1
|
Ahmed A, Kato N, Gautier J. Replication-Independent ICL Repair: From Chemotherapy to Cell Homeostasis. J Mol Biol 2024; 436:168618. [PMID: 38763228 PMCID: PMC11227339 DOI: 10.1016/j.jmb.2024.168618] [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: 03/18/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Interstrand crosslinks (ICLs) are a type of covalent lesion that can prevent transcription and replication by inhibiting DNA strand separation and instead trigger cell death. ICL inducing compounds are commonly used as chemotherapies due to their effectiveness in inhibiting cell proliferation. Naturally occurring crosslinking agents formed from metabolic processes can also pose a challenge to genome stability especially in slowly or non-dividing cells. Cells maintain a variety of ICL repair mechanisms to cope with this stressor within and outside the S phase of the cell cycle. Here, we discuss the mechanisms of various replication-independent ICL repair pathways and how crosslink repair efficiency is tied to aging and disease.
Collapse
Affiliation(s)
- Arooba Ahmed
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Niyo Kato
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA.
| |
Collapse
|
2
|
Islam T, Shim G, Melton D, Lewis CD, Lei Z, Gates KS. Ultrafast Reaction of the Drug Hydralazine with Apurinic/Apyrimidinic Sites in DNA Gives Rise to a Stable Triazolo[3,4- a]phthalazine Adduct. Chem Res Toxicol 2024; 37:1023-1034. [PMID: 38743824 DOI: 10.1021/acs.chemrestox.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The clinically used antihypertensive agent hydralazine rapidly generates hydrazone-derived adducts by reaction with apurinic/apyrimidinic (also known as abasic or AP) sites in many different sequences of duplex DNA. The reaction rates are comparable to those of some AP-trapping reagents previously described as "ultrafast." Initially, reversible formation of a hydrazone adduct is followed by an oxidative cyclization reaction that generates a chemically stable triazolo[3,4-a]phthalazine adduct. The net result is that the reaction of hydralazine with AP sites in duplex DNA yields a rapid and irreversible adduct formation. Although the hydrazone and triazolo[3,4-a]phthalazine adducts differ by only two mass units, it was possible to use MALDI-TOF-MS and ESI-QTOF-nanospray-MS to quantitatively characterize mixtures of these adducts by deconvolution of overlapping isotope envelopes. Reactions of hydralazine with the endogenous ketone pyruvate do not prevent the formation of the hydralazine-AP adducts, providing further evidence that these adducts have the potential to form in cellular DNA. AP sites are ubiquitous in cellular DNA, and rapid, irreversible adduct formation by hydralazine could be relevant to the pathogenesis of systemic drug-induced lupus erythematosus experienced by some patients. Finally, hydralazine might be developed as a probe for the detection of AP sites, the study of cellular BER, and marking the location of AP sites in DNA-sequencing analyses.
Collapse
Affiliation(s)
- Tanhaul Islam
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Garam Shim
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Douglas Melton
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Calvin D Lewis
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Zhentian Lei
- University of Missouri, MU Metabolomics Center, 240f Christopher S. Bond Life Science Center, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| |
Collapse
|
3
|
Wang Y, Wang F, Li L, Zhang L, Song M, Jiang G. Comprehensive Toxicological Assessment of Halobenzoquinones in Drinking Water at Environmentally Relevant Concentration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9125-9134. [PMID: 38743861 DOI: 10.1021/acs.est.4c03308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Halobenzoquinones (HBQs), an emerging unregulated category of disinfection byproduct (DBP) in drinking water, have aroused an increasing concern over their potential health risks. However, the chronic toxicity of HBQs at environmentally relevant concentrations remains largely unknown. Here, the occurrence and concentrations of 13 HBQs in drinking water from a northern megacity in China were examined using ultrahigh performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-MS/MS). Four HBQs, including 2,6-dichloro-1,4-benzoquinone (2,6-DCBQ), 2,6-dibromo-1,4-benzoquinone (2,6-DBBQ), 2,3,6-trichloro-1,4-benzoquinone (TriCBQ), and 2,5-dibromo-1,4-benzoquinone (2,5-DBBQ), were detected beyond 50% occurrence frequency and at median concentrations from 4 to 50 ng/L. The chronic toxicity of these four HBQs to normal human colon and liver cells (FHC and THLE-2) was investigated at these concentrations. After 90 days of exposure, 2,5-DBBQ and 2,6-DCBQ induced the highest levels of oxidative stress and deoxyribonucleic acid (DNA) damage in colon and liver cells, respectively. Moreover, 2,5-DBBQ and 2,6-DCBQ were also found to induce epithelial-mesenchymal transition (EMT) in normal human liver cells via the extracellular signal regulated kinase (ERK) signaling pathway. Importantly, heating to 100 °C (boiling) was found to efficiently reduce the levels of these four HBQs in drinking water. These results suggested that environmentally relevant concentrations of HBQs could induce cytotoxicity and genotoxicity in normal human cells, and boiling is a highly efficient way of detoxification for HBQs.
Collapse
Affiliation(s)
- Yuanyuan Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Fengbang Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Li
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Lan Zhang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
Wang J, Takyi NA, Hsiao YC, Tang Q, Chen YT, Liu CW, Ma J, Qi R, Bian K, Peng Z, Essigmann JM, Lu K, Wetmore SD, Li D. Stable Interstrand Cross-Links Generated from the Repair of 1, N6-Ethenoadenine in DNA by α-Ketoglutarate/Fe(II)-Dependent Dioxygenase ALKBH2. J Am Chem Soc 2024; 146:10381-10392. [PMID: 38573229 PMCID: PMC11060877 DOI: 10.1021/jacs.3c12890] [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] [Indexed: 04/05/2024]
Abstract
DNA cross-links severely challenge replication and transcription in cells, promoting senescence and cell death. In this paper, we report a novel type of DNA interstrand cross-link (ICL) produced as a side product during the attempted repair of 1,N6-ethenoadenine (εA) by human α-ketoglutarate/Fe(II)-dependent enzyme ALKBH2. This stable/nonreversible ICL was characterized by denaturing polyacrylamide gel electrophoresis analysis and quantified by high-resolution LC-MS in well-matched and mismatched DNA duplexes, yielding 5.7% as the highest level for cross-link formation. The binary lesion is proposed to be generated through covalent bond formation between the epoxide intermediate of εA repair and the exocyclic N6-amino group of adenine or the N4-amino group of cytosine residues in the complementary strand under physiological conditions. The cross-links occur in diverse sequence contexts, and molecular dynamics simulations rationalize the context specificity of cross-link formation. In addition, the cross-link generated from attempted εA repair was detected in cells by highly sensitive LC-MS techniques, giving biological relevance to the cross-link adducts. Overall, a combination of biochemical, computational, and mass spectrometric methods was used to discover and characterize this new type of stable cross-link both in vitro and in human cells, thereby uniquely demonstrating the existence of a potentially harmful ICL during DNA repair by human ALKBH2.
Collapse
Affiliation(s)
- Jie Wang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| |
Collapse
|
5
|
Price NE, Gates KS. Novel Processes Associated with the Repair of Interstrand Cross-Links Derived from Abasic Sites in Duplex DNA: Roles for the Base Excision Repair Glycosylase NEIL3 and the SRAP Protein HMCES. Chem Res Toxicol 2024; 37:199-207. [PMID: 38198604 DOI: 10.1021/acs.chemrestox.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Recent studies have defined a novel pathway for the repair of interstrand cross-links derived from the reaction of an adenine residue with an apurinic/apyrimidinic (AP) site on the opposing strand of DNA (dA-AP ICL). Stalling of a replication fork at the dA-AP ICL triggers TRAIP-dependent ubiquitylation of the CMG helicase that recruits the base excision repair glycosylase NEIL3 to the lesion. NEIL3 unhooks the dA-AP ICL to regenerate the native adenine residue on one strand and an AP site on the other strand. Covalent capture of the abasic site by the SRAP protein HMCES protects against genomic instability that would result from cleavage of the abasic site in the context of single-stranded DNA at the replication fork. After repair synthesis moves the HMCES-AP adduct into the context of double-stranded DNA, the DNA-protein cross-link is resolved by a nonproteolytic mechanism involving dissociation of thiazolidine attachment. The AP site in duplex DNA is then repaired by the base excision repair pathway.
Collapse
Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| |
Collapse
|
6
|
Gomina A, Islam T, Shim G, Lei Z, Gates KS. Formation and Properties of DNA Adducts Generated by Reactions of Abasic Sites with 1,2-Aminothiols Including Cysteamine, Cysteine Methyl Ester, and Peptides Containing N-Terminal Cysteine Residues. Chem Res Toxicol 2024; 37:395-406. [PMID: 38181204 DOI: 10.1021/acs.chemrestox.3c00344] [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] [Indexed: 01/07/2024]
Abstract
The reaction of 1,2-aminothiol groups with aldehyde residues in aqueous solution generates thiazolidine products, and this process has been developed as a catalyst-free click reaction for bioconjugation. The work reported here characterized reactions of the biologically relevant 1,2-aminothiols including cysteamine, cysteine methyl ester, and peptides containing N-terminal cysteine residues with the aldehyde residue of apurinic/apyrimidinic (AP) sites in DNA oligomers. These 1,2-aminothiol-containing compounds rapidly generated adducts with AP sites in single-stranded and double-stranded DNA. NMR and MALDI-TOF-MS analyses provided evidence that the reaction generated a thiazolidine product. Conversion of an AP site to a thiazolidine-AP adduct protected against the rapid cleavage normally induced at AP sites by the endonuclease action of the enzyme APE1 and the AP-lyase activity of the biogenic amine spermine. In the presence of excess 1,2-aminothiols, the thiazolidine-AP adducts underwent slow strand cleavage via a β-lyase reaction that generated products with 1,2-aminothiol-modified sugar residues on the 3'-end of the strand break. In the absence of excess 1,2-aminothiols, the thiazolidine-AP adducts dissociated to release the parent AP-containing oligonucleotide. The properties of the thiazolidine-AP adducts described here mirror critical properties of SRAP proteins HMCES and YedK that capture AP sites in single-stranded regions of cellular DNA and protect them from cleavage.
Collapse
Affiliation(s)
- Anuoluwapo Gomina
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Garam Shim
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Zhentian Lei
- MU Metabolomics Center, University of Missouri, 240F Christopher S. Bond Life Science Center, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| |
Collapse
|
7
|
Rama-Garda R, Martin-Ortega MD, Sánchez ADJ, Priego J, de Blas J, Torrado A, Domínguez E, Haro R, Rivera-Sagredo A, Román JP, Lorite MJ, Johansson HE, Loza MI, Amigo J, Sobrino B, Lallena MJ, Toledo MÁ. Design, synthesis and validation of a new Crimped Head-Piece for DNA-Encoded libraries generation. Bioorg Med Chem 2024; 99:117596. [PMID: 38232459 DOI: 10.1016/j.bmc.2024.117596] [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: 10/13/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Codification of DNA Encoded Libraries (DELs) is critical for successful ligand identification of molecules that bind a protein of interest (POI). There are different encoding strategies that permit, for instance, the customization of a DEL for testing single or dual pharmacophores (single strand DNA) or for producing and screening large diversity libraries of small molecules (double strand DNA). Both approaches challenges, either from the synthetic and encoding point of view, or from the selection methodology to be utilized for the screening. The Head-Piece contains the DNA sequence that is attached to a chemical compound, allowing the encoding of each molecule with a unique DNA tag. Designing the Head-Piece for a DNA-encoded library involves careful consideration of several key aspects including DNA barcode identity, sequence length and attachment chemistry. Here we describe a double stranded DNA versatile Head-Piece that can be used for the generation of single or dual pharmacophore libraries, but also shows other advanced DEL functionalities, stability and enlarged encoding capacity.
Collapse
Affiliation(s)
- Ramón Rama-Garda
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain; BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain.
| | - María Dolores Martin-Ortega
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - Julián Priego
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Jesús de Blas
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alicia Torrado
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Eduardo Domínguez
- Genomic Medicine, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña, Spain
| | - Rubén Haro
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alfonso Rivera-Sagredo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - José Pablo Román
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - María José Lorite
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - María Isabel Loza
- BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain
| | - Jorge Amigo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - Beatriz Sobrino
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - María José Lallena
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Miguel Ángel Toledo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| |
Collapse
|
8
|
Gusti Ngurah Putu EP, Cattiaux L, Lavergne T, Pommier Y, Bombard S, Granzhan A. Unprecedented reactivity of polyamines with aldehydic DNA modifications: structural determinants of reactivity, characterization and enzymatic stability of adducts. Nucleic Acids Res 2023; 51:10846-10866. [PMID: 37850658 PMCID: PMC10639052 DOI: 10.1093/nar/gkad837] [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: 05/23/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3'-tetrahydrofuro[2,3,4-ef]-1,4-diazepane ('ribodiazepane') scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3'-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3' end-blocking DNA lesions.
Collapse
Affiliation(s)
- Eka Putra Gusti Ngurah Putu
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Laurent Cattiaux
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Thomas Lavergne
- DCM, CNRS UMR5250, Université Grenoble Alpes, 38000 Grenoble, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology & Developmental Therapeutics Branch, CCR-NCI, NIH, Bethesda, MD 20892, USA
| | - Sophie Bombard
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anton Granzhan
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| |
Collapse
|
9
|
Bellamri M, Terrell JT, Brandt K, Gruppi F, Turesky RJ, Rizzo CJ. Anthracyclines React with Apurinic/Apyrimidinic Sites in DNA. ACS Chem Biol 2023; 18:1315-1323. [PMID: 37200590 PMCID: PMC10391585 DOI: 10.1021/acschembio.3c00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The combination of doxorubicin (Adriamycin) and cyclophosphamide, referred to as AC chemotherapy, is commonly used for the clinical treatment of breast and other cancers. Both agents target DNA with cyclophosphamide causing alkylation damage and doxorubicin stabilizing the topoisomerase II-DNA complex. We hypothesize a new mechanism of action whereby both agents work in concert. DNA alkylating agents, such as nitrogen mustards, increase the number of apurinic/apyrimidinic (AP) sites through deglycosylation of labile alkylated bases. Herein, we demonstrate that anthracyclines with aldehyde-reactive primary and secondary amines form covalent Schiff base adducts with AP sites in a 12-mer DNA duplex, calf thymus DNA, and MDA-MB-231 human breast cancer cells treated with nor-nitrogen mustard and the anthracycline mitoxantrone. The anthracycline-AP site conjugates are characterized and quantified by mass spectrometry after NaB(CN)H3 or NaBH4 reduction of the Schiff base. If stable, the anthracycline-AP site conjugates represent bulky adducts that may block DNA replication and contribute to the cytotoxic mechanism of therapies involving combinations of anthracyclines and DNA alkylating agents.
Collapse
|
10
|
Nagatsugi F, Onizuka K. Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids. CHEM REC 2023; 23:e202200194. [PMID: 36111635 DOI: 10.1002/tcr.202200194] [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: 08/03/2022] [Revised: 08/31/2022] [Indexed: 11/06/2022]
Abstract
DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T-T/U-U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.
Collapse
Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| |
Collapse
|
11
|
Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [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: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
Collapse
Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| |
Collapse
|
12
|
Cui Y, Wang Y. Mass spectrometry-based DNA adductomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
13
|
Amin SM, Islam T, Price NE, Wallace A, Guo X, Gomina A, Heidari M, Johnson KM, Lewis CD, Yang Z, Gates KS. Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA. ACS OMEGA 2022; 7:36888-36901. [PMID: 36278095 PMCID: PMC9583646 DOI: 10.1021/acsomega.2c05736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.
Collapse
Affiliation(s)
- Saosan
Binth Md. Amin
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Amanda Wallace
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Xu Guo
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Anuoluwapo Gomina
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Marjan Heidari
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Calvin D. Lewis
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| |
Collapse
|
14
|
Huskova A, Dinesh DC, Srb P, Boura E, Veverka V, Silhan J. Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model. Nucleic Acids Res 2022; 50:10436-10448. [PMID: 36155818 PMCID: PMC9561275 DOI: 10.1093/nar/gkac793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block the replication machinery that can cause a genomic instability. Ubiquitous abasic DNA sites are particularly susceptible to spontaneous cross-linking with a base from the opposite DNA strand. Detection of a crosslink induces the DNA helicase ubiquitination that recruits NEIL3, a DNA glycosylase responsible for the lesion removal. NEIL3 utilizes several zinc finger domains indispensable for its catalytic NEI domain repairing activity. They recruit NEIL3 to the repair site and bind the single-stranded DNA. However, the molecular mechanism underlying their roles in the repair process is unknown. Here, we report the structure of the tandem zinc-finger GRF domain of NEIL3 and reveal the molecular details of its interaction with DNA. Our biochemical data indicate the preferential binding of the GRF domain to the replication fork. In addition, we obtained a structure for the catalytic NEI domain in complex with the DNA reaction intermediate that allowed us to construct and validate a model for the interplay between the NEI and GRF domains in the recognition of an interstrand cross-link. Our results suggest a mechanism for recognition of the DNA replication X-structure by NEIL3, a key step in the interstrand cross-link repair.
Collapse
Affiliation(s)
- Andrea Huskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Dhurvas Chandrasekaran Dinesh
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| |
Collapse
|
15
|
Onizuka K, Yamano Y, Abdelhady AM, Nagatsugi F. Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids. Org Biomol Chem 2022; 20:4699-4708. [PMID: 35622064 DOI: 10.1039/d2ob00551d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.
Collapse
Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| |
Collapse
|
16
|
Jha JS, Yin J, Haldar T, Wang Y, Gates KS. Reconsidering the Chemical Nature of Strand Breaks Derived from Abasic Sites in Cellular DNA: Evidence for 3'-Glutathionylation. J Am Chem Soc 2022; 144:10471-10482. [PMID: 35612610 DOI: 10.1021/jacs.2c02703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydrolytic loss of coding bases from cellular DNA is a common and unavoidable reaction. The resulting abasic sites can undergo β-elimination of the 3'-phosphoryl group to generate a strand break with an electrophilic α,β-unsaturated aldehyde residue on the 3'-terminus. The work reported here provides evidence that the thiol residue of the cellular tripeptide glutathione rapidly adds to the alkenal group on the 3'-terminus of an AP-derived strand break. The resulting glutathionylated adduct is the only major cleavage product observed when β-elimination occurs at an AP site in the presence of glutathione. Formation of the glutathionylated cleavage product is reversible, but in the presence of physiological concentrations of glutathione, the adduct persists for days. Biochemical experiments provided evidence that the 3'-phosphodiesterase activity of the enzyme apurinic/apyrimidinic endonuclease (APE1) can remove the glutathionylated sugar remnant from an AP-derived strand break to generate the 3'OH residue required for repair via base excision or single-strand break repair pathways. The results suggest that a previously unrecognized 3'glutathionylated sugar remnant─and not the canonical α,β-unsaturated aldehyde end group─may be the true strand cleavage product arising from β-elimination at an abasic site in cellular DNA. This work introduces the 3'glutathionylated cleavage product as the major blocking group that must be trimmed to enable repair of abasic site-derived strand breaks by the base excision repair or single-strand break repair pathways.
Collapse
|
17
|
Huskova A, Landova B, Boura E, Silhan J. The rate of formation and stability of abasic site interstrand crosslinks in the DNA duplex. DNA Repair (Amst) 2022; 113:103300. [PMID: 35255312 DOI: 10.1016/j.dnarep.2022.103300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/03/2022]
Abstract
DNA interstrand crosslinks (ICLs) strands pose an impenetrable barrier for DNA replication. Different ICLs are known to recruit distinct DNA repair pathways. NEIL3 glycosylase has been known to remove an abasic (Ap) site derived DNA crosslink (Ap-ICL). An Ap-ICL forms spontaneously from the Ap site with an adjacent adenine in the opposite strand. Lack of genetic models and a poor understanding of the fate of these lesions leads to many questions about the occurrence and the toxicity of Ap-ICL in cells. Here, we investigate the circumstances of Ap-ICL formation. With an array of different oligos, we have investigated the rates of formation, the yields, and the stability of Ap-ICL. Our findings point out how different bases in the vicinity of the Ap site change crosslink formation in vitro. We reveal that AT-rich rather than GC-rich regions in the surrounding Ap site lead to higher rates of Ap-ICL formation. Overall, our data reveal that Ap-ICL can be formed in virtually any DNA sequence context surrounding a hot spot of a 5'-Ap-dT pair, albeit with significantly different rates and yields. Based on Ap-ICL formation in vitro, we attempt to predict the number of Ap-ICLs in the cell.
Collapse
Affiliation(s)
- Andrea Huskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Barbora Landova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.
| |
Collapse
|
18
|
Facile preparation of model DNA interstrand cross-link repair intermediates using ribonucleotide-containing DNA. DNA Repair (Amst) 2022; 111:103286. [PMID: 35124371 PMCID: PMC8939895 DOI: 10.1016/j.dnarep.2022.103286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 01/13/2023]
Abstract
DNA interstrand cross-links (ICLs) are lesions with a covalent bond formed between DNA strands. ICLs are extremely toxic to cells because they prevent the separation of the two strands, which are necessary for the genetic interpretation of DNA. ICLs are repaired via Fanconi anemia and replication-independent pathways. The formation of so-called unhooked repair intermediates via a dual strand incision flanking the ICL site on one strand is an essential step in nearly all ICL repair pathways. Recently, ICLs derived from endogenous sources, such as those from ubiquitous DNA lesions, abasic (AP) sites, have emerged as an important class of ICLs. Despite the earlier efforts in preparing AP-ICLs in high yield using nucleotide analogs, little information is available for preparing AP-ICL unhooked intermediates with varying lengths of overhangs. In this study, we devise a simple approach to prepare model ICL unhooked intermediates derived from AP sites. We exploited the alkaline lability of ribonucleotides (rNMPs) and the high cross-linking efficiency between an AP lesion and a nucleotide analog, 2-aminopurine, via reductive amination. We designed chimeric DNA/RNA substrates with rNMPs flanking the cross-linking residue (2-aminopurine) to facilitate subsequent strand cleavage under our optimized conditions. Mass spectrometric analysis and primer extension assays confirmed the structures of ICL substrates. The method is straightforward, requires no synthetic chemistry expertise, and should be broadly accessible to all researchers in the DNA repair community. For step-by-step descriptions of the method, please refer to the companion manuscript in MethodsX.
Collapse
|
19
|
Haldar T, Jha JS, Yang Z, Nel C, Housh K, Cassidy OJ, Gates KS. Unexpected Complexity in the Products Arising from NaOH-, Heat-, Amine-, and Glycosylase-Induced Strand Cleavage at an Abasic Site in DNA. Chem Res Toxicol 2022; 35:218-232. [PMID: 35129338 PMCID: PMC9482271 DOI: 10.1021/acs.chemrestox.1c00409] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hydrolytic loss of nucleobases from the deoxyribose backbone of DNA is one of the most common unavoidable types of damage in synthetic and cellular DNA. The reaction generates abasic sites in DNA, and it is important to understand the properties of these lesions. The acidic nature of the α-protons of the ring-opened abasic aldehyde residue facilitates the β-elimination of the 3'-phosphoryl group. This reaction is expected to generate a DNA strand break with a phosphoryl group on the 5'-terminus and a trans-α,β-unsaturated aldehyde residue on the 3'-terminus; however, a handful of studies have identified noncanonical sugar remnants on the 3'-terminus, suggesting that the products arising from strand cleavage at apurinic/apyrimidinic sites in DNA may be more complex than commonly thought. We characterized the strand cleavage induced by the treatment of an abasic site-containing DNA oligonucleotide with heat, NaOH, piperidine, spermine, and the base excision repair glycosylases Fpg and Endo III. The results showed that under multiple conditions, cleavage at an abasic site in a DNA oligomer generated noncanonical sugar remnants including cis-α,β-unsaturated aldehyde, 2-deoxyribose, and 3-thio-2,3-dideoxyribose products on the 3'-terminus of the strand break.
Collapse
Affiliation(s)
- Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Jay S. Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Zhiyu Yang
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Orla J. Cassidy
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211,University of Missouri, Department of Biochemistry, Columbia, MO 65211,Address correspondence to Kent S. Gates – Departments of Chemistry and Biochemistry, 125 Chemistry Bldg. University of Missouri, Columbia, MO 65211, United States; ORCHID ID: 0000-0002-4218-7411; Phone: (573) 882-6763;
| |
Collapse
|
20
|
Chan W, Jin L. DNA-Protein Cross-Links Formed by Reacting Lysine with Apurinic/Apyrimidinic Sites in DNA and Human Cells: Quantitative Analysis by Liquid Chromatography-Tandem Mass Spectrometry Coupled with Stable Isotope Dilution. Anal Chem 2021; 94:803-810. [PMID: 34971314 DOI: 10.1021/acs.analchem.1c03356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Accumulating evidence suggests that DNA lesion-induced DNA-protein cross-links (DPCs) interrupt normal DNA metabolic processes, such as transcription, replication, and repair, resulting in profound biological consequences, including the development of many human diseases, such as cancers. Although apurinic/apyrimidinic (AP) sites are among the most predominant DNA lesions and are in close proximity to the histone proteins that they wrap around in the nucleosome, knowledge of the chemical structure or biological consequences of their associated DPCs is limited in part due to a lack of sensitive and selective analytical methods. We developed liquid chromatography-tandem mass spectrometry coupled with a stable isotope dilution method for rigorous quantitation of DPCs formed by reacting a DNA AP site with a lysine residue. In combination with chemical derivatization with fluorenylmethoxycarbonyl chloride to form a hydrophobic conjugate, the developed LC-MS/MS method allows sensitive detection of AP site-Lys cross-links down to sub-1 adduct per 106 nt. After validation using a synthetic AP site-lysine-cross-linked peptide and an oligodeoxyribonucleotide, the method was used to determine the concentration of AP site-lysine cross-links in hot acid-treated DNA and in human cells exposed to methyl methanesulfonate.
Collapse
Affiliation(s)
- Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Long Jin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
21
|
Rozelle AL, Lee S. Genotoxic C8-Arylamino-2'-deoxyadenosines Act as Latent Alkylating Agents to Induce DNA Interstrand Cross-Links. J Am Chem Soc 2021; 143:18960-18976. [PMID: 34726902 DOI: 10.1021/jacs.1c07234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA interstrand cross-links (ICLs) are extremely deleterious and structurally diverse, driving the evolution of ICL repair pathways. Discovering ICL-inducing agents is, thus, crucial for the characterization of ICL repair pathways and Fanconi anemia, a genetic disease caused by mutations in ICL repair genes. Although several studies point to oxidative stress as a cause of ICLs, oxidative stress-induced cross-linking events remain poorly characterized. Also, polycyclic aromatic amines, potent environmental carcinogens, have been implicated in producing ICLs, but their identities and sequences are unknown. To close this knowledge gap, we tested whether ICLs arise by the oxidation of 8-arylamino-2'-deoxyadenosine (ArNHdA) lesions, adducts produced by arylamino carcinogens. Herein, we report that ArNHdA acts as a latent cross-linking agent to generate ICLs under oxidative conditions. The formation of an ICL from 8-aminoadenine, but not from 8-aminoguanine, highlights the specificity of 8-aminopurine-mediated ICL production. Under the influence of the reactive oxygen species (ROS) nitrosoperoxycarbonate, ArNHdA (Ar = biphenyl, fluorenyl) lesions were selectively oxidized to generate ICLs. The cross-linking reaction may occur between the C2-ArNHdA and N2-dG, presumably via oxidation of ArNHdA into a reactive diiminoadenine intermediate followed by the nucleophilic attack of the N2-dG on the diiminoadenine. Overall, ArNHdA-mediated ICLs represent rare examples of ROS-induced ICLs and polycyclic aromatic amine-mediated ICLs. These results reveal novel cross-linking chemistry and the genotoxic effects of arylamino carcinogens and support the hypothesis that C8-modified adenines with low redox potential can cause ICLs in oxidative stress.
Collapse
Affiliation(s)
- Aaron L Rozelle
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States.,McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Seongmin Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
22
|
Housh K, Gates KS. Synthesis of DNA Duplexes Containing Site-Specific Interstrand Cross-Links via Sequential Reductive Amination Reactions Involving Diamine Linkers and Abasic Sites on Complementary Oligodeoxynucleotides. Chem Res Toxicol 2021; 34:2384-2391. [PMID: 34694787 PMCID: PMC8650211 DOI: 10.1021/acs.chemrestox.1c00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interstrand DNA cross-links are important in biology, medicinal chemistry, and materials science. Accordingly, methods for the targeted installation of interstrand cross-links in DNA duplexes may be useful in diverse fields. Here, a simple procedure is reported for the preparation of DNA duplexes containing site-specific, chemically defined interstrand cross-links. The approach involves sequential reductive amination reactions between diamine linkers and two abasic (apurinic/apyrimidinic, AP) sites on complementary oligodeoxynucleotides. Use of the symmetrical triamine, tris(2-aminoethyl)amine, in this reaction sequence enabled the preparation of a cross-linked DNA duplex bearing a derivatizable aminoethyl group.
Collapse
Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| |
Collapse
|
23
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
24
|
Housh K, Jha JS, Yang Z, Haldar T, Johnson KM, Yin J, Wang Y, Gates KS. Formation and Repair of an Interstrand DNA Cross-Link Arising from a Common Endogenous Lesion. J Am Chem Soc 2021; 143:15344-15357. [PMID: 34516735 DOI: 10.1021/jacs.1c06926] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interstrand DNA cross-links (ICLs) are cytotoxic because they block the strand separation required for read-out and replication of the genetic information in duplex DNA. The unavoidable formation of ICLs in cellular DNA may contribute to aging, neurodegeneration, and cancer. Here, we describe the formation and properties of a structurally complex ICL derived from an apurinic/apyrimidinic (AP) site, which is one of the most common endogenous lesions in cellular DNA. The results characterize a cross-link arising from aza-Michael addition of the N2-amino group of a guanine residue to the electrophilic sugar remnant generated by spermine-mediated strand cleavage at an AP site in duplex DNA. An α,β-unsaturated iminium ion is the critical intermediate involved in ICL formation. Studies employing the bacteriophage φ29 polymerase provided evidence that this ICL can block critical DNA transactions that require strand separation. The results of biochemical studies suggest that this complex strand break/ICL might be repaired by a simple mechanism in which the 3'-exonuclease action of the enzyme apurinic/apyrimidinic endonuclease (APE1) unhooks the cross-link to initiate repair via the single-strand break repair pathway.
Collapse
Affiliation(s)
- Kurt Housh
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jay S Jha
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Tuhin Haldar
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Kevin M Johnson
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jiekai Yin
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States.,University of Missouri Department of Biochemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| |
Collapse
|
25
|
Varela JG, Pierce LE, Guo X, Price NE, Johnson KM, Yang Z, Wang Y, Gates KS. Interstrand Cross-Link Formation Involving Reaction of a Mispaired Cytosine Residue with an Abasic Site in Duplex DNA. Chem Res Toxicol 2021; 34:1124-1132. [PMID: 33784065 PMCID: PMC8650171 DOI: 10.1021/acs.chemrestox.1c00004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of interstrand cross-links in duplex DNA is important in biology, medicine, and biotechnology. Interstrand cross-links arising from the reaction of the aldehyde residue of an abasic (apurinic or AP) site with the exocyclic amino groups of guanine or adenine residues on the opposing strand of duplex DNA have previously been characterized. The canonical nucleobase cytosine has an exocyclic amino group but its ability to form interstrand cross-links by reaction with an AP site has not been characterized before now. Here it is shown that substantial yields of interstrand cross-links are generated in sequences having a mispaired cytosine residue located one nucleotide to the 3'-side of the AP site on the opposing strand (e.g., 5'XA/5'CA, where X = AP). Formation of the dC-AP cross-link is pH-dependent, with significantly higher yields at pH 5 than pH 7. Once formed, the dC-AP cross-link is quite stable, showing less than 5% dissociation over the course of 96 h at pH 7 and 37 °C. No significant yields of cross-link are observed when the cytosine residue is paired with its Watson-Crick partner guanine. It was also shown that a single AP site can engage with multiple nucleobase cross-linking partners in some sequences. Specifically, the dG-AP and dC-AP cross-links coexist in dynamic equilibrium in the sequence 5'CXA/5'CAG (X = AP). In this sequence, the dC-AP cross-link dominates. However, in the presence of NaBH3CN, irreversible reduction of small amounts of the dG-AP cross-link present in the mixture shifts the equilibria away from the dC-AP cross-link toward good yields of the dG-APred cross-link.
Collapse
Affiliation(s)
- Jacqueline Gamboa Varela
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Luke E. Pierce
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Nathan E. Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kevin M. Johnson
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Zhiyu Yang
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Housh K, Jha JS, Haldar T, Amin SBM, Islam T, Wallace A, Gomina A, Guo X, Nel C, Wyatt JW, Gates KS. Formation and repair of unavoidable, endogenous interstrand cross-links in cellular DNA. DNA Repair (Amst) 2021; 98:103029. [PMID: 33385969 PMCID: PMC8882318 DOI: 10.1016/j.dnarep.2020.103029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
Genome integrity is essential for life and, as a result, DNA repair systems evolved to remove unavoidable DNA lesions from cellular DNA. Many forms of life possess the capacity to remove interstrand DNA cross-links (ICLs) from their genome but the identity of the naturally-occurring, endogenous substrates that drove the evolution and retention of these DNA repair systems across a wide range of life forms remains uncertain. In this review, we describe more than a dozen chemical processes by which endogenous ICLs plausibly can be introduced into cellular DNA. The majority involve DNA degradation processes that introduce aldehyde residues into the double helix or reactions of DNA with endogenous low molecular weight aldehyde metabolites. A smaller number of the cross-linking processes involve reactions of DNA radicals generated by oxidation.
Collapse
Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jay S Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Saosan Binth Md Amin
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Tanhaul Islam
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Amanda Wallace
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Anuoluwapo Gomina
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Jesse W Wyatt
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, Columbia, MO 65211, United States.
| |
Collapse
|
28
|
Kellum AH, Qiu DY, Voehler MW, Martin W, Gates KS, Stone MP. Structure of a Stable Interstrand DNA Cross-Link Involving a β- N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site. Biochemistry 2020; 60:41-52. [PMID: 33382597 DOI: 10.1021/acs.biochem.0c00596] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abasic (AP) sites are one of the most common forms of DNA damage. The deoxyribose ring of AP sites undergoes anomerization between α and β configurations, via an electrophilic aldehyde intermediate. In sequences where an adenine residue is located on the opposing strand and offset 1 nt to the 3' side of the AP site, the nucleophilic N6-dA amino group can react with the AP aldehyde residue to form an interstrand cross-link (ICL). Here, we present an experimentally determined structure of the dA-AP ICL by NMR spectroscopy. The ICL was constructed in the oligodeoxynucleotide 5'-d(T1A2T3G4T5C6T7A8A9G10T11T12C13A14T15C16T17A18)-3':5'-d(T19A20G21A22T23G24A25A26C27X28T29A30G31A32C33A34T35A36)-3' (X=AP site), with the dA-AP ICL forming between A8 and X28. The NMR spectra indicated an ordered structure for the cross-linked DNA duplex and afforded detailed spectroscopic resonance assignments. Structural refinement, using molecular dynamics calculations restrained by NOE data (rMD), revealed the structure of the ICL. In the dA-AP ICL, the 2'-deoxyribosyl ring of the AP site was ring-closed and in the β configuration. Juxtapositioning the N6-dA amino group and the aldehydic C1 of the AP site within bonding distance while simultaneously maintaining two flanking unpaired A9 and T29 bases stacked within the DNA is accomplished by the unwinding of the DNA at the ICL. The structural data is discussed in the context of recent studies describing the replication-dependent unhooking of the dA-AP ICL by the base excision repair glycosylase NEIL3.
Collapse
Affiliation(s)
- Andrew H Kellum
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David Y Qiu
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - William Martin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, Missouri 65221, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
29
|
Rogers CM, Simmons Iii RH, Fluhler Thornburg GE, Buehler NJ, Bochman ML. Fanconi anemia-independent DNA inter-strand crosslink repair in eukaryotes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 158:33-46. [PMID: 32877700 DOI: 10.1016/j.pbiomolbio.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
DNA inter-strand crosslinks (ICLs) are dangerous lesions that can be caused by a variety of endogenous and exogenous bifunctional compounds. Because covalently linking both strands of the double helix locally disrupts DNA replication and transcription, failure to remove even a single ICL can be fatal to the cell. Thus, multiple ICL repair pathways have evolved, with the best studied being the canonical Fanconi anemia (FA) pathway. However, recent research demonstrates that different types of ICLs (e.g., backbone distorting vs. non-distorting) can be discriminated by the cell, which then mounts a specific repair response using the FA pathway or one of a variety of FA-independent ICL repair pathways. This review focuses on the latter, covering current work on the transcription-coupled, base excision, acetaldehyde-induced, and SNM1A/RecQ4 ICL repair pathways and highlighting unanswered questions in the field. Answering these questions will provide mechanistic insight into the various pathways of ICL repair and enable ICL-inducing agents to be more effectively used as chemotherapeutics.
Collapse
Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Robert H Simmons Iii
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Gabriella E Fluhler Thornburg
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA.
| |
Collapse
|
30
|
Abe YS, Sasaki S. The adduct formation between the thioguanine-polyamine ligands and DNA with the AP site under UVA irradiated and non-irradiated conditions. Bioorg Med Chem 2019; 27:115160. [PMID: 31706680 DOI: 10.1016/j.bmc.2019.115160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
Abstract
The AP sites are representative of DNA damage and known as an intermediate in the base excision repair (BER) pathway which is involved in the repair of damaged nucleobases by reactive oxygen species, UVA irradiation, and DNA alkylating agents. Therefore, it is expected that the inhibition or modulation of the AP site repair pathway may be a new type of anticancer drug. In this study, we investigated the effects of the thioguanine-polyamine ligands (SG-ligands) on the affinity and the reactivity for the AP site under UVA irradiated and non-irradiated conditions. The SG-ligands have a photo-reactivity with the A-F-C sequence where F represents a tetrahydrofuran AP site analogue. Interestingly, the SG-ligands promoted the β-elimination of the AP site followed by the formation of a covalent bond with the β-eliminated fragment without UVA irradiation.
Collapse
Affiliation(s)
- Yukiko S Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| |
Collapse
|
31
|
Nejad MI, Guo X, Housh K, Nel C, Yang Z, Price NE, Wang Y, Gates KS. Preparation and Purification of Oligodeoxynucleotide Duplexes Containing a Site-Specific, Reduced, Chemically Stable Covalent Interstrand Cross-Link Between a Guanine Residue and an Abasic Site. Methods Mol Biol 2019; 1973:163-175. [PMID: 31016701 DOI: 10.1007/978-1-4939-9216-4_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Methods for the preparation of DNA duplexes containing interstrand covalent cross-links may facilitate research in the fields of biochemistry, molecular biology, nanotechnology, and materials science. Here we report methods for the synthesis and isolation of DNA duplexes containing a site-specific, chemically stable, reduced covalent interstrand cross-link between a guanine residue and an abasic site. The method uses experimental techniques and equipment that are common in most biochemical laboratories and inexpensive, commercially available oligonucleotides and reagents.
Collapse
Affiliation(s)
| | - Xu Guo
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Kurt Housh
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Christopher Nel
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Zhiyu Yang
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Nathan E Price
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
32
|
Nejad MI, Price NE, Haldar T, Lewis C, Wang Y, Gates KS. Interstrand DNA Cross-Links Derived from Reaction of a 2-Aminopurine Residue with an Abasic Site. ACS Chem Biol 2019; 14:1481-1489. [PMID: 31259519 DOI: 10.1021/acschembio.9b00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient methods for the site-specific installation of structurally defined interstrand cross-links in duplex DNA may be useful in a wide variety of fields. The work described here developed a high-yield synthesis of chemically stable interstrand cross-links resulting from a reductive amination reaction between an abasic site and the noncanonical nucleobase 2-aminopurine in duplex DNA. Results from footprinting, liquid chromatography-mass spectrometry, and stability studies support the formation of an N2-alkylamine attachment between the 2-aminopurine residue and the Ap site. The reaction performs best when the 2-aminopurine residue on the opposing strand is offset 1 nt to the 5'-side of the abasic site. The cross-link confers substantial resistance to thermal denaturation (melting). The cross-linking reaction is fast (complete in 4 h), employs only commercially available reagents, and can be used to generate cross-linked duplexes in sufficient quantities for biophysical, structural, and DNA repair studies.
Collapse
Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Tuhin Haldar
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Calvin Lewis
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| |
Collapse
|
33
|
Chan W, Ham YH, Jin L, Chan HW, Wong YL, Chan CK, Chung PY. Quantification of a Novel DNA–Protein Cross-Link Product Formed by Reacting Apurinic/Apyrimidinic Sites in DNA with Cysteine Residues in Protein by Liquid Chromatography-Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. Anal Chem 2019; 91:4987-4994. [DOI: 10.1021/acs.analchem.8b04306] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
34
|
Shen X, Gates KS. Enzyme-Activated Generation of Reactive Oxygen Species from Heterocyclic N-Oxides under Aerobic and Anaerobic Conditions and Its Relevance to Hypoxia-Selective Prodrugs. Chem Res Toxicol 2019; 32:348-361. [PMID: 30817135 DOI: 10.1021/acs.chemrestox.9b00036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymatic one-electron reduction of heterocyclic N-oxides can lead to the intracellular generation of reactive oxygen species via several different chemical pathways. These reactions may be relevant to hypoxia-selective anticancer drugs, antimicrobial agents, and unwanted toxicity of heterocylic nitrogen compounds.
Collapse
|
35
|
Caron C, Duong XNT, Guillot R, Bombard S, Granzhan A. Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts. Chemistry 2019; 25:1949-1962. [DOI: 10.1002/chem.201805555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Coralie Caron
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Xuan N. T. Duong
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Régis Guillot
- CNRS UMR8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO)Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| |
Collapse
|
36
|
Guo X, Nejad MI, Gu LQ, Gates KS. Selective covalent capture of a DNA sequence corresponding to a cancer-driving C>G mutation in theKRASgene by a chemically reactive probe: optimizing a cross-linking reaction with non-canonical duplex structures. RSC Adv 2019; 9:32804-32810. [PMID: 35529740 PMCID: PMC9073178 DOI: 10.1039/c9ra08009k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
A covalent cross-linking reaction used for selective capture of a disease-relevant DNA sequence.
Collapse
Affiliation(s)
- Xu Guo
- Department of Chemistry
- University of Missouri
- Columbia
- USA
| | | | - Li-Qun Gu
- Department of Bioengineering
- Dalton Cardiovascular Research Center
- University of Missouri
- Columbia
- USA
| | - Kent S. Gates
- Department of Chemistry
- University of Missouri
- Columbia
- USA
- Department of Biochemistry
| |
Collapse
|
37
|
Shi R, Nejad MI, Zhang X, Gu LQ, Gates KS. Generation and Single-Molecule Characterization of a Sequence-Selective Covalent Cross-Link Mediated by Mechlorethamine at a C–C Mismatch in Duplex DNA for Discrimination of a Disease-Relevant Single Nucleotide Polymorphism. Bioconjug Chem 2018; 29:3810-3816. [DOI: 10.1021/acs.bioconjchem.8b00663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ruicheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | | | - Xinyue Zhang
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | | |
Collapse
|
38
|
Wang R, Yang K, Banerjee S, Greenberg MM. Rotational Effects within Nucleosome Core Particles on Abasic Site Reactivity. Biochemistry 2018; 57:3945-3952. [PMID: 29894168 DOI: 10.1021/acs.biochem.8b00493] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
An abasic (AP) site is a ubiquitous DNA lesion that is produced via several cellular processes. Although AP sites are cytotoxic and mutagenic, cells are protected from them by different DNA damage tolerance and repair pathways, including base excision repair (BER). AP lesions are alkali-labile, but the half-life for strand scission is several weeks in free DNA at around neutral pH. The AP lifetime is reduced ∼100-fold in nucleosome core particles (NCPs) because the histone proteins promote strand scission. The reactivity of other DNA lesions to BER enzymes and exogenous reagents is highly dependent upon rotational positioning within the NCP. We examined strand scission at AP sites as a function of rotational position over approximately one helical turn of DNA. The rate constant for strand scission at AP varies ∼4-fold, a range of reactivity much smaller than that observed for processes that involve reaction with diffusible reagents in solution. In addition, the change in rate constant does not exhibit an obvious pattern with respect to rotational position. The small dependence of reactivity on rotational position is attributed to interactions with histone proteins. A molecular model based upon NCP X-ray crystal structures indicates that histone protein tails access AP sites via the major or minor groove and are therefore not limited to regions where one particular groove is exposed to solvent. Determining the roles of individual proteins is difficult because of the unstructured nature of the histone tails and the chemical mechanism, which involves reversible Schiff base formation, followed by irreversible elimination.
Collapse
Affiliation(s)
- Ruixiang Wang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kun Yang
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Samya Banerjee
- 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
| |
Collapse
|
39
|
Liu CW, Tian X, Hartwell HJ, Leng J, Chi L, Lu K, Swenberg JA. Accurate Measurement of Formaldehyde-Induced DNA–Protein Cross-Links by High-Resolution Orbitrap Mass Spectrometry. Chem Res Toxicol 2018; 31:350-357. [DOI: 10.1021/acs.chemrestox.8b00040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xu Tian
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hadley J. Hartwell
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jiapeng Leng
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James A. Swenberg
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
40
|
Price NE, Li L, Gates KS, Wang Y. Replication and repair of a reduced 2΄-deoxyguanosine-abasic site interstrand cross-link in human cells. Nucleic Acids Res 2017; 45:6486-6493. [PMID: 28431012 PMCID: PMC5499640 DOI: 10.1093/nar/gkx266] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/13/2017] [Indexed: 02/02/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites, or abasic sites, which are a common type of endogenous DNA damage, can forge interstrand DNA–DNA cross-links via reaction with the exocyclic amino group on a nearby 2΄-deoxyguanosine or 2΄-deoxyadenosine in the opposite strand. Here, we utilized a shuttle vector method to examine the efficiency and fidelity with which a reduced dG–AP cross-link-containing plasmid was replicated in cultured human cells. Our results showed that the cross-link constituted strong impediments to DNA replication in HEK293T cells, with the bypass efficiencies for the dG- and AP-containing strands being 40% and 20%, respectively. While depletion of polymerase (Pol) η did not perturb the bypass efficiency of the lesion, the bypass efficiency was markedly reduced (to 1–10%) in the isogenic cells deficient in Pol κ, Pol ι or Pol ζ, suggesting the mutual involvement of multiple translesion synthesis polymerases in bypassing the lesion. Additionally, replication of the cross-linked AP residue in HEK293T cells was moderately error-prone, inducing a total of ∼26% single-nucleobase substitutions at the lesion site, whereas replication past the cross-linked dG component occurred at a mutation frequency of ∼8%. Together, our results provided important insights into the effects of an AP-derived interstrand cross-link on the efficiency and accuracy of DNA replication in human cells.
Collapse
Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Lin Li
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| |
Collapse
|
41
|
Yang Z, Price NE, Johnson KM, Wang Y, Gates KS. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA. Nucleic Acids Res 2017; 45:6275-6283. [PMID: 28531327 PMCID: PMC5499897 DOI: 10.1093/nar/gkx394] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/02/2017] [Indexed: 01/04/2023] Open
Abstract
Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems.
Collapse
Affiliation(s)
- Zhiyu Yang
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Nathan E Price
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Kevin M Johnson
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA.,Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| |
Collapse
|
42
|
Wilson DM, Rieckher M, Williams AB, Schumacher B. Systematic analysis of DNA crosslink repair pathways during development and aging in Caenorhabditis elegans. Nucleic Acids Res 2017; 45:9467-9480. [PMID: 28934497 PMCID: PMC5766164 DOI: 10.1093/nar/gkx660] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/18/2017] [Indexed: 01/12/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are generated by endogenous sources and chemotherapeutics, and pose a threat to genome stability and cell survival. Using Caenorhabditis elegans mutants, we identify DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g. XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan. Compensatory roles for global-genome (XPC-1) and transcription-coupled (CSB-1) NER in ICL sensing were exposed. The analysis also revealed contributions of homologous recombination (BRC-1/BRCA1), the MUS-81, EXO-1, SLX-1 and FAN-1 nucleases, and the DOG-1 (FANCJ) helicase in ICL resolution, influenced by the replicative-status of the cell/tissue. No obvious or critical role in ICL repair was seen for non-homologous end-joining (cku-80) or base excision repair (nth-1, exo-3), the Fanconi-related proteins BRC-2 (BRCA2/FANCD1) and FCD-2 (FANCD2), the WRN-1 or HIM-6 (BLM) helicases, or the GEN-1 or MRT-1 (SNM1) nucleases. Our efforts uncover replication-dependent and -independent ICL repair networks, and establish nematodes as a model for investigating the repair and consequences of DNA crosslinks in metazoan development and in adult post-mitotic and proliferative germ cells.
Collapse
Affiliation(s)
- David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ashley B Williams
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| |
Collapse
|
43
|
Poudyal RR, Nguyen PDM, Lokugamage MP, Callaway MK, Gavette JV, Krishnamurthy R, Burke DH. Nucleobase modification by an RNA enzyme. Nucleic Acids Res 2017; 45:1345-1354. [PMID: 28180302 PMCID: PMC5388400 DOI: 10.1093/nar/gkw1199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/26/2022] Open
Abstract
Ribozymes can catalyze phosphoryl or nucleotidyl transfer onto ribose hydroxyls of RNA chains. We report a single ribozyme that performs both reactions, with a nucleobase serving as initial acceptor moiety. This unprecedented combined reaction was revealed while investigating potential contributions of ribose hydroxyls to catalysis by kinase ribozyme K28. For a 58nt, cis-acting form of K28, each nucleotide could be replaced with the corresponding 2΄F analog without loss of activity, indicating that no particular 2΄OH is specifically required. Reactivities of two-stranded K28 variants with oligodeoxynucleotide acceptor strands devoid of any 2΄OH moieties implicate modification on an internal guanosine N-2, rather than a ribose hydroxyl. Product mass suggests formation of a GDP(S) adduct along with a second thiophosphorylation, implying that the ribozyme catalyzes both phosphoryl and nucleotidyl transfers. This is further supported by transfer of radiolabels into product from both α and γ phosphates of donor molecules. Furthermore, periodate reactivity of the final product signifies acquisition of a ribose sugar with an intact 2΄-3΄ vicinal diol. Neither nucleobase modification nor nucleotidyl transfer has previously been reported for a kinase ribozyme, making this a first-in-class ribozyme. Base-modifying ribozymes may have played important roles in early RNA world evolution by enhancing nucleic acid functions.
Collapse
Affiliation(s)
- Raghav R Poudyal
- Dept. of Biochemistry, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Phuong D M Nguyen
- Dept. of Biochemistry, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Melissa P Lokugamage
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Department of Biological Engineering, University of Missouri, Columbia, MO, USA
| | - Mackenzie K Callaway
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Department of Biological Engineering, University of Missouri, Columbia, MO, USA
| | - Jesse V Gavette
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Donald H Burke
- Dept. of Biochemistry, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Department of Biological Engineering, University of Missouri, Columbia, MO, USA.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| |
Collapse
|
44
|
Bignon E, Dršata T, Morell C, Lankaš F, Dumont E. Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics. Nucleic Acids Res 2017; 45:2188-2195. [PMID: 27986856 PMCID: PMC5389527 DOI: 10.1093/nar/gkw1253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Oxidatively-generated interstrand cross-links rank among the most deleterious DNA lesions. They originate from abasic sites, whose aldehyde group can form a covalent adduct after condensation with the exocyclic amino group of purines, sometimes with remarkably high yields. We use explicit solvent molecular dynamics simulations to unravel the structures and mechanical properties of two DNA sequences containing an interstrand cross-link. Our simulations palliate the absence of experimental structural and stiffness information for such DNA lesions and provide an unprecedented insight into the DNA embedding of lesions that represent a major challenge for DNA replication, transcription and gene regulation by preventing strand separation. Our results based on quantum chemical calculations also suggest that the embedding of the ICL within the duplex can tune the reaction profile, and hence can be responsible for the high difference in yields of formation.
Collapse
Affiliation(s)
- Emmanuelle Bignon
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.,Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Christophe Morell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.,Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Praha 6, Czech Republic
| | - Elise Dumont
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| |
Collapse
|
45
|
Nejad MI, Shi R, Zhang X, Gu LQ, Gates KS. Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence. Chembiochem 2017; 18:1383-1386. [PMID: 28422400 PMCID: PMC6139021 DOI: 10.1002/cbic.201700204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/12/2023]
Abstract
Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes.
Collapse
Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyue Zhang
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Li-Qun Gu
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. DNA Repair (Amst) 2017; 52:1-11. [PMID: 28262582 PMCID: PMC5424475 DOI: 10.1016/j.dnarep.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are "unhooked" by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.
Collapse
Affiliation(s)
- Zhiyu Yang
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Maryam Imani Nejad
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Jacqueline Gamboa Varela
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Nathan E Price
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Yinsheng Wang
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States; University of Missouri Department of Biochemistry, 125 Chemistry Building Columbia, MO 65211, United States.
| |
Collapse
|
48
|
Nejad MI, Johnson KM, Price NE, Gates KS. A New Cross-Link for an Old Cross-Linking Drug: The Nitrogen Mustard Anticancer Agent Mechlorethamine Generates Cross-Links Derived from Abasic Sites in Addition to the Expected Drug-Bridged Cross-Links. Biochemistry 2016; 55:7033-7041. [PMID: 27992994 DOI: 10.1021/acs.biochem.6b01080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrogen mustard anticancer drugs generate highly reactive aziridinium ions that alkylate DNA. Monoadducts arising from reaction with position N7 of guanine residues are the major DNA adducts generated by these agents. Interstrand cross-links in which the drug bridges position N7 of two guanine residues are formed in low yields relative to those of the monoadducts but are generally thought to be central to medicinal activity. The N7-alkylguanine residues generated by nitrogen mustards are depurinated to yield abasic (Ap) sites in duplex DNA. Here, we show that Ap sites generated by the nitrogen mustard mechlorethamine lead to interstrand cross-links of a type not previously associated with this drug. Gel electrophoretic data were consistent with early evolution of the expected drug-bridged cross-links, followed by the appearance of Ap-derived cross-links. The evidence is further consistent with a reaction pathway involving alkylation of a guanine residue in a 5'-GT sequence, followed by depurination to generate the Ap site, and cross-link formation via reaction of the Ap aldehyde residue with the opposing adenine residue at this site [Price, N. E., Johnson, K. M., Wang, J., Fekry, M. I., Wang, Y., and Gates, K. S. (2014) J. Am. Chem. Soc. 136, 3483-3490]. The monofunctional DNA-alkylating agents 2-chloro-N,N-diethylethanamine 5, (2-chloroethyl)ethylsulfide 6, and natural product leinamycin similarly were found to induce the formation of Ap-derived cross-links in duplex DNA. This work provides the first characterization of Ap-derived cross-links at sequences in which a cytosine residue is located directly opposing the Ap site. Cross-linking processes of this type could be relevant in medicine and biology because Ap sites with directly opposing cytosine residues occur frequently in genomic DNA via spontaneous or enzymatic depurination of guanine and N7-alkylguanine residues.
Collapse
Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri , 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kevin M Johnson
- Department of Chemistry, University of Missouri , 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Nathan E Price
- Department of Chemistry, University of Missouri , 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri , 125 Chemistry Building, Columbia, Missouri 65211, United States.,Department of Biochemistry, University of Missouri , 125 Chemistry Building, Columbia, Missouri 65211, United States
| |
Collapse
|
49
|
Guo C, Asamitsu S, Kashiwazaki G, Sato S, Bando T, Sugiyama H. DNA Interstrand Crosslinks by H-pin Polyamide (S
)-seco
-CBI Conjugates. Chembiochem 2016; 18:166-170. [DOI: 10.1002/cbic.201600425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Chuanxin Guo
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
| |
Collapse
|
50
|
Gamboa Varela J, Gates KS. Simple, High-Yield Syntheses of DNA Duplexes Containing Interstrand DNA-DNA Cross-Links Between an N(4) -Aminocytidine Residue and an Abasic Site. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2016; 65:5.16.1-5.16.15. [PMID: 27248783 PMCID: PMC5000854 DOI: 10.1002/cpnc.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N(4) -aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially available chemicals and enzymes to carry out post-synthetic modification of commercially available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| |
Collapse
|