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Shi H, Hu X, Zhang J, Li W, Xu J, Hu B, Ma L, Lou L. Soil minerals and organic matters affect ARGs transformation by changing the morphology of plasmid and bacterial responses. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131727. [PMID: 37257383 DOI: 10.1016/j.jhazmat.2023.131727] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
Soil environment is a vital place for the occurrence and spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Extracellular DNA-mediated transformation is an important pathway for ARGs horizontal transfer and widely exists in soil environment. However, little information is available on how common soil components affect ARGs transformation. Here, three minerals (quartz, kaolinite, and montmorillonite) and three organic matters (humic acid, biochar, and soot) were selected as typical soil components. A small amount in suspension (0.2 g/L) of most soil components (except for quartz and montmorillonite) promoted transformant production by 1.1-1.6 folds. For a high amount (8 g/L), biochar significantly promoted transformant production to 1.5 times, kaolinite exerted a 30 % inhibitory effect. From the perspective of plasmid, biochar induced a higher proportion of supercoiled plasmid than kaolinite; more dissolved organic matter and metal ions facilitated plasmid aggregation under the near-neutral pH, thus promoted transformation. As for the influence of materials on recipient, although biochar and kaolinite both increased reactive oxygen species (ROS) level and membrane permeability, biochar up-regulated more ROS related genes, resulting in intracellular ROS production and up-regulating the expression of carbohydrate metabolism and transformation related genes. While kaolinite inhibited transformation mainly by causing nutrient deficiency.
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Affiliation(s)
- Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jin Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Wenxuan Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jiang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China.
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Mandal B, Mondal HK, Das S. In situ reactivity of electrochemically generated semiquinone on Emodin and its CuII/MnII complexes with pyrimidine based nucleic acid bases and calf thymus DNA: Insight into free radical induced cytotoxicity of anthracyclines. Biochem Biophys Res Commun 2019; 515:505-509. [DOI: 10.1016/j.bbrc.2019.05.140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 11/26/2022]
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Electrochemical, spectroscopic and theoretical monitoring of anthracyclines' interactions with DNA and ascorbic acid by adopting two routes: Cancer cell line studies. PLoS One 2018; 13:e0205764. [PMID: 30372448 PMCID: PMC6205586 DOI: 10.1371/journal.pone.0205764] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/01/2018] [Indexed: 01/08/2023] Open
Abstract
Pharmacodynamic interactions of three anthracycline antibiotics namely doxorubicin (DXH), epirubicin (EpiDXH) and daunorubicin (DNR) with DNA in the absence and presence of ascorbic acid (AA) as natural additive were monitored under physiological conditions (pH = 7.4, 4.7 and T = 309.5K). Route–1 (Anthracycline–AA–DNA) and Route–2 (Anthracycline–DNA–AA) were adopted to see the interactional behavior by cyclic voltammetry (CV) and UV-visible spectroscopy. In comparison to Route–2; voltammetric and spectral responses as well as binding constant (Kb) and Gibb’s free energy change (ΔG) values revealed strongest and more favorable interaction of anthracycline–AA complex with DNA via Route–1. Kb, s (binding site sizes) and ΔG evaluated from experimental (CV, UV-Vis) and theoretical (molecular docking) findings showed enhanced binding strength of tertiary complexes as compared to binary drug–DNA complexes. The results were found comparatively better at pH 7.4. Consistency was observed in binding parameters evaluated from experimental and theoretical techniques. Diffusion coefficients (Do) and heterogeneous electron transfer rate constant (ks,h) confirmed the formation of complexes via slow diffusion kinetics. Percent cell inhibition (%Cinh) of anthracyclines for non-small cell cancer cell lines (NSCCLs) H-1299 and H-157 were evaluated higher in the presence of AA which further complimented experimental and theoretical results.
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Mukherjee Chatterjee S, Jain CK, Singha S, Das P, Roychoudhury S, Majumder HK, Das S. Activity of Co II-Quinalizarin: A Novel Analogue of Anthracycline-Based Anticancer Agents Targets Human DNA Topoisomerase, Whereas Quinalizarin Itself Acts via Formation of Semiquinone on Acute Lymphoblastic Leukemia MOLT-4 and HCT 116 Cells. ACS OMEGA 2018; 3:10255-10266. [PMID: 31459155 PMCID: PMC6644896 DOI: 10.1021/acsomega.8b00706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/23/2018] [Indexed: 05/13/2023]
Abstract
Quinalizarin (THAQ), a hydroxy-9,10-anthraquinone analogue of the family of anthracycline anticancer drugs and an inhibitor of protein kinase, was observed for its anticancer activity. Because apart from showing anticancer activity, anthracyclines and their analogues also show cardiotoxic side effects, believed to be addressed through metal complex formation; an effort was made to realize this by preparing a CoII complex of THAQ. The aim of this study was to find out if complex formation leads to a decrease in the generation of intermediates that are responsible for toxic side effects. However, because this also meant that efficacy on cancer cells would be compromised, studies were undertaken on two cancer cell lines, namely, acute lymphoblastic leukemia (ALL) MOLT-4 and HCT116 cells. The complex decreases the flow of electrons from NADH to molecular oxygen (O2) in the presence of NADH dehydrogenase forming less semiquinone than THAQ. It showed increased affinity toward DNA with binding constant values remaining constant over the physiological pH range unlike THAQ (for which decrease in binding constant values with increase in pH was observed). The complex is probably a human DNA topoisomerase I and human DNA topoisomerase II poison acting by stabilizing the covalent topoisomerase-cleaved DNA adduct, a phenomenon not observed for THAQ. Activity of the compounds on cancer cells suggests that THAQ was more effective on ALL MOLT-4 cells, whereas the complex performed better on HCT116 cells. Results suggest that the formation of semiquinone probably dominates the action because of THAQ, whereas the performance of the complex is attributed to increased DNA binding, inhibition of topoisomerase, and so forth. Inspite of a decrease in the generation of superoxide by the complex, it did not hamper efficacy on either cell line, probably compensated by improved DNA binding and inhibition of topoisomerase enzymes which are positive attributes of complex formation. A decrease in superoxide formation suggests that the complex could be less cardiotoxic, thus increasing its therapeutic index.
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Affiliation(s)
| | - Chetan Kumar Jain
- Cancer Biology & Inflammatory
Disorder Division and Infectious Diseases and Immunology
Division, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Soumen Singha
- Department
of Chemistry (Inorganic Section) and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Piyal Das
- Department
of Chemistry (Inorganic Section) and Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Susanta Roychoudhury
- Cancer Biology & Inflammatory
Disorder Division and Infectious Diseases and Immunology
Division, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Hemanta Kumar Majumder
- Cancer Biology & Inflammatory
Disorder Division and Infectious Diseases and Immunology
Division, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Saurabh Das
- Department
of Chemistry (Inorganic Section) and Department of Physics, Jadavpur University, Kolkata 700032, India
- E-mail: , . Phone: +91 33
24572148, +91 33 8902087756. Fax: +91
33 24146223 (S.D.)
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Construction of the DEF-ring system of nogalamycin and menogaril via an efficient Suzuki-Miyaura reaction. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.04.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Banerjee T, Banerjee S, Sett S, Ghosh S, Rakshit T, Mukhopadhyay R. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy. PLoS One 2016; 11:e0154666. [PMID: 27183010 PMCID: PMC4868319 DOI: 10.1371/journal.pone.0154666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.
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Affiliation(s)
- T. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - T. Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - R. Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
- * E-mail:
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Mandal B, Singha S, Dey SK, Mazumdar S, Mondal TK, Karmakar P, Kumar S, Das S. Synthesis, crystal structure from PXRD of a MnII(purp)2complex, interaction with DNA at different temperatures and pH and lack of stimulated ROS formation by the complex. RSC Adv 2016. [DOI: 10.1039/c6ra09387f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
MnII(purpurin)2crystal structure done from PXRD is the second report on hydroxy-9,10-anthraquinone with a 3d-transition metal. DNA binding of complex is better and ROS generation less than purpurin. Complex maintains biological activity of purpurin.
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Affiliation(s)
- Bitapi Mandal
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
| | - Soumen Singha
- Department of Physics
- Jadavpur University
- Kolkata-700032
- India
| | | | - Swagata Mazumdar
- Department of Life Science and Biotechnology
- Jadavpur University
- Kolkata-700032
- India
| | - Tapan Kumar Mondal
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology
- Jadavpur University
- Kolkata-700032
- India
| | - Sanjay Kumar
- Department of Physics
- Jadavpur University
- Kolkata-700032
- India
| | - Saurabh Das
- Department of Chemistry (Inorganic Section)
- Jadavpur University
- Kolkata-700032
- India
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Mohamadi M, Afzali D, Esmaeili-Mahani S, Mostafavi A, Torkzadeh-Mahani M. Spectroscopic and electrochemical studies of the interaction between oleuropein, the major bio-phenol in olives, and salmon sperm DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 148:260-265. [PMID: 25909900 DOI: 10.1016/j.saa.2015.03.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/28/2015] [Accepted: 03/31/2015] [Indexed: 06/04/2023]
Abstract
Interaction of oleuropein, the major bio-phenol in olive leaf and fruit, with salmon sperm double-stranded DNA was investigated by employing electronic absorption titrations, fluorescence quenching spectroscopy, competitive fluorescence spectroscopy, thermal denaturation and voltammetric studies. Titration of oleuropein with the DNA caused a hypochromism accompanied with a red shift indicating an intercalative mode of interaction. Binding constant of 1.4×10(4) M(-1) was obtained for this interaction. From the curves of fluorescence titration of oleuropein with the DNA, binding constant and binding sites were calculated to be 8.61×10(3) M(-1) and 1.05, respectively. Competitive studies with ethidium bromide (a well-known DNA intercalator) showed that the bio-phenol could take the place of ethidium bromide in the DNA intercalation sites. The interaction of oleuropein with DNA was also studied electrochemically. In the presence of the DNA, the anodic and cathodic peak currents of oleuropein decreased accompanied with increases in peak-to-peak potential separation and formal potential, indicating the intercalation of oleuropein into the DNA double helix. Moreover, melting temperature of the DNA was found to increase in the presence of oleuropein, indicating the stabilization of the DNA double helix due to an intercalative interaction.
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Affiliation(s)
- Maryam Mohamadi
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Chemistry, Payame Noor University (PNU), 19395-4697 Tehran, Iran.
| | - Daryoush Afzali
- Department of Environment, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Saeed Esmaeili-Mahani
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Mostafavi
- Department of Chemistry, Payame Noor University (PNU), 19395-4697 Tehran, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
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Mukherjee A, Boujedaini N, Khuda-Bukhsh AR. Homeopathic Thuja 30C ameliorates benzo(a)pyrene-induced DNA damage, stress and viability of perfused lung cells of mice in vitro. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2014; 11:397-404. [PMID: 24299603 DOI: 10.3736/jintegrmed2013054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To examine if the ultra-highly diluted homeopathic remedy Thuja 30C can ameliorate benzo(a)pyrene (BaP)-induced DNA damage, stress and viability of perfused lung cells of Swiss albino mice in vitro. METHODS Perfused normal lung cells from mice were cultured in 5% Roswell Park Memorial Institute medium and exposed to BaP, a potent carcinogen, at the half maximal inhibitory concentration dose (2.2 μmol/L) for 24 h. Thereafter, the intoxicated cells were either treated with Thuja 30C (used against tumor or cancer) or its vehicle media, succussed alcohol 30C. Relevant parameters of study involving reactive oxygen species (ROS) accumulation, total glutathione (GSH) content, and generations of heat shock protein (hsp)-90 were measured; the cell viability and other test parameters were measured after treatment with either Thuja 30C or its vehicle media. Circular dichroism spectroscopy was performed to examine if Thuja 30C directly interacted with calf thymus DNA as target. For ascertaining if DNA damaged by BaP could be partially repaired and restituted by the remedy, 4',6-diamidino-2-phenylindole staining was performed. RESULTS Thuja 30C increased cell viability of BaP-intoxicated cells significantly, as compared to drug-untreated or drug-vehicle control. A minimal dose of Thuja 30C significantly inhibited BaP-induced stress level, by down-regulating ROS and hsp-90, and increasing GSH content. Thuja 30C itself had no DNA-damaging effect, and no direct drug-DNA interaction. However, it showed quite striking ability to repair DNA damage caused by BaP. CONCLUSION Thuja 30C ameliorates BaP-induced toxicity, stress and DNA damage in perfused lung cells of mice and it apparently has no effect on normal lung cells.
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Affiliation(s)
- Avinaba Mukherjee
- Cytogenetics and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani-741235, West Bengal, India; E-mail: ;
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Verebová V, Adamcik J, Danko P, Podhradský D, Miškovský P, Staničová J. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA. Biochem Biophys Res Commun 2014; 444:50-5. [PMID: 24434150 DOI: 10.1016/j.bbrc.2014.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022]
Abstract
The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.
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Affiliation(s)
- Valéria Verebová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia
| | - Jozef Adamcik
- Food and Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Patrik Danko
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Dušan Podhradský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Pavol Miškovský
- Department of Biophysics, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Jana Staničová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia.
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Alonso-Sarduy L, Longo G, Dietler G, Kasas S. Time-lapse AFM imaging of DNA conformational changes induced by daunorubicin. NANO LETTERS 2013; 13:5679-5684. [PMID: 24125039 DOI: 10.1021/nl403361f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cancer is a major health issue that absorbs the attention of a large part of the biomedical research. Intercalating agents bind to DNA molecules and can inhibit their synthesis and transcription; thus, they are increasingly used as drugs to fight cancer. In this work, we show how atomic force microscopy in liquid can characterize, through time-lapse imaging, the dynamical influence of intercalating agents on the supercoiling of DNA, improving our understanding of the drug's effect.
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Affiliation(s)
- Livan Alonso-Sarduy
- Laboratoire de Physique de la Matière Vivante, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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Nanjunda R, Musetti C, Kumar A, Ismail MA, Farahat AA, Wang S, Sissi C, Palumbo M, Boykin DW, Wilson WD. Heterocyclic dications as a new class of telomeric G-quadruplex targeting agents. Curr Pharm Des 2012; 18:1934-47. [PMID: 22380518 DOI: 10.2174/138161212799958422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 11/22/2022]
Abstract
Small molecules that can induce and stabilize G-quadruplex DNA structures represent a novel approach for anti-cancer and anti-parasitic therapy and extensive efforts have been directed towards discovering lead compounds that are capable of stabilizing quadruplexes. The purpose of this study is to explore conformational modifications in a series of heterocyclic dications to discover structural motifs that can selectively bind and stabilize specific G-quadruplexes, such as those present in the human telomere. The G-quadruplex has various potential recognition sites for small molecules; however, the primary interaction site of most of these ligands is the terminal tetrads. Similar to duplex-DNA groove recognition, quadruplex groove recognition by small molecules offers the potential for enhanced selectivity that can be developed into a viable therapeutic strategy. The compounds investigated were selected based on preliminary studies with DB832, a bifuryl-phenyl diamidine with a unique telomere interaction. This compound provides a paradigm that can help in understanding the optimum compound-DNA interactions that lead to quadruplex groove recognition. DNA recognition by the DB832 derivatives was investigated by biophysical experiments such as thermal melting, circular dichroism, mass spectrometry and NMR. Biological studies were also performed to complement the biophysical data. The results suggest a complex binding mechanism which involves the recognition of grooves for some ligands as well as stacking at the terminal tetrads of the human telomeric G-quadruplex for most of the ligands. These molecules represent an excellent starting point for further SAR analysis for diverse modes of quadruplex recognition and subsequent structure optimization for drug development.
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Affiliation(s)
- Rupesh Nanjunda
- Dept. of Chemistry, Georgia State University, Atlanta GA 30303, USA
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Banerjee T, Dubey P, Mukhopadhyay R. DNA compaction by mononuclear platinum cancer drug cisplatin and the trisplatinum anticancer agent BBR3464: Differences and similarities. Biochimie 2012; 94:494-502. [DOI: 10.1016/j.biochi.2011.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/24/2011] [Indexed: 10/17/2022]
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Ghosh A, Bera S, Ray S, Banerjee T, Ray M. Methylglyoxal induces mitochondria-dependent apoptosis in sarcoma. BIOCHEMISTRY (MOSCOW) 2011; 76:1164-71. [DOI: 10.1134/s0006297911100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mukherjee S, Das P, Das S. Exploration of small hydroxy-9,10-anthraquinones as anthracycline analogues: physicochemical characteristics and DNA binding for comparison. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1928] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Piyal Das
- Department of Chemistry; Jadavpur University; Kolkata; 700032; India
| | - Saurabh Das
- Department of Chemistry; Jadavpur University; Kolkata; 700032; India
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Time-resolved chloroquine-induced relaxation of supercoiled plasmid DNA. Anal Bioanal Chem 2011; 402:373-80. [PMID: 21766217 DOI: 10.1007/s00216-011-5213-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/17/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
Herein, we report on the in vitro change of DNA conformation of plasmids bound to a 3-aminopropyl-modified mica surface and monitoring the events by atomic force microscopy (AFM) imaging under near physiological conditions. In our study, we used an intercalating drug, chloroquine, which is known to decrease the twist of the double helix and thus altered the conformation of the whole DNA. During our experiments, a chloroquine solution was added while imaging a few highly condensed plasmid nanoparticles in solution. AFM images recorded after the drug addition clearly show a time-resolved relaxation of these bionanoparticles into a mixture of loose DNA strands.
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Guin PS, Das S, Mandal PC. Interaction of 1,4-Dihydroxy–9,10-Anthraquinone with Calf Thymus DNA: A Comparison with Anthracycline Anticancer Drugs. J SOLUTION CHEM 2011. [DOI: 10.1007/s10953-011-9654-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Das P, Guin PS, Mandal PC, Paul M, Paul S, Das S. Cyclic voltammetric studies of 1,2,4-trihydroxy-9,10-anthraquinone, its interaction with calf thymus DNA and anti-leukemic activity on MOLT-4 cell lines: a comparison with anthracycline anticancer drugs. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1827] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Xiao Z, Cao L, Zhu D, Lu Z. Atomic force microscopy studies on circular DNA structural changes by vincristine and aspirin. Methods Mol Biol 2011; 736:425-435. [PMID: 21660742 DOI: 10.1007/978-1-61779-105-5_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this chapter, we have presented materials and methods to study the interaction between DNA and small molecule drugs by AFM. The detailed AFM imaging of the circular DNA after incubation with -various concentrations of vincristine and aspirin have been demonstrated. The immobilization of DNA fragments on mica surface as well as the force between tip and sample plays an important role for successful imaging of DNA-drug complexes. How to quantitatively describe the conformations and structures of circular DNA molecules and their changes is also introduced. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.
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Affiliation(s)
- Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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Dhar S, Rana DK, Sarkar A, Mandal TK, Bhattacharya SC. Fluorescence resonance energy transfer from serum albumins to 1-anthracene sulphonate entrapped in reverse micellar nanocavities. Colloids Surf A Physicochem Eng Asp 2010. [DOI: 10.1016/j.colsurfa.2010.07.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang J, Coffey PD, Swann MJ, Yang F, Lu JR, Yang X. Optical extinction combined with phase measurements for probing DNA-small-molecule interactions using an evanescent waveguide biosensor. Anal Chem 2010; 82:5455-62. [PMID: 20524624 DOI: 10.1021/ac9027164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the use of both optical extinction and phase measurements for probing the interactions between DNA and small molecules by dual polarization interferometry. On binding to DNA at the interface, mitoxantrone (MTX) and methylene blue (MB) induced reversible concentration-dependent optical extinction due to light absorption, which clearly revealed the association and dissociation of small molecules with DNA in real time. The binding constants of MTX-DNA and MB-DNA determined from the masses derived from optical extinction are 1.8 x 10(5) and 4.2 x 10(4) M(-1), respectively, and shown to be buffer salt concentration-dependent. Apart from optical extinction, phase measurements reflected the overall change of the interaction; namely, a combined result of the binding of small molecules and any changes in DNA structure. The masses derived from phase could be very different from those derived from optical extinction. The structural changes detected by phase measurements showed a contraction and densification of DNA upon intercalation by MTX or MB. The combination of optical extinction and phase measurements allows a detailed understanding of the interaction process.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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Banerjee T, Dubey P, Mukhopadhyay R. Compacting effect of BBR3464, a new-generation trisplatinum anticancer agent, on DNA. Biochimie 2010; 92:846-51. [DOI: 10.1016/j.biochi.2010.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/18/2010] [Indexed: 11/26/2022]
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Wang J, Xu X, Zhang Z, Yang F, Yang X. Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry. Anal Chem 2009; 81:4914-21. [DOI: 10.1021/ac900591k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
| | - Xiaowen Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
| | - Zhanxia Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
| | - Fan Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
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Cai HH, Yang PH, Chen J, Liang ZH, Chen Q, Cai J. Visual characterization and quantitative measurement of artemisinin-induced DNA breakage. Electrochim Acta 2009. [DOI: 10.1016/j.electacta.2009.01.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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