1
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Liao X, Li M, Zou L. Target-induced activation of DNAzyme for highly sensitive colorimetric detection of bleomycin via DNA scission. RSC Adv 2022; 12:18296-18300. [PMID: 35799941 PMCID: PMC9215162 DOI: 10.1039/d2ra02816f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/16/2022] [Indexed: 12/01/2022] Open
Abstract
In this work, a label-free and sensitive colorimetric sensing strategy for the detection of bleomycin (BLM) was developed on the basis of BLM-mediated activation of G-quadruplex DNAzyme via DNA strand scission. A G-quadruplex based hairpin probe (G4HP) containing the scission site (5'-GT-3') of BLM at the loop region and guanine (G)-rich sequences at its 5'-end was employed in this protocol. In the presence of BLM, it may cleave the 5'-GT-3' site of the hairpin probe with Fe(ii) as a cofactor, releasing the G-tetrads DNA fragment, which may further bind hemin to form a catalytic G-quadruplex-hemin DNAzyme. The resultant G-quadruplex DNAzyme has notable peroxidase-like activity, which effectively catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid) (ABTS) by H2O2 to produce the blue-green-colored free-radical cation (ABTS·+). Therefore, the detection of BLM can be achieved by observing the color transition with the naked eye or measuring the absorbance at a wavelength of 420 nm using a UV-Vis spectrophotometer. Attributing to the specific BLM-induced DNA strand scission and the effective locking of G-tetrads in the stem of the G4HP, the colorimetric sensing strategy exhibits high sensitivity and selectivity for detection of BLM in human serum samples, which might hold great promise for BLM assay in biomedical and clinical research.
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Affiliation(s)
- Xiaofei Liao
- School of Pharmacy, Guangdong Pharmaceutical University Guangzhou 510006 PR China
| | - Mengyan Li
- School of Pharmacy, Guangdong Pharmaceutical University Guangzhou 510006 PR China
| | - Li Zou
- School of Pharmacy, Guangdong Pharmaceutical University Guangzhou 510006 PR China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University Guangzhou 510699 PR China
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2
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Zhu S, Liu L, Sun J, Shi F, Zhao XE. A ratiometric fluorescence assay for bleomycin based on dual-emissive chameleon DNA-templated silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119521. [PMID: 33581576 DOI: 10.1016/j.saa.2021.119521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/26/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
The authors design dual-emissive DNA-templated silver nanoclusters (DNA-AgNCs) for ratiometric fluorescence sensing bleomycin (BLM) for the first time. A hairpin probe containing two different C-rich DNA templates at two terminals is used to synthesize chameleon DNA-AgNCs, which possess two emission peaks when they are in close proximity. A strong emission is founded at 622 nm (λex = 570 nm) while a weak one is located at 572 nm (λex = 504 nm). Meanwhile, the loop of this probe contains the scission site (5'-GC-3') of BLM. The loop can be cleaved into two parts by BLM-Fe(II) complex, inducing the two DNA-AgNCs away from each other. The fluorescence intensity at 572 nm and 622 nm increases and decreases, respectively. Such chameleon DNA-AgNCs exhibit an obvious fluorescence discoloration from orange to yellow. Therefore, a sensitive ratiometric fluorescent strategy for BLM detection has been proposed with the detection limit of 67 pM. Finally, this ratiometric method is used to detect BLM in serum samples.
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Affiliation(s)
- Shuyun Zhu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Lingyuan Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Jing Sun
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Fengjin Shi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China.
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3
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Detection of bleomycin and its hydrolase by the cationic surfactant-doped liquid crystal-based sensing platform. Anal Chim Acta 2021; 1150:338247. [PMID: 33583545 DOI: 10.1016/j.aca.2021.338247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/07/2023]
Abstract
Bleomycin (BLM) is a broadly used antibiotic to treat different types of cancer. It can be hydrolyzed by bleomycin hydrolase (BLMH), which eventually influences the anti-tumor efficacy of BLM. Therefore, it is particularly important to detect BLM and BLMH. Herein, we demonstrated highly sensitive detection of BLM and BLMH by a simple and convenient liquid crystal (LC)-based sensing platform for the first time. 5CB (a nematic LC) doped with the cationic surfactant OTAB was working as the sensing platform. When the OTAB-laden 5CB interface was in contact with an aqueous solution of ssDNA, LCs displayed a bright image due to disruption of the arrangement of OTAB monolayers by ssDNA, indicating the planar orientation of LCs at the aqueous/LC interface. When BLM·Fe(II) and ssDNA were both present in the aqueous solution, ssDNA underwent irreversible cleavage, which prevented disruption of the arrangement of OTAB monolayers. Accordingly, LCs showed a dark image, suggesting the homeotropic orientation of LCs at the aqueous/LC interface. However, when BLM·Fe(II) was enzymatically hydrolyzed by BLMH, LCs remained the bright image. This approach showed high sensitivity for the detection of BLM and BLMH with the limits of detection of 0.2 nM and 0.3 ng/mL, respectively. Besides, the detection of BLM and BLMH was successfully achieved in human serum. This method has the advantages of high sensitivity, robust stability, simple operation, low cost, and easy detection through naked eyes, which makes it a potential candidate for applications in clinical analysis.
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4
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Liu L, Zhu S, Sun J, Xia M, Zhao X, Xu G. Ratiometric fluorescence detection of bleomycin based on proximity-dependent fluorescence conversion of DNA-templated silver nanoclusters. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.07.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Baig MMFA, Lai WF, Akhtar MF, Saleem A, Mikrani R, Farooq MA, Ahmed SA, Tahir A, Naveed M, Abbas M, Ansari MT. Targeting folate receptors (α1) to internalize the bleomycin loaded DNA-nanotubes into prostate cancer xenograft CWR22R cells. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Murray V, Chen JK, Yang D, Shen B. The genome-wide sequence specificity of DNA cleavage by bleomycin analogues in human cells. Bioorg Med Chem 2018; 26:4168-4178. [PMID: 30006142 DOI: 10.1016/j.bmc.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/26/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023]
Abstract
Bleomycin (BLM) is a cancer chemotherapeutic agent that cleaves cellular DNA at specific sequences. Using next-generation Illumina sequencing, the genome-wide sequence specificity of DNA cleavage by two BLM analogues, 6'-deoxy-BLM Z and zorbamycin (ZBM), was determined in human HeLa cells and compared with BLM. Over 200 million double-strand breaks were examined for each sample, and the 50,000 highest intensity cleavage sites were analysed. It was found that the DNA sequence specificity of the BLM analogues in human cells was different to BLM, especially at the cleavage site (position "0") and the "+1" position. In human cells, the 6'-deoxy-BLM Z had a preference for 5'-GTGY*MC (where * is the cleavage site, Y is C or T, M is A or C); it was 5'-GTGY*MCA for ZBM; and 5'-GTGT*AC for BLM. With cellular DNA, the highest ranked tetranucleotides were 5'-TGC*C and 5'-TGT*A for 6'-deoxy-BLM Z; 5'-TGC*C, 5'-TGT*A and 5'-TGC*A for ZBM; and 5'-TGT*A for BLM. In purified human genomic DNA, the DNA sequence preference was 5'-TGT*A for 6'-deoxy-BLM, 5'-RTGY*AYR (where R is G or A) for ZBM, and 5'-TGT*A for BLM. Thus, the sequence specificity of the BLM analogue, 6'-deoxy-BLM Z, was similar to BLM in purified human DNA, while ZBM was different.
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Affiliation(s)
- Vincent Murray
- 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
| | - Dong Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ben Shen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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7
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Murray V, Chen JK, Chung LH. The Interaction of the Metallo-Glycopeptide Anti-Tumour Drug Bleomycin with DNA. Int J Mol Sci 2018; 19:E1372. [PMID: 29734689 PMCID: PMC5983701 DOI: 10.3390/ijms19051372] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/17/2022] Open
Abstract
The cancer chemotherapeutic drug, bleomycin, is clinically used to treat several neoplasms including testicular and ovarian cancers. Bleomycin is a metallo-glycopeptide antibiotic that requires a transition metal ion, usually Fe(II), for activity. In this review, the properties of bleomycin are examined, especially the interaction of bleomycin with DNA. A Fe(II)-bleomycin complex is capable of DNA cleavage and this process is thought to be the major determinant for the cytotoxicity of bleomycin. The DNA sequence specificity of bleomycin cleavage is found to at 5′-GT* and 5′-GC* dinucleotides (where * indicates the cleaved nucleotide). Using next-generation DNA sequencing, over 200 million double-strand breaks were analysed, and an expanded bleomycin sequence specificity was found to be 5′-RTGT*AY (where R is G or A and Y is T or C) in cellular DNA and 5′-TGT*AT in purified DNA. The different environment of cellular DNA compared to purified DNA was proposed to be responsible for the difference. A number of bleomycin analogues have been examined and their interaction with DNA is also discussed. In particular, the production of bleomycin analogues via genetic manipulation of the modular non-ribosomal peptide synthetases and polyketide synthases in the bleomycin gene cluster is reviewed. The prospects for the synthesis of bleomycin analogues with increased effectiveness as cancer chemotherapeutic agents is also explored.
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Affiliation(s)
- Vincent Murray
- 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.
| | - Long H Chung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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8
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Abstract
Covering: July 2012 to June 2015. Previous review: Nat. Prod. Rep., 2013, 30, 869-915The structurally diverse imidazole-, oxazole-, and thiazole-containing secondary metabolites are widely distributed in terrestrial and marine environments, and exhibit extensive pharmacological activities. In this review the latest progress involving the isolation, biological activities, and chemical and biogenetic synthesis studies on these natural products has been summarized.
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Affiliation(s)
- Zhong Jin
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China. and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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9
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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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10
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Pei H, Zheng Y, Kong R, Xia L, Qu F. Niche nanoparticle-based FRET assay for bleomycin detection via DNA scission. Biosens Bioelectron 2016; 85:76-82. [DOI: 10.1016/j.bios.2016.04.085] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 12/11/2022]
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11
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Yu Z, Paul R, Bhattacharya C, Bozeman TC, Rishel MJ, Hecht SM. Structural features facilitating tumor cell targeting and internalization by bleomycin and its disaccharide. Biochemistry 2015; 54:3100-9. [PMID: 25905565 PMCID: PMC4440614 DOI: 10.1021/acs.biochem.5b00277] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have shown previously that the bleomycin (BLM) carbohydrate moiety can recapitulate the tumor cell targeting effects of the entire BLM molecule, that BLM itself is modular in nature consisting of a DNA-cleaving aglycone which is delivered selectively to the interior of tumor cells by its carbohydrate moiety, and that there are disaccharides structurally related to the BLM disaccharide which are more efficient than the natural disaccharide at tumor cell targeting/uptake. Because BLM sugars can deliver molecular cargoes selectively to tumor cells, and thus potentially form the basis for a novel antitumor strategy, it seemed important to consider additional structural features capable of affecting the efficiency of tumor cell recognition and delivery. These included the effects of sugar polyvalency and net charge (at physiological pH) on tumor cell recognition, internalization, and trafficking. Since these parameters have been shown to affect cell surface recognition, internalization, and distribution in other contexts, this study has sought to define the effects of these structural features on tumor cell recognition by bleomycin and its disaccharide. We demonstrate that both can have a significant effect on tumor cell binding/internalization, and present data which suggests that the metal ions normally bound by bleomycin following clinical administration may significantly contribute to the efficiency of tumor cell uptake, in addition to their characterized function in DNA cleavage. A BLM disaccharide-Cy5** conjugate incorporating the positively charged dipeptide d-Lys-d-Lys was found to associate with both the mitochondria and the nuclear envelope of DU145 cells, suggesting possible cellular targets for BLM disaccharide-cytotoxin conjugates.
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Affiliation(s)
- Zhiqiang Yu
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Trevor C Bozeman
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael J Rishel
- ‡GE Global Research, 1 Research Circle, Niskayuna, New York 12309, United States
| | - Sidney M Hecht
- †Center for Bioenergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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12
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Tang C, Paul A, Alam MP, Roy B, Wilson WD, Hecht SM. A short DNA sequence confers strong bleomycin binding to hairpin DNAs. J Am Chem Soc 2014; 136:13715-26. [PMID: 25188011 PMCID: PMC4183661 DOI: 10.1021/ja505733u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Bleomycins A5 and B2 were used to study the
structural features in hairpin DNAs conducive to strong BLM–DNA
interaction. Two members of a 10-hairpin DNA library previously found
to bind most tightly to these BLMs were subsequently noted to share
the sequence 5′-ACGC (complementary strand sequence 5′-GCGT).
Each underwent double-strand cleavage at five sites within, or near,
an eight base pair region of the DNA duplex which had been randomized
to create the original library. A new hairpin DNA library was selected
based on affinity for immobilized Fe(III)·BLM A5.
Two of the 30 newly identified DNAs also contained the sequence 5′-ACGC/5′-GCGT.
These DNAs bound to the Fe(II)·BLMs more tightly than any DNA
characterized previously. Surface plasmon resonance confirmed tight
Fe(III)·BLM B2 binding and gave an excellent fit for
a 1:1 binding model, implying the absence of significant secondary
binding sites. Fe(II)·BLM A5 was used to assess sites
of double-strand DNA cleavage. Both hairpin DNAs underwent double-strand
cleavage at five sites within or near the original randomized eight
base region. For DNA 12, four of the five double-strand
cleavages involved independent single-strand cleavage reactions; DNA 13 underwent double-strand DNA cleavage by independent single-strand
cleavages at all five sites. DNA 14, which bound Fe·BLM
poorly, was converted to a strong binder (DNA 15) by
insertion of the sequence 5′-ACGC/5′-GCGT. These findings
reinforce the idea that tighter DNA binding by Fe·BLM leads to
increased double-strand cleavage by a novel mechanism and identify
a specific DNA motif conducive to strong BLM binding and cleavage.
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Affiliation(s)
- Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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13
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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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14
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Li Q, van der Wijst MG, Kazemier HG, Rots MG, Roelfes G. Efficient nuclear DNA cleavage in human cancer cells by synthetic bleomycin mimics. ACS Chem Biol 2014; 9:1044-51. [PMID: 24527883 DOI: 10.1021/cb500057n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Iron complexes of N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)-methylamine (N4Py) have proven to be excellent synthetic mimics of the Bleomycins (BLMs), which are a family of natural antibiotics used clinically in the treatment of certain cancers. However, most investigations of DNA cleavage activity of these and related metal complexes were carried out in cell-free systems using plasmid DNA as substrate. The present study evaluated nuclear DNA cleavage activity and cell cytotoxicity of BLM and its synthetic mimics based on the ligand N4Py. The N4Py-based reagents induced nuclear DNA cleavage in living cells as efficiently as BLM and Fe(II)-BLM. Treatment of 2 cancer cell lines and 1 noncancerous cell line indicated improved cytotoxicity of N4Py when compared to BLM. Moreover, some level of selectivity was observed for N4Py on cancerous versus noncancerous cells. It was demonstrated that N4Py-based reagents and BLM induce cell death via different mechanistic pathways. BLM was shown to induce cell cycle arrest, ultimately resulting in mitotic catastrophe. In contrast, N4Py-based reagents were shown to induce apoptosis effectively. To the best of our knowledge, the present study is the first demonstration of efficient nuclear DNA cleavage activity of a synthetic BLM mimic within cells. The results presented here show that it is possible to design synthetic bioinorganic model complexes that are at least as active as the parent natural product and thereby are potentially interesting alternatives for BLM to induce antitumor activity.
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Affiliation(s)
- Qian Li
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Monique G.P. van der Wijst
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Hinke G. Kazemier
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Marianne G. Rots
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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15
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Murray V, Chen JK, Galea AM. The anti-tumor drug bleomycin preferentially cleaves at the transcription start sites of actively transcribed genes in human cells. Cell Mol Life Sci 2014; 71:1505-12. [PMID: 23982755 PMCID: PMC11113418 DOI: 10.1007/s00018-013-1456-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 08/06/2013] [Accepted: 08/12/2013] [Indexed: 11/26/2022]
Abstract
The genome-wide pattern of DNA cleavage at transcription start sites (TSSs) for the anti-tumor drug bleomycin was examined in human HeLa cells using next-generation DNA sequencing. It was found that actively transcribed genes were preferentially cleaved compared with non-transcribed genes. The 143,600 identified human TSSs were split into non-transcribed genes (82,596) and transcribed genes (61,004) for HeLa cells. These transcribed genes were further split into quintiles of 12,201 genes comprising the top 20, 20-40, 40-60, 60-80, and 80-100 % of expressed genes. The bleomycin cleavage pattern at highly transcribed gene TSSs was greatly enhanced compared with purified DNA and non-transcribed gene TSSs. The top 20 and 20-40 % quintiles had a very similar enhanced cleavage pattern, the 40-60 % quintile was intermediate, while the 60-80 and 80-100 % quintiles were close to the non-transcribed and purified DNA profiles. The pattern of bleomycin enhanced cleavage had peaks that were approximately 200 bp apart, and this indicated that bleomycin was identifying the presence of phased nucleosomes at TSSs. Hence bleomycin can be utilized to detect chromatin structures that are present at actively transcribed genes. In this study, for the first time, the pattern of DNA damage by a clinically utilized cancer chemotherapeutic agent was performed on a human genome-wide scale at the nucleotide level.
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Affiliation(s)
- Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia,
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16
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Roy B, Hecht SM. Hairpin DNA sequences bound strongly by bleomycin exhibit enhanced double-strand cleavage. J Am Chem Soc 2014; 136:4382-93. [PMID: 24548300 PMCID: PMC3988684 DOI: 10.1021/ja500414a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Clinically
used bleomycin A5 has been employed in a
study of double-strand cleavage of a library of 10 hairpin DNAs originally
selected on the basis of their strong binding to bleomycin. Each of
the DNAs underwent double-strand cleavage at more than one site, and
all of the cleavage sites were within, or in close proximity to, an
eight-base-pair region of the duplex that had been randomized to create
the original library. A total of 31 double-strand cleavage sites were
identified on the 10 DNAs, and 14 of these sites were found to represent
coupled cleavage sites, that is, events in which one of the two strands
was always cleaved first, followed by the associated site on the opposite
strand. Most of these coupled sites underwent cleavage by a mechanism
described previously by the Povirk laboratory and afforded cleavage
patterns entirely analogous to those reported. However, at least one
coupled cleavage event was noted that did not conform to the pattern
of those described previously. More surprisingly, 17 double-strand
cleavages were found not to result from coupled double-strand cleavage,
and we posit that these cleavages resulted from a new mechanism not
previously described. Enhanced double-strand cleavages at these sites
appear to be a consequence of the dynamic nature of the interaction
of Fe·BLM A5 with the strongly bound hairpin DNAs.
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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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17
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Segerman ZJ, Roy B, Hecht SM. Characterization of bleomycin-mediated cleavage of a hairpin DNA library. Biochemistry 2013; 52:5315-27. [PMID: 23834496 DOI: 10.1021/bi400779r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal-free BLM. The ability of Fe(II)·BLM to affect cleavage on both the 3' and 5' arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe·BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5'-AT-3' dinucleotide sequence. This dinucleotide sequence and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates were apparent when examining the library of 10 hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe·BLM A5. The existence of multiple sites of cleavage on both the 3' and 5' arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method and gave results consistent with earlier reports of double-strand DNA cleavage but with a sequence selectivity that was different from those reported previously.
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Affiliation(s)
- Zachary J Segerman
- Center for BioEnergetics, Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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