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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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Luo H, Liang Y, Zhang H, Liu Y, Xiao Q, Huang S. Comparison on binding interactions of quercetin and its metal complexes with calf thymus DNA by spectroscopic techniques and viscosity measurement. J Mol Recognit 2021; 34:e2933. [PMID: 34432328 DOI: 10.1002/jmr.2933] [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: 07/16/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/08/2022]
Abstract
Quercetin (Qu) and its metal complexes have received great attention during the last years, due to their good antioxidant, antibacterial, and anticancer activities. In this contribution, binding interactions of Qu and Qu-metal complexes with calf thymus DNA (ctDNA) were investigated and compared systematically by using spectroscopic techniques and viscosity measurement. UV-vis absorption spectra of ctDNA-compound systems showed obvious hypochromic effect. Relative viscosity and melting temperature of ctDNA increased after the addition of Qu and Qu-metal complexes, and the change tendency is Qu-Cr(III) > Qu-Mn(II) > Qu-Zn(II) > Qu-Cu(II) > Qu. Fluorescence competition experiments show that hydrogen bonds and van der Waals interaction play an important role in the intercalative binding of Qu and Qu-metal complexes with ctDNA. Qu and Qu-metal complexes could unwind the right-handed B-form helicity of ctDNA and further affect its base pair stacking. Space steric hindrance might be responsible for the differences in the intercalative binding between ctDNA and different Qu-metal complexes. These results provide new information for the molecular understanding of binding interactions of Qu-metal complexes with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Yu Liang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Huiying Zhang
- College of Chemistry and Biological Engineering, Hechi University, Hechi, China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China.,State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry and Chemical Engineering, Tiangong University, Tianjin, China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
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3
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He YQ, Gao Y, Gu HW, Meng XZ, Yi HC, Chen Y, Sun WY. Target-induced activation of DNAzyme for sensitive detection of bleomycin by using a simple MOF-modified electrode. Biosens Bioelectron 2021; 178:113034. [DOI: 10.1016/j.bios.2021.113034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/28/2020] [Accepted: 01/20/2021] [Indexed: 12/26/2022]
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4
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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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5
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Dual-mode visible light-induced aptasensing platforms for bleomycin detection based on CdS-In 2S 3 heterojunction. Biosens Bioelectron 2019; 145:111712. [PMID: 31563064 DOI: 10.1016/j.bios.2019.111712] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 11/22/2022]
Abstract
CdS-In2S3 heterojunction with enhanced photoelectrochemical (PEC) performance was synthesized to construct dual-mode visible light-induced biosensors for highly sensitive and selective detection of bleomycin (BLM). Due to improved absorption in the visible region and suppressed recombination of electron-hole pairs in the heterojunction, CdS-In2S3 composite exhibited enhanced photocurrent response under visible light illumination. Using CdS-In2S3 as photoactive materials and BLM-binding aptamer as recognition element, a PEC aptasensor displaying a declined photocurrent response to BLM was facilely constructed, which was linear to BLM concentration in the range of 5.0-250 nM. On the other hand, the CdS-In2S3 photoanode was employed to construct a photofuel cell (PFC). In such a PFC, the oxidation of water on CdS-In2S3 photoanode under visible light illumination and the reduction of oxygen on Pt cathode led to the generation of electricity. When BLM-binding aptamer was immobilized on CdS-In2S3 photoanode, the output power of the PFC was inversely proportional to the logarithm of BLM concentration from 10 to 250 nM, offering a visible light-induced self-powered sensing platform for BLM detection. Both of the proposed sensors showed high selectivity, good reproducibility and high stability. They were successfully applied to the determination of BLM in human serum samples.
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6
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Follett SE, Murray SA, Ingersoll AD, Reilly TM, Lehmann TE. Structural changes of Zn(II)bleomycin complexes when bound to DNA hairpins containing the 5'-GT-3' and 5'-GC-3' binding sites studied through NMR spectroscopy. MAGNETOCHEMISTRY 2018; 4. [PMID: 30464999 DOI: 10.3390/magnetochemistry4010004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bleomycins are antitumor antibiotics that can chelate a metal center and cause site-specific DNA cleavage at 5'-Gpyrimidine-3' regions of DNA. These antibiotics are successful in the treatment of various cancers, but are known to cause pulmonary fibrosis to patients under bleomycin regimes. Substantial research has resulted in the development of over 300 bleomycin analogs, aiming to improve the therapeutic index of the drug. Previous studies have proposed that the lung toxicity caused by bleomycin is related to the C-terminal regions of these drugs, which have been shown to closely interact with DNA in metal-bleomycin-DNA complexes. Some of the research studying metallo-bleomycin-DNA interactions have suggested three different binding modes of the metal form of the drug to DNA, including total and/or partial intercalation, and minor groove binding. However, there is still lack of consensus regarding this matter, and solid conclusions on the subject have not yet been established. Previously we investigated the diverse levels of disruption caused to DNA hairpins containing 5'-GC-3' and 5'-GT-3' binding sites, which are consequence of the binding of bleomycins with different C-termini. The results of these investigation indicate that both the DNA-binding site and the bleomycin C-termini have an impact on the final conformations of drug and target. The present study focuses on the structural alterations exhibited by Zn(II)bleomycin-A2, -B2, -A5 and Zn(II)peplomycin upon binding to DNA hairpins containing 5'-GC-3' and 5'-GT-3' binding sites. Evidence that each Zn(II)bleomycin is structurally affected depending on both its C-terminus and the DNA-binding site present in the hairpin is provided.
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Affiliation(s)
- Shelby E Follett
- Department of Chemistry, University of Wyoming, Laramie, WY, United Sates of America
| | - Sally A Murray
- Department of Chemistry, University of Wyoming, Laramie, WY, United Sates of America
| | - Azure D Ingersoll
- Department of Chemistry, University of Wyoming, Laramie, WY, United Sates of America
| | - Teresa M Reilly
- Department of Chemical Engineering, University of Wyoming, Laramie, WY, United Sates of America
| | - Teresa E Lehmann
- Department of Chemistry, University of Wyoming, Laramie, WY, United Sates of America
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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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Li H, Chang J, Hou T, Li F. HRP-Mimicking DNAzyme-Catalyzed in Situ Generation of Polyaniline To Assist Signal Amplification for Ultrasensitive Surface Plasmon Resonance Biosensing. Anal Chem 2016; 89:673-680. [DOI: 10.1021/acs.analchem.6b02988] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Haiyin Li
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Jiafu Chang
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Ting Hou
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Feng Li
- College of Chemistry and
Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
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9
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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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10
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Huang S, Liang Y, Huang C, Su W, Lei X, Liu Y, Xiao Q. Systematical investigation of binding interaction between novel ruthenium(II) arene complex with curcumin analogs and ctDNA. LUMINESCENCE 2016; 31:1384-1394. [DOI: 10.1002/bio.3119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/17/2016] [Accepted: 01/24/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Shan Huang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Yu Liang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
| | - Chusheng Huang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Wei Su
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Xiaolin Lei
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
| | - Yi Liu
- State Key Laboratory of Virology; Wuhan University; Wuhan 430072 People's Republic of China
| | - Qi Xiao
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
- State Key Laboratory of Virology; Wuhan University; Wuhan 430072 People's Republic of China
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11
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Kundu N, Roy A, Banik D, Sarkar N. Unveiling the Mode of Interaction of Berberine Alkaloid in Different Supramolecular Confined Environments: Interplay of Surface Charge between Nano-Confined Charged Layer and DNA. J Phys Chem B 2016; 120:1106-20. [PMID: 26756221 DOI: 10.1021/acs.jpcb.5b10121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this Article, we demonstrate a detailed characterization of binding interaction of berberine chloride (BBCl) with calf-thymus DNA (CT-DNA) in buffer solution as well as in two differently charged reverse micelles (RMs). The photophyscial properties of this alkaloid have been modulated within these microheterogeneous bioassemblies. The mode of binding of this alkaloid with DNA is of debate to date. However, fluorescence spectroscopic measurements, circular dichroism (CD) measurement, and temperature-dependent study unambiguously establish that BBCl partially intercalates into the DNA base pairs. The nonplanarity imposed by partial saturation in their structure causes the nonclassical types of intercalation into DNA. Besides the intercalation, electrostatic interactions also play a significant role in the binding between BBCl and DNA. DNA structure turns into a condensed form after encapsulation into RMs, which is followed by the CD spectra and microscopy study. The probe location and dynamics in the nanopool of the RMs depended on the electrostatic interaction between the charged surfactants and cationic berberine. The structural alteration of CT-DNA from B form to condensed form and the interplay of surface charge between RMs and DNA determine the interaction between the alkaloid and DNA in RMs. Time-resolved study and fluorescence anisotropy measurements successfully provide the binding interaction of BBCl in the nanopool of the RMs in the absence and in the presence of DNA. This study motivates us to judge further the potential applicability of this alkaloid in other biological systems or other biomimicking organized assemblies.
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Affiliation(s)
- Niloy Kundu
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Arpita Roy
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Debasis Banik
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
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12
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Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA–Protein Interaction. Biochemistry 2015; 54:7457-69. [DOI: 10.1021/acs.biochem.5b01085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Poulami Talukder
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Petro Yakovchuk
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michelle M. Spiering
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad P. Alam
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Manikandadas M. Madathil
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Stephen J. Benkovic
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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13
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Li ZJ, Hou Y, Qin DA, Jin ZM, Hu ML. Two half-sandwiched ruthenium (II) compounds containing 5-fluorouracil derivatives: synthesis and study of DNA intercalation. PLoS One 2015; 10:e0120211. [PMID: 25789618 PMCID: PMC4366203 DOI: 10.1371/journal.pone.0120211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
Two novel coordination compounds of half-sandwiched ruthenium(II) containing 2-(5-fluorouracil)-yl-N-(pyridyl)-acetamide were synthesized, and their intercalation binding modes with calf thymus DNA were revealed by hyperchromism of ultraviolet-visible spectroscopy; the binding constants were determined according to a Langmuir adsorption equation that was deduced on the base of careful cyclic voltammetry measurements. The two compounds exhibited DNA intercalation binding activities with the binding constants of 1.13×106 M-1 and 5.35 ×105 M-1, respectively.
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Affiliation(s)
- Zhao-Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, China
| | - Yong Hou
- Institute of Biotechnology and Nucleic Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Da-An Qin
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, China
| | - Zhi-Min Jin
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- * E-mail: (ZMJ); (MLH)
| | - Mao-Lin Hu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, China
- * E-mail: (ZMJ); (MLH)
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14
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Huang S, Zhu F, Xiao Q, Liang Y, Zhou Q, Su W. Thermodynamic investigation of the interaction between the [(η6-p-cymene)Ru(benzaldehyde-N4-phenylthiosemicarbazone)Cl]Cl anticancer drug and ctDNA: multispectroscopic and electrochemical studies. RSC Adv 2015. [DOI: 10.1039/c5ra03979g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The interaction between the [(η6-p-cymene)Ru(benzaldehyde-N4-phenylthiosemicarbazone)Cl]Cl anticancer drug and ctDNA was systematically investigated by multispectroscopic and electrochemical studies.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Fawei Zhu
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Qi Xiao
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Yu Liang
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Quan Zhou
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Wei Su
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
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15
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Kong RM, Sun NN, Qu F, Wu H, Wang H, You J. Sensitive fluorescence “turn-on” detection of bleomycin based on a superquenched perylene–DNA complex. RSC Adv 2015. [DOI: 10.1039/c5ra18227a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We introduced a superquenched perylene–DNA complex based method for sensitive fluorescence “turn-on” detection of bleomycin.
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Affiliation(s)
- Rong-Mei Kong
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Ni-Na Sun
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Fengli Qu
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Haiyan Wu
- Tianjin Hexi District Environmental Monitoring Station
- Tianjin 300201
- P. R. China
| | - Hua Wang
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
| | - Jinmao You
- The Key Laboratory of Life-Organic Analysis
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu Shandong 273165
- P. R. China
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16
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Tyagi N, Chakraborty A, Singh UP, Roy P, Ghosh K. Mononuclear iron(iii) complexes of tridentate ligands with efficient nuclease activity and studies of their cytotoxicity. Org Biomol Chem 2015; 13:11445-58. [DOI: 10.1039/c5ob01623a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mono- and bis-chelated iron(iii) complexes derived from phenolato-based tridentate ligands have been synthesised and characterized. These complexes show electrostatic DNA interactions and efficient DNA cleavage via OH˙ radicals, and induce cytotoxicity in MCF7 cell lines.
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Affiliation(s)
- Nidhi Tyagi
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Ajanta Chakraborty
- Department of Biochemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Udai P. Singh
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Partha Roy
- Department of Biochemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Kaushik Ghosh
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
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17
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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
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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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18
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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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19
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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
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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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20
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Microbial natural products: molecular blueprints for antitumor drugs. J Ind Microbiol Biotechnol 2013; 40:1181-210. [PMID: 23999966 DOI: 10.1007/s10295-013-1331-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.
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21
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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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22
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Gao F, Lei J, Ju H. Ultrasensitive fluorescence detection of bleomycin via exonuclease III-aided DNA recycling amplification. Chem Commun (Camb) 2013; 49:7561-3. [DOI: 10.1039/c3cc44275f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Bozeman TC, Nanjunda R, Tang C, Liu Y, Segerman ZJ, Zaleski PA, Wilson WD, Hecht SM. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA. J Am Chem Soc 2012; 134:17842-5. [PMID: 23072568 PMCID: PMC3840713 DOI: 10.1021/ja306233e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.
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Affiliation(s)
- Trevor C. Bozeman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zachary J. Segerman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul A. Zaleski
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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24
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Li XL, Hu YJ, Wang H, Yu BQ, Yue HL. Molecular spectroscopy evidence of berberine binding to DNA: comparative binding and thermodynamic profile of intercalation. Biomacromolecules 2012; 13:873-80. [PMID: 22316074 DOI: 10.1021/bm2017959] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Berberine (BH) is an important traditional medicinal herb endowed with diverse pharmacological and biological activities. In this work, the binding characteristics and molecular mechanism of the interaction between the BH and herring sperm DNA were explored by UV-vis absorbance and fluorescence spectroscopy. In the mechanism discussion, fluorescence quenching, absorption spectra, competition experiment, and iodide quenching experiment studies hinted at an intercalative mode of binding for BH to DNA. Fluorescence studies revealed the binding constant (K) of BH-DNA was ∼10(4) L·mol(-1). The effects of temperature, chemical denaturants, thermal denaturation, and pH were studied to show the factors of the interaction and provided further support for the intercalative binding mode. The results of thermodynamic parameters ΔG, ΔH, and ΔS at different temperatures indicated that the hydrogen bonds and van der Waals interactions played major roles in the reaction, and the effect of ionic strength indicated that electrostatic attraction between the BH and DNA was also a component of the interaction.
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Affiliation(s)
- Xiao-Ling Li
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, PR China
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25
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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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26
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Hara K, Kasahara E, Takahashi N, Konishi M, Inoue J, Jikumaru M, Kubo S, Okamura H, Sato E, Inoue M. Mitochondria Determine the Efficacy of Anticancer Agents that Interact with DNA but Not the Cytoskeleton. J Pharmacol Exp Ther 2011; 337:838-45. [DOI: 10.1124/jpet.111.179473] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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27
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28
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Liu M, Zhao H, Chen S, Yu H, Quan X. Salt-controlled assembly of stacked-graphene for capturing fluorescence and its application in chemical genotoxicity screening. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12772a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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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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30
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Iron(III) Schiff base complexes of arginine and lysine as netropsin mimics showing AT-selective DNA binding and photonuclease activity. J Inorg Biochem 2010; 104:477-84. [DOI: 10.1016/j.jinorgbio.2010.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 12/14/2009] [Accepted: 01/04/2010] [Indexed: 11/20/2022]
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31
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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32
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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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