1
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Olatunji M, Liu Y. RNA damage and its implications in genome stability. DNA Repair (Amst) 2025; 147:103821. [PMID: 40043352 DOI: 10.1016/j.dnarep.2025.103821] [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: 11/26/2024] [Revised: 02/19/2025] [Accepted: 02/25/2025] [Indexed: 03/17/2025]
Abstract
Endogenous and environmental stressors can damage DNA and RNA to compromise genome and transcriptome stability and integrity in cells, leading to genetic instability and diseases. Recent studies have demonstrated that RNA damage can also modulate genome stability via RNA-templated DNA synthesis, suggesting that it is essential to maintain RNA integrity for the sustainment of genome stability. However, little is known about RNA damage and repair and their roles in modulating genome stability. Current efforts have mainly focused on revealing RNA surveillance pathways that detect and degrade damaged RNA, while the critical role of RNA repair is often overlooked. Due to their abundance and susceptibility to nucleobase damaging agents, it is essential for cells to evolve robust RNA repair mechanisms that can remove RNA damage, maintaining RNA integrity during gene transcription. This is supported by the discovery of the alkylated RNA nucleobase repair enzyme human AlkB homolog 3 that can directly remove the methyl group on damaged RNA nucleobases, predominantly in the nucleus of human cells, thereby restoring the integrity of the damaged RNA nucleobases. This is further supported by the fact that several DNA repair enzymes can also process RNA damage. In this review, we discuss RNA damage and its effects on cellular function, DNA repair, genome instability, and potential RNA damage repair mechanisms. Our review underscores the necessity for future research on RNA damage and repair and their essential roles in modulating genome stability.
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Affiliation(s)
- Mustapha Olatunji
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA; Department of Chemistry and Biochemistry, and Florida International University, Miami, FL, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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2
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Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells. Cell Rep 2021; 31:107532. [PMID: 32320655 DOI: 10.1016/j.celrep.2020.107532] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/07/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Cisplatin is an antineoplastic drug administered at suboptimal and intermittent doses to avoid life-threatening effects. Although this regimen shortly improves symptoms in the short term, it also leads to more malignant disease in the long term. We describe a multilayered analysis ranging from chromatin to translation-integrating chromatin immunoprecipitation sequencing (ChIP-seq), global run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and ribosome profiling-to understand how cisplatin confers (pre)malignant features by using a well-established ovarian cancer model of cisplatin exposure. This approach allows us to segregate the human transcriptome into gene modules representing distinct regulatory principles and to characterize that the most cisplatin-disrupted modules are associated with underlying events of super-enhancer plasticity. These events arise when cancer cells initiate without ultimately ending the program of drug-stimulated death. Using a PageRank-based algorithm, we predict super-enhancer regulator ISL1 as a driver of this plasticity and validate this prediction by using CRISPR/dCas9-KRAB inhibition (CRISPRi) and CRISPR/dCas9-VP64 activation (CRISPRa) tools. Together, we propose that cisplatin reprograms cancer cells when inducing them to undergo near-to-death experiences.
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Affiliation(s)
- Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos Mackintosh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ranveer Singh Jayani
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Soohwan Oh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunyu Jin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sreejith Janardhanan Nair
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Allen
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Angels Almenar-Queralt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Abstract
Similar to many other biological molecules, RNA is vulnerable to chemical insults from endogenous and exogenous sources. Noxious agents such as reactive oxygen species or alkylating chemicals have the potential to profoundly affect the chemical properties and hence the function of RNA molecules in the cell. Given the central role of RNA in many fundamental biological processes, including translation and splicing, changes to its chemical composition can have a detrimental impact on cellular fitness, with some evidence suggesting that RNA damage has roles in diseases such as neurodegenerative disorders. We are only just beginning to learn about how cells cope with RNA damage, with recent studies revealing the existence of quality-control processes that are capable of recognizing and degrading or repairing damaged RNA. Here, we begin by reviewing the most abundant types of chemical damage to RNA, including oxidation and alkylation. Focusing on mRNA damage, we then discuss how alterations to this species of RNA affect its function and how cells respond to these challenges to maintain proteostasis. Finally, we briefly discuss how chemical damage to noncoding RNAs such as rRNA, tRNA, small nuclear RNA, and small nucleolar RNA is likely to affect their function.
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Affiliation(s)
- Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, To whom correspondence should be addressed:
Dept. of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Dr., St. Louis, MO 63130. Tel.:
314-935-7662; Fax:
314-935-4432; E-mail:
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4
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Dávila–Rodríguez M, Barolli JP, de Oliveira KM, Colina–Vegas L, da Silva Miranda F, Castellano EE, Von Poelhsitz G, Batista AA. Carbonyl–heterobimetallic Ru(II)/Fe(II)–complexes containing polypyridyl ligands: Synthesis, characterization, cellular viability assays and interactions with biomolecules. Arch Biochem Biophys 2018; 660:156-167. [DOI: 10.1016/j.abb.2018.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/18/2022]
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5
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Nicholas BD, Francis S, Wagner EL, Zhang S, Shin JB. Protein Synthesis Inhibition and Activation of the c-Jun N-Terminal Kinase Are Potential Contributors to Cisplatin Ototoxicity. Front Cell Neurosci 2017; 11:303. [PMID: 29033791 PMCID: PMC5627031 DOI: 10.3389/fncel.2017.00303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/12/2017] [Indexed: 11/29/2022] Open
Abstract
Cisplatin has been regarded as an effective and versatile chemotherapeutic agent for nearly 40 years. Though the associated dose-dependent ototoxicity is known, the cellular mechanisms by which cochleovestibular hair cell death occur are not well understood. We have previously shown that aminoglycoside ototoxicity is mediated in part by cytosolic protein synthesis inhibition. Despite a lack of molecular similarity, aminoglycosides were shown to elicit similar stress pathways to cisplatin. We therefore reasoned that there may be some role of protein synthesis inhibition in cisplatin ototoxicity. Employing a modification of the bioorthogonal noncanonical amino acid tagging (BONCAT) method, we evaluated the effects of cisplatin on cellular protein synthesis. We show that cisplatin inhibits cellular protein synthesis in organ of Corti explant cultures. Similar to what was found after gentamicin exposure, cisplatin activates both the c-Jun N-terminal kinase (JNK) and mammalian target of rapamycin (mTOR) pathways. In contrast to aminoglycosides, cisplatin also inhibits protein synthesis in all cochlear cell types. We further demonstrate that the multikinase inhibitor sorafenib completely prevents JNK activation, while providing only moderate hair cell protection. Simultaneous stimulation of cellular protein synthesis by insulin, however, significantly improved hair cell survival in culture. The presented data provides evidence for a potential role of protein synthesis inhibition in cisplatin-mediated ototoxicity.
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Affiliation(s)
- Brian D Nicholas
- Department of Neuroscience, University of Virginia, Charlottesville, VA, United States
| | - Shimon Francis
- Department of Neuroscience, University of Virginia, Charlottesville, VA, United States
| | - Elizabeth L Wagner
- Department of Neuroscience, University of Virginia, Charlottesville, VA, United States
| | - Sibo Zhang
- Department of Neuroscience, University of Virginia, Charlottesville, VA, United States
| | - Jung-Bum Shin
- Department of Neuroscience, University of Virginia, Charlottesville, VA, United States
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6
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Simms CL, Zaher HS. Quality control of chemically damaged RNA. Cell Mol Life Sci 2016; 73:3639-53. [PMID: 27155660 DOI: 10.1007/s00018-016-2261-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 01/10/2023]
Abstract
The "central dogma" of molecular biology describes how information contained in DNA is transformed into RNA and finally into proteins. In order for proteins to maintain their functionality in both the parent cell and subsequent generations, it is essential that the information encoded in DNA and RNA remains unaltered. DNA and RNA are constantly exposed to damaging agents, which can modify nucleic acids and change the information they encode. While much is known about how cells respond to damaged DNA, the importance of protecting RNA has only become appreciated over the past decade. Modification of the nucleobase through oxidation and alkylation has long been known to affect its base-pairing properties during DNA replication. Similarly, recent studies have begun to highlight some of the unwanted consequences of chemical damage on mRNA decoding during translation. Oxidation and alkylation of mRNA appear to have drastic effects on the speed and fidelity of protein synthesis. As some mRNAs can persist for days in certain tissues, it is not surprising that it has recently emerged that mRNA-surveillance and RNA-repair pathways have evolved to clear or correct damaged mRNA.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA.
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7
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Melnikov SV, Söll D, Steitz TA, Polikanov YS. Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome. Nucleic Acids Res 2016; 44:4978-87. [PMID: 27079977 PMCID: PMC4889946 DOI: 10.1093/nar/gkw246] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin-RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome-the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Department of Chemistry, Yale University, New Haven, CT 06520, USA Howard Hughes Medical Institute at Yale University, New Haven, CT 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
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8
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Dedduwa-Mudalige GNP, Chow CS. Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins. Int J Mol Sci 2015; 16:21392-409. [PMID: 26370969 PMCID: PMC4613259 DOI: 10.3390/ijms160921392] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/26/2015] [Accepted: 08/29/2015] [Indexed: 01/11/2023] Open
Abstract
Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA) intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA) including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.
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Affiliation(s)
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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9
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Electron microscopy in rat brain slices reveals rapid accumulation of Cisplatin on ribosomes and other cellular components only in glia. CHEMOTHERAPY RESEARCH AND PRACTICE 2014; 2014:174039. [PMID: 25610648 PMCID: PMC4291194 DOI: 10.1155/2014/174039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/16/2014] [Indexed: 01/24/2023]
Abstract
Cisplatin is a widely used, effective anticancer drug. Its use, however, is associated with several side effects including nephrotoxicity and neurotoxicity. It is known that cisplatin is accumulated in cells by the organic cation transport system and reacts with nucleotides, damaging them, but the precise target of cisplatin-induced neurotoxicity remains obscure. Here we report direct visualization of cisplatin inside brain cells using in vivo "cisplatin staining," a technique that takes advantage of the high electron density of cisplatin, which contains platinum (atomic mass = 195). After applying 0.1% cisplatin to living brain slices for 30 min, we fixed the tissue and observed the accumulated cisplatin using electron microscopy. We found that cisplatin was localized mainly to ribosomes associated with endoplasmic reticulum (EPR) in glial cells and to the myelin sheath formed by oligodendrocytes around neuronal axons. Staining of nuclear DNA was moderate. Our in vivo "cisplatin staining" method validated that the main target of cisplatin is a direct attack on myelin and the RNA contained in ribosomes.
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10
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Felício DF, Vidal LDS, Irineu RS, Leitão AC, von Kruger WA, Britto CDP, Cardoso A, Cardoso JS, Lage C. Overexpression of Escherichia coli nucleotide excision repair genes after cisplatin-induced damage. DNA Repair (Amst) 2013; 12:63-72. [DOI: 10.1016/j.dnarep.2012.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 10/25/2012] [Accepted: 10/30/2012] [Indexed: 12/12/2022]
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11
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Perin N, Martin-Kleiner I, Nhili R, Laine W, David-Cordonnier MH, Vugrek O, Karminski-Zamola G, Kralj M, Hranjec M. Biological activity and DNA binding studies of 2-substituted benzimidazo[1,2-a]quinolines bearing different amino side chains. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00193h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Hostetter AA, Osborn MF, DeRose VJ. RNA-Pt adducts following cisplatin treatment of Saccharomyces cerevisiae. ACS Chem Biol 2012; 7:218-25. [PMID: 22004017 DOI: 10.1021/cb200279p] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The numerous regulatory roles of cellular RNAs suggest novel potential drug targets, but establishing intracellular drug-RNA interactions is challenging. Cisplatin (cis-diamminedichloridoplatinum(II)) is a leading anticancer drug that forms exchange-inert complexes with nucleic acids, allowing its distribution on cellular RNAs to be followed ex vivo. Although Pt adduct formation on DNA is well-known, a complete characterization of cellular RNA-Pt adducts has not been performed. In this study, the action of cisplatin on S. cerevisiae in minimal media was established with growth curves, clonogenic assays, and tests for apoptotic markers. Despite high toxicity, cisplatin-induced apoptosis in S. cerevisiae was not observed under these conditions. In-cell Pt concentrations and Pt accumulation on poly(A)-mRNA, rRNA, total RNA, and DNA quantified via ICP-MS indicate ∼4- to 20-fold more Pt accumulation in total cellular RNA than in DNA. Interestingly, similar Pt accumulation is observed on rRNA and total RNA, corresponding to one Pt per (14,600 ± 1,500) and (5760 ± 580) nucleotides on total RNA following 100 and 200 μM cisplatin treatments, respectively. Specific Pt adducts mapped by primer extension analysis of a solvent-accessible 18S rRNA helix occur at terminal and internal loop regions and appear as soon as 1 h post-treatment. Pt per nucleotide accumulation on poly(A)-mRNA is 4- to 6-fold lower than on rRNA but could have consequences for low copy-number or highly regulated transcripts. Taken together, these data demonstrate significant accumulation of Pt adducts on cellular RNA species following in cellulo cisplatin treatment. These and other small molecule-RNA interactions could disrupt processes regulated by RNA.
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Affiliation(s)
- Alethia A. Hostetter
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Maire F. Osborn
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
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13
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Martha KRM, Rosangkima G, Amenla L, Rongpi T, Prasad SB. Cisplatin- and dietary ascorbic acid-mediated changes in the mitochondria of Dalton's lymphoma-bearing mice. Fundam Clin Pharmacol 2011; 27:329-38. [PMID: 22211279 DOI: 10.1111/j.1472-8206.2011.01019.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cisplatin treatment caused a significant increase in the life span of ascites Dalton's lymphoma (DL) Tumor-bearing (TB) mice. However, as compared to cisplatin (CP) alone, combination treatment with ascorbic acid plus CP resulted in better therapeutic efficacy against murine DL. Cisplatin treatment of TB mice resulted in the appearance of thickened and irregular arrangement of mitochondrial cristae in the liver, kidney and DL tumor cells. Combination treatment of the hosts with ascorbic acid and CP lessened deformities in the mitochondria of liver and kidney, while in tumor cells, this increased the formation of vacuoles and disruption in mitochondrial cristae. Cisplatin treatment decreased the succinate dehydrogenase (SDH) activity in the mitochondria of kidney and DL cells and combination treatment caused further decrease in SDH activity in kidney and DL cells during 24-48 h of treatment. After CP treatment, the protein content in the mitochondria of these tissues decreased, and during combination treatment, it showed significant improvement. Mitochondrial lipid peroxidation (LPO) increased in these tissues after CP treatment. However, combination treatment significantly decreased mitochondrial LPO in liver and kidney but increased in DL cells. This increase in mitochondrial LPO in DL cells and decrease in liver and kidney could play an important role in the antitumor activity of combination treatment and at the same time reduce CP-induced toxicity in the host. However, further study may be desirable to explore some aspects of the mechanism(s) involved in these changes in mitochondria.
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Affiliation(s)
- Kham R M Martha
- Cell & Tumor Biology Lab., Department of Zoology, North-Eastern Hill University, Shillong-973022, India
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14
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Hostetter AA, Miranda ML, DeRose VJ, McFarlane Holman KL. Ru binding to RNA following treatment with the antimetastatic prodrug NAMI-A in Saccharomyces cerevisiae and in vitro. J Biol Inorg Chem 2011; 16:1177-85. [PMID: 21739255 DOI: 10.1007/s00775-011-0806-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/11/2011] [Indexed: 11/24/2022]
Abstract
[ImH][trans-Ru(III)Cl(4)(DMSO)(Im)] (where DMSO is dimethyl sulfoxide and Im is imidazole) (NAMI-A) is an antimetastatic prodrug currently in phase II clinical trials. The mechanisms of action of this and related Ru-based anticancer agents are not well understood, but several cellular targets have been suggested. Although Ru has been observed to bind to DNA following in vitro NAMI-A exposure, little is known about Ru-DNA interactions in vivo and even less is known about how this or related metallodrugs might influence cellular RNA. In this study, Ru accumulation in cellular RNA was measured following treatment of Saccharomyces cerevisiae with NAMI-A. Drug-dependent growth and cell viability indicate relatively high tolerance, with approximately 40% cell death occurring at 6 h for 450 μM NAMI-A. Significant dose-dependent accumulation of Ru in cellular RNA was observed by inductively coupled plasma mass spectrometry measurements on RNA extracted from yeast treated with NAMI-A. In vitro, binding of Ru species to drug-treated model DNA and RNA oligonucleotides at pH 6.0 and 7.4 was characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the presence and absence of the reductant ascorbate. The extent of Ru-nucleotide interactions increases slightly with lower pH and significantly in the presence of ascorbate, with differences in observed species distribution. Taken together, these studies demonstrate the accumulation of aquated and reduced derivatives of NAMI-A on RNA in vitro and in cellulo, and enhanced binding with nucleic acid targets in a tumorlike acidic, reducing environment. To our knowledge, this is also the first study to characterize NAMI-A treatment of S. cerevisiae, a genetically tractable model organism.
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15
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Chapman EG, Hostetter AA, Osborn MF, Miller AL, DeRose VJ. Binding of kinetically inert metal ions to RNA: the case of platinum(II). Met Ions Life Sci 2011; 9:347-77. [PMID: 22010278 PMCID: PMC4080900 DOI: 10.1039/9781849732512-00347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter several aspects of Pt(II) are highlighted that focus on the properties of Pt(II)-RNA adducts and the possibility that they influence RNA-based processes in cells. Cellular distribution of Pt(II) complexes results in significant platination of RNA, and localization studies find Pt(II) in the nucleus, nucleolus, and a distribution of other sites in cells. Treatment with Pt(II) compounds disrupts RNA-based processes including enzymatic processing, splicing, and translation, and this disruption may be indicative of structural changes to RNA or RNA-protein complexes. Several RNA-Pt(II) adducts have been characterized in vitro by biochemical and other methods. Evidence for Pt(II) binding in non-helical regions and for Pt(II) cross-linking of internal loops has been found. Although platinated sites have been identified, there currently exists very little in the way of detailed structural characterization of RNA-Pt(II) adducts. Some insight into the details of Pt(II) coordination to RNA, especially RNA helices, can be gained from DNA model systems. Many RNA structures, however, contain complex tertiary folds and common, purine-rich structural elements that present suitable Pt(II) nucleophiles in unique arrangements which may hold the potential for novel types of platinum-RNA adducts. Future research aimed at structural characterization of platinum-RNA adducts may provide further insights into platinum-nucleic acid binding motifs, and perhaps provide a rationale for the observed inhibition by Pt(II) complexes of splicing, translation, and enzymatic processing.
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Affiliation(s)
- Erich G. Chapman
- Department of Chemistry University of Oregon Eugene OR 97403 USA
| | | | - Maire F. Osborn
- Department of Chemistry University of Oregon Eugene OR 97403 USA
| | - Amanda L. Miller
- Department of Chemistry University of Oregon Eugene OR 97403 USA
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16
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Nakai T, Ando M, Okamoto Y, Ueda K, Kojima N. Modulation of oxidative DNA damage and DNA-crosslink formation induced by cis-diammine-tetrachloro-platinum(IV) in the presence of endogenous reductants. J Inorg Biochem 2011; 105:1-5. [DOI: 10.1016/j.jinorgbio.2010.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/17/2010] [Accepted: 10/01/2010] [Indexed: 10/19/2022]
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17
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Prasad SB, Rosangkima G, Kharbangar A. Structural and biochemical changes in mitochondria after cisplatin treatment of Dalton’s lymphoma-bearing mice. Mitochondrion 2010; 10:38-45. [DOI: 10.1016/j.mito.2009.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Revised: 09/07/2009] [Accepted: 09/11/2009] [Indexed: 10/20/2022]
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18
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Gaillard H, Aguilera A. A novel class of mRNA-containing cytoplasmic granules are produced in response to UV-irradiation. Mol Biol Cell 2008; 19:4980-92. [PMID: 18768757 DOI: 10.1091/mbc.e08-02-0193] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nucleic acids are substrates for different types of damage, but little is known about the fate of damaged RNAs. We addressed the existence of an RNA-damage response in yeast. The decay kinetics of GAL1p-driven mRNAs revealed a dose-dependent mRNA stabilization upon UV-irradiation that was not observed after heat or saline shocks, or during nitrogen starvation. UV-induced mRNA stabilization did not depend on DNA repair, damage checkpoint or mRNA degradation machineries. Notably, fluorescent in situ hybridization revealed that after UV-irradiation, polyadenylated mRNA accumulated in cytoplasmic foci that increased in size with time. In situ colocalization showed that these foci are not processing-bodies, eIF4E-, eIF4G-, and Pab1-containing bodies, stress granules, autophagy vesicles, or part of the secretory or endocytic pathways. These results point to the existence of a specific eukaryotic RNA-damage response, which leads to new polyadenylated mRNA-containing granules (UV-induced mRNA granules; UVGs). We propose that potentially damaged mRNAs, which may be deleterious to the cell, are temporarily stored in UVG granules to safeguard cell viability.
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Affiliation(s)
- Hélène Gaillard
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Centro Andaluz de Biología Molecular and Medicina Regenativa CABIMER, 41092 Sevilla, Spain
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Cisplatin and siRNA interference with structure and function of Wnt-5a mRNA: design and in vitro evaluation of targeting AU-rich elements in the 3′ UTR. J Biol Inorg Chem 2007; 13:385-99. [DOI: 10.1007/s00775-007-0327-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 11/15/2007] [Indexed: 12/20/2022]
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Falnes PØ, Klungland A, Alseth I. Repair of methyl lesions in DNA and RNA by oxidative demethylation. Neuroscience 2006; 145:1222-32. [PMID: 17175108 DOI: 10.1016/j.neuroscience.2006.11.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 10/27/2006] [Accepted: 11/01/2006] [Indexed: 11/29/2022]
Abstract
It was established several decades ago that it is crucial for all organisms to repair their DNA to maintain genome integrity and numerous proteins are dedicated to this purpose. However, it is becoming increasingly clear that it is also important to prevent and repair lesions in the macromolecules encoded by the DNA, i.e. RNA and protein. Many neurological disorders such as Alzheimer's disease and Parkinson's disease are associated with the aggregation of defective, misfolded proteins, and several mechanisms exist to prevent such aggregation, both through direct protein repair and through the elimination and repair of faulty or damaged RNAs. A few years ago, it was discovered that the E. coli AlkB protein represented an iron and 2-oxoglutarate dependent oxygenase capable of repairing methyl lesions in DNA by a novel mechanism, termed oxidative demethylation. Furthermore, it was found that both human and bacterial AlkB proteins were able to demethylate lesions also in RNA, thus representing the first example of RNA repair. In the present review, recent findings on the AlkB mechanism, as well as on RNA damage in general, will be discussed.
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Affiliation(s)
- P Ø Falnes
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, N-0316 Oslo, Norway.
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Brégeon D, Sarasin A. Hypothetical role of RNA damage avoidance in preventing human disease. Mutat Res 2005; 577:293-302. [PMID: 15916782 DOI: 10.1016/j.mrfmmm.2005.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 03/31/2005] [Accepted: 04/02/2005] [Indexed: 01/21/2023]
Abstract
Most of nucleic acids damaging agents are not only restricted to DNA but equally affect DNA and RNA molecules. Considering that RNA damage could be very toxic for the cell, a property used by some cancer treatments, it would not be unexpected to find out that several proteins may be involved in RNA damage avoidance mechanisms helping cells to counteract such cytotoxic effects. Up to now, only one specific repair mechanism allowing cells to deal with toxic effects of methylated RNA have been described. However, there are in the literature several data suggesting that this study may only be the tip of the iceberg and that cells might be able to counteract the deleterious effects of a large variety of RNA damage. In this review, we will discuss the different proteins that may be involved in the mechanism of RNA damage avoidance and their potential role in human diseases.
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Affiliation(s)
- Damien Brégeon
- Institut Gustave Roussy PR2, CNRS UPR-2169, 39 rue Camille Desmoulins 94805 Villejuif Cedex, France
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Delehanty JB, Stuart TC, Knight DA, Goldman ER, Thach DC, Bongard JE, Chang EL. RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex. RNA (NEW YORK, N.Y.) 2005; 11:831-836. [PMID: 15840822 PMCID: PMC1370767 DOI: 10.1261/rna.7156805] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 01/18/2005] [Indexed: 05/24/2023]
Abstract
Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.
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Affiliation(s)
- James B Delehanty
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
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Wozniak K, Czechowska A, Blasiak J. Cisplatin-evoked DNA fragmentation in normal and cancer cells and its modulation by free radical scavengers and the tyrosine kinase inhibitor STI571. Chem Biol Interact 2004; 147:309-18. [PMID: 15135086 DOI: 10.1016/j.cbi.2004.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2004] [Indexed: 11/17/2022]
Abstract
Cis-diamminedichloroplatinum(II) (cisplatin, cis-DDP) is well studied anticancer drug, whose activity can be attributed to its ability to form adducts with DNA, but this drug can also form DNA-damaging free radicals, however this mechanism of cisplatin action is far less explored. Using the comet assay we studied cisplatin-induced DNA damage in the presence of spin traps: DMPO and PBN, Vitamins A, C and E as well as the tyrosine kinases inhibitor STI571 in normal human lymphocytes and leukemic K562 cells. The latter cells express the BCR/ABL fusion protein, which can be a target of the tyrosine kinase inhibitor STI571. A 20 h incubation with cisplatin at 1-10 microM induced DNA cross-links and DNA fragmentation in normal and cancer cells. Cisplatin could induce intra- and interstrand DNA-DNA cross-links as well as DNA-protein cross-links. DNA damage in K562 cells was more pronounced than in normal lymphocytes. In the presence of spin traps and vitamins we noticed a decrease in the DNA fragmentation in both cell types. Co-treatment of the lymphocytes with cisplatin at 10 microM and STI571 at 0.25 microg/ml caused an increase of DNA fragmentation in comparison with DNA fragmentation induced by cisplatin alone. In the case of K562 cells, an increase of DNA fragmentation was observed after treatment with cisplatin at 1 microM. Our results indicate that the free radicals scavengers could decrease DNA fragmentation induced by cisplatin in the normal and cancer cells, but probably they have no effect on DNA cross-linking induced by the drug. The results obtained with the BCR/ABL inhibitor suggest that K562 cells could be more sensitive towards co-treatment of cisplatin and STI571. Our results suggest also that aside from the BCR/ABL other factors such as p53 level, signal transduction pathways and DNA repair processes can be responsible for the increased sensitivity of K562 cells to cisplatin compared with normal lymphocytes.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Molecular Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
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Leitão AA, Leite CA, Santos BC, Boim MA. HSP70 induced by hyperosmotic stress partially protects LLC-PK1 cells against nephrotoxic drugs. NEPHRON. EXPERIMENTAL NEPHROLOGY 2003; 94:e94-102. [PMID: 12902619 DOI: 10.1159/000072027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2002] [Accepted: 04/14/2003] [Indexed: 11/19/2022]
Abstract
Accumulation of HSP70 is related to the cytoprotection. It was evaluated whether hyperosmotic stress induces HSP70 accumulation in LLC-PK1 cells, and protects cells against toxicity provoked by cisplatin (Cis) and cyclosporine A (CyA). Cells were maintained in isosmotic (Iso) or hyperosmotic (H) culture medium for 24 h and then exposed to Cis or CyA for an additional period of 12 or 24 h (groups H+Cis and H+CyA). The H medium did not induce cell death and increased both HSP70 mRNA and protein levels, suggesting a role in cell adaptation to H condition. H medium produced partial cytoprotection against Cis and CyA compared with control cells. Despite the cytoprotection, there was a reduction in HSP70 mRNA and protein levels in H+Cis group. In contrast, the H+CyA group presented high levels of HSP70 mRNA and protein. The induction of HSP70 by H medium was associated with tolerance of LLC-PK1 cells against Cis and CyA cytotoxicity but this protection was induced by different mechanisms and depended on the characteristics of the drug used.
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Affiliation(s)
- Aurilucia A Leitão
- Nephrology Division, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brasil
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Abstract
RNA in a cell is subject to many of the same insults as DNA. RNA damage can induce apoptosis and may be exploited for anti-cancer chemotherapy. It is a surprise, however, to learn that cells may repair RNA damage, suggesting a far greater significance of RNA in genotoxic stress.
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Volckova E, Dudones LP, Bose RN. HPLC determination of binding of cisplatin to DNA in the presence of biological thiols: implications of dominant platinum-thiol binding to its anticancer action. Pharm Res 2002; 19:124-31. [PMID: 11883638 DOI: 10.1023/a:1014268729658] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
PURPOSE The purpose of this work is to evaluate the extent of the binding of cisplatin (cis-diamminedichloroplatinum(II)) to DNA in the presence and absence of biological thiols, glutathione, and cysteine, and to test the hypothesis whether the platinum-thiol complexes can serve as a drug reservoir for subsequent binding to DNA. METHODS Reactions of cisplatin (50 microM to 1.0 mM) with calf thymus DNA (870 microM to 6.75 mM) in the presence and absence of glutathione and cysteine (0 to 10 mM) were carried out at pH 4.4, 7.0, and 7.3. Following the reactions, the DNA was enzymatically digested with nucleases, separated by RP HPLC, and analyzed to determine the extent of DNA binding. The method was independently verified by proton NMR measurements. RESULTS At neutral pH, and equimolar concentrations of DNA and thiols, only a very small amount of platinum (<5%) was coordinated to DNA, and most of the platinum was coordinated to the thiols. At pH 4.4, binding to DNA was dominant over the binding to thiols. No conversion of platinum-thiol to platinum-DNA complexes was observed up to 7 days of incubation. CONCLUSION At physiological pH, the cisplatin was exclusively coordinated to biological thiols and platinum-DNA was a minor adduct. Data presented in this paper does not support the "drug reservoir" hypothesis.
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Affiliation(s)
- Erika Volckova
- Department of Chemistry, Kent State University, Ohio 44242, USA
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