1
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Sharma S, Canman CE. REV1 and DNA polymerase zeta in DNA interstrand crosslink repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:725-40. [PMID: 23065650 PMCID: PMC5543726 DOI: 10.1002/em.21736] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 08/09/2012] [Accepted: 08/15/2012] [Indexed: 05/06/2023]
Abstract
DNA interstrand crosslinks (ICLs) are covalent linkages between two strands of DNA, and their presence interferes with essential metabolic processes such as transcription and replication. These lesions are extremely toxic, and their repair is essential for genome stability and cell survival. In this review, we will discuss how the removal of ICLs requires interplay between multiple genome maintenance pathways and can occur in the absence of replication (replication-independent ICL repair) or during S phase (replication-coupled ICL repair), the latter being the predominant pathway used in mammalian cells. It is now well recognized that translesion DNA synthesis (TLS), especially through the activities of REV1 and DNA polymerase zeta (Polζ), is necessary for both ICL repair pathways operating throughout the cell cycle. Recent studies suggest that the convergence of two replication forks upon an ICL initiates a cascade of events including unhooking of the lesion through the actions of structure-specific endonucleases, thereby creating a DNA double-stranded break (DSB). TLS across the unhooked lesion is necessary for restoring the sister chromatid before homologous recombination repair. Biochemical and genetic studies implicate REV1 and Polζ as being essential for performing lesion bypass across the unhooked crosslink, and this step appears to be important for subsequent events to repair the intermediate DSB. The potential role of Fanconi anemia pathway in the regulation of REV1 and Polζ-dependent TLS and the involvement of additional polymerases, including DNA polymerases kappa, nu, and theta, in the repair of ICLs is also discussed in this review.
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Affiliation(s)
- Shilpy Sharma
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109-2200, USA
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2
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Mukherjee A, Vasquez KM. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis. Biochimie 2011; 93:1197-208. [PMID: 21501652 DOI: 10.1016/j.biochi.2011.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 04/01/2011] [Indexed: 12/18/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences.
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Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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3
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Gantchev TG, Hunting DJ. Modeling the interactions of the nucleotide excision repair UvrA(2) dimer with DNA. Biochemistry 2010; 49:10912-24. [PMID: 21090726 DOI: 10.1021/bi1012035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The UvrA protein initiates the DNA damage recognition process by the bacterial nucleotide excision repair (NER) system. Recently, crystallographic structures of holo-UvrA(2) dimers from two different microorganisms have been released (Protein Data Bank entries 2r6f , 2vf7 , and 2vf8 ). However, the details of the DNA binding by UvrA(2) and other peculiarities involved in the damage recognition process remain unknown. We have undertaken a molecular modeling approach to appraise the possible modes of DNA-UvrA(2) interaction using molecular docking and short-scale guided molecular dynamics [continuum field, constrained, and/or unrestricted simulated annealing (SA)], taking into account the three-dimensional location of a series of mutation-identified UvrA residues implicated in DNA binding. The molecular docking was based on the assumptions that the UvrA(2) dimer is preformed prior to DNA binding and that no major protein conformational rearrangements, except moderate domain reorientations, are required for binding of undamaged DNA. As a first approximation, DNA was treated as a rigid ligand. From the electrostatic relief of the ventral surface of UvrA(2), we initially identified three, noncollinear DNA binding paths. Each of the three resulting nucleoprotein complexes (C1, C2, and C3) was analyzed separately, including calculation of binding energies, the number and type of interaction residues (including mutated ones), and the predominant mode of translational and rotational motion of specific protein domains after SA to ensure improved DNA binding. The UvrA(2) dimer can accommodate DNA in all three orientations, albeit with different binding strengths. One of the UvrA(2)-DNA complexes (C1) fulfilled most of the requirements (high interaction energy, proximity of DNA to mutated residues, etc.) expected for a natural, high-affinity DNA binding site. This nucleoprotein presents a structural organization that is designed to clamp and bend double-stranded DNA. We examined the binding site in more detail by docking DNAs of significantly different (AT- vs CG-enriched) sequences and by submitting the complexes to DNA-unrestricted SA. It was found that in a manner independent of the DNA sequence and applied MD protocols, UvrA(2) favors binding of a bent and unwound undamaged DNA, with a kink positioned in the proximity of the Zn3 hairpins, anticollinearly aligned at the bottom of the ventral protein surface. It is further hypothesized that the Zn3 modules play an essential role in the damage recognition process and that the apparent existence of a family of DNA binding sites might be biologically relevant. Our data should prove to be useful in rational (structure-based) mutation studies.
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Affiliation(s)
- Tsvetan G Gantchev
- Center for Research in Radio-Oncology (CR2), Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Life Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4 Canada.
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4
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Vasquez KM. Targeting and processing of site-specific DNA interstrand crosslinks. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:527-39. [PMID: 20196133 PMCID: PMC2895014 DOI: 10.1002/em.20557] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA interstrand crosslinks (ICLs) are among the most cytotoxic types of DNA damage, and thus ICL-inducing agents such as cyclophosphamide, melphalan, cisplatin, psoralen, and mitomycin C have been used clinically as anticancer drugs for decades. ICLs can also be formed endogenously as a consequence of cellular metabolic processes. ICL-inducing agents continue to be among the most effective chemotherapeutic treatments for many cancers; however, treatment with these agents can lead to secondary malignancies, in part due to mutagenic processing of the DNA lesions. The mechanisms of ICL repair have been characterized more thoroughly in bacteria and yeast than in mammalian cells. Thus, a better understanding of the molecular mechanisms of ICL processing offers the potential to improve the efficacy of these drugs in cancer therapy. In mammalian cells, it is thought that ICLs are repaired by the coordination of proteins from several pathways, including nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous recombination (HR), translesion synthesis (TLS), and proteins involved in Fanconi anemia (FA). In this review, we focus on the potential functions of NER, MMR, and HR proteins in the repair of and response to ICLs in human cells and in mice. We will also discuss a unique approach, using psoralen covalently linked to triplex-forming oligonucleotides to direct ICLs to specific sites in the mammalian genome.
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Affiliation(s)
- Karen M Vasquez
- Department of Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA.
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5
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McVey M. Strategies for DNA interstrand crosslink repair: insights from worms, flies, frogs, and slime molds. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:646-658. [PMID: 20143343 DOI: 10.1002/em.20551] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA interstrand crosslinks (ICLs) are complex lesions that covalently link both strands of the DNA double helix and impede essential cellular processes such as DNA replication and transcription. Recent studies suggest that multiple repair pathways are involved in their removal. Elegant genetic analysis has demonstrated that at least three distinct sets of pathways cooperate in the repair and/or bypass of ICLs in budding yeast. Although the mechanisms of ICL repair in mammals appear similar to those in yeast, important differences have been documented. In addition, mammalian crosslink repair requires other repair factors, such as the Fanconi anemia proteins, whose functions are poorly understood. Because many of these proteins are conserved in simpler metazoans, nonmammalian models have become attractive systems for studying the function(s) of key crosslink repair factors. This review discusses the contributions that various model organisms have made to the field of ICL repair. Specifically, it highlights how studies performed with C. elegans, Drosophila, Xenopus, and the social amoeba Dictyostelium serve to complement those from bacteria, yeast, and mammals. Together, these investigations have revealed that although the underlying themes of ICL repair are largely conserved, the complement of DNA repair proteins utilized and the ways in which each of the proteins is used can vary substantially between different organisms.
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Affiliation(s)
- Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA.
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6
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Liu Y, Nairn RS, Vasquez KM. Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells. Nucleic Acids Res 2009; 37:6378-88. [PMID: 19726585 PMCID: PMC2770658 DOI: 10.1093/nar/gkp678] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Correction of a defective gene is a promising approach for both basic research and clinical gene therapy. However, the absence of site-specific targeting and the low efficiency of homologous recombination in human cells present barriers to successful gene targeting. In an effort to overcome these barriers, we utilized triplex-forming oligonucleotides (TFOs) conjugated to a DNA interstrand crosslinking (ICL) agent, psoralen (pTFO-ICLs), to improve the gene targeting efficiency at a specific site in DNA. Gene targeting events were monitored by the correction of a deletion on a recipient plasmid with the homologous sequence from a donor plasmid in human cells. The mechanism underlying this event is stimulation of homologous recombination by the pTFO-ICL. We found that pTFO-ICLs are efficient in inducing targeted gene conversion (GC) events in human cells. The deletion size in the recipient plasmid influenced both the recombination frequency and spectrum of recombinants; i.e. plasmids with smaller deletions had a higher frequency and proportion of GC events. The polarity of the pTFO-ICL also had a prominent effect on recombination. Our results suggest that pTFO-ICL induced intermolecular recombination provides an efficient method for targeted gene correction in mammalian cells.
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Affiliation(s)
- Yaobin Liu
- Department of Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park-Research Division, Smithville, Texas, USA
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7
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Chin JY, Glazer PM. Repair of DNA lesions associated with triplex-forming oligonucleotides. Mol Carcinog 2009; 48:389-99. [PMID: 19072762 DOI: 10.1002/mc.20501] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) are gene targeting tools that can bind in the major groove of duplex DNA in a sequence-specific manner. When bound to DNA, TFOs can inhibit gene expression, can position DNA-reactive agents to specific locations in the genome, or can induce targeted mutagenesis and recombination. There is evidence that third strand binding, alone or with an associated cross-link, is recognized and metabolized by DNA repair factors, particularly the nucleotide excision repair pathway. This review examines the evidence for DNA repair of triplex-associated lesions.
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Affiliation(s)
- Joanna Y Chin
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, 15 York Street, New Haven, CT 06510, USA
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8
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Lehoczký P, McHugh PJ, Chovanec M. DNA interstrand cross-link repair in Saccharomyces cerevisiae. FEMS Microbiol Rev 2006; 31:109-33. [PMID: 17096663 DOI: 10.1111/j.1574-6976.2006.00046.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA interstrand cross-links (ICL) present a formidable challenge to the cellular DNA repair apparatus. For Escherichia coli, a pathway which combines nucleotide excision repair (NER) and homologous recombination repair (HRR) to eliminate ICL has been characterized in detail, both genetically and biochemically. Mechanisms of ICL repair in eukaryotes have proved more difficult to define, primarily as a result of the fact that several pathways appear compete for ICL repair intermediates, and also because these competing activities are regulated in the cell cycle. The budding yeast Saccharomyces cerevisiae has proven a powerful tool for dissecting ICL repair. Important roles for NER, HRR and postreplication/translesion synthesis pathways have all been identified. Here we review, with reference to similarities and differences in higher eukaryotes, what has been discovered to date concerning ICL repair in this simple eukaryote.
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Affiliation(s)
- Peter Lehoczký
- Department of Molecular Genetics, Cancer Research Institute, Bratislava, Slovak Republic
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9
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Varganov Y, Amosova O, Fresco JR. Third strand-mediated psoralen-induced correction of the sickle cell mutation on a plasmid transfected into COS-7 cells. Gene Ther 2006; 14:173-9. [PMID: 16943853 DOI: 10.1038/sj.gt.3302850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A significant level of correction of the mutation responsible for sickle cell anemia has been achieved in monkey COS-7 cells on a plasmid containing a beta-globin gene fragment. The plasmid was treated in vitro with a nucleic acid 'third strand' bearing a terminal photoreactive psoralen moiety that binds immediately adjacent to the mutant base pair. Following covalent attachment of the psoralen by monoadduct or diadduct formation to the mutant T-residue on the coding strand, the treated plasmid was transfected into the cells, which were then incubated for 48 h to allow the cellular DNA repair mechanisms to remove the photoadducts. Upon re-isolation and amplification of the transfected plasmid, sickle cell mutation correction, as determined by sequence analysis of both complementary strands, was established in a full 1%. This result encourages extension of the approach to correct the mutation directly on the chromosome.
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Affiliation(s)
- Y Varganov
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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10
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Colton SL, Xu XS, Wang YA, Wang G. The involvement of ataxia-telangiectasia mutated protein activation in nucleotide excision repair-facilitated cell survival with cisplatin treatment. J Biol Chem 2006; 281:27117-25. [PMID: 16849332 DOI: 10.1074/jbc.m602826200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA damage can lead to either DNA repair with cell survival or to apoptotic cell death. Although the biochemical processes underlying DNA repair and apoptosis have been extensively studied, the mechanisms by which cells determine whether the damage will be repaired or the apoptotic pathway will be activated is largely unknown. We have studied the role of nucleotide excision repair (NER) in cisplatin DNA damage-induced apoptotic cell death using both normal human fibroblasts and NER-defective xeroderma pigmentosum (XP) XPA and XPG cells. The caspase-3 activation experiment demonstrated a greatly increased casapse-3 activation in the NER-defective cells following cisplatin treatment. The flow cytometry experiment revealed an altered cell cycle arrest pattern of the NER-defective cells following cisplatin treatment. The results obtained from the Western blot experiment showed that NER defects resulted in enhanced CHK1 phosphorylation and p21 induction after cisplatin treatment. The cisplatin treatment-induced ATM phosphorylation, however, was attenuated in NER-defective cells. The results obtained from our immunoprecipitation experiment further demonstrated that the ATM protein interacted with the TFIIH basal transcription factor and the XPG protein of the NER pathway. It also showed that a functional XPC protein was required for the association of the ATM protein to genomic DNA. These results suggest that the NER process may prevent the cisplatin treatment-induced apoptosis by activating the ATM protein, and that the presence of the XPC protein is essential for recruiting the ATM protein to the DNA template.
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Affiliation(s)
- Stephanie L Colton
- Institute of Environmental Health Sciences, Karmanos Cancer Research Institute, Wayne State University, Detroit, Michigan 48201, USA
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11
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Truglio JJ, Croteau DL, Van Houten B, Kisker C. Prokaryotic nucleotide excision repair: the UvrABC system. Chem Rev 2006; 106:233-52. [PMID: 16464004 DOI: 10.1021/cr040471u] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James J Truglio
- Department of Pharmacological Sciences, State University of New York at Stony Brook, 11794-5115, USA
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12
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Richards S, Liu ST, Majumdar A, Liu JL, Nairn RS, Bernier M, Maher V, Seidman MM. Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways. Nucleic Acids Res 2005; 33:5382-93. [PMID: 16186129 PMCID: PMC1236719 DOI: 10.1093/nar/gki851] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Revised: 09/03/2005] [Accepted: 09/03/2005] [Indexed: 12/02/2022] Open
Abstract
We have synthesized triple helix forming oligonucleotides (TFOs) that target a psoralen (pso) interstrand crosslink to a specific chromosomal site in mammalian cells. Mutagenesis of the targeted crosslinks results in base substitutions and deletions. Identification of the gene products involved in mutation formation is important for developing practical applications of pso-TFOs, and may be informative about the metabolism of other interstrand crosslinks. We have studied mutagenesis of a pso-TFO genomic crosslink in repair proficient and deficient cells. Deficiencies in non homologous end joining and mismatch repair do not influence mutation patterns. In contrast, the frequency of base substitutions is dependent on the activity of ERCC1/XPF and polymerase zeta, but independent of other nucleotide excision repair (NER) or transcription coupled repair (TCR) genes. In NER/TCR deficient cells the frequency of deletions rises, indicating that in wild-type cells NER/TCR functions divert pso-TFO crosslinks from processes that result in deletions. We conclude that targeted pso-TFO crosslinks can enter genetically distinct mutational routes that resolve to base substitutions or deletions.
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Affiliation(s)
- Sally Richards
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health5600 Nathan Shock Dr, Baltimore, MD 21224, USA
- University of Texas, MD Anderson Cancer Center, Department of CarcinogenesisPO Box 389, 1808 Park Road 1C, Smithville, TX 78957, USA
- Laboratory of Clinical Investigation, NIA/NIHBaltimore, MD 21224, USA
- Carcinogenesis Laboratory, Michigan State UniversityEast Lansing, MI 48824, USA
| | - Su-Ting Liu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health5600 Nathan Shock Dr, Baltimore, MD 21224, USA
- University of Texas, MD Anderson Cancer Center, Department of CarcinogenesisPO Box 389, 1808 Park Road 1C, Smithville, TX 78957, USA
- Laboratory of Clinical Investigation, NIA/NIHBaltimore, MD 21224, USA
- Carcinogenesis Laboratory, Michigan State UniversityEast Lansing, MI 48824, USA
| | - Alokes Majumdar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health5600 Nathan Shock Dr, Baltimore, MD 21224, USA
- University of Texas, MD Anderson Cancer Center, Department of CarcinogenesisPO Box 389, 1808 Park Road 1C, Smithville, TX 78957, USA
- Laboratory of Clinical Investigation, NIA/NIHBaltimore, MD 21224, USA
- Carcinogenesis Laboratory, Michigan State UniversityEast Lansing, MI 48824, USA
| | - Ji-Lan Liu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health5600 Nathan Shock Dr, Baltimore, MD 21224, USA
- University of Texas, MD Anderson Cancer Center, Department of CarcinogenesisPO Box 389, 1808 Park Road 1C, Smithville, TX 78957, USA
- Laboratory of Clinical Investigation, NIA/NIHBaltimore, MD 21224, USA
- Carcinogenesis Laboratory, Michigan State UniversityEast Lansing, MI 48824, USA
| | - Rodney S. Nairn
- University of Texas, MD Anderson Cancer Center, Department of CarcinogenesisPO Box 389, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - Michel Bernier
- Laboratory of Clinical Investigation, NIA/NIHBaltimore, MD 21224, USA
| | - Veronica Maher
- Carcinogenesis Laboratory, Michigan State UniversityEast Lansing, MI 48824, USA
| | - Michael M. Seidman
- To whom correspondence should be addressed. Tel: +1 410 558 8565; Fax: +1 410 558 8157;
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13
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Van Houten B, Croteau DL, DellaVecchia MJ, Wang H, Kisker C. 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat Res 2005; 577:92-117. [PMID: 15927210 DOI: 10.1016/j.mrfmmm.2005.03.013] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 03/11/2005] [Accepted: 03/11/2005] [Indexed: 05/02/2023]
Abstract
DNA damage recognition represents a long-standing problem in the field of protein-DNA interactions. This article reviews our current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins.
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Affiliation(s)
- Bennett Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, MD D3-01, Research Triangle Park, NC 27709, USA
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14
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Chen Z, Xu XS, Harrison J, Wang G. Defining the function of xeroderma pigmentosum group F protein in psoralen interstrand cross-link-mediated DNA repair and mutagenesis. Biochem J 2004; 379:71-8. [PMID: 14728600 PMCID: PMC1224063 DOI: 10.1042/bj20031143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2003] [Revised: 11/10/2003] [Accepted: 01/16/2004] [Indexed: 11/17/2022]
Abstract
Many commonly used drugs, such as psoralen and cisplatin, can generate a very unique type of DNA damage, namely ICL (interstrand cross-link). An ICL can severely block DNA replication and transcription and cause programmed cell death. The molecular mechanism of repairing the ICL damage has not been well established. We have studied the role of XPF (xeroderma pigmentosum group F) protein in psoralen-induced ICL-mediated DNA repair and mutagenesis. The results obtained from our mutagenesis studies revealed a very similar mutation frequency in both human normal fibroblast cells and XPF cells. The mutation spectra generated in both cells, however, were very different: most of the mutations generated in the normal fibroblast cells were T167-->A transversions, whereas most of the mutations generated in the XPF cells were T167-->G transversions. When a wild-type XPF gene cDNA was stably transfected into the XPF cells, the T167-->A mutations were increased and the T167-->G mutations were decreased. We also determined the DNA repair capability of the XPF cells using both the host-cell reactivation and the in vitro DNA repair assays. The results obtained from the host-cell reactivation experiments revealed an effective reactivation of a luciferase reporter gene from the psoralen-damaged plasmid in the XPF cells. The results obtained from the in vitro DNA repair experiments demonstrated that the XPF nuclear extract is normal in introducing dual incisions during the nucleotide excision repair process. These results suggest that the XPF protein has important roles in the psoralen ICL-mediated DNA repair and mutagenesis.
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MESH Headings
- Base Sequence
- Cells, Cultured/drug effects
- Cells, Cultured/metabolism
- Cells, Cultured/radiation effects
- Cross-Linking Reagents/pharmacology
- DNA Adducts/metabolism
- DNA Damage
- DNA Repair/genetics
- DNA Repair/physiology
- DNA, Complementary/genetics
- DNA, Recombinant/drug effects
- DNA, Recombinant/genetics
- DNA, Recombinant/radiation effects
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Fibroblasts/drug effects
- Fibroblasts/metabolism
- Fibroblasts/radiation effects
- Genes, Reporter
- Genes, Suppressor
- Genes, Synthetic/drug effects
- Genes, Synthetic/radiation effects
- Humans
- Luciferases/biosynthesis
- Luciferases/genetics
- Molecular Sequence Data
- Mutagenesis
- Mutagenesis, Site-Directed
- Oligonucleotides/pharmacology
- Photochemistry
- Plasmids/drug effects
- Plasmids/radiation effects
- RNA, Transfer/genetics
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Transfection
- Trioxsalen/analogs & derivatives
- Trioxsalen/pharmacology
- Ultraviolet Rays
- Xeroderma Pigmentosum/genetics
- Xeroderma Pigmentosum/metabolism
- Xeroderma Pigmentosum/pathology
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Affiliation(s)
- Zhiwen Chen
- Institute of Environmental Health Sciences, Wayne State University, 2727 Second Avenue, Detroit, MI 48201, USA
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15
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Saffran WA, Ahmed S, Bellevue S, Pereira G, Patrick T, Sanchez W, Thomas S, Alberti M, Hearst JE. DNA repair defects channel interstrand DNA cross-links into alternate recombinational and error-prone repair pathways. J Biol Chem 2004; 279:36462-9. [PMID: 15213235 DOI: 10.1074/jbc.m402323200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The repair of psoralen interstrand cross-links in the yeast Saccharomyces cerevisiae involves the DNA repair groups nucleotide excision repair (NER), homologous recombination (HR), and post-replication repair (PRR). In repair-proficient yeast cells cross-links induce double-strand breaks, in an NER-dependent process; the double-strand breaks are then repaired by HR. An alternate error-prone repair pathway generates mutations at cross-link sites. We have characterized the repair of plasmid molecules carrying a single psoralen cross-link, psoralen monoadduct, or double-strand break in yeast cells with deficiencies in NER, HR, or PRR genes, measuring the repair efficiencies and the levels of gene conversions, crossing over, and mutations. Strains with deficiencies in the NER genes RAD1, RAD3, RAD4, and RAD10 had low levels of cross-link-induced recombination but higher mutation frequencies than repair-proficient cells. Deletion of the HR genes RAD51, RAD52, RAD54, RAD55, and RAD57 also decreased induced recombination and increased mutation frequencies above those of NER-deficient yeast. Strains lacking the PRR genes RAD5, RAD6, and RAD18 did not have any cross-link-induced mutations but showed increased levels of recombination; rad5 and rad6 cells also had altered patterns of cross-link-induced gene conversion in comparison with repair-proficient yeast. Our observations suggest that psoralen cross-links can be repaired by three pathways: an error-free recombinational pathway requiring NER and HR and two PRR-dependent error-prone pathways, one NER-dependent and one NER-independent.
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Affiliation(s)
- Wilma A Saffran
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA.
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16
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Carbone GM, McGuffie E, Napoli S, Flanagan CE, Dembech C, Negri U, Arcamone F, Capobianco ML, Catapano CV. DNA binding and antigene activity of a daunomycin-conjugated triplex-forming oligonucleotide targeting the P2 promoter of the human c-myc gene. Nucleic Acids Res 2004; 32:2396-410. [PMID: 15121897 PMCID: PMC419437 DOI: 10.1093/nar/gkh527] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Triplex-forming oligonucleotides (TFO) that bind DNA in a sequence-specific manner might be used as selective repressors of gene expression and gene-targeted therapeutics. However, many factors, including instability of triple helical complexes in cells, limit the efficacy of this approach. In the present study, we tested whether covalent linkage of a TFO to daunomycin, which is a potent DNA-intercalating agent and anticancer drug, could increase stability of the triple helix and activity of the oligonucleotide in cells. The 11mer daunomycin-conjugated GT (dauno-GT11) TFO targeted a sequence upstream of the P2 promoter, a site known to be critical for transcription of the c-myc gene. Band-shift assays showed that the dauno-GT11 formed triplex DNA with enhanced stability compared to the unmodified TFO. Band shift and footprinting experiments demonstrated that binding of dauno-GT11 was highly sequence-specific with exclusive binding to the 11 bp target site in the c-myc promoter. The daunomycin-conjugated TFO inhibited transcription in vitro and reduced c-myc promoter activity in prostate and breast cancer cells. The daunomycin-conjugated TFO was taken up by cells with a distinctive intracellular distribution compared to free daunomycin. However, cationic lipid-mediated delivery was required for enhanced cellular uptake, nuclear localization and biological activity of the TFO in cells. Dauno-GT11 reduced transcription of the endogenous c-myc gene in cells, but did not affect expression of non-target genes, such as ets-1 and ets-2, which contained very similar target sequences in their promoters. Daunomycin-conjugated control oligonucleotides unable to form triplex DNA with the target sequence did not have any effect in these assays, indicating that daunomycin was not directly responsible for the activity of daunomycin-conjugated TFO. Thus, attachment of daunomycin resulted in increased triplex stability and biological activity of the 11mer GT-rich TFO without compromising its specificity. These results encourage further testing of this approach to develop novel antigene therapeutics.
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Affiliation(s)
- Giuseppina M Carbone
- Laboratory of Experimental Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Via Vela 6, 6500 Bellinzona, Switzerland
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17
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Guillonneau F, Guieysse AL, Nocentini S, Giovannangeli C, Praseuth D. Psoralen interstrand cross-link repair is specifically altered by an adjacent triple-stranded structure. Nucleic Acids Res 2004; 32:1143-53. [PMID: 14966263 PMCID: PMC373402 DOI: 10.1093/nar/gkh267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 01/16/2004] [Accepted: 01/16/2004] [Indexed: 11/14/2022] Open
Abstract
Targeting DNA-damaging agents to specific DNA sites by using sequence-specific DNA ligands has been successful in directing genomic modifications. The understanding of repair processing of such targeted damage and the influence of the adjacent complex is largely unknown. In this way, directed interstrand cross-links (ICLs) have already been generated by psoralen targeting. The mechanisms responsible for ICL removal are far from being understood in mammalian cells, with the proposed involvement of both mutagenic and recombinogenic pathways. Here, a unique ICL was introduced at a selected site by photoactivation of a psoralen moiety with the use of psoralen conjugates of triplex-forming oligonucleotides. The processing of psoralen ICL was evaluated in vitro and in cells for two types of cross-linked substrates, either containing a psoralen ICL alone or with an adjacent triple-stranded structure. We show that the presence of a neighbouring triplex structure interferes with different stages of psoralen ICL processing: (i) the ICL-induced DNA repair synthesis in HeLa cell extracts is inhibited by the triplex structure, as measured by the efficiency of 'true' and futile repair synthesis, stopping at the ICL site; (ii) in HeLa cells, the ICL removal via a nucleotide excision repair (NER) pathway is delayed in the presence of a neighbouring triplex; and (iii) the binding to ICL of recombinant xeroderma pigmentosum A protein, which is involved in pre-incision recruitment of NER factors is impaired by the presence of the third DNA strand. These data characterize triplex-induced modulation of ICL repair pathways at specific steps, which might have implications for the controlled induction of targeted genomic modifications and for the associated cellular responses.
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Affiliation(s)
- F Guillonneau
- Laboratoire de Biophysique, INSERM U565, CNRS UMR5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris Cedex 05, France
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18
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Broitman SL, Amosova O, Fresco JR. Repairing the Sickle Cell mutation. III. Effect of irradiation wavelength on the specificity and type of photoproduct formed by a 3'-terminal psoralen on a third strand directed to the mutant base pair. Nucleic Acids Res 2003; 31:4682-8. [PMID: 12907707 PMCID: PMC169894 DOI: 10.1093/nar/gkg658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Using a psoralen delivery system mediated by a DNA third strand that binds selectively to linear target duplexes immediately downstream from the Sickle Cell beta-globin gene mutation and the comparable wild-type beta-globin gene sequence, the kinetics of formation and yield of psoralen monoadducts and crosslinks with pyrimidine residues at and near the mutant base pair site and its wild-type counterpart were determined. By exploiting irradiation specificities at 300, 365 and 419 nm, it was possible to evaluate the orientation equilibrium of 3'-linked intercalated psoralen and to develop conditions that lead to preferential formation of each type of photoproduct in both the mutant and wild-type sequences. This makes possible the preparation of each type of photoproduct for use as a substrate for DNA repair. In this way, the base pair change(s) that each generates can be established.
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Affiliation(s)
- Steven L Broitman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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19
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Majumdar A, Puri N, Cuenoud B, Natt F, Martin P, Khorlin A, Dyatkina N, George AJ, Miller PS, Seidman MM. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide. J Biol Chem 2003; 278:11072-7. [PMID: 12538585 DOI: 10.1074/jbc.m211837200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Successful gene-targeting reagents must be functional under physiological conditions and must bind chromosomal target sequences embedded in chromatin. Triple helix-forming oligonucleotides (TFOs) recognize and bind specific sequences via the major groove of duplex DNA and may have potential for gene targeting in vivo. We have constructed chemically modified, psoralen-linked TFOs that mediate site-specific mutagenesis of a chromosomal gene in living cells. Here we show that targeting efficiency is sensitive to the biology of the cell, specifically, cell cycle status. Targeted mutagenesis was variable across the cycle with the greatest activity in S phase. This was the result of differential TFO binding as measured by cross-link formation. Targeted cross-linking was low in quiescent cells but substantially enhanced in S phase cells with adducts in approximately 20-30% of target sequences. 75-80% of adducts were repaired faithfully, whereas the remaining adducts were converted into mutations (>5% mutation frequency). Clones with mutations could be recovered by direct screening of colonies chosen at random. These results demonstrate high frequency target binding and target mutagenesis by TFOs in living cells. Successful protocols for TFO-mediated manipulation of chromosomal sequences are likely to reflect a combination of appropriate oligonucleotide chemistry and manipulation of the cell biology.
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Affiliation(s)
- Alokes Majumdar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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20
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Ziemba A, Derosier LC, Methvin R, Song CY, Clary E, Kahn W, Milesi D, Gorn V, Reed M, Ebbinghaus S. Repair of triplex-directed DNA alkylation by nucleotide excision repair. Nucleic Acids Res 2001; 29:4257-63. [PMID: 11691913 PMCID: PMC60196 DOI: 10.1093/nar/29.21.4257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are being investigated as highly specific DNA binding agents to inhibit the expression of clinically relevant genes. So far, they have been shown to inhibit transcription from the HER-2/neu gene in vitro, whereas their use in vivo has been studied to a limited extent. This study uses a TFO-chlorambucil (chl) conjugate capable of forming site-specific covalent guanine adducts within the HER-2/neu promoter. We demonstrate that nucleotide excision repair (NER) represents a mechanism of cellular resistance to TFO-directed DNA alkylation. In vitro repair assays demonstrate that triplex-directed chl-guanine adducts are substrates for repair by NER competent cell extracts but not XP12BE cell extracts deficient in NER. The degree of repair is estimated by a ligation-mediated polymerase chain reaction with a pre-formed triplex in a plasmid transfected into repair competent cells, indicating that approximately 25% of the guanine adducts are removed after 24 h. These data indicate that guanine adducts from TFO-directed alkylation are a substrate for NER and that DNA repair is a significant barrier to the intracellular persistence of target gene binding by TFOs.
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Affiliation(s)
- A Ziemba
- Arizona Cancer Center, University of Arizona, 1515 North Campbell Avenue, Tucson, AZ 85724-5024, USA
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21
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Wollowitz S. Fundamentals of the psoralen-based Helinx technology for inactivation of infectious pathogens and leukocytes in platelets and plasma. Semin Hematol 2001; 38:4-11. [PMID: 11727280 DOI: 10.1016/s0037-1963(01)90118-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Psoralens plus ultraviolet A (UVA) light inactivate viruses and bacteria as well as leukocytes. A system employing the synthetic psoralen compound amotosalen hydrochloride (S-59), in combination with UVA light, is being developed to decontaminate platelet concentrates and plasma in a blood-bank setting. S-59 is a heterocyclic psoralen compound that reacts by a three-step process with nucleic acids (NAs): (1) S-59 intercalates into the double helix; (2) upon illumination with long-wavelength ultraviolet light (UVA), it covalently attaches to a single strand, forming a monoadduct; and (3) additional illumination causes a photoreaction of the monoadduct with the second NA strand, resulting in an interstrand crosslink. The reaction occurs with the genomic material of DNA- and RNA-based viruses and occurs in genomes that are single stranded as well as double stranded. Inactivation rate is related to genome size. Large genomes such as those in leukocytes are far more susceptible to inactivation than are viruses such as hepatitis B virus (HBV), which is inactivated (>10(5) logs) under conditions being developed for blood-bank use. The efficiency of the process is affected by a number of practical considerations such as solution components and light source. The S-59 photochemical treatment process (PCT) has been optimized for platelet concentrates as currently processed for transfusion.
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Affiliation(s)
- S Wollowitz
- Department of Chemical Technology, Cerus Corporation, Concord, CA 94520, USA
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22
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Abstract
DNA interstrand cross-links (ICLs) are very toxic to dividing cells, because they induce mutations, chromosomal rearrangements and cell death. Inducers of ICLs are important drugs in cancer treatment. We discuss the main properties of several classes of ICL agents and the types of damage they induce. The current insights in ICL repair in bacteria, yeast and mammalian cells are reviewed. An intriguing aspect of ICLs is that a number of multi-step DNA repair pathways including nucleotide excision repair, homologous recombination and post-replication/translesion repair all impinge on their repair. Furthermore, the breast cancer-associated proteins Brca1 and Brca2, the Fanconi anemia-associated FANC proteins, and cell cycle checkpoint proteins are involved in regulating the cellular response to ICLs. We depict several models that describe possible pathways for the repair or replicational bypass of ICLs.
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Affiliation(s)
- M L Dronkert
- Department of Cell Biology and Genetics, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
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23
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Greenberg RB, Alberti M, Hearst JE, Chua MA, Saffran WA. Recombinational and mutagenic repair of psoralen interstrand cross-links in Saccharomyces cerevisiae. J Biol Chem 2001; 276:31551-60. [PMID: 11390398 DOI: 10.1074/jbc.m103588200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Psoralen photoreacts with DNA to form interstrand cross-links, which can be repaired by both nonmutagenic nucleotide excision repair and recombinational repair pathways and by mutagenic pathways. In the yeast Saccharomyces cerevisiae, psoralen cross-links are processed by nucleotide excision repair to form double-strand breaks (DSBs). In yeast, DSBs are repaired primarily by homologous recombination, predicting that cross-link and DSB repair should induce similar recombination end points. We compared psoralen cross-link, psoralen monoadduct, and DSB repair using plasmid substrates with site-specific lesions and measured the patterns of gene conversion, crossing over, and targeted mutation. Psoralen cross-links induced both recombination and mutations, whereas DSBs induced only recombination, and monoadducts were neither recombinogenic nor mutagenic. Although the cross-link- and DSB-induced patterns of plasmid integration and gene conversion were similar in most respects, they showed opposite asymmetries in their unidirectional conversion tracts: primarily upstream from the damage site for cross-links but downstream for DSBs. Cross-links induced targeted mutations in 5% of the repaired plasmids; all were base substitutions, primarily T --> C transitions. The major pathway of psoralen cross-link repair in yeast is error-free and involves the formation of DSB intermediates followed by homologous recombination. A fraction of the cross-links enter an error-prone pathway, resulting in mutations at the damage site.
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Affiliation(s)
- R B Greenberg
- Department of Chemistry and Biochemistry, Queens College, City University of New York, Flushing, New York 11367, USA
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24
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Abstract
The ability to specifically manipulate gene expression has wide-ranging applications in experimental biology and in gene-based therapeutics. The design of molecules that recognise specific sequences on the DNA double helix provides us with interesting tools to interfere with DNA information processing at an early stage of gene expression. Triplex-forming molecules specifically recognise oligopyrimidine-oligopurine sequences by hydrogen bonding interactions. Applications of such triplex-forming molecules (TFMs) are the subject of the present review. In cell cultures, TFMs have been successfully used to down- or up-regulate transcription in a gene-specific manner and to induce genomic DNA modifications at a selected site. The first evidence of a triplex-based activity in animals has been provided recently. In addition, TFMs are also powerful tools for gene-specific chemistry, in particular for gene transfer applications.
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Affiliation(s)
- M Faria
- Department of Microbiologia, Immunologia e Parasitologia, UNIFESP, Sao Paulo, SP, Brazil
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25
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Biet E, Maurisse R, Dutreix M. Stimulation of RecA-mediated D-loop formation by oligonucleotide-directed triple-helix formation: guided homologous recombination (GOREC). Biochemistry 2001; 40:1779-86. [PMID: 11327840 DOI: 10.1021/bi001605a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligonucleotide-directed triple helix formation provides an elegant rational basis for gene-specific DNA targeting and has been widely used to interfere with gene expression ("antigene" strategies) and as a molecular tool for biological studies. Various strategies have been developed to introduce sequence modifications in genomes. However, the low efficiency of the overall process in eucaryotic cells impairs efficient recovery of recombinant genomes. Since one limiting step in homologous recombination is the targeting to the homologous sequence, we have tested the contribution of an oligonucleotide-directed triple helix formation on the RecA-dependent association of an oligonucleotide and its homologous target on duplex DNA (D-loop formation). For this study, the recombinant ssDNA fragment was noncovalently associated to a triple helix-forming oligonucleotide. The physicochemical and biochemical characteristics of the triple helix and D-loop structures formed by the complex molecules in the presence or in the absence of RecA protein were determined. We have demonstrated that the triple helix-forming oligonucleotide increases the efficiency of D-loop formation and the RecA protein speeds up also the triple helix formation. The so-called "GOREC" (for guided homologous recombination) approach can be developed as a novel tool to improve the efficiency of directed mutagenesis and gene alteration in living organisms.
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Affiliation(s)
- E Biet
- Laboratoire de Biophysique, UMR 8646 CNRS-Muséum National d'Histoire Naturelle, INSERM U201, 43 rue Cuvier, 75231 Paris Cedex 05, France
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26
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Hoque AT, Sedelnikova OA, Luu AN, Swaim WD, Panyutin IG, Baum BJ. Use of polyethylenimine-adenovirus complexes to examine triplex formation in intact cells. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:229-41. [PMID: 10984117 DOI: 10.1089/108729000421411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) show potential for sequence-specific DNA binding and inhibition of gene expression. We have applied this antigene strategy using a TFO incorporating an Auger-emitting radionucleotide, 125I, to study the production of double-strand breaks (dsb) in the rat aquaporin 5 (rAQP5) cDNA. 125I-TFO bound to the pCMVrAQP5 plasmid in vitro in a dose-dependent manner and formed stable triplexes up to 65 degrees C and in the presence of 140 mM KCl. Further, 125I-TFO resulted in a predictable dsb when analyzed by Southern hybridization. To deliver TFOs to epithelial cells, we employed 125I-TFO-polyethyleneimine-adenovirus (125I-TFO-PEI-Ad) complexes. We hypothesized that these complexes would take advantage of adenoviral characteristics to transfer 125I-TFO to the cell nucleus. Adenovirus-containing complexes brought about greater uptake and nuclear localization of TFOs compared with delivery with 125I-TFO-PEI complexes alone. No significant degradation of 125I-TFO was found after delivery into cells using PEI-Ad complexes and freezing and thawing. We next used PEI-Ad complexes to deliver 125I-TFO and pCMVrAQP5 separately to epithelial cells to determine if triplexes can form de novo within cells, resulting in the specific dsb in the rAQP5 cDNA. After delivery, cell pellets were stored at -80 degrees C for more than 60 days. Thereafter, plasmid DNA was isolated from cells and analyzed for dsb by Southern hybridization. However, none were detected. We conclude that under the experimental conditions employed, effective triplexes, with 125I-TFO and pCMVrAQP5, do not form de novo inside cells.
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Affiliation(s)
- A T Hoque
- Gene Therapy and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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27
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Barre FX, Ait-Si-Ali S, Giovannangeli C, Luis R, Robin P, Pritchard LL, Helene C, Harel-Bellan A. Unambiguous demonstration of triple-helix-directed gene modification. Proc Natl Acad Sci U S A 2000; 97:3084-8. [PMID: 10716704 PMCID: PMC16196 DOI: 10.1073/pnas.97.7.3084] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Triple-helix-forming oligonucleotides (TFOs), which can potentially modify target genes irreversibly, represent promising tools for antiviral therapies. However, their effectiveness on endogenous genes has yet to be unambiguously demonstrated. To monitor endogenous gene modification by TFOs in a yeast model, we inactivated an auxotrophic marker gene by inserting target sequences of interest into its coding region. The genetically engineered yeast cells then were treated with psoralen-linked TFOs followed by UV irradiation, thus generating highly mutagenic covalent crosslinks at the target site whose repair could restore gene function; the number of revertants and spectrum of mutations generated were quantified. Results showed that a phosphoramidate TFO indeed reaches its target sequence, forms crosslinks, and generates mutations at the expected site via a triplex-mediated mechanism: (i) under identical conditions, no mutations were generated by the same TFO at two other loci in the target strain, nor in an isogenic control strain carrying a modified target sequence incapable of supporting triple-helix formation; (ii) for a given target sequence, whether the triplex was formed in vivo on an endogenous gene or in vitro on an exogenous plasmid, the nature of the mutations generated was identical, and consistent with the repair of a psoralen crosslink at the target site. Although the mutation efficiency was probably too low for therapeutic applications, our results confirm the validity of the triple-helix approach and provide a means of evaluating the effectiveness of new chemically modified TFOs and analogs.
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Affiliation(s)
- F X Barre
- Centre National de la Recherche Scientifique UPR 9079, 7 rue Guy Moquet, B.P.8, 94801 Villejuif, France
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28
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Abstract
Triple-helix-forming oligonucleotides (TFOs), which can potentially modify target genes irreversibly, represent promising tools for antiviral therapies. However, their effectiveness on endogenous genes has yet to be unambiguously demonstrated. To monitor endogenous gene modification by TFOs in a yeast model, we inactivated an auxotrophic marker gene by inserting target sequences of interest into its coding region. The genetically engineered yeast cells then were treated with psoralen-linked TFOs followed by UV irradiation, thus generating highly mutagenic covalent crosslinks at the target site whose repair could restore gene function; the number of revertants and spectrum of mutations generated were quantified. Results showed that a phosphoramidate TFO indeed reaches its target sequence, forms crosslinks, and generates mutations at the expected site via a triplex-mediated mechanism: (i) under identical conditions, no mutations were generated by the same TFO at two other loci in the target strain, nor in an isogenic control strain carrying a modified target sequence incapable of supporting triple-helix formation; (ii) for a given target sequence, whether the triplex was formed in vivo on an endogenous gene or in vitro on an exogenous plasmid, the nature of the mutations generated was identical, and consistent with the repair of a psoralen crosslink at the target site. Although the mutation efficiency was probably too low for therapeutic applications, our results confirm the validity of the triple-helix approach and provide a means of evaluating the effectiveness of new chemically modified TFOs and analogs.
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29
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Guieysse AL, Praseuth D, Giovannangeli C, Asseline U, Hélène C. Psoralen adducts induced by triplex-forming oligonucleotides are refractory to repair in HeLa cells. J Mol Biol 2000; 296:373-83. [PMID: 10669595 DOI: 10.1006/jmbi.1999.3466] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The use of triple helix-forming oligonucleotides constitutes an attractive strategy to regulate gene expression by inhibition of transcription. Psoralen-oligonucleotide conjugates form, upon irradiation, covalent triplexes and thereby modify the specific target sequence. The processing of such photoproducts on the promoter of the gene coding for the interleukin-2 receptor alpha chain was investigated in HeLa cells and HeLa nuclear extracts. We demonstrate that psoralen cross-links are not repaired within the cell extracts nor inside cells. The mechanism of repair inhibition was elucidated in vitro: the presence of the third strand oligonucleotide inhibits the incision step of the damaged target by repair endonucleases. These results demonstrate the possibility of using this approach to induce a persistent intracellular DNA damage at a specific site and to afford prolonged transcription inhibition.
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Affiliation(s)
- A L Guieysse
- Laboratoire de Biophysique, INSERM U 201 - CNRS UMR 8646, Muséum National d'Histoire Naturelle, 43, rue Cuvier, Paris, 75005, France.
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