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Analyte-driven self-assembly of graphene oxide sheets onto hydroxycamptothecin-functionalized upconversion nanoparticles for the determination of type I topoisomerases in cell extracts. Anal Bioanal Chem 2018; 410:6761-6769. [PMID: 30019082 DOI: 10.1007/s00216-018-1234-0] [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: 04/20/2018] [Revised: 05/28/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022]
Abstract
Type I topoisomerases (TOPOI), a potential diagnostic biomarker and a target for chemotherapeutic agents, play essential roles in DNA replication, transcription, chromosome segregation, and recombination. It is essential to develop analytical methods for accurate detection of TOPOI in biological fluids for early diagnosis of diseases. Here we show an assay for TOPOI on the basis of the target-induced self-assembly of graphene oxide (GO) sheets onto hydroxycamptothecin-functionalized upconversion nanoparticles (HCPT-UCNPs). The dipole-dipole coupling of HCPT-UCNPs (donor) and GO (acceptor) regulated by TOPOI enables Förster resonance energy transfer between the donor and the acceptor. Integration of minimal autofluorescence and highly specific affinity into the developed nanosensor allows reliable detection of TOPOI in the nanomolar range with the detection limit of 0.29 nM. The detection of TOPOI in breast cancer cells with recoveries from 96.3 to 103.7% shows the availability of the proposed assay in complicated samples. Graphical abstract ᅟ.
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2
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Wang Z, Ouyang H, Tesauro C, Ottaviani A, He Y, Fiorani P, Xie H, Desideri A, Fu Z. Real-time analysis of cleavage and religation activity of human topoisomerase 1 based on ternary fluorescence resonance energy transfer DNA substrate. Arch Biochem Biophys 2018; 643:1-6. [PMID: 29458004 DOI: 10.1016/j.abb.2018.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 12/22/2022]
Abstract
Human topoisomerase 1B is a ubiquitous and essential enzyme involved in relaxing the topological state of supercoiled DNA to allow the progression of fundamental DNA metabolism. Its enzymatic catalytic cycle consists of cleavage and religation reaction. A ternary fluorescence resonance energy transfer biosensor based on a suicide DNA substrate conjugated with three fluorophores has been developed to monitor both cleavage and religation Topoisomerase I catalytic function. The presence of fluorophores does not alter the specificity of the enzyme catalysis on the DNA substrate. The enzyme-mediated reaction can be tracked in real-time by simple fluorescence measurement, avoiding the use of risky radioactive substrate labeling and time-consuming denaturing gel electrophoresis. The method is applied to monitor the perturbation brought by single mutation on the cleavage or religation reaction and to screen the effect of the camptothecin anticancer drug monitoring the energy transfer decrease during religation reaction. Pathological mutations usually affect only the cleavage or the religation reaction and the proposed approach represent a fast protocol for assessing chemotherapeutic drug efficacy and analyzing mutant's properties.
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Affiliation(s)
- Zhenxing Wang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China; Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hui Ouyang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Yong He
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome 00133, Italy
| | - Hui Xie
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
| | - Zhifeng Fu
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China.
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3
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. NANOSCALE 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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4
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Jepsen ML, Harmsen C, Godbole AA, Nagaraja V, Knudsen BR, Ho YP. Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor. NANOSCALE 2016; 8:358-364. [PMID: 26616006 DOI: 10.1039/c5nr06326d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.
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Affiliation(s)
- Morten Leth Jepsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Charlotte Harmsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Birgitta R Knudsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
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5
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Zuccaro L, Tesauro C, Kurkina T, Fiorani P, Yu HK, Knudsen BR, Kern K, Desideri A, Balasubramanian K. Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene. ACS NANO 2015; 9:11166-76. [PMID: 26445172 DOI: 10.1021/acsnano.5b05709] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.
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Affiliation(s)
- Laura Zuccaro
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
- Department of Molecular Biology & Genetics, Aarhus University , DK-8000 Aarhus, Denmark
| | - Tetiana Kurkina
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
- Institute of Translational Pharmacology , National Research Council CNR, I-00133 Rome, Italy
| | - Hak Ki Yu
- Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Birgitta R Knudsen
- Department of Molecular Biology & Genetics, Aarhus University , DK-8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , DK-8000 Aarhus, Denmark
| | - Klaus Kern
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
- Institut de Physique de la Matière Condensée, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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Kristoffersen EL, Jørgensen LA, Franch O, Etzerodt M, Frøhlich R, Bjergbæk L, Stougaard M, Ho YP, Knudsen BR. Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations. NANOSCALE 2015; 7:9825-9834. [PMID: 25963854 DOI: 10.1039/c5nr01474c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.
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7
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Abstract
Recent progress in quantum dot (QD) based chemo- and biosensors for various applications is summarized.
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Affiliation(s)
- Lei Cui
- College of Science
- School of Environment and Architecture
- University of Shanghai for Science and Technology
- Shanghai 200293
- PR China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology (ECUST)
- Shanghai 200237
- PR China
| | - Guo-Rong Chen
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology (ECUST)
- Shanghai 200237
- PR China
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