with UV light at wavelengths longer than 300 nm, and two products generated from 2′-deoxycytidine were identified. In the present study, UV reactions of acetylated derivatives of 2′-deoxyguansoine and 2′-deoxyadenosine were conducted and their products were identified.
Findings
Each reaction of 3′,5′-di-O-acetyl-2′-deoxyguansoine or 3′,5′-di-O-acetyl-2′-deoxyadenosine with UV light at wavelengths longer than 300 nm in the presence of uric acid generated several products. The products were separated by HPLC and identified by comparing UV and MS spectra of the products with previously reported values. The major products were spiroiminodihydantoin, imidazolone, and dehydro-iminoallantoin nucleosides for 3′,5′-di-O-acetyl-2′-deoxyguansoine, and an adenine base and a formamidopyrimidine nucleoside for 3′,5′-di-O-acetyl-2′-deoxyadenosine.
Conclusions
If these damages caused by uric acid with sunlight occur in DNA of skin cells, mutations may arise. We should pay attention to the genotoxicity of uric acid in terms of DNA damage to dGuo and dAdo sites mediated by sunlight.
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17
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Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4. Biochem J 2021; 478:1769-1781. [PMID: 33881499 DOI: 10.1042/bcj20210162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022]
Abstract
Nucleobases within DNA are attacked by reactive oxygen species to produce 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as major oxidative lesions. The high mutagenicity of oxoG is attributed to the lesion's ability to adopt syn-oxoG:anti-dA with Watson-Crick-like geometry. Recent studies have revealed that Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) inserts nucleotide opposite oxoA in an error-prone manner and accommodates syn-oxoA:anti-dGTP with Watson-Crick-like geometry, highlighting a promutagenic nature of oxoA. To gain further insights into the bypass of oxoA by Dpo4, we have conducted kinetic and structural studies of Dpo4 extending oxoA:dT and oxoA:dG by incorporating dATP opposite templating dT. The extension past oxoA:dG was ∼5-fold less efficient than that past oxoA:dT. Structural studies revealed that Dpo4 accommodated dT:dATP base pair past anti-oxoA:dT with little structural distortion. In the Dpo4-oxoA:dG extension structure, oxoA was in an anti conformation and did not form hydrogen bonds with the primer terminus base. Unexpectedely, the dG opposite oxoA exited the primer terminus site and resided in an extrahelical site, where it engaged in minor groove contacts to the two immediate upstream bases. The extrahelical dG conformation appears to be induced by the stabilization of anti-oxoA conformation via bifurcated hydrogen bonds with Arg332. This unprecedented structure suggests that Dpo4 may use Arg332 to sense 8-oxopurines at the primer terminus site and slow the extension from the mismatch by promoting anti conformation of 8-oxopurines.
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18
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Rozelle AL, Cheun Y, Vilas CK, Koag MC, Lee S. DNA interstrand cross-links induced by the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine. Nat Commun 2021; 12:1897. [PMID: 33772030 PMCID: PMC7997976 DOI: 10.1038/s41467-021-22273-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/11/2021] [Indexed: 12/21/2022] Open
Abstract
Oxidative damage to DNA generates 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as two major lesions. Despite the comparable prevalence of these lesions, the biological effects of oxoA remain poorly characterized. Here we report the discovery of a class of DNA interstrand cross-links (ICLs) involving oxidized nucleobases. Under oxidative conditions, oxoA, but not oxoG, readily reacts with an opposite base to produce ICLs, highlighting a latent alkylating nature of oxoA. Reactive halogen species, one-electron oxidants, and the myeloperoxidase/H2O2/Cl− system induce oxoA ICLs, suggesting that oxoA-mediated cross-links may arise endogenously. Nucleobase analog studies suggest C2-oxoA is covalently linked to N2-guanine and N3-adenine for the oxoA-G and oxoA-A ICLs, respectively. The oxoA ICLs presumably form via the oxidative activation of oxoA followed by the nucleophilic attack by an opposite base. Our findings provide insights into oxoA-mediated mutagenesis and contribute towards investigations of oxidative stress-induced ICLs and oxoA-based latent alkylating agents. 7,8-dihydro-8-oxoguanine and 7,8-dihydro-8-oxoadenine (oxoA) are generated upon oxidative damage to DNA, but the biological effects of oxoA are not well known. Here, the authors report that only oxoA forms DNA interstrand crosslinks (ICLs) upon secondary oxidation and that these ICLs can be induced by reactive halogen species, one-electron oxidants and the myeloperoxidase/H2O2/Cl- system.
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Affiliation(s)
- Aaron L Rozelle
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Young Cheun
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Caroline K Vilas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Myong-Chul Koag
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Seongmin Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.
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19
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Translesion synthesis of the major nitrogen mustard-induced DNA lesion by human DNA polymerase η. Biochem J 2021; 477:4543-4558. [PMID: 33175093 DOI: 10.1042/bcj20200767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022]
Abstract
Nitrogen mustards are among the first modern anticancer chemotherapeutics that are still widely used as non-specific anticancer alkylating agents. While the mechanism of action of mustard drugs involves the generation of DNA interstrand cross-links, the predominant lesions produced by these drugs are nitrogen half-mustard-N7-dG (NHMG) adducts. The bulky major groove lesion NHMG, if left unrepaired, can be bypassed by translesion synthesis (TLS) DNA polymerases. However, studies of the TLS past NHMG have not been reported so far. Here, we present the first synthesis of an oligonucleotide containing a site-specific NHMG. We also report kinetic and structural characterization of human DNA polymerase η (polη) bypassing NHMG. The templating NHMG slows dCTP incorporation ∼130-fold, while it increases the misincorporation frequency ∼10-30-fold, highlighting the promutagenic nature of NHMG. A crystal structure of polη incorporating dCTP opposite NHMG shows a Watson-Crick NHMG:dCTP base pair with a large propeller twist angle. The nitrogen half-mustard moiety fits snugly into an open cleft created by the Arg61-Trp64 loop of polη, suggesting a role of the Arg61-Trp64 loop in accommodating bulky major groove adducts during lesion bypass. Overall, our results presented here to provide first insights into the TLS of the major DNA adduct formed by nitrogen mustard drugs.
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20
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Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4. Biochem J 2021; 477:2859-2871. [PMID: 32686822 DOI: 10.1042/bcj20200449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 01/28/2023]
Abstract
Reactive oxygen species induced by ionizing radiation and metabolic pathways generate 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as two major forms of oxidative damage. The mutagenicity of oxoG, which promotes G to T transversions, is attributed to the lesion's conformational flexibility that enables Hoogsteen base pairing with dATP in the confines of DNA polymerases. The mutagenesis mechanism of oxoA, which preferentially causes A to C transversions, remains poorly characterized. While structures for oxoA bypass by human DNA polymerases are available, that of prokaryotic DNA polymerases have not been reported. Herein, we report kinetic and structural characterizations of Sulfolobus solfataricus Dpo4 incorporating a nucleotide opposite oxoA. Our kinetic studies show oxoA at the templating position reduces the replication fidelity by ∼560-fold. The catalytic efficiency of the oxoA:dGTP insertion is ∼300-fold greater than that of the dA:dGTP insertion, highlighting the promutagenic nature of oxoA. The relative efficiency of the oxoA:dGTP misincorporation is ∼5-fold greater than that of the oxoG:dATP misincorporation, suggesting the mutagenicity of oxoA is comparable to that of oxoG. In the Dpo4 replicating base pair site, oxoA in the anti-conformation forms a Watson-Crick base pair with an incoming dTTP, while oxoA in the syn-conformation assumes Hoogsteen base pairing with an incoming dGTP, displaying the dual coding potential of the lesion. Within the Dpo4 active site, the oxoA:dGTP base pair adopts a Watson-Crick-like geometry, indicating Dpo4 influences the oxoA:dGTP base pair conformation. Overall, the results reported here provide insights into the miscoding properties of the major oxidative adenine lesion during translesion synthesis.
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21
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Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase. Biochem J 2020; 477:4797-4810. [PMID: 33258913 DOI: 10.1042/bcj20200800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022]
Abstract
The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e., xanthine) forms three Watson-Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson-Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.
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