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Akiyama Y, Kimura K, Komatsu S, Takarada T, Maeda M, Kikuchi A. A Simple Colorimetric Assay of Bleomycin-Mediated DNA Cleavage Utilizing Double-Stranded DNA-Modified Gold Nanoparticles. Chembiochem 2023; 24:e202200451. [PMID: 36156837 PMCID: PMC10092608 DOI: 10.1002/cbic.202200451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/23/2022] [Indexed: 01/05/2023]
Abstract
A colorimetric assay of DNA cleavage by bleomycin (BLM) derivatives was developed utilizing high colloidal stability on double-stranded (ds) DNA-modified gold nanoparticles (dsDNA-AuNPs) possessing a cleavage site. The assay was performed using dsDNA-AuNPs treated with inactive BLM or activated BLM (Fe(II)⋅BLM). A 10-min exposure in dsDNA-AuNPs with inactive BLM treatment resulted in a rapid color change from red to purple because of salt-induced non-crosslinking aggregation of dsDNA-AuNPs. In contrast, the addition of active Fe(II)⋅BLM retained the red color, probably because of the formation of protruding structures at the outermost phase of dsDNA-AuNPs caused by BLM-mediated DNA cleavage. Furthermore, the results of our model experiments indicate that oxidative base release and DNA-cleavage pathways could be visually distinguished with color change. The present methodology was also applicable to model screening assays using several drugs with different mechanisms related to antitumor activity. These results strongly suggest that this assay with a rapid color change could lead to simple and efficient screening of potent antitumor agents.
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Affiliation(s)
- Yoshitsugu Akiyama
- Katsushika Division, Institute of Arts and Sciences, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan.,Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Kazunori Kimura
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Syuuhei Komatsu
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Tohru Takarada
- Surface and Interface Science Laboratory, RIKEN, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Mizuo Maeda
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Akihiko Kikuchi
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
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Cai X, Zaleski PA, Cagir A, Hecht SM. Deglycobleomycin A6 analogues modified in the methylvalerate moiety. Bioorg Med Chem 2011; 19:3831-44. [DOI: 10.1016/j.bmc.2011.04.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 04/22/2011] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
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Würthner F, Bräse S, Sewald N, Herges R, Senge MO, Bach T, Gottwald T, Kopf T, Ŝpehar K, Hartung J, Plattner D, Gansäuer A, Oestreich M, Brückner R, Pietruszka J, Süßmuth R, Müller M, Weinhold E, Jäschke A, Albrecht M, Priepke H, Roth G, Ditrich K, Ernst A, Wortmann L, Ag S. Organische Chemie 2002. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/nadc.20030510309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Akiyama Y, Ma Q, Edgar E, Laikhter A, Hecht SM. A Novel DNA Hairpin Substrate for Bleomycin. Org Lett 2008; 10:2127-30. [DOI: 10.1021/ol800445x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yoshitsugu Akiyama
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Erin Edgar
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Andrei Laikhter
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
| | - Sidney M. Hecht
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, and Integrated DNA Technologies, 1710 Commercial Park, Coralville, Iowa 52241
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Chandrasekhar V, Athimoolam A, Krishnan V, Azhakar R, Madhavaiah C, Verma S. A Copper-Metalated, Hybrid Inorganic-Organic Polymer as an Oxidative Nuclease. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200400727] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
The bleomycins (BLMs) are used clinically in combination chemotherapy, their clinical usefulness being limited by the accompanying pulmonary toxicity. Much has been learned about the structure and function of BLMs in vitro. However, the mechanism of their cytoxicity in vivo, including their target(s), metal cofactor(s) effecting nucleic acid cleavage and its (their) oxidation state, concentrations of BLM in the nucleus of the cell, BLM metabolism, hot spots for double-strand DNA cleavage, and their repair, have remained elusive. New methods offer new opportunities to revisit and solve old problems, which could ultimately lead to development of a more effective therapeutic.
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Affiliation(s)
- Jingyang Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
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Chandrasekhar V, Deria P, Krishnan V, Athimoolam A, Singh S, Madhavaiah C, Srivatsan SG, Verma S. Metalated hybrid polymers as catalytic reagents for phosphate ester hydrolysis and plasmid modification. Bioorg Med Chem Lett 2004; 14:1559-62. [PMID: 15006403 DOI: 10.1016/j.bmcl.2003.12.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 12/22/2003] [Accepted: 12/22/2003] [Indexed: 11/23/2022]
Abstract
Pendant pyrazolylcyclophosphazene containing hybrid cross-linked polymer (CPPL) has been utilized for binding Zn(II). The metalated polymer (CPPL-Zn) has been found to be very effective catalyst for the hydrolysis of a RNA model phosphodiester substrate [2-(hydroxypropyl)-p-nitrophenyl phosphate, hNPP]. In addition, CPPL-Zn also cleaved supercoiled plasmid DNA pBR322 thus providing a novel structural motif of inorganic-organic hybrid polymers as synthetic nucleases.
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Girard C, Tranchant I, Gorteau V, Potey L, Herscovici J. Development of a DNA Interaction Test with Small Molecules Still Grafted on Solid Phase. ACTA ACUST UNITED AC 2004; 6:275-8. [PMID: 15002977 DOI: 10.1021/cc0499744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Girard
- Synthèse, Imagerie et Nanochimie, Laboratoire de Pharmacologie Chimique et Génétique (FRE 2463 CNRS/U266 INSERM), Ecole Nationale Supérieure de Chimie de Paris, 75005 Paris, France
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Cagir A, Tao ZF, Sucheck SJ, Hecht SM. Solid-phase synthesis and biochemical evaluation of conformationally constrained analogues of deglycobleomycin A5. Bioorg Med Chem 2003; 11:5179-87. [PMID: 14604681 DOI: 10.1016/j.bmc.2003.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Deglycobleomycin binds to and degrades the self-complementary oligonucleotide d(CGCTAGCG)(2) in a sequence selective fashion. A previous modeling study [J. Am. Chem. Soc. 120, (1998), 7450] had shown that, during binding to double stranded DNA, the conformation of the methylvalerate domain of deglycoBLM approximated that of S-proline. In the belief that an analogue of deglycoBLM structurally constrained to mimic the DNA-bound conformation might exhibit facilitated DNA binding and cleavage, an analogue of deglycoBLM was prepared in which the methylvalerate moiety was replaced by S-proline. This deglycoBLM analogue, as well as the related analogue containing R-proline, was synthesized on a TentaGel resin. Both of the analogues were found to be capable of binding Fe(2+) and activating O(2) for transfer to styrene. However, both deglycoBLM analogues exhibited diminished abilities to effect the relaxation of supercoiled plasmid DNA, and neither mediated sequence selective DNA cleavage.
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Affiliation(s)
- Ali Cagir
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22901, USA
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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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Leitheiser CJ, Smith KL, Rishel MJ, Hashimoto S, Konishi K, Thomas CJ, Li C, McCormick MM, Hecht SM. Solid-phase synthesis of bleomycin group antibiotics. Construction of a 108-member deglycobleomycin library. J Am Chem Soc 2003; 125:8218-27. [PMID: 12837092 DOI: 10.1021/ja021388w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycins (BLMs) are structurally related glycopeptide antibiotics isolated from Streptomyces verticillus that mediate the sequence-selective oxidative damage of DNA and RNA. Deglycobleomycin, which lacks the carbohydrate moiety, cleaves DNA analogously to bleomycin itself, albeit less potently, and has been used successfully for analyzing the functional domains of bleomycin. Although structural modifications to bleomycin and deglycobleomycin have been reported, no bleomycin or deglycobleomycin analogue having enhanced DNA cleavage activity has yet been described. The successful synthesis of a deglycobleomycin on a solid support has permitted the facile solid-phase synthesis of 108 unique deglycobleomycin analogues through parallel solid-phase synthesis. Each of the deglycobleomycin analogues was synthesized efficiently; the purity of each crude product was greater than 60%, as determined by HPLC integration. The solid-phase synthesis of the deglycobleomycin library provided near-milligram to milligram quantities of each deglycobleomycin, thereby permitting characterization by (1)H NMR and high-resolution mass spectrometry. Each analogue demonstrated supercoiled plasmid DNA relaxation above background cleavage; the library included two analogues that mediated plasmid relaxation to a greater extent than the parent deglycobleomycin molecule.
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Madhavaiah C, Srivatsan S, Verma S. Heterogeneously active nucleolytic reagents: flexible design of reusable catalysts for nucleic acid scission. CATAL COMMUN 2003. [DOI: 10.1016/s1566-7367(03)00050-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Thomas CJ, Chizhov AO, Leitheiser CJ, Rishel MJ, Konishi K, Tao ZF, Hecht SM. Solid-phase synthesis of bleomycin A(5) and three monosaccharide analogues: exploring the role of the carbohydrate moiety in RNA cleavage. J Am Chem Soc 2002; 124:12926-7. [PMID: 12405801 DOI: 10.1021/ja0208916] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid-phase synthesis of bleomycin A5 (BLM A5) and three monosaccharide analogues is presented. The monosaccharide analogues incorporated alpha-d-mannose, alpha-l-gulose, and alpha-l-rhamnose moieties in lieu of the disaccharide normally present in BLM A5. Also explored were the abilities of each of the monosaccharide congeners to cleave a 53-nt RNA. The elaboration of these carbohydrate-modified bleomycin analogues helps to define the role of the disaccharide moiety during the RNA cleavage event. The relatively facile solid-phase synthesis of bleomycin A5 and each of the carbohydrate analogues constitutes an important advance in the continuing mechanistic studies of bleomycin.
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Affiliation(s)
- Craig J Thomas
- Department of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA
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