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Zuin Fantoni N, McGorman B, Molphy Z, Singleton D, Walsh S, El-Sagheer AH, McKee V, Brown T, Kellett A. Development of Gene-Targeted Polypyridyl Triplex-Forming Oligonucleotide Hybrids. Chembiochem 2020; 21:3563-3574. [PMID: 32755000 DOI: 10.1002/cbic.202000408] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/30/2020] [Indexed: 02/02/2023]
Abstract
In the field of nucleic acid therapy there is major interest in the development of libraries of DNA-reactive small molecules which are tethered to vectors that recognize and bind specific genes. This approach mimics enzymatic gene editors, such as ZFNs, TALENs and CRISPR-Cas, but overcomes the limitations imposed by the delivery of a large protein endonuclease which is required for DNA cleavage. Here, we introduce a chemistry-based DNA-cleavage system comprising an artificial metallo-nuclease (AMN) that oxidatively cuts DNA, and a triplex-forming oligonucleotide (TFO) that sequence-specifically recognises duplex DNA. The AMN-TFO hybrids coordinate CuII ions to form chimeric catalytic complexes that are programmable - based on the TFO sequence employed - to bind and cut specific DNA sequences. Use of the alkyne-azide cycloaddition click reaction allows scalable and high-throughput generation of hybrid libraries that can be tuned for specific reactivity and gene-of-interest knockout. As a first approach, we demonstrate targeted cleavage of purine-rich sequences, optimisation of the hybrid system to enhance stability, and discrimination between target and off-target sequences. Our results highlight the potential of this approach where the cutting unit, which mimics the endonuclease cleavage machinery, is directly bound to a TFO guide by click chemistry.
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Affiliation(s)
- Nicolò Zuin Fantoni
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Present address: Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
| | - Daniel Singleton
- ATDBio Ltd., School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sarah Walsh
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,ATDBio Ltd., Magdalen Centre, Oxford Science Park, Oxford, OX4 4GA, UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
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Abstract
In a recent study, we described the enhanced double-strand cleavage of hairpin DNAs by Fe·bleomycin (Fe·BLM) that accompanies increasingly strong binding of this antitumor agent and suggested that this effect may be relevant to the mechanism by which BLM mediates its antitumor effects. Because the DNA in tumor cells is known to be hypomethylated on cytidine relative to that in normal cells, it seemed of interest to study the possible effects of methylation status on BLM-induced double-strand DNA cleavage. Three hairpin DNAs found to bind strongly to bleomycin, and their methylated counterparts, were used to study the effect of methylation on bleomycin-induced DNA degradation. Under conditions of limited DNA cleavage, there was a significant overall decrease in the cleavage of methylated hairpin DNAs. Cytidine methylation was found to result in decreased BLM-induced cleavage at the site of methylation and to result in enhanced cleavage at adjacent nonmethylated sites. For two of the three hairpin DNAs studied, methylation was accompanied by a dramatic decrease in the binding affinity for Fe·BLM, suggesting the likelihood of diminished double-strand cleavage. The source of the persistent binding of BLM by the third hairpin DNA was identified. Also identified was the probable molecular mechanism for diminished binding and cleavage of the methylated DNAs by BLM. The possible implications of these findings for the antitumor selectivity of bleomycin are discussed.
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Affiliation(s)
- Basab Roy
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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Ma Q, Akiyama Y, Xu Z, Konishi K, Hecht SM. Identification and Cleavage Site Analysis of DNA Sequences Bound Strongly by Bleomycin. J Am Chem Soc 2009; 131:2013-22. [DOI: 10.1021/ja808629s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Yoshitsugu Akiyama
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Zhidong Xu
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Kazuhide Konishi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Sidney M. Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904
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Calafat AM, Marzilli LG. Chiralities of Complexes of BleomycirvType Ligands, a Neglected Feature in Structural Studies Relevant to Anticancer Drug Action. COMMENT INORG CHEM 2006. [DOI: 10.1080/02603599808012255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rishel MJ, Thomas CJ, Tao ZF, Vialas C, Leitheiser CJ, Hecht SM. Conformationally constrained analogues of bleomycin A5. J Am Chem Soc 2003; 125:10194-205. [PMID: 12926941 DOI: 10.1021/ja030057w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bleomycin (BLM) group antitumor antibiotics are glycopeptide-derived natural products shown to cause sequence selective lesions in DNA. Prior studies have indicated that the linker region, composed of the methylvalerate and threonine residues, may be responsible for a conformational bend in the agent required for efficient DNA cleavage. We have synthesized a number of conformationally constrained methylvalerate analogues and incorporated them into deglycobleomycin A(5) congeners using our recently reported procedure for the solid phase construction of (deglyco)bleomycin and its analogues. These analogues were designed to probe the effects of conformational constraint of the native valerate moiety. Initial experiments indicated that the constrained molecules, none of which mimic the conformation proposed for the natural valerate linker, possessed DNA cleavage activity, albeit with potencies less than that of (deglyco)BLM and lacking sequence selectivity. Further experiments demonstrated that these analogues failed to produce alkali-labile lesions in DNA or sequence selective oxidative damage in RNA. However, two of the conformationally constrained deglycoBLM analogues were shown to mediate RNA cleavage in the absence of added Fe(2+). The ability of the analogues to mediate the oxygenation of small molecules was also assayed, and it was shown that they were as competent in the transfer of oxygen to low molecular weight substrates as the parent compound.
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Affiliation(s)
- Michael J Rishel
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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Ramotar D, Wang H. Protective mechanisms against the antitumor agent bleomycin: lessons from Saccharomyces cerevisiae. Curr Genet 2003; 43:213-24. [PMID: 12698269 DOI: 10.1007/s00294-003-0396-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2003] [Revised: 03/17/2003] [Accepted: 03/18/2003] [Indexed: 10/26/2022]
Abstract
Bleomycin is a small glycopeptide antibiotic used in combination therapy for the treatment of a few types of human cancer. The antitumor effect of bleomycin is most likely caused by its ability to bind to DNA and induce the formation of toxic DNA lesions via a free radical reactive (Fe.bleomycin) complex. However, the chemotherapeutic potential of bleomycin is limited, as it causes pulmonary fibrosis and tumor resistance at high doses. The chemical structure and modes of action of bleomycin have been extensively studied and these provide a foundation towards improving the therapeutic value of the drug. This review provides a first account of the current state of knowledge of the cellular processes that can allow the yeast Saccharomyces cerevisiae to evade the lethal effects of bleomycin. This model organism is likely to provide rapid clues in our understanding of bleomycin resistance in tumor cells.
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Affiliation(s)
- Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Guy-Bernier Research Center, 5415 Boulevard de l'Assomption, H1T 2M4, Montreal, Quebec, Canada.
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Lentzen O, Constant JF, Defrancq E, Prévost M, Schumm S, Moucheron C, Dumy P, Kirsch-De Mesmaeker A. Photocrosslinking in ruthenium-labelled duplex oligonucleotides. Chembiochem 2003; 4:195-202. [PMID: 12616633 DOI: 10.1002/cbic.200390031] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The formation of a photoadduct between a [Ru(1,4,5,8-tetraazaphenanthrene)(2)4,7-diphenylphenanthroline](2+) complex chemically attached to a synthetic oligonucleotide, and a guanine moiety in a complementary targeted single-stranded DNA molecule was studied for ten 17-mer duplexes by denaturing gel electrophoresis. This photoadduct formation leads to photocrosslinking of the two strands. The percentage quenching of luminescence of the complex by electron transfer was compared to the resulting yield of photocrosslinked product. This yield does not only depend on the ionisation potential of the guanine bases, which are electron donors, but also on other factors, such as the position of the guanine bases as compared to the site of attachment of the complex. The photocrosslinking yield is higher when the guanine moieties are towards the 3' end on the complementary strand as compared to the tethering site. Computer modelling results are in agreement with this preference for the 3' side for the photoreaction. Interestingly, the photocrosslink is not alkali labile. Moreover, a type III exonuclease enzyme is blocked at the position of photocrosslinking.
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Affiliation(s)
- O Lentzen
- Université Libre de Bruxelles, Organic Chemistry and Photochemistry, CP. 160/08, 50 Avenue F. D. Roosevelt, Belgium
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Alberti P, Arimondo PB, Mergny JL, Garestier T, Hélène C, Sun JS. A directional nucleation-zipping mechanism for triple helix formation. Nucleic Acids Res 2002; 30:5407-15. [PMID: 12490709 PMCID: PMC140048 DOI: 10.1093/nar/gkf675] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T.A base pair by a C.G pair at either the 5' or the 3' end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5' side of the triplex (referred to as the 5' side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5' end to the 3' end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5' than at the 3' duplex-triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression.
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Affiliation(s)
- Patrizia Alberti
- Laboratoire de Biophysique, USM0503 Muséum National d'Histoire Naturelle, UMR8646 CNRS-MNHN, U565 INSERM, 43 rue Cuvier 75231 Paris cedex 05, France
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Katano K, An H, Aoyagi Y, Overhand M, Sucheck SJ, Stevens WC, Hess CD, Zhou X, Hecht SM. Total Synthesis of Bleomycin Group Antibiotics. Total Syntheses of Bleomycin Demethyl A2, Bleomycin A2, and Decarbamoyl Bleomycin Demethyl A2. J Am Chem Soc 1998. [DOI: 10.1021/ja9819458] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kiyoaki Katano
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Haoyun An
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Yoshiaki Aoyagi
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Mark Overhand
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Steven J. Sucheck
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - William C. Stevens
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Cynthia D. Hess
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Xiang Zhou
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Sidney M. Hecht
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
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Holmes CE, Abraham AT, Hecht SM, Florentz C, Giegé R. Fe.bleomycin as a probe of RNA conformation. Nucleic Acids Res 1996; 24:3399-406. [PMID: 8811095 PMCID: PMC146117 DOI: 10.1093/nar/24.17.3399] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.
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Affiliation(s)
- C E Holmes
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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