1
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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.
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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
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2
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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.
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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
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3
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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.
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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.
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4
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Pumuye PP, Evison BJ, Konda SK, Collins JG, Kelso C, Medan J, Sleebs BE, Watson K, Phillips DR, Cutts SM. Formaldehyde-activated WEHI-150 induces DNA interstrand crosslinks with unique structural features. Bioorg Med Chem 2020; 28:115260. [PMID: 31870833 DOI: 10.1016/j.bmc.2019.115260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022]
Abstract
Mitoxantrone is an anticancer anthracenedione that can be activated by formaldehyde to generate covalent drug-DNA adducts. Despite their covalent nature, these DNA lesions are relatively labile. It was recently established that analogues of mitoxantrone featuring extended side-chains terminating in primary amino groups typically yielded high levels of stable DNA adducts following their activation by formaldehyde. In this study we describe the DNA sequence-specific binding properties of the mitoxantrone analogue WEHI-150 which is the first anthracenedione to form apparent DNA crosslinks mediated by formaldehyde. The utility of this compound lies in the versatility of the covalent binding modes displayed. Unlike other anthracenediones described to date, WEHI-150 can mediate covalent adducts that are independent of interactions with the N-2 of guanine and is capable of adduct formation at novel DNA sequences. Moreover, these covalent adducts incorporate more than one formaldehyde-mediated bond with DNA, thus facilitating the formation of highly lethal DNA crosslinks. The versatility of binding observed is anticipated to allow the next generation of anthracenediones to interact with a broader spectrum of nucleic acid species than previously demonstrated by the parent compounds, thus allowing for more diverse biological activities.
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Affiliation(s)
- Paul P Pumuye
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Benny J Evison
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Shyam K Konda
- School of Science, University of New South Wales, Canberra 2610, Australia
| | - J Grant Collins
- School of Science, University of New South Wales, Canberra 2610, Australia
| | - Celine Kelso
- School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jelena Medan
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia; Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Keith Watson
- Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia
| | - Don R Phillips
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Suzanne M Cutts
- La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia.
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5
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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.
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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
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6
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Brayboy LM, Clark H, Knapik LO, Schnirman RE, Wessel GM. Nitrogen mustard exposure perturbs oocyte mitochondrial physiology and alters reproductive outcomes. Reprod Toxicol 2018; 82:80-87. [PMID: 30308227 DOI: 10.1016/j.reprotox.2018.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/28/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022]
Abstract
Nitrogen mustard (NM) is an alkylating chemical warfare agent, and its derivatives are used in chemotherapy. Alkylating agents can cause mitochondrial damage, so exposed females may transmit damaged genomes to their children, since mitochondria are maternally inherited and oocytes are not thought to undergo mitophagy (Boudoures et al. [1]). The objective of this study is to investigate NM's effects on oocyte mitochondria to understand risks facing female soldiers, cancer patients, and their children. Mice were injected intraperitoneally with NM, monitored for reproductive outcomes, and ovaries and oocytes were isolated for analysis. Escalating doses of NM increased oxidative stress in parental and F1 generation oocytes, suggesting that mitochondrial damage by NM is enhanced by mitochondrial superoxide. NM-treated ovaries in vitro exhibited smaller mitochondrial volume, more electron-dense and multivesicular structures, and lower birth weight litters. These results demonstrate that females must be protected from alkylating agents for their health, and the health of their offspring.
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Affiliation(s)
- Lynae M Brayboy
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Women & Infants Hospital of Rhode Island, Alpert Medical School of Brown University, 101 Dudley Street, Providence, RI, 02905, USA; Alpert Medical School of Brown University, Providence, RI, 02903, USA; Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
| | - Haley Clark
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Laura O Knapik
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Women & Infants Hospital of Rhode Island, Alpert Medical School of Brown University, 101 Dudley Street, Providence, RI, 02905, USA
| | - Ruby E Schnirman
- University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA
| | - Gary M Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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7
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Ye J, Farrington CR, Millard JT. Polymerase bypass of N7-guanine monoadducts of cisplatin, diepoxybutane, and epichlorohydrin. Mutat Res 2018; 809:6-12. [PMID: 29579534 PMCID: PMC5962418 DOI: 10.1016/j.mrfmmm.2018.03.002] [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: 10/19/2017] [Revised: 01/31/2018] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
DNA oligonucleotides containing site-specific N7-guanine monoadducts of cisplatin, diepoxybutane, and epichlorohydrin were used as templates for DNA synthesis by two bacterial DNA polymerases and human polymerase β. These polymerases were able to bypass the lesions effectively, although the efficiency was decreased, with inhibition increasing with the size of the lesion. Fidelity of incorporation was essentially unaltered, suggesting that N7-guanine monoadducts do not significantly contribute to the mutational spectra of these agents.
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Affiliation(s)
- Jiayu Ye
- Department of Chemistry, Colby College, Waterville, ME 04901, United States
| | | | - Julie T Millard
- Department of Chemistry, Colby College, Waterville, ME 04901, United States.
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8
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Chang SM, Christian W, Wu MH, Chen TL, Lin YW, Suen CS, Pidugu HB, Detroja D, Shah A, Hwang MJ, Su TL, Lee TC. Novel indolizino[8,7- b ]indole hybrids as anti-small cell lung cancer agents: Regioselective modulation of topoisomerase II inhibitory and DNA crosslinking activities. Eur J Med Chem 2017; 127:235-249. [DOI: 10.1016/j.ejmech.2016.12.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 01/01/2023]
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9
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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.
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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
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10
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Abstract
The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug-target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
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11
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Schiesser S, Hackner B, Vrabel M, Beck W, Carell T. Synthesis and DNA-Damaging Properties of Cisplatin-N-Mustard Conjugates. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Price N, Johnson KM, Wang J, Fekry MI, Wang Y, Gates KS. Interstrand DNA-DNA cross-link formation between adenine residues and abasic sites in duplex DNA. J Am Chem Soc 2014; 136:3483-90. [PMID: 24506784 PMCID: PMC3954461 DOI: 10.1021/ja410969x] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Indexed: 01/28/2023]
Abstract
The loss of a coding nucleobase from the structure of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating mixture of a cyclic hemiacetal and a ring-opened aldehyde. Aldehydes are electrophilic functional groups that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially reactive aldehyde as part of the internal structure of DNA. Here we report evidence that the aldehyde group of Ap sites in duplex DNA can form a covalent adduct with the N(6)-amino group of adenine residues on the opposing strand. The resulting interstrand DNA-DNA cross-link occurs at 5'-ApT/5'-AA sequences in remarkably high yields (15-70%) under physiologically relevant conditions. This naturally occurring DNA-templated reaction has the potential to generate cross-links in the genetic material of living cells.
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Affiliation(s)
- Nathan
E. Price
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Jin Wang
- Department
of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Mostafa I. Fekry
- Department of Chemistry and Department of Biochemistry, University of Missouri, 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 and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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13
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Johnson KM, Price NE, Wang J, Fekry MI, Dutta S, Seiner DR, Wang Y, Gates KS. On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an abasic site with the opposing guanine residue of 5'-CAp sequences in duplex DNA. J Am Chem Soc 2013; 135:1015-25. [PMID: 23215239 DOI: 10.1021/ja308119q] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5'-CAp sequence under conditions of reductive amination (NaCNBH(3), pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions, and the cross-link, once formed, was stable to a variety of workup conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LC-MS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N(2)-amino group of the opposing guanine residue in 5'-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH(3)/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N(2)-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH(3).
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Affiliation(s)
- Kevin M Johnson
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, USA
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14
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Loss of Neil3, the major DNA glycosylase activity for removal of hydantoins in single stranded DNA, reduces cellular proliferation and sensitizes cells to genotoxic stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1157-64. [PMID: 23305905 DOI: 10.1016/j.bbamcr.2012.12.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/13/2012] [Accepted: 12/26/2012] [Indexed: 11/21/2022]
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative base lesions in normal tissues induced by a variety of endogenous and exogenous agents. Hydantoins are products of 8-oxoG oxidation and as 8-oxoG, they have been shown to be mutagenic lesions. Oxidative DNA damage has been implicated in the etiology of various age-associated pathologies, such as cancer, cardiovascular diseases, arthritis, and several neurodegenerative diseases. The mammalian endonuclease VIII-like 3 (Neil3) is one of the four DNA glycosylases found to recognize and remove hydantoins in the first step of base excision repair (BER) pathway. We have generated mice lacking Neil3 and by using total cell extracts we demonstrate that Neil3 is the main DNA glycosylase that incises hydantoins in single stranded DNA in tissues. Using the neurosphere culture system as a model to study neural stem/progenitor (NSPC) cells we found that lack of Neil3 impaired self renewal but did not affect differentiation capacity. Proliferation was also reduced in mouse embryonic fibroblasts (MEFs) derived from Neil3(-/-) embryos and these cells were sensitive to both the oxidative toxicant paraquat and interstrand cross-link (ICL)-inducing agent cisplatin. Our data support the involvement of Neil3 in removal of replication blocks in proliferating cells.
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Basu S, Kandiyal PS, Ampapathi RS, Chakraborty TK. Ti(iii)-mediated radical cyclization of epoxy-β-aminoacrylate in the synthesis of the substituted pyrrolidine core of necine bases: synthesis of 2-epi-rosmarinecine. RSC Adv 2013. [DOI: 10.1039/c3ra42315h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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16
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Lando DY, Galyuk EN, Chang CL, Hu CK. Temporal behavior of DNA thermal stability in the presence of platinum compounds. Role of monofunctional and bifunctional adducts. J Inorg Biochem 2012; 117:164-70. [DOI: 10.1016/j.jinorgbio.2012.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/24/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
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17
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Polavarapu A, Stillabower JA, Stubblefield SGW, Taylor WM, Baik MH. The mechanism of guanine alkylation by nitrogen mustards: a computational study. J Org Chem 2012; 77:5914-21. [PMID: 22681226 DOI: 10.1021/jo300351g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermodynamics and kinetics for the monofunctional binding of nitrogen mustard class of anticancer drugs to purine bases of DNA were studied computationally using guanine and adenine as model substrates. Mechlorethamine and melphalan are used as model systems in order to better understand the difference in antitumor activity of aliphatic and aromatic mustards, respectively. In good agreement with experiments that suggested the accumulation of a reactive intermediate in the case of mechlorethamine, our model predicts a significant preference for the formation of corresponding aziridinium ion for mechlorethamine, while the formation of the aziridinium ion is not computed to be preferred when melphalan is used. Two effects are found that contribute to this difference. First, the ground state of the drug shows a highly delocalized lone pair on the amine nitrogen of the melphalan, which makes the subsequent cyclization more difficult. Second, because of the aromatic substituent connected to the amine nitrogen of melphalan, a large energy penalty has to be paid for solvation. A detailed study of energy profiles for the two-step mechanism for alkylation of guanine and adenine was performed. Alkylation of guanine is ∼6 kcal mol(-1) preferred over adenine, and the factors contributing to this preference were explained in our previous study of cisplatin binding to purine bases. A detailed analysis of energy profiles of mechlorethamine and melphalan binding to guanine and adenine are presented to provide an insight into rate limiting step and the difference in reactivity and stability of the intermediate in both nitrogen mustards, respectively.
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Affiliation(s)
- Abhigna Polavarapu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, Indiana 47405, USA
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18
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Millard JT, McGowan EE, Bradley SQ. Diepoxybutane interstrand cross-links induce DNA bending. Biochimie 2011; 94:574-7. [PMID: 21839139 DOI: 10.1016/j.biochi.2011.07.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/26/2011] [Indexed: 12/26/2022]
Abstract
The bifunctional alkylating agent 1,2,3,4-diepoxybutane (DEB) is thought to be a major contributor to the carcinogenicity of 1,3-butadiene, from which it is derived in vivo. DEB forms DNA interstrand cross-links primarily between distal deoxyguanosine residues at the duplex sequence 5'-GNC. In order for the short butanediol tether to span this distance, distortion of the DNA target has been postulated. We determined that the electrophoretic mobility of ligated DNA oligomers containing DEB cross-links was retarded in comparison with control, uncross-linked DNA. Our data are consistent with DNA bending of ∼34° per lesion towards the major groove.
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Affiliation(s)
- Julie T Millard
- Department of Chemistry, Colby College, 5757 Mayflower Hill Drive, Waterville, ME 04901, USA.
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Nadas J, Zhang X, Hay BP. Shapes of Sulfur, Oxygen, and Nitrogen Mustards. J Phys Chem A 2011; 115:6709-16. [DOI: 10.1021/jp203120c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janos Nadas
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6119, United States
| | - Xiaohua Zhang
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6119, United States
| | - Benjamin P. Hay
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6119, United States
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20
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Wadugu BA, Ng C, Bartley BL, Rowe RJ, Millard JT. DNA interstrand cross-linking activity of (1-Chloroethenyl)oxirane, a metabolite of beta-chloroprene. Chem Res Toxicol 2010; 23:235-9. [PMID: 20030381 DOI: 10.1021/tx9003769] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
With the goal of elucidating the molecular and cellular mechanisms of chloroprene toxicity, we examined the potential DNA cross-linking of the bifunctional chloroprene metabolite, (1-chloroethenyl)oxirane (CEO). We used denaturing polyacrylamide gel electrophoresis to monitor the possible formation of interstrand cross-links by CEO within synthetic DNA duplexes. Our data suggest interstrand cross-linking at deoxyguanosine residues within 5'-GC and 5'-GGC sites, with the rate of cross-linking depending on pH (pH 5.0 > pH 6.0 > pH 7.0). A comparison of the cross-linking efficiencies of CEO and the structurally similar cross-linkers diepoxybutane (DEB) and epichlorohydrin (ECH) revealed that DEB > CEO > or = ECH. Furthermore, we found that cytotoxicity correlates with cross-linking efficiency, supporting a role for interstrand cross-links in the genotoxicology of chloroprene.
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Affiliation(s)
- Brian A Wadugu
- Department of Chemistry, Colby College, Waterville, Maine 04901, USA
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21
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Smith S, Guziec FS, Guziec L, Brodbelt JS. Interactions of sulfur-containing acridine ligands with DNA by ESI-MS. Analyst 2009; 134:2058-66. [PMID: 19768213 PMCID: PMC2892893 DOI: 10.1039/b905071j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alkylating proficiency of sulfur-containing mustards may be increased by using an acridine moiety to guide the sulfur mustard to its cellular target. In this study, the interactions of a new series of sulfur-containing acridine ligands, some that also function as alkylating mustards, with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/acridine mixtures. The extent of binding observed for the series of sulfur-containing acridines was similar, presumably because the intercalating acridine moiety was identical. Upon infrared multi-photon dissociation (IRMPD) of the resulting oligonucleotide/sulfur-containing acridine complexes, ejection of the ligand was the dominant pathway for most of the complexes. However, for AS4, an acridine sulfide mustard, and AN1, an acridine nitrogen mustard, strand separation with the ligand remaining on one of the single strands was observed. At higher irradiation times, a variety of sequence ions were observed, some retaining the AS4/AN1 ligand, which was indicative of covalent binding.
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Affiliation(s)
- Suncerae Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
| | - Frank S. Guziec
- Department of Chemistry, Southwestern University, Georgetown, TX 79626
| | - Lynn Guziec
- Department of Chemistry, Southwestern University, Georgetown, TX 79626
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
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22
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Pentikäinen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ. Lennard−Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases. J Chem Theory Comput 2009; 5:396-410. [DOI: 10.1021/ct800135k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulla Pentikäinen
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Katherine E. Shaw
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Kittusamy Senthilkumar
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Christopher J. Woods
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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23
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Petrović ZD, Hadjipavlou-Litina D, Petrović VP. New Pd(II)–mechlorethamine complex: Synthesis, NMR study of hydrolytic activity and in vitro evaluation of antiradical property of new complex and its alkylating precursor. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2008.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Fridman AS, Galyuk EN, Vorob'ev VI, Skvortsov AN, Lando DY. Melting of Crosslinked DNA: VI. Comparison of Influence of Interstrand Crosslinks and Other Chemical Modifications Formed by Antitumor Compounds on DNA Stability. J Biomol Struct Dyn 2008; 26:175-85. [DOI: 10.1080/07391102.2008.10507233] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Antsypovitch SI, Oretskaya TS. Double-helical nucleic acids with cross-linked strands: synthesis and applications in molecular biology. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1998v067n03abeh000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Romano KP, Newman AG, Zahran RW, Millard JT. DNA interstrand cross-linking by epichlorohydrin. Chem Res Toxicol 2007; 20:832-8. [PMID: 17441735 PMCID: PMC2727797 DOI: 10.1021/tx700066h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epichlorohydrin (ECH), an important industrial chemical, is a bifunctional alkylating agent with the potential to form DNA cross-links. Occupational exposure to this suspect carcinogen leads to chromosomal aberrations, and ECH has been shown previously to undergo reaction with DNA in vivo and in vitro. We used denaturing polyacrylamide gel electrophoresis to monitor the possible formation of interstrand cross-links within DNA oligomers by ECH and the related compound, epibromohydrin (EBH). Although both compounds did indeed form cross-links between deoxyguanosine residues, EBH was a more efficient cross-linker than ECH. The optimal pH for cross-linking also varied, with ECH more efficient at pH 5.0 and EBH more efficient at pH 7.0. Both agents were relatively flexible in the sequences targeted, with comparable efficiencies for 5'-GGC and 5'GC sites. Furthermore, interstrand cross-linking by the two optical isomers of ECH correlated with their relative cytotoxicities, with R-ECH about twice as potent as S-ECH.
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Affiliation(s)
- Keith P Romano
- Department of Chemistry, Colby College, Waterville Maine 04901, USA
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27
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Sawyer GA, Frederick ED, Millard JT. Flanking sequences modulate diepoxide and mustard cross-linking efficiencies at the 5'-GNC site. Chem Res Toxicol 2005; 17:1057-63. [PMID: 15310237 DOI: 10.1021/tx0499057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diepoxybutane, diepoxyoctane, and mechlorethamine are cytotoxic agents that induce interstrand cross-links between the N7 positions of deoxyguanosine residues on opposite strands of the DNA duplex preferentially at 5'-GNC sequences. We have systematically varied the identity of either the base 5' to the cross-linked deoxyguanosine residues or the intervening base pair to determine flanking sequence effects on cross-linking efficiency. We used synthetic DNA oligomers containing four 5'-N(1)GN(2)C sites that varied either N(1) or N(2). Interstrand cross-links were purified through denaturing polyacrylamide gel electrophoresis and then subjected to piperidine cleavage. The amount of cleavage at each deoxyguanosine residue, representative of cross-linking efficiency at that site, was determined by sequencing gel analysis. Our data suggest that cross-linking efficiency varies with the identity of N(1) similarly (purines > pyrimidines) for diepoxybutane, diepoxyoctane, and mechlorethamine but that the effects of N(2) differ for the three compounds.
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Affiliation(s)
- Gregory A Sawyer
- Department of Chemistry, 5757 Mayflower Hill Drive, Colby College, Waterville, Maine 04901, USA
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28
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Wang Y, Wang Y. Structure elucidation of DNA interstrand cross-link by a combination of nuclease P1 digestion with mass spectrometry. Anal Chem 2004; 75:6306-13. [PMID: 14616015 DOI: 10.1021/ac034683n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA interstrand cross-link reagents are among the most powerful agents for cancer treatment. Here we report a combined nuclease P1 digestion/mass spectrometry method for the structure elucidation of duplex oligodeoxynucleotides (ODNs) containing an interstrand cross-link. Our results demonstrate that nuclease P1 digestion of a double-stranded ODN containing an interstrand cross-link (ICL) of 4,5',8-trimethylpsoralen or mitomycin C gives a tetranucleotide bearing the cross-linked nucleobase moiety. Product ion spectra of the deprotonated ions of the tetranucleotides provide information about the structure of the cross-link. Furthermore, product-ion spectra of tetranucleotides containing two orientation isomers of mitomycin C interstrand cross-link are distinctive. We believe that the method described in this paper can be generally applicable for investigating the structures of other DNA ICLs.
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Affiliation(s)
- Yuesong Wang
- Department of Chemistry-027, University of California at Riverside, Riverside, California 92521-0403, USA
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29
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Bando T, Narita A, Saito I, Sugiyama H. Highly efficient sequence-specific DNA interstrand cross-linking by pyrrole/imidazole CPI conjugates. J Am Chem Soc 2003; 125:3471-85. [PMID: 12643709 DOI: 10.1021/ja028459b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have developed a novel type of DNA interstrand cross-linking agent by synthesizing dimers of a pyrrole (Py)/imidazole (Im)-diamide-CPI conjugate, ImPyLDu86 (1), connected using seven different linkers. The tetramethylene linker compound, 7b, efficiently produces DNA interstrand cross-links at the nine-base-pair sequence, 5'-PyGGC(T/A)GCCPu-3', only in the presence of a partner triamide, ImImPy. For efficient cross-linking by 7b with ImImPy, one A.T base pair between two recognition sites was required to accommodate the linker region. Elimination of the A.T base pair and insertion of an additional A.T base pair and substitution with a G.C base pair significantly reduced the degree of cross-linking. The sequence specificity of the interstrand cross-linking by 7b was also examined in the presence of various triamides. The presence of ImImIm slightly reduced the formation of a cross-linked product compared to ImImPy. The mismatch partners, ImPyPy and PyImPy, did not produce an interstrand cross-link product with 7b, whereas ImPyPy and PyImPy induced efficient alkylation at their matching site with 7b. The interstrand cross-linking abilities of 7b were further examined using denaturing polyacrylamide gel electrophoresis with 5'-Texas Red-labeled 400- and 67-bp DNA fragments. The sequencing gel analysis of the 400-bp DNA fragment with ImImPy demonstrated that 7b alkylates several sites on the top and bottom strands, including one interstrand cross-linking match site, 5'-PyGGC(T/A)GCCPu-3'. To obtain direct evidence of interstrand cross-linkages on longer DNA fragments, a simple method using biotin-labeled complementary strands was developed, which produced a band corresponding to the interstrand cross-linked site on both top and bottom strands. Densitometric analysis indicated that the contribution of the interstrand cross-link in the observed alkylation bands was approximately 40%. This compound efficiently cross-linked both strands at the target sequence. The present system consisted of a 1:2 complex of the alkylating agent and its partner ImImPy and caused an interstrand cross-linking in a sequence-specific fashion according to the base-pair recognition rule of Py-Im polyamides.
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Affiliation(s)
- Toshikazu Bando
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda, Tokyo 101-0062, Japan
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30
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DNA-alkylating events associated with nitrogen mustard based anticancer drugs and the metabolic byproduct Acrolein. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1067-568x(02)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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31
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Affiliation(s)
- R A Luce
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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32
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Affiliation(s)
- A M Snow
- Memorial High School, Elmwood Park, New Jersey 07407, USA
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33
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Millard JT, Wilkes EE. Diepoxybutane and diepoxyoctane interstrand cross-linking of the 5S DNA nucleosomal core particle. Biochemistry 2001; 40:10677-85. [PMID: 11524013 DOI: 10.1021/bi0109663] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diepoxyalkanes form interstrand cross-links in DNA oligomers preferentially at 5'-GNC sites. We have examined cross-linking by 1,2,3,4-diepoxybutane (DEB) and 1,2,7,8-diepoxyoctane (DEO) within a fragment of the 5S RNA gene of Xenopus borealis in both the free and nucleosomal states. Sites and efficiencies of interstrand cross-linking were probed through denaturing polyacrylamide gel electrophoresis and quantitative phosphorimagery. Both agents targeted 5'-GNC sites for cross-linking in the restriction fragment in its free state, and DEO also targeted 5'-GNNC sites. Monoalkylation occurred at all deoxyguanosines. The sites for both monoalkylation and interstrand cross-linking were similar in nucleosomal and free DNA, and cross-linked DNA was cleanly incorporated into the core particle structure. These findings suggest that the 5S core particle is able to tolerate any structural abnormalities induced by diepoxide cross-linking.
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Affiliation(s)
- J T Millard
- Department of Chemistry, Colby College, Waterville, Maine 04901, USA.
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34
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Bando T, Iida H, Saito I, Sugiyama H. Sequence-specific DNA interstrand cross-linking by imidazole--pyrrole CPI conjugate. J Am Chem Soc 2001; 123:5158-9. [PMID: 11457371 DOI: 10.1021/ja003660c] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T Bando
- CREST, Japan Science and Technology Corporation (JST), Japan
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35
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Boga C, Bonamartini A, Forlani L, Modarelli V, Righi L, Sgarabotto P, Todesco P. Reactions of Hydroxypyridines with 1-Chloro-2,4,6-trinitrobenzene − Product Structure, Kinetics, and Tautomerism. European J Org Chem 2001. [DOI: 10.1002/1099-0690(200103)2001:6<1175::aid-ejoc1175>3.0.co;2-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Millard JT, Wilkes EE. cis- and trans-diamminedichloroplatinum(II) interstrand cross-linking of a defined sequence nucleosomal core particle. Biochemistry 2000; 39:16046-55. [PMID: 11123932 DOI: 10.1021/bi0022285] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interstrand cross-linking studies with the antitumor drug cis-diamminedichloroplatinum(II) and its clinically inactive isomer, trans-diamminedichloroplatinum(II), were performed on a fragment of the 5S rRNA gene of Xenopus borealis in the free and nucleosomal state. 5S nucleosomes were formed via histone octamer exchange from chicken erythrocyte core particles. Native polyacrylamide gel electrophoresis was used to probe the ability of platinated DNA to reconstitute into core particles. Both isomers negatively impacted reconstitution when histones were present during incubation with the drug. When histones were not present during the drug treatment, platinated DNA was successfully reconstituted into core particles. These results suggest that platination of histones impedes reconstitution of free DNA. However, already-formed core particles were not disrupted upon platination. Sites of interstrand cross-linking were probed through denaturing polyacrylamide gel electrophoresis and quantitative phosphorimagery. We found both site-specific enhancement and depression of cis-diamminedichloroplatinum(II) cross-linking in the nucleosomal samples relative to free DNA at both drug concentrations that were tested (0.01 and 0.0025 mM). trans-Diamminedichloroplatinum(II) exhibited no detectable differences in the interstrand cross-linking of free and nucleosomal samples.
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Affiliation(s)
- J T Millard
- Department of Chemistry, Colby College, Waterville, Maine 04901, USA.
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37
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Alcaro S, Coleman RS. A molecular model for DNA cross-linking by the antitumor agent azinomycin B. J Med Chem 2000; 43:2783-8. [PMID: 10956185 DOI: 10.1021/jm990362l] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A computational model for the covalent interstrand DNA cross-linking of the antitumor agent azinomycin B is reported and is based on Monte Carlo simulations of the four possible monoalkylation species and an examination of the low energy conformations of the cross-linked agent. The model was developed using a suitably modified version of the AMBER* force field with the experimentally determined triplet DNA target sequence 5'-d(GCT)-3' in both the native B-form and containing a preformed intercalation site.
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Affiliation(s)
- S Alcaro
- Dipartimento di Scienze Farmaco-Biologiche, Università di Catanzaro Magna Graecia, Catanzaro, Italy
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38
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Malinge JM, Giraud-Panis MJ, Leng M. Interstrand cross-links of cisplatin induce striking distortions in DNA. J Inorg Biochem 1999; 77:23-9. [PMID: 10626349 DOI: 10.1016/s0162-0134(99)00148-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the reaction between cellular DNA and cisplatin, different bifunctional adducts are formed including intrastrand and interstrand cross-links. The respective role of these lesions in the cytotoxicity of the drug is not yet elucidated. This paper deals with the current knowledge on cisplatin interstrand cross-links and presents results on the formation, stability and structure of these adducts. A key step in the studies of these lesions is the recent determination of solution and crystallographic structures of double-stranded oligonucleotides containing a unique interstrand cross-link. The DNA distortions induced by this adduct exhibit unprecedented features such as the location of the platinum residue in the minor groove, the extrusion of the cytosines of the cross-linked d(GpC).d(GpC) site, the bending of the helix axis towards the minor groove and a large DNA unwinding. In addition to a detailed determination of the distortions, the high resolution of the crystal structure allowed us to locate the water molecules surrounding the adduct. The possible implications of this structure for the chemical properties and the cellular processing of cisplatin interstrand cross-links are discussed.
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Affiliation(s)
- J M Malinge
- Centre de Biophysique Moléculaire, CNRS, Orléans, France.
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Picada JN, Khromov-Borisov NN, Henriques JA. Deletogenic activity of 1,2:7,8-diepoxyoctane in the Salmonella typhimurium tester strain TA102. Mutat Res 1999; 437:165-73. [PMID: 10556620 DOI: 10.1016/s1383-5742(99)00082-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
1,2:7,8-Diepoxyoctane (DEO), whose deletogenic activity was first demonstrated in ad-3 system of Neurospora crassa and then in different species, has been tested in Salmonella typhimurium tester strain TA102 (hisG428(Ochre)). It was confirmed that it is a direct acting mutagen and was found that its activity is stimulated with the S9 mix. Obtained His(+) revertants were screened on their response to the histidine analog, N-(2-thiazolyl)-DL-alanine (ThiAla). Thirty-two percent of spontaneous and 52% of DEO-induced revertants were resistant to the analog while no resistance was observed among those induced with 4-nitroquinoline-N-oxide (4NQO). Resistance to ThiAla was interpreted as due to small deletions surrounding the target TAA codon in hisG428(Ochre). Thus, at least two simple test-systems, ad-3 of N. crassa and hisG428(Ochre) of S. typhimurium, gave compatible results and might be useful in searching of deletogens.
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Affiliation(s)
- J N Picada
- Departamento de Biofsica, GENOTOX-Laboratório de Genotoxicidade/Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Bloco IV, Prdio 43.421, Caixa Postal 15.005, Campus do Vale/UFRGS, CEP 91501-970, Porto Alegre, RS, Brazil
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40
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Bierbach U, Qu Y, Hambley TW, Peroutka J, Nguyen HL, Doedee M, Farrell N. Synthesis, Structure, Biological Activity, and DNA Binding of Platinum(II) Complexes of the Type trans-[PtCl(2)(NH(3))L] (L = Planar Nitrogen Base). Effect of L and Cis/Trans Isomerism on Sequence Specificity and Unwinding Properties Observed in Globally Platinated DNA. Inorg Chem 1999; 38:3535-3542. [PMID: 11671101 DOI: 10.1021/ic981181x] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to establish fundamental structural requirements for the antitumor activation of the trans-platinum geometry, complexes of the general formulas [PtCl(2)(NH(3))L] (L = planar N donor) have been synthesized. The trans isomers, trans-[PtCl(2)(NH(3))(quinoline)] (3), trans-[PtCl(2)(NH(3))(thiazole)] (5), trans-[PtCl(2)(NH(3))(benzothiazole)] (7), and trans-[PtCl(2)(NH(3))(isoquinoline)] (8) and the cis isomers cis-[PtCl(2)(NH(3))(quinoline)] (4) and cis-[PtCl(2)(NH(3))(thiazole)] (6) were characterized by (1)H NMR and analytical data. In addition, the crystal structures of 3, 5, 7, and 8 were determined: 3, monoclinic, P2(1)/c, with a = 8.414(1) Å, b = 12.373(3) Å, c = 21.266(3) Å, beta = 96.78(1) degrees, V = 2198.3(6) Å(3), and Z = 8; 5, monoclinic, P2(1)/n, with a = 8.815(4) Å, b = 19.917(8) Å, c = 14.498(5) Å, beta = 103.30(3) degrees, V = 2477(2) Å(3), and Z = 12; 7, monoclinic, P2(1)/c, with a = 8.150(4) Å, b = 23.196(9) Å, c = 11.297(7) Å, beta = 90.94(4) degrees, V = 2135.3(2) Å(3), and Z = 8; 8, monoclinic, C2/c, with a = 19.043(4) Å, b = 8.570(2) Å, c = 29.127(6) Å, beta_ = 111.59(2) degrees, V = 4420(2) Å(3), and Z = 16. In all cases, the Pt coordination plane and L are mutually twisted with angles between planes of 50-68 degrees. Bulky quinoline in 3 produces intramolecular steric strain as evidenced by a short, nonbonding Pt.H8(quin) contact of 2.77 Å and concomitantly distorted Pt-N(quin)-C bond angles. The trans complexes 3, 5, 7, and 8 showed a significantly higher cytotoxicity in cisplatin-sensitive L1210 leukemia than trans-[PtCl(2)(NH(3))(2)] (2), with 3 and 5 being as potent as the corresponding cis isomers 4 and 6. In addition, the presence of the planar ligand greatly enhanced the activity of all of the compounds in cells resistant to cisplatin, cis-[PtCl(2)(NH(3))(2)] (1). Complex geometry and L play an important role in the binding of 1-7 to DNA. For synthetic poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) the order of binding affinities (r(b), drug-to-nucleotide ratio) was 2 > 1 > 6 > 5 > 4 > 7 > 3 and 5 > 6 > 7 > 3 > 2 > 1 > 4, respectively. Furthermore, 3 and 7, carrying large planar ligands, were remarkably effective at unwinding negatively supercoiled, closed circular pUC19 DNA (phi = 15 degrees and 17 degrees, respectively). The consequences of structural effects caused by L on target DNA with respect to possible biological consequences are discussed.
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Affiliation(s)
- Ulrich Bierbach
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, and School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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41
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Coste F, Malinge JM, Serre L, Shepard W, Roth M, Leng M, Zelwer C. Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. Nucleic Acids Res 1999; 27:1837-46. [PMID: 10101191 PMCID: PMC148391 DOI: 10.1093/nar/27.8.1837] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.
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Affiliation(s)
- F Coste
- Centre de Biophysique Moléculaire, Centre de National de la Recherche Scientifique, affiliated to the Université d'Orléans, rue Charles Sadron, 45071 Orleans Cedex, France
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42
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Tomasz M, Das A, Tang KS, Ford MGJ, Minnock A, Musser SM, Waring MJ. The Purine 2-Amino Group as the Critical Recognition Element for Sequence-Specific Alkylation and Cross-Linking of DNA by Mitomycin C. J Am Chem Soc 1998. [DOI: 10.1021/ja9824019] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maria Tomasz
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Arunangshu Das
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Kit S. Tang
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Marjin G. J. Ford
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Andrew Minnock
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Steven M. Musser
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
| | - Michael J. Waring
- Contribution from the Department of Chemistry, Hunter College, City University of New York, New York, New York 10021, U.S. Food and Drug Administration, Washington, D.C. 20204, and Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QJ, UK
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43
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Yaghi BM, Turner PM, Denny WA, Turner PR, O'Connor CJ, Ferguson LR. Comparative mutational spectra of the nitrogen mustard chlorambucil and its half-mustard analogue in Chinese hamster AS52 cells. Mutat Res 1998; 401:153-64. [PMID: 9639696 DOI: 10.1016/s0027-5107(98)00005-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nitrogen mustards play an important role in current cancer chemotherapy. The most effective antitumour agents are those carrying two alkylating functions, probably through their ability to form interstrand cross-links in DNA. Such lesions appear to create more of a block in DNA replication and are more difficult to repair than are most monoadducts. Although there were early reports that monofunctional drugs were more mutagenic than the bifunctional drugs, this has not been formally proved using structurally related drugs in a mutagenicity assay capable of detecting a range of different events. We have studied both the mutagenic potency and spectrum of events caused by treatment with the clinical agent, chlorambucil, compared with its half-mustard analogue, in Chinese hamster ovary (CHO)-AS52 cells. Although both drugs caused comparable increases in mutation frequency at doses killing 90% of cells (from around 9x10-6 to around 9x10-5 mutant cells), the nature of events differed significantly between the drugs. By far the majority of mutations caused by the half-mustard were transversion mutations, and almost all of these could be interpreted in relation to the DNA adducts that are known to be formed. In contrast, the majority of chlorambucil-induced mutations were major deletions, and point mutations were only identified from a few clones. Parallel micronucleus assays verified that chlorambucil has a stronger ability to break chromosomes than the half-mustard. These two drugs are thought to form similar monoadducts, but only the full mustard can form interstrand cross-links. The data suggest that DNA cross-links, although only a minor fraction of the total lesions, dominate the mutagenic spectrum and lead to gross changes at the chromosome level that can not be readily associated with individual lesions produced by the drug.
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Affiliation(s)
- B M Yaghi
- Cancer Research Laboratory, Faculty of Medicine and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1000, New Zealand
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44
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Millard JT, Spencer RJ, Hopkins PB. Effect of nucleosome structure on DNA interstrand cross-linking reactions. Biochemistry 1998; 37:5211-9. [PMID: 9548752 DOI: 10.1021/bi972862r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antitumor agents of the nitrogen mustard family and mitomycin C form interstrand cross-links in duplex DNA. To provide information about the cellular mechanism by which these compounds exert their cytotoxic effects, we examined cross-linking of a nucleosomal core particle formed on a fragment of the 5S RNA gene of Xenopus borealis. For the mustards mechlorethamine, chlorambucil, and melphalan, both sites of monoalkylation and interstrand cross-linking were similar in nucleosomal and free DNA. Some small (two- to three- fold) differences in intensity of cross-linking at some sites were apparent. However, these differences did not appear to correlate with rotational or translational positioning. For mitomycin C, cross-linking was inhibited five- to ten-fold at the nucleosomal dyad and showed attenuation of inhibition toward the ends. Furthermore, rotational positioning also appeared to be a factor, with sites facing inward in the nucleosome less accessible for mitomycin cross-linking. None of these agents demonstrated the 10-base pair periodicity exhibited by hydroxyl radical cleavage of nucleosomal DNA.
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Affiliation(s)
- J T Millard
- Department of Chemistry, Colby College, Waterville, Maine 04901, USA.
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45
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Hicks M, Wharton G, Huchital DH, Murphy WR, Sheardy RD. Assessing the sequence specificity in the binding of Co(III) to DNA via a thermodynamic approach. Biopolymers 1997; 42:549-59. [PMID: 9322443 DOI: 10.1002/(sici)1097-0282(19971015)42:5<549::aid-bip5>3.0.co;2-q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction specificities of Co(III) with DNA were investigated via consideration of thermodynamic characteristics of the duplex to single strand transition for DNA oligomers incubated in the presence of [Co(NH3)5(OH2)](ClO4)3. It has previously been demonstrated that incubation of the DNA oligomer [(5medC-dG)4]2 with this cobalt complex leads to coordination of the cobalt center to the DNA, presumably at N7 of guanine bases [D. C. Calderone, E. J. Mantilla, M. Hicks, D. H. Huchital, W. R. Murphy, Jr. and R. D. Sheardy, (1995) Biochemistry 34, 13841]. In this report, DNA oligomers of different sequence were incubated with [Co(NH3)5(OH2)](ClO4)3 via protocols developed previously and the treated oligomers were subjected to thermal denaturation for comparison to the untreated oligomers. The DNA oligomers were designed in order to investigate the sequence specificity, if any, in the reaction of the cobalt complex with DNA. The values of Tm, delta HvH, and delta n (the differential ion binding term) obtained from the thermal denaturations were used to assess the sequence specificity of the interaction. For all oligomers, treated or untreated, Tm and delta HvH vary linearly with log [Na+] and hence the value of delta n is a function of the Na+ concentration. The results indicate no significant reaction between the cobalt complex and oligomers possessing isolated -GA- or -CG- sites; however, the thermodynamic characteristics of DNA oligomers possessing either an isolated -GG- site or an isolated -GC- site were altered by the treatment. Atomic absorption studies of the treated oligomers demonstrate that only the DNA oligomers possessing isolated -GG- or -GC- sites bind cobalt. Hence, the changes in the thermodynamic properties of these oligomers are a result of cobalt binding with a remarkable sequence specificity.
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Affiliation(s)
- M Hicks
- Department of Chemistry, Seton Hall University, South Orange, NJ 07079-2694, USA
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46
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Tomasz M, Palom Y. The mitomycin bioreductive antitumor agents: cross-linking and alkylation of DNA as the molecular basis of their activity. Pharmacol Ther 1997; 76:73-87. [PMID: 9535170 DOI: 10.1016/s0163-7258(97)00088-0] [Citation(s) in RCA: 212] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This review focuses on the chemical and enzymatic aspects of the reductive activation of mitomycin C, its disulfide analogs KW-2149 and BMS-181174, and, in less detail, FR66979 and FR900482, newly discovered antitumor antibiotics related to mitomycins. Furthermore, structural aspects of DNA damage induced by these drugs in vitro and in vivo are described, including the chemical and conformational characteristics of DNA interstrand and intrastrand cross-links and monofunctional alkylation products, with emphasis on DNA adducts of mitomycin C. The DNA sequence specificity of the damage and its mechanism is reviewed. The relationship between the chemical and structural properties of the DNA damage on the one hand, and the antitumor and other biological activities of the mitomycins on the other, is discussed.
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Affiliation(s)
- M Tomasz
- Hunter College, The City University of New York, New York 10021, USA
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47
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Bierbach U, Farrell N. Modulation of Nucleotide Binding of trans Platinum(II) Complexes by Planar Ligands. A Combined Proton NMR and Molecular Mechanics Study. Inorg Chem 1997; 36:3657-3665. [PMID: 11670057 DOI: 10.1021/ic970154o] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonclassical trans platinum complexes containing planar nitrogen bases show biological activity different from that of trans-diamminedichloroplatinum(II) (trans-DDP). In search of the mechanism of action of such compounds, a comparative study on the nucleobase chemistry of trans-DDP and trans-[PtCl(2)(NH(3))(quinoline)] (trans-QUIN) was performed using 1D and 2D NMR spectroscopy and molecular modeling techniques. The two simple monofunctional adducts trans-[PtCl(9-ethylguanine-N7)(NH(3))L]NO(3) (L = NH(3), 1; L = quinoline, 2) were synthesized by employing the AgNO(3)/DMF method. Reactions of these species with 5'-guanosine monophosphate (5'-GMP) and 5'-cytidine monophosphate (5'-CMP) were used to simulate potential second binding steps on DNA. Guanine-N7 proved to be the kinetically preferred binding site for both 1 and 2. Reactions with 2 proceeded significantly slower than those with 1 under the same conditions. These differences in reactivity are attributed to an altered hydrolytic behavior of 2 due to steric influences of quinoline upon associative substitution reactions. This is supported by interligand NOEs observed in the 2D NOESY spectrum of 2 and by AMBER-based geometries for different conformers of 2. Signal splittings observed in the (1)H NMR spectra of 2 and the bifunctional adducts trans-[Pt(9-EtGua-N7)(5'-GMP-N7)(NH(3))L] (4) andtrans-[Pt(9-EtGua-N7)(2)(NH(3))L](2+) (6) (L = quinoline) indicate hindered rotation about the Pt-N (guanine and quinoline) bonds. Temperature-dependent NMR spectra and molecular mechanics results are in agreement with frozen rotamers in solution at room temperature where unfavorable repulsive interligand interactions result in different head-to-head and head-to-tail orientations of the bases. For the different rotamers of 4, a high barrier of interconversion of 87 kJ mol(-)(1) was estimated from NMR data. The consequences of these kinetic and geometric effects with respect to target DNA are discussed.
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Affiliation(s)
- Ulrich Bierbach
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006
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48
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Pérez C, Leng M, Malinge JM. Rearrangement of interstrand cross-links into intrastrand cross-links in cis-diamminedichloroplatinum(II)-modified DNA. Nucleic Acids Res 1997; 25:896-903. [PMID: 9016644 PMCID: PMC146515 DOI: 10.1093/nar/25.4.896] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the reaction of the anticancer drug cis-diamminedichloroplatinum(II) (cis-DDP) with DNA, bifunctional intrastrand and interstrand cross-links are formed. In this work, we show that at 37 degrees C interstrand cross-links (ICL) are labile and rearrange into intrastrand cross-links. The ICL instability was first studied with a 10 base pairs (bp) double-stranded oligonucleotide containing a unique site-specific ICL resulting from chelation of the N7 position of two guanine residues on the opposite strands of DNA at the d(GC/GC) site by a cis-diammineplatinum(II) residue. The bonds between the platinum and the N7 of guanine residues within the interstrand adduct are cleaved. In 50 mM NaCl or NaClO4, this cleavage results in the formation of monofunctional adducts which subsequently form intrastrand cross-links. One cleavage reaction takes place per cross-linked duplex in either of both DNA strands. Whereas the starting cross-linked 10 bp duplex is hydrogen bonded, the two complementary DNA strands separate after the cleavage of the ICL. Under these conditions, the cleavage reaction is irreversible allowing its rate measurement (t1/2= 29+/-2 h) and closure of monofunctional adducts to intrastrand cross-links occurs within single-stranded DNA. Within a longer cross-linked oligonucleotide (20 bp), ICL are apparently more stable (t1/2= 120+/-12 h) as a consequense of monofunctional adducts closure back to ICL. We propose that the ICL cleavage is reversible in DNA and that these adducts rearrange finally into intrastrand cross-links. Our results could explain an 'ICL unhooking' in previously reported in vivo repair studies [Zhenet al. (1993)Carcinogenesis14, 919-924].
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Affiliation(s)
- C Pérez
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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49
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Park HJ, Kelly RC, Hurley LH. The Chemical Evolution of DNA−DNA Interstrand Cross-Linkers That Recognize Defined Mixed AT and GC Sequences. J Am Chem Soc 1996. [DOI: 10.1021/ja961678a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Hyun-Ju Park
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Robert C. Kelly
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Laurence H. Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
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50
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Seaman FC, Hurley L. Manipulative Interplay of the Interstrand Cross-Linker Bizelesin with d(TAATTA)2 To Achieve Sequence Recognition of DNA. J Am Chem Soc 1996. [DOI: 10.1021/ja961924i] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frederick C. Seaman
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
| | - Laurence Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
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