1
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Petersen KV, Tesauro C, Hede MS, Pages C, Marcussen LB, Keller JG, Bugge M, Holm K, Bjergbæk L, Stougaard M, Wejse C, Knudsen BR. Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts. SENSORS (BASEL, SWITZERLAND) 2022; 22:7763. [PMID: 36298113 PMCID: PMC9608553 DOI: 10.3390/s22207763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The method is based on rolling circle amplification of circular DNA products that can only be formed upon restriction digestion of specially designed DNA substrates. By combining the activity of the target restriction endonuclease with the highly specific Cre recombinase to generate DNA circles, we demonstrate specific detection of selected restriction endonuclease activities even in crude cell extracts. This is, to our knowledge, the first example of a sensor system that allows activity measurements of restriction endonucleases in crude samples. The presented sensor system may prove valuable for future characterization of bacteria species or strains based on their expression of restriction endonucleases as well as for quantification of restriction endonuclease activities directly in extracts from recombinant cells.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
| | | | | | - Camilla Pages
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Josephine Geertsen Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Bugge
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Lotte Bjergbæk
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Christian Wejse
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
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2
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Petersen KV, Selas A, Hymøller KM, Mizielinski K, Thorsager M, Stougaard M, Alonso C, Palacios F, Pérez-Pertejo Y, Reguera RM, Balaña-Fouce R, Knudsen BR, Tesauro C. Simple and Fast DNA Based Sensor System for Screening of Small-Molecule Compounds Targeting Eukaryotic Topoisomerase 1. Pharmaceutics 2021; 13:1255. [PMID: 34452216 PMCID: PMC8401307 DOI: 10.3390/pharmaceutics13081255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Eukaryotic topoisomerase 1 is a potential target of anti-parasitic and anti-cancer drugs. Parasites require topoisomerase 1 activity for survival and, consequently, compounds that inhibit topoisomerase 1 activity may be of interest. All effective topoisomerase 1 drugs with anti-cancer activity act by inhibiting the ligation reaction of the enzyme. Screening for topoisomerase 1 targeting drugs, therefore, should involve the possibility of dissecting which step of topoisomerase 1 activity is affected. Methods: Here we present a novel DNA-based assay that allows for screening of the effect of small-molecule compounds targeting the binding/cleavage or the ligation steps of topoisomerase 1 catalysis. This novel assay is based on the detection of a rolling circle amplification product generated from a DNA circle resulting from topoisomerase 1 activity. Results: We show that the binding/cleavage and ligation reactions of topoisomerase 1 can be investigated separately in the presented assay termed REEAD (C|L) and demonstrate that the assay can be used to investigate, which of the individual steps of topoisomerase 1 catalysis are affected by small-molecule compounds. The assay is gel-free and the results can be detected by a simple colorimetric readout method using silver-on-gold precipitation rendering large equipment unnecessary. Conclusion: REEAD (C|L) allows for easy and quantitative investigations of topoisomerase 1 targeting compounds and can be performed in non-specialized laboratories.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark;
| | - Asier Selas
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Kirstine Mejlstrup Hymøller
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
| | | | - Maria Thorsager
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark;
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Concepcion Alonso
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Francisco Palacios
- Department of Organic Chemistry, University of Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (A.S.); (C.A.); (F.P.)
| | - Yolanda Pérez-Pertejo
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Rosa M. Reguera
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Rafael Balaña-Fouce
- Department of Biomedical Sciences, University of Leon (ULE), 24071 Leon, Spain; (Y.P.-P.); (R.M.R.); (R.B.-F.)
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; (K.V.P.); (K.M.H.); (B.R.K.)
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
| | - Cinzia Tesauro
- VPCIR Biosciences ApS., 8000 Aarhus, Denmark; (K.M.); (M.T.)
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3
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A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors. SENSORS 2021; 21:s21144832. [PMID: 34300575 PMCID: PMC8309759 DOI: 10.3390/s21144832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.
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4
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Different Camptothecin Sensitivities in Subpopulations of Colon Cancer Cells Correlate with Expression of Different Phospho-Isoforms of Topoisomerase I with Different Activities. Cancers (Basel) 2020; 12:cancers12051240. [PMID: 32423158 PMCID: PMC7281652 DOI: 10.3390/cancers12051240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 12/25/2022] Open
Abstract
The heterogeneity of tumor cells and the potential existence of rare cells with reduced chemotherapeutic response is expected to play a pivotal role in the development of drug resistant cancers. Herein, we utilized the colon cancer cell lines, Caco2 and DLD1, to investigate heterogeneity of topoisomerase 1 (TOP1) activity in different cell subpopulations, and the consequences for the chemotherapeutic response towards the TOP1 targeting drug, camptothecin. The cell lines consisted of two subpopulations: one (the stem-cell-like cells) divided asymmetrically, was camptothecin resistant, had a differently phosphorylated TOP1 and a lower Casein Kinase II (CKII) activity than the camptothecin sensitive non-stem-cell-like cells. The tumor suppressor p14ARF had a different effect in the two cell subpopulations. In the stem-cell-like cells, p14ARF suppressed TOP1 activity and downregulation of this factor increased the sensitivity towards camptothecin. It had the opposite effect in non-stem-cell-like cells. Since it is only the stem-cell-like cells that have tumorigenic activity our results point towards new considerations for future cancer therapy. Moreover, the data underscore the importance of considering cell-to-cell variations in the analysis of molecular processes in cell lines.
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Franch O, Han X, Marcussen LB, Givskov A, Andersen MB, Godbole AA, Harmsen C, Nørskov-Lauritsen N, Thomsen J, Pedersen FS, Wang Y, Shi D, Wejse C, Pødenphant L, Nagaraja V, Bertl J, Stougaard M, Ho YP, Hede MS, Labouriau R, Knudsen BR. A new DNA sensor system for specific and quantitative detection of mycobacteria. NANOSCALE 2019; 11:587-597. [PMID: 30556557 DOI: 10.1039/c8nr07850e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.
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Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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6
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Hede MS, Fjelstrup S, Lötsch F, Zoleko RM, Klicpera A, Groger M, Mischlinger J, Endame L, Veletzky L, Neher R, Simonsen AKW, Petersen E, Mombo-Ngoma G, Stougaard M, Ho YP, Labouriau R, Ramharter M, Knudsen BR. Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker. Sci Rep 2018. [PMID: 29515150 PMCID: PMC5841400 DOI: 10.1038/s41598-018-22378-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite. Subsequent rolling circle amplification of the generated DNA circle in the presence of biotin conjugated deoxynucleotides resulted in long tandem repeat products that was visualized colorimetrically upon binding of horse radish peroxidase (HRP) and addition of 3,3′,5,5′-Tetramethylbenzidine that was converted to a blue colored product by HRP. The assay was directly quantitative, specific for Plasmodium parasites, and allowed detection of Plasmodium infection in a single drop of saliva from 35 out of 35 infected individuals tested. The results could be determined directly by the naked eye and documented by quantifying the color intensity using a standard paper scanner.
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Affiliation(s)
| | - Søren Fjelstrup
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
| | - Felix Lötsch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Anna Klicpera
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Johannes Mischlinger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Lilian Endame
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Luzia Veletzky
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Ronja Neher
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | | | - Eskild Petersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Infectious Diseases, The Royal Hospital, Muscat, Oman
| | - Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Magnus Stougaard
- Department of Clinical Medicine, University of Aarhus, Aarhus, Denmark
| | - Yi-Ping Ho
- Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | | | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark.
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7
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Kjeldsen E, Nielsen CJF, Roy A, Tesauro C, Jakobsen AK, Stougaard M, Knudsen BR. Characterization of Camptothecin-induced Genomic Changes in the Camptothecin-resistant T-ALL-derived Cell Line CPT-K5. Cancer Genomics Proteomics 2018; 15:91-114. [PMID: 29496689 PMCID: PMC5892604 DOI: 10.21873/cgp.20068] [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: 11/17/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022] Open
Abstract
Acquisition of resistance to topoisomerase I (TOP1)-targeting camptothecin (CPT) derivatives is a major clinical problem. Little is known about the underlying chromosomal and genomic mechanisms. We characterized the CPT-K5 cell line expressing mutant CPT-resistant TOP1 and its parental T-cell derived acute lymphoblastic leukemia CPT-sensitive RPMI-8402 cell line by karyotyping and molecular genetic methods, including subtractive oligo-based array comparative genomic hybridization (soaCGH) analysis. Karyotyping revealed that CPT-K5 cells had acquired additional structural aberrations and a reduced modal chromosomal number compared to RPMI-8402. soaCGH analysis identified vast copy number alterations and >200 unbalanced DNA breakpoints distributed unevenly across the chromosomal complement in CPT-K5. In addition, the short tandem repeat alleles were found to be highly different between CPT-K5 and its parental cell line. We identified copy number alterations affecting genes important for maintaining genome integrity and reducing CPT-induced DNA damage. We show for the first time that short tandem repeats are targets for TOP1 cleavage, that can be differentially stimulated by CPT.
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Affiliation(s)
- Eigil Kjeldsen
- Cancer Cytogenetics Section, HemoDiagnostic Laboratory, Aarhus University Hospital, Aarhus, Denmark
| | - Christine J F Nielsen
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | - Amit Roy
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
| | | | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C.F. Møllers Allé, Aarhus University, Aarhus, Denmark
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8
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Kristoffersen EL, Givskov A, Jørgensen LA, Jensen PW, W Byl JA, Osheroff N, Andersen AH, Stougaard M, Ho YP, Knudsen BR. Interlinked DNA nano-circles for measuring topoisomerase II activity at the level of single decatenation events. Nucleic Acids Res 2017; 45:7855-7869. [PMID: 28541438 PMCID: PMC5570003 DOI: 10.1093/nar/gkx480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/22/2017] [Indexed: 12/23/2022] Open
Abstract
DNA nano-structures present appealing new means for monitoring different molecules. Here, we demonstrate the assembly and utilization of a surface-attached double-stranded DNA catenane composed of two intact interlinked DNA nano-circles for specific and sensitive measurements of the life essential topoisomerase II (Topo II) enzyme activity. Topo II activity was detected via the numeric release of DNA nano-circles, which were visualized at the single-molecule level in a fluorescence microscope upon isothermal amplification and fluorescence labeling. The transition of each enzymatic reaction to a micrometer sized labeled product enabled quantitative detection of Topo II activity at the single decatenation event level rendering activity measurements in extracts from as few as five cells possible. Topo II activity is a suggested predictive marker in cancer therapy and, consequently, the described highly sensitive monitoring of Topo II activity may add considerably to the toolbox of individualized medicine where decisions are based on very sparse samples.
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Affiliation(s)
- Emil L Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
| | - Asger Givskov
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Line A Jørgensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Pia W Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Anni H Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark.,Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center - iNANO, Aarhus University, 8000 Aarhus C, Denmark
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9
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Keller JG, Tesauro C, Coletta A, Graversen AD, Ho YP, Kristensen P, Stougaard M, Knudsen BR. On-slide detection of enzymatic activities in selected single cells. NANOSCALE 2017; 9:13546-13553. [PMID: 28872165 DOI: 10.1039/c7nr05125e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
With increasing recognition of the importance in addressing cell-to-cell heterogeneity for the understanding of complex biological systems, there is a growing need for assays capable of single cell analyses. In the current study, we describe the measurement of human topoisomerase I activity in single CD44 positive Caco2 cells specifically captured from a mixed population on glass slides, which were dual functionalized with anti-CD44-antibodies and specific DNA primers. On-slide lysis of captured CD44 positive cells, resulted in the release of human topoisomerase I, allowing the enzyme to circularize a specific linear DNA substrate added to the slides. The generated circles hybridized to the anchored DNA primers and acted as templates for a solid support rolling circle amplification reaction leading to the generation of long tandem repeat products that were detected at the single molecule level in a fluorescent microscope upon hybridization of fluorescent labelled probes. The on-slide detection system was demonstrated to be directly quantitative and specific towards CD44 positive cells. Moreover, it allowed reproducible detection of human topoisomerase I activity in single cells.
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Affiliation(s)
- Josephine Geertsen Keller
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg. 1131, Aarhus University, 8000 Aarhus C, Denmark.
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10
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Optimized Detection of Plasmodium falciparum Topoisomerase I Enzyme Activity in a Complex Biological Sample by the Use of Molecular Beacons. SENSORS 2016; 16:s16111916. [PMID: 27854277 PMCID: PMC5134575 DOI: 10.3390/s16111916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/31/2016] [Accepted: 11/04/2016] [Indexed: 12/16/2022]
Abstract
The so-called Rolling Circle Amplification allows for amplification of circular DNA structures in a manner that can be detected in real-time using nucleotide-based molecular beacons that unfold upon recognition of the DNA product, which is being produced during the amplification process. The unfolding of the molecular beacons results in a fluorescence increase as the Rolling Circle Amplification proceeds. This can be measured in a fluorometer. In the current study, we have investigated the possibility of using two different molecular beacons to detect two distinct Rolling Circle Amplification reactions proceeding simultaneously and in the same reaction tube by measurement of fluorescence over time. We demonstrate the application of this fluorometric readout method, for automated and specific detection of the activity of the type IB topoisomerase from the malaria parasite Plasmodium falciparum in the presence of human cell extract containing the related topoisomerase I from humans. The obtained results point towards a future use of the presented assay setup for malaria diagnostics or drug screening purposes. In longer terms the method may be applied more broadly for real-time sensing of various Rolling Circle Amplification reactions.
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11
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Jensen NF, Agama K, Roy A, Smith DH, Pfister TD, Rømer MU, Zhang HL, Doroshow JH, Knudsen BR, Stenvang J, Brünner N, Pommier Y. Characterization of DNA topoisomerase I in three SN-38 resistant human colon cancer cell lines reveals a new pair of resistance-associated mutations. J Exp Clin Cancer Res 2016; 35:56. [PMID: 27029323 PMCID: PMC4815242 DOI: 10.1186/s13046-016-0335-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/23/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND DNA topoisomerase I (Top1) is a DNA unwinding protein and the specific target of the camptothecin class of chemotherapeutic drugs. One of these, irinotecan, acting through its active metabolite SN-38, is used in the treatment of metastatic colorectal cancer. However, resistance to irinotecan represents a major clinical problem. Since molecular alterations in Top1 may result in resistance to irinotecan, we characterized Top1 in three human colon cancer cell lines with acquired resistance to SN-38. METHODS Three SN-38 resistant (20-67 fold increased resistance) cell lines were generated and compared to wild-type parental cells with regards to: TOP1 gene copy number and gene sequence, Top1 expression (mRNA and protein), Top1 enzymatic activity in the absence and presence of drug, and Top1-DNA cleavage complexes in drug treated cells. TOP1 mutations were validated by PCR using mutant specific primers. Furthermore, cross-resistance to two indenoisoquinoline Top1-targeting drugs (NSC 725776 and NSC 743400) and two Top2-targeting drugs (epirubicin and etoposide) was investigated. RESULTS Two of three SN-38 resistant cell lines carried TOP1 gene copy number aberrations: A TOP1 gene copy gain and a loss of chromosome 20, respectively. One resistant cell line harbored a pair of yet unreported TOP1 mutations (R364K and G717R) in close proximity to the drug binding site. Mutant TOP1 was expressed at a markedly higher level than wild-type TOP1. None or very small reductions were observed in Top1 expression or Top1 activity in the absence of drug. In all three SN-38 resistant cell lines Top1 activity was maintained in the presence of high concentrations of SN-38. None or only partial cross-resistance were observed for etoposide and epirubicin, respectively. SN-38 resistant cells with wild-type TOP1 remained sensitive to NSC 743400, while cells with mutant TOP1 was fully cross-resistant to both indenoisoquinolines. Top1-DNA cleavage complex formation following drug treatment supported the other findings. CONCLUSIONS This study adds to the growing knowledge about resistance mechanisms for Top1-targeting chemotherapeutic drugs. Importantly, two yet unreported TOP1 mutations were identified, and it was underlined that cross-resistance to the new indenoisoquinoline drugs depends on the specific underlying molecular mechanism of resistance to SN-38.
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Affiliation(s)
- Niels Frank Jensen
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Keli Agama
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
| | - Amit Roy
- />Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
- />Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali 844102 India
| | - David Hersi Smith
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- />Dako Denmark A/S, R&D, Produktionsvej 42, DK-2600 Glostrup, Denmark
| | - Thomas D. Pfister
- />Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Maria Unni Rømer
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- />Department for Clinical Physiology and Nuclear Medicine, Frederiksberg Hospital, Nordre Fasanvej 57, DK-2000 Frederiksberg C, Denmark
| | - Hong-Liang Zhang
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
| | - James H. Doroshow
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
- />Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Birgitta R. Knudsen
- />Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Jan Stenvang
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Nils Brünner
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yves Pommier
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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Juul S, Obliosca JM, Liu C, Liu YL, Chen YA, Imphean DM, Knudsen BR, Ho YP, Leong KW, Yeh HC. NanoCluster Beacons as reporter probes in rolling circle enhanced enzyme activity detection. NANOSCALE 2015; 7:8332-7. [PMID: 25901841 PMCID: PMC4441223 DOI: 10.1039/c5nr01705j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
As a newly developed assay for the detection of endogenous enzyme activity at the single-catalytic-event level, Rolling Circle Enhanced Enzyme Activity Detection (REEAD) has been used to measure enzyme activity in both single human cells and malaria-causing parasites, Plasmodium sp. Current REEAD assays rely on organic dye-tagged linear DNA probes to report the rolling circle amplification products (RCPs), the cost of which may hinder the widespread use of REEAD. Here we show that a new class of activatable probes, NanoCluster Beacons (NCBs), can simplify the REEAD assays. Easily prepared without any need for purification and capable of large fluorescence enhancement upon hybridization, NCBs are cost-effective and sensitive. Compared to conventional fluorescent probes, NCBs are also more photostable. As demonstrated in reporting the human topoisomerases I (hTopI) cleavage-ligation reaction, the proposed NCBs suggest a read-out format attractive for future REEAD-based diagnostics.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Judy M. Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Cong Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Darren M. Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
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14
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Roy A, Tesauro C, Frøhlich R, Hede MS, Nielsen MJ, Kjeldsen E, Bonven B, Stougaard M, Gromova I, Knudsen BR. Decreased camptothecin sensitivity of the stem-cell-like fraction of Caco2 cells correlates with an altered phosphorylation pattern of topoisomerase I. PLoS One 2014; 9:e99628. [PMID: 24960044 PMCID: PMC4069021 DOI: 10.1371/journal.pone.0099628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 05/17/2014] [Indexed: 12/27/2022] Open
Abstract
The CD44+ and CD44− subpopulations of the colorectal cancer cell line Caco2 were analyzed separately for their sensitivities to the antitumor drug camptothecin. CD44+ cells were less sensitive to camptothecin than CD44− cells. The relative resistance of CD44+ cells was correlated with (i) reduced activity of the nuclear enzyme topoisomerase I and (ii) insensitivity of this enzyme to camptothecin when analyzed in extracts. In contrast, topoisomerase I activity was higher in extracts from CD44− cells and the enzyme was camptothecin sensitive. Topoisomerase I from the two subpopulations were differentially phosphorylated in a manner that appeared to determine the drug sensitivity and activity of the enzyme. This finding was further supported by the fact that phosphorylation of topoisomerase I in CD44+ cell extract by protein kinase CK2 converted the enzyme to a camptothecin sensitive, more active form mimicking topoisomerase I in extracts from CD44− cells. Conversely, dephosphorylation of topoisomerase I in extracts from CD44− cells rendered the enzyme less active and camptothecin resistant. These findings add to our understanding of chemotherapy resistance in the Caco2 CD44+ cancer stem cell model.
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Affiliation(s)
- Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria J. Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eigil Kjeldsen
- Hemodiagnostic Laboratory, Cancercytogenetic Section, Aarhus University Hospital, Aarhus, Denmark
| | - Bjarne Bonven
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Irina Gromova
- Genome Integrity Unit, Proteomics in Cancer, Danish Cancer Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- * E-mail:
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15
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Chiu YL, Chan HF, Phua KKL, Zhang Y, Juul S, Knudsen BR, Ho YP, Leong KW. Synthesis of fluorosurfactants for emulsion-based biological applications. ACS NANO 2014; 8:3913-20. [PMID: 24646088 PMCID: PMC4004322 DOI: 10.1021/nn500810n] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Microemulsion represents an attractive platform for fundamental and applied biomedical research because the emulsified droplets can serve as millions of compartmentalized micrometer-sized reactors amenable to high-throughput screening or online monitoring. However, establishing stable emulsions with surfactants that are compatible with biological applications remains a significant challenge. Motivated by the lack of commercially available surfactants suitable for microemulsion-based biological assays, this study describes the facile synthesis of a biocompatible fluorosurfactant with nonionic tris(hydroxymethyl)methyl (Tris) polar head groups. We have further demonstrated compatibility of the developed surfactant with diverse emulsion-based applications, including DNA polymeric nanoparticle synthesis, enzymatic activity assay, and bacterial or mammalian cell culture, in the setup of both double- and multiphases of emulsions.
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Affiliation(s)
- Ya-Ling Chiu
- Department of Biomedical Engineering, Duke University , North Carolina 27708, United States
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16
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Stougaard M, Ho YP. DNA-based nanosensors for next-generation clinical diagnostics via detection of enzyme activity. Expert Rev Mol Diagn 2013; 14:1-3. [PMID: 24308335 DOI: 10.1586/14737159.2014.863151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specific and sensitive detection of DNA-modifying enzymes represents a cornerstone in modern medical diagnostics. Many of the currently prevalent methods are not preferred in the clinics because they rely heavily on pre-amplification or post-separation steps. This editorial highlights the potential of adopting DNA-based nanosensors for the assessment of the activities of DNA-modifying enzymes, with emphasis on the topoisomerase and tyrosyl-DNA phosphodiesterase families. By underlining the existing challenges, we expect that the DNA-nanosensors may soon be promoted to clinical diagnostics via enzyme detection.
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Affiliation(s)
- Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Noerrebrogade 44, building 18B, 8000 Aarhus C, Denmark +45 7846 3672
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17
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Tesauro C, Juul S, Arnò B, Nielsen CJF, Fiorani P, Frøhlich RF, Andersen FF, Desideri A, Stougaard M, Petersen E, Knudsen BR. Specific detection of topoisomerase I from the malaria causing P. falciparum parasite using isothermal rolling circle amplification. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2012:2416-9. [PMID: 23366412 DOI: 10.1109/embc.2012.6346451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a Rolling-Circle-Enhance-Enzyme-Activity-Detection (REEAD) system with potential use for future point-of-care diagnosis of malaria. In the developed setup, specific detection of malaria parasites in crude blood samples is facilitated by the conversion of single Plasmodium falciparum topoisomerase I (pfTopI) mediated cleavage-ligation events, happening within nanometer dimensions, to micrometer-sized products readily detectable at the single molecule level in a fluorescence microscope. In principle, REEAD requires no special equipment and the readout is adaptable to simple colorimetric detection systems. Moreover, with regard to detection limit the presented setup is likely to outcompete standard gold immuno-based diagnostics. Hence, we believe the presented assay forms the basis for a new generation of easy-to-use diagnostic tools suitable for the malaria epidemic areas in developing countries.
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Affiliation(s)
- Cinzia Tesauro
- Department of Biology and Center of Biostatistics and Bioinformatics & NAST Nanoscience & Nanotechnology & Innovative Instrumentation, University of Rome Tor Vergata, Rome, Italy
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18
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Jensen PW, Falconi M, Kristoffersen EL, Simonsen AT, Cifuentes JB, Marcussen LB, Frøhlich R, Vagner J, Harmsen C, Juul S, Ho YP, Withers MA, Lupski JR, Koch J, Desideri A, Knudsen BR, Stougaard M. Real-time detection of TDP1 activity using a fluorophore-quencher coupled DNA-biosensor. Biosens Bioelectron 2013; 48:230-7. [PMID: 23693093 DOI: 10.1016/j.bios.2013.04.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/13/2013] [Indexed: 12/16/2022]
Abstract
Real-time detection of enzyme activities may present the easiest and most reliable way of obtaining quantitative analyses in biological samples. We present a new DNA-biosensor capable of detecting the activity of the potential anticancer drug target tyrosyl-DNA phosphodiesterase 1 (TDP1) in a very simple, high throughput, and real-time format. The biosensor is specific for Tdp1 even in complex biological samples, such as human cell extracts, and may consequently find future use in fundamental studies as well as a cancer predictive tool allowing fast analyses of diagnostic cell samples such as biopsies. TDP1 removes covalent 3'DNA adducts in DNA single-strand break repair. This enzymatic activity forms the basis of the design of the TDP1-biosensor, which consists of a short hairpin-forming oligonucleotide having a 5'fluorophore and a 3'quencher brought in close proximity by the secondary structure of the biosensor. The specific action of TDP1 removes the quencher, thereby enabling optical detection of the fluorophore. Since the enzymatic action of TDP1 is the only "signal amplification" the increase in fluorescence may easily be followed in real-time and allows quantitative analyses of TDP1 activity in pure enzyme fractions as well as in crude cell extracts. In the present study we demonstrate the specificity of the biosensor, its ability to quantitatively detect up- or down-regulated TDP1 activity, and that it may be used for measuring and for analyzing the mechanism of TDP1 inhibition.
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Affiliation(s)
- Pia W Jensen
- Department of Pathology, Aarhus University Hospital, Denmark
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19
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Chen F, Zhao Y. Methylation-blocked enzymatic recycling amplification for highly sensitive fluorescence sensing of DNA methyltransferase activity. Analyst 2013; 138:284-9. [DOI: 10.1039/c2an36329a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Juul S, Nielsen CJF, Labouriau R, Roy A, Tesauro C, Jensen PW, Harmsen C, Kristoffersen EL, Chiu YL, Frøhlich R, Fiorani P, Cox-Singh J, Tordrup D, Koch J, Bienvenu AL, Desideri A, Picot S, Petersen E, Leong KW, Ho YP, Stougaard M, Knudsen BR. Droplet microfluidics platform for highly sensitive and quantitative detection of malaria-causing Plasmodium parasites based on enzyme activity measurement. ACS NANO 2012; 6:10676-83. [PMID: 23121492 PMCID: PMC3528816 DOI: 10.1021/nn3038594] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present an attractive new system for the specific and sensitive detection of the malaria-causing Plasmodium parasites. The system relies on isothermal conversion of single DNA cleavage-ligation events catalyzed specifically by the Plasmodium enzyme topoisomerase I to micrometer-sized products detectable at the single-molecule level. Combined with a droplet microfluidics lab-on-a-chip platform, this design allowed for sensitive, specific, and quantitative detection of all human-malaria-causing Plasmodium species in single drops of unprocessed blood with a detection limit of less than one parasite/μL. Moreover, the setup allowed for detection of Plasmodium parasites in noninvasive saliva samples from infected patients. During recent years malaria transmission has declined worldwide, and with this the number of patients with low-parasite density has increased. Consequently, the need for accurate detection of even a few parasites is becoming increasingly important for the continued combat against the disease. We believe that the presented droplet microfluidics platform, which has a high potential for adaptation to point-of-care setups suitable for low-resource settings, may contribute significantly to meet this demand. Moreover, potential future adaptation of the presented setup for the detection of other microorganisms may form the basis for the development of a more generic platform for diagnosis, fresh water or food quality control, or other purposes within applied or basic science.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | | | - Rodrigo Labouriau
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Cinzia Tesauro
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Pia W. Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Charlotte Harmsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Ya-Ling Chiu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Janet Cox-Singh
- School of Medicine, University of St Andrews, Fife KY16 9TF, Scotland and The Malaria Research Centre, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - David Tordrup
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jørn Koch
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Anne-Lise Bienvenu
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Alessandro Desideri
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Stephane Picot
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Eskild Petersen
- Department of Infectious Diseases, Institute of Clinical Medicine, Aarhus University Hospital-Skejby, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
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Juul S, Ho YP, Stougaard M, Koch J, Andersen FF, Leong KW, Knudsen BR. Microfluidics-mediated isothermal detection of enzyme activity at the single molecule level. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2012; 2011:3258-61. [PMID: 22255034 DOI: 10.1109/iembs.2011.6090885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Conventional analysis of enzymatic activity, often carried out on pools of cells, is blind to heterogeneity in the population. Here, we combine microfluidics with a previously developed isothermal rolling circle amplification-based assay to investigate multiple enzymatic activities in down to single cells. This microfluidics-meditated assay performs at very high sensitivity in picoliter incubators with small quantities of biological materials. Furthermore, we demonstrate the assay's capability of multiplexed detection of at least three enzyme activities at the single molecule level.
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Affiliation(s)
- Sissel Juul
- Department of Molecular Biology and Interdisciplinary Nanoscience Center, iNANO, Aarhus University, Denmark
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22
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Juul S, Ho YP, Koch J, Andersen FF, Stougaard M, Leong KW, Knudsen BR. Detection of single enzymatic events in rare or single cells using microfluidics. ACS NANO 2011; 5:8305-10. [PMID: 21936557 PMCID: PMC3823540 DOI: 10.1021/nn203012q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In the present study we demonstrate highly sensitive detection of rare, aberrant cells in a population of wild-type human cells by combining a rolling-circle-enhanced enzyme activity single-molecule detection assay with a custom-designed microfluidic device. Besides reliable detection of low concentrations of aberrant cells, the integrated system allowed multiplexed detection of individual enzymatic events at the single cell level. The single cell sensitivity of the presented setup relies on the combination of single-molecule rolling-circle-enhanced enzyme activity detection with the fast reaction kinetics provided by a picoliter droplet reaction volume and subsequent concentration of signals in a customized drop-trap device. This setup allows the fast reliable analyses of enzyme activities in a vast number of single cells, thereby offering a valuable tool for basic research as well as theranostics.
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Affiliation(s)
- Sissel Juul
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yi-Ping Ho
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Jørn Koch
- Department of Pathology and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Hospital, Denmark
| | - Felicie F. Andersen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology and Interdisciplinary Nanoscience Center (iNANO), Aarhus University Hospital, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Corresponding authorship shared between KWL and BRK. Contact information, KWL: ; BRK:
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
- Corresponding authorship shared between KWL and BRK. Contact information, KWL: ; BRK:
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Claridge SA, Schwartz JJ, Weiss PS. Electrons, photons, and force: quantitative single-molecule measurements from physics to biology. ACS NANO 2011; 5:693-729. [PMID: 21338175 PMCID: PMC3043607 DOI: 10.1021/nn103298x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 01/10/2011] [Indexed: 05/19/2023]
Abstract
Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.
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Affiliation(s)
| | | | - Paul S. Weiss
- California NanoSystems Institute
- Department of Chemistry and Biochemistry
- Department of Materials Science and Engineering
- Address correspondence to
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Hu J, Zhang CY. Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy. Anal Chem 2010; 82:8991-7. [DOI: 10.1021/ac1019599] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Juan Hu
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun-yang Zhang
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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