1
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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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2
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Yang D, Hindra, Dong LB, Crnovcic I, Shen B. Engineered production and evaluation of 6'-deoxy-tallysomycin H-1 revealing new insights into the structure-activity relationship of the anticancer drug bleomycin. J Antibiot (Tokyo) 2017; 71:ja201793. [PMID: 28831149 DOI: 10.1038/ja.2017.93] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022]
Abstract
The bleomycins (BLMs), a family of glycopeptide antibiotics, are currently used clinically in combination with a number of other agents for the treatment of malignant tumors. Other members of the BLM family include tallysomycins (TLMs), phleomycins and zorbamycin (ZBM). We previously cloned and characterized the biosynthetic gene clusters for BLMs, TLMs and ZBM. Applications of combinatorial biosynthesis strategies to the three biosynthetic machineries enabled the engineered production of several BLM analogs with unique structural characteristics and varying DNA cleavage activities, thereby providing an outstanding opportunity to study the structure-activity relationship (SAR) for the BLM family of anticancer drugs. We now report the engineered production of a new BLM-TLM-ZBM hybrid metabolite, named 6'-deoxy-TLM H-1, which consists of the 22-desmethyl-BLM aglycone, the TLM A C-terminal amine and the ZBM disaccharide, by heterologous expression of the zbmGL genes from the ZBM biosynthetic gene cluster in the Streptoalloteichus hindustanus ΔtlmH mutant strain SB8005. Evaluation of the DNA cleavage activities of 6'-deoxy-TLM H-1 as a measurement for its potential anticancer activity, in comparison with TLM H-1 and BLM A2, reveals new insight into the SAR of BLM family of anticancer drugs.The Journal of Antibiotics advance online publication, 23 August 2017; doi:10.1038/ja.2017.93.
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Affiliation(s)
- Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Liao-Bin Dong
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA
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3
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Gautam SD, Chen JK, Murray V. The DNA sequence specificity of bleomycin cleavage in a systematically altered DNA sequence. J Biol Inorg Chem 2017; 22:881-892. [PMID: 28509989 DOI: 10.1007/s00775-017-1466-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/11/2017] [Indexed: 12/20/2022]
Abstract
Bleomycin is an anti-tumour agent that is clinically used to treat several types of cancers. Bleomycin cleaves DNA at specific DNA sequences and recent genome-wide DNA sequencing specificity data indicated that the sequence 5'-RTGT*AY (where T* is the site of bleomycin cleavage, R is G/A and Y is T/C) is preferentially cleaved by bleomycin in human cells. Based on this DNA sequence, we constructed a plasmid clone to explore this bleomycin cleavage preference. By systematic variation of single nucleotides in the 5'-RTGT*AY sequence, we were able to investigate the effect of nucleotide changes on bleomycin cleavage efficiency. We observed that the preferred consensus DNA sequence for bleomycin cleavage in the plasmid clone was 5'-YYGT*AW (where W is A/T). The most highly cleaved sequence was 5'-TCGT*AT and, in fact, the seven most highly cleaved sequences conformed to the consensus sequence 5'-YYGT*AW. A comparison with genome-wide results was also performed and while the core sequence was similar in both environments, the surrounding nucleotides were different.
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Affiliation(s)
- Shweta D Gautam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Jon K Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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4
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Hindra, Yang D, Teng Q, Dong LB, Crnovčić I, Huang T, Ge H, Shen B. Genome Mining of Streptomyces mobaraensis DSM40847 as a Bleomycin Producer Providing a Biotechnology Platform To Engineer Designer Bleomycin Analogues. Org Lett 2017; 19:1386-1389. [PMID: 28256838 DOI: 10.1021/acs.orglett.7b00283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Streptomyces mobaraensis DSM40847 has been identified by genome mining and confirmed to be a new bleomycin (BLM) producer. Manipulation of BLM biosynthesis in S. mobaraensis has been demonstrated, as exemplified by the engineered production of 6'-deoxy-BLM A2, providing a biotechnology platform for BLM biosynthesis and engineering. Comparison of DNA cleavage efficiency and kinetics among 6'-deoxy-BLM A2 and selected analogues supports the wisdom of altering the disaccharide moiety to fine-tune BLM activity.
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Affiliation(s)
- Hindra
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Qihui Teng
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Liao-Bin Dong
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ivana Crnovčić
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Tingting Huang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Huiming Ge
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
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5
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Chitrapriya N, Shin JH, Hwang IH, Kim Y, Kim C, Kim SK. Synthesis, DNA binding profile and DNA cleavage pathway of divalent metal complexes. RSC Adv 2015. [DOI: 10.1039/c5ra10695h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Divalent metal complexes of dipyridylamine ligand with an anthracene moiety induced considerable oxidative DNA cleavage in the presence hydrogen peroxide and dioxygen.
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Affiliation(s)
| | - Jong Heon Shin
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
| | - In Hong Hwang
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Youngmee Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Republic of Korea
| | - Cheal Kim
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Seog K. Kim
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
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6
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Potentiometric sensing of nuclease activities and oxidative damage of single-stranded DNA using a polycation-sensitive membrane electrode. Biosens Bioelectron 2013; 47:559-65. [DOI: 10.1016/j.bios.2013.03.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/13/2013] [Accepted: 03/26/2013] [Indexed: 01/09/2023]
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7
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Li Y, Huang C, Zheng J, Qi H, Cao W, Wei Y. Label-free electrogenerated chemiluminescence biosensing method for trace bleomycin detection based on a Ru(phen)32+–hairpin DNA composite film electrode. Biosens Bioelectron 2013; 44:177-82. [DOI: 10.1016/j.bios.2012.12.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/27/2012] [Accepted: 12/30/2012] [Indexed: 10/27/2022]
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8
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Ultrasensitive electrogenerated chemiluminescent DNA-based biosensing switch for the determination of bleomycin. Talanta 2012. [PMID: 23200351 DOI: 10.1016/j.talanta.2012.09.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An ultrasensitive electrogenerated chemiluminescent (ECL) DNA-based biosensing switch for the determination of bleomycin (BLM) was developed based on Fe(II) · BLM-mediated hairpin DNA strand cleavage and a structure-switching ECL-dequenching mechanism. A thiolated ss-DNA was used as a substrate for BLMs: one terminus was tethered onto an electrode surface, and the other terminus was labelled with the ECL quencher ferrocene to form a hairpin structure. This thiolated ss-DNA self-assembled on to the tris(2,2'-bipyridine)ruthenium-gold nanoparticle composite modified gold electrode. In the presence of Fe(II) · BLM, the ECL DNA biosensing switch undergoes an irreversible cleavage event that can trigger a significant increase in ECL intensity. The relationship of ECL intensity and the concentration of BLMs was found to be linear in the range of 5 fM - 5000 fM with a detection limit of 2 fM. This work demonstrates that the design of a highly sensitive ECL DNA-based biosensing switch that uses the sequence selectivity of DNA cleavage mediated by the antitumor drug BLM in combination with a chemical quencher, such as ferrocene, to quench ECL signal(s), offers a promising approach for the determination of ultratrace amounts of antitumor drugs.
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9
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Viso A, Fernández de la Pradilla R, Tortosa M, García A, Flores A. Update 1 of: α,β-Diamino Acids: Biological Significance and Synthetic Approaches. Chem Rev 2011; 111:PR1-42. [DOI: 10.1021/cr100127y] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Alma Viso
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | | | - Mariola Tortosa
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Ana García
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Aida Flores
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
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10
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Singh V, Zharnikov M, Gulino A, Gupta T. DNA immobilization, delivery and cleavage on solid supports. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm04359a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Giroux RA, Hecht SM. Characterization of Bleomycin Cleavage Sites in Strongly Bound Hairpin DNAs. J Am Chem Soc 2010; 132:16987-96. [DOI: 10.1021/ja107228c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rachel A. Giroux
- Center for BioEnergetics, Biodesign Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287, United States
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12
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Yin BC, Wu D, Ye BC. Sensitive DNA-Based Electrochemical Strategy for Trace Bleomycin Detection. Anal Chem 2010; 82:8272-7. [DOI: 10.1021/ac101761q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin-Cheng Yin
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Di Wu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
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13
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Oligonucleotides are potent antioxidants acting primarily through metal ion chelation. J Biol Inorg Chem 2010; 15:601-20. [PMID: 20155378 DOI: 10.1007/s00775-010-0628-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
We report on a rather unknown feature of oligonucleotides, namely, their potent antioxidant activity. Previously, we showed that nucleotides are potent antioxidants in Fe(II)/Cu(I/II)-H(2)O(2) systems. Here, we explored the potential of 2'-deoxyoligonucleotides as inhibitors of the Fe(II)/Cu(I/II)-induced *OH formation from H(2)O(2). The oligonucleotides [d(A)(5,7,20); d(T)(20); (2'-OMe-A)(5)] proved to be highly potent antioxidants with IC(50) values of 5-17 or 48-85 microM in inhibiting Fe(II)/Cu(I)- or Cu(II)-induced H(2)O(2) decomposition, respectively, thus representing a 40-215-fold increase in potency as compared with Trolox, a standard antioxidant. The antioxidant activity is only weakly dependent on the oligonucleotides' length or base identity. We analyzed by matrix-assisted laser desorption/ionization time of flight mass spectrometry and (1)H-NMR spectroscopy the composition of the d(A)(5) solution exposed to the aforementioned oxidative conditions for 4 min or 24 h. We concluded that the primary (rapid) inhibition mechanism by oligonucleotides is metal ion chelation and the secondary (slow) mechanism is radical scavenging. We characterized the Cu(I)-d(A)(5) and Cu(II)-d(A)(7) complexes by (1)H-NMR and (31)P-NMR or frozen-solution ESR spectroscopy, respectively. Cu(I) is probably coordinated to d(A)(5) via N1 and N7 of two adenine residues and possibly also via two phosphate/bridging water molecules. The ESR data suggest Cu(II) chelation through two nitrogen atoms of the adenine bases and two oxygen atoms (phosphates or water molecules). We conclude that oligonucleotides at micromolar concentrations prevent Fe(II)/Cu(I/II)-induced oxidative damage, primarily through metal ion chelation. Furthermore, we propose the use of a short, metabolically stable oligonucleotide, (2'-OMe-A)(5), as a highly potent and relatively long lived (t(1/2) approximately 20 h) antioxidant.
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14
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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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15
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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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16
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Yamada H, Tanabe K, Nishimoto SI. Fluorometric identification of 5-methylcytosine modification in DNA: combination of photosensitized oxidation and invasive cleavage. Bioconjug Chem 2007; 19:20-3. [PMID: 18038964 DOI: 10.1021/bc7003318] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient fluorometric detection system of DNA methylation has been developed by a combination of a photooxidative DNA cleavage reaction with 2-methyl-1,4-naphthoquinone (NQ) chromophore and an invasive cleavage reaction with human Flap endonuclease-1. Enzymatic treatment of a mixture of photochemically fragmented target oligodeoxynucleotides (ODNs) at 5-methylcytosine mC) and hairpin-like probe oligomer possessing a fluorophore (F) and a quencher (D) resulted in a dramatic enhancement of fluorescence. In contrast, fluorescence emission for the ODN containing cytosine but not mC at the target sequence was extremely weak. In addition, by monitoring the fluorescence change, this system allows for the detection of mC in DNA at subfemtomole amounts. This system would provide a highly sensitive protocol for determining the methylation status in DNA by fluorescence emission.
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Affiliation(s)
- Hisatsugu Yamada
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
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17
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Tang Y, Feng F, He F, Wang S, Li Y, Zhu D. Direct visualization of enzymatic cleavage and oxidative damage by hydroxyl radicals of single-stranded DNA with a cationic polythiophene derivative. J Am Chem Soc 2007; 128:14972-6. [PMID: 17105308 DOI: 10.1021/ja065159b] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new method has been developed for the label-free, convenient, and real-time monitoring of the cleavage of single-stranded DNA by single-strand-specific S1 nuclease and hydroxyl radical based on cationic water-soluble poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-thiophene hydrochloride](PMNT). The PMNT can form an interpolyelectrolyte complex with ssDNA (duplex) through electrostatic interactions, in which PMNT takes a highly conjugated and planar conformation, and thus PMNT exhibits a relatively red-shifted absorption wavelength. When ssDNA is hydrolyzed by S1 nuclease or hydroxyl radical into small fragments, the PMNT/ssDNA duplex cannot form. In this case, the PMNT remains in random-coil conformation and exhibits a relatively short absorption wavelength. The nuclease digestion or oxidative damage by hydroxyl radical of DNA can be monitored by absorption spectra or just visualized by the "naked-eye" in view of the observed PMNT color changes in aqueous solutions. This assay is simple and rapid, and there is no need to label DNA substrates. The most important characteristic of the assay is direct visualization of the DNA cleavage by the "naked-eye", which makes it more convenient than other methods that rely on instrumentation. The assay also provides a promising application in drug screening based on the inhibition of oxidative damage of DNA.
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Affiliation(s)
- Yanli Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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18
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Maheswari PU, Lappalainen K, Sfregola M, Barends S, Gamez P, Turpeinen U, Mutikainen I, van Wezel GP, Reedijk J. Structure and DNA cleavage properties of two copper(ii) complexes of the pyridine-pyrazole-containing ligands mbpzbpy and Hmpzbpya. Dalton Trans 2007:3676-83. [PMID: 17700831 DOI: 10.1039/b704390b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA-cleavage properties of the two copper(II) complexes, [Cu(mbpzbpy)Br(2)](H(2)O)(2.5) (1) and [Cu(mpzbpya)Cl](CH(3)OH) (2), obtained from the ligands 6,6'-bis(3,5-dimethyl-N-pyrazolmethyl)-2,2'-bipyridine) (mbpzbpy) and 6'-(3,5-dimethyl-N-pyrazolmethyl)-2,2'-bipyridine-6-carboxylic acid) (Hmpzbpya), respectively, are reported. Upon coordination to Cu(II) chloride in methanol, one arm of the ligand mbpzbpy is hydrolyzed to form mpzbpya. Under the same experimental conditions, the reaction of mbpzbpy with CuBr(2) does not lead to ligand hydrolysis. The ligand mpzbpya is coordinated to a copper(ii) ion generating a CuN(3)OCl chromophore, resulting in a distorted square-pyramidal environment, whereas with the N(4) mbpzbpy ligand, the Cu(II) ion is four-coordinated in a distorted square planar geometry. Both complexes promote the oxidative DNA cleavage of phiX174 phage DNA in the absence of reductant. The oxidative nature of the DNA cleavage reaction has been confirmed by religation and cell-transformation experiments. Studies using standard radical scavengers suggest the involvement of hydroxyl radicals in the oxidative cleavage of DNA. Although both compounds do convert form I (supercoiled) DNA to form II (nicked, relaxed form), only complex 1 is able to produce small amounts of form III (linearized DNA). This observation may be explained either by the attack of the copper(ii) complexes to only one single strand of DNA, or by a single cleavage event. Statistical analysis of relative DNA quantities present after the treatment with both copper(ii) complexes supports a random mode of DNA cleavage.
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Affiliation(s)
- Palanisamy Uma Maheswari
- Leiden Institute of Chemistry, Leiden University, P.O. Box, 9502, 2300, RA Leiden, The Netherlands
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19
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Viso A, Fernández de la Pradilla R, García A, Flores A. α,β-Diamino Acids: Biological Significance and Synthetic Approaches. Chem Rev 2005; 105:3167-96. [PMID: 16092828 DOI: 10.1021/cr0406561] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alma Viso
- Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain.
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20
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Oliveira M, Couto M, Severino P, Foppa T, Martins G, Szpoganicz B, Peralta R, Neves A, Terenzi H. Nucleic acid cleavage by a Cu(II) polyaza macrocyclic complex. Polyhedron 2005. [DOI: 10.1016/j.poly.2004.12.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Caputo R, De Nisco M, Festa P, Guaragna A, Palumbo G, Pedatella S. Synthesis of 4-Deoxy-l-(and d-)hexoses from Chiral Noncarbohydrate Building Blocks. J Org Chem 2004; 69:7033-7. [PMID: 15471449 DOI: 10.1021/jo0493774] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
4-Deoxy-l-hexoses were synthesized starting from our previously reported reagent 1 and (R)-benzyl glycidyl ether, which led in few steps to a substituted dihydropyran 6. The stereocontrolled hydroxylation of the latter afforded the corresponding 4-deoxy-l-hexoses 7a, 9, and 11. The same procedure, starting from (S)-benzyl glycidyl ether, enabled the preparation of their d-series enantiomers.
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Affiliation(s)
- Romualdo Caputo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Via Cynthia, 4 80126 Naples, Italy
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Chang JC, Yang CH, Chou PY, Yang WH, Chou IC, Lu CT, Lin PH, Hou RCW, Jeng KCG, Cheng CC, Sheh L. DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs. Bioorg Med Chem 2004; 12:53-61. [PMID: 14697770 DOI: 10.1016/j.bmc.2003.10.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Three peptide amides, HPRK(Py)(4)HPRK-NH(2) (PyH-12), HPRK(Py)(3)HPRK-NH(2) (PyH-11) and HPRK(Py)(2)HPRK-NH(2) (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5'-32P-labeled 158-mer DNA duplex (Watson fragment) and to a 5'-32P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105-112 and 76-79, corresponding to the sequences 5'-GAGAAAAT-3' and 5'-CGGT-3', respectively. However, on the complementary Crick strand, only PyH-12 strongly discriminates the 5'-TTT-3' site around positions 108-110 whereas both PyH-11 and PyH-10 have moderate binding around positions 102-112 comprising the sequence 5'-ATTTTCTCCTT-3'. Possible bidentate and single interactions of the side-chain functions and alpha-amino protons of the peptides with DNA bases are discussed.
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Affiliation(s)
- Jung-Cheng Chang
- Department of Chemistry, Tunghai Christian University, 407, ROC, Taichung, Taiwan
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Kundu LM, Burgdorf LT, Kleiner O, Batschauer A, Carell T. Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity. Chembiochem 2002; 3:1053-60. [PMID: 12404629 DOI: 10.1002/1439-7633(20021104)3:11<1053::aid-cbic1053>3.0.co;2-#] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In order to gain deeper insight into the function and interplay of proteins in cells it is essential to develop methods that allow the profiling of protein function in real time, in solution, in cells, and in cell organelles. Here we report the development of a U-type oligonucleotide (molecular beacon) that contains a fluorophore and a quencher at the tips, and in addition a substrate analogue in the loop structure. This substrate analogue induces a hairpin cleavage in response to enzyme action, which is translated into a fluorescence signal. The molecular beacon developed here was used to characterize DNA-photolyase activity. These enzymes represent a challenge for analytical methods because of their low abundance in cells. The molecular beacon made it possible to measure the activity of purified class I and class II photolyases. Photolyase activity was even detectable in crude cell extracts.
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Affiliation(s)
- Lal Mohan Kundu
- Fachbereich Chemie, Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg, Germany
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Liang Y, Du F, Zhou BR, Zhou H, Zou GL, Wang CX, Qu SS. Thermodynamics and kinetics of the cleavage of DNA catalyzed by bleomycin A5. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:2851-9. [PMID: 12071947 DOI: 10.1046/j.1432-1033.2002.02948.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Microcalorimetry and UV-vis spectroscopy were used to conduct thermodynamic and kinetic investigations of the scission of calf thymus DNA catalyzed by bleomycin A5 (BLM-A5) in the presence of ferrous ion and oxygen. The molar reaction enthalpy for the cleavage, the Michaelis-Menten constant for calf thymus DNA and the turnover number of BLM-A5 were calculated by a novel thermokinetic method for an enzyme-catalyzed reaction to be -577 +/- 19 kJ.mol-1, 20.4 +/- 3.8 microm and 2.28 +/- 0.49 x 10-2 s-1, respectively, at 37.0 degrees C. This DNA cleavage was a largely exothermic reaction. The catalytic efficiency of BLM-A5 is of the same order of magnitude as that of lysozyme but several orders of magnitude lower than those of TaqI restriction endonuclease, NaeI endonuclease and BamHI endonuclease. By comparing the molar enthalpy change for the cleavage of calf thymus DNA induced by BLM-A5 with those for the scission of calf thymus DNA mediated by adriamycin and by (1,10-phenanthroline)-copper, it was found that BLM-A5 possessed the highest DNA cleavage efficiency among these DNA-damaging agents. These results suggest that BLM-A5 is not as efficient as a DNA-cleaving enzyme although the cleavage of DNA by BLM-A5 follows Michaelis-Menten kinetics. Binding of BLM-A5 to calf thymus DNA is driven by a favorable entropy increase with a less favorable enthalpy decrease, in line with a partial intercalation mode involved in BLM-catalyzed breakage of DNA.
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Affiliation(s)
- Yi Liang
- College of Life Sciences and College of Chemistry and Molecular Science, Wuhan University, China.
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Abstract
The specific structural features of stem-loop (hairpin) DNA constructs provide increased specificity of target recognition. Recently, several robust assays have been developed that exploit the potential of structurally constrained oligonucleotides to hybridize with their cognate targets. Here, I review new diagnostic approaches based on the formation of stem-loop DNA oligonucleotides: molecular beacon methodology, suppression PCR approaches and the use of hairpin probes in DNA microarrays. The advantages of these techniques over existing ones for sequence-specific DNA detection, amplification and manipulation are discussed.
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Affiliation(s)
- Natalia E Broude
- Center for Advanced Biotechnology and Dept of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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