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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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Mudeppa DG, Kumar S, Kokkonda S, White J, Rathod PK. Topoisomerase II from Human Malaria Parasites: EXPRESSION, PURIFICATION, AND SELECTIVE INHIBITION. J Biol Chem 2015; 290:20313-24. [PMID: 26055707 DOI: 10.1074/jbc.m115.639039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 11/06/2022] Open
Abstract
Historically, type II topoisomerases have yielded clinically useful drugs for the treatment of bacterial infections and cancer, but the corresponding enzymes from malaria parasites remain understudied. This is due to the general challenges of producing malaria proteins in functional forms in heterologous expression systems. Here, we express full-length Plasmodium falciparum topoisomerase II (PfTopoII) in a wheat germ cell-free transcription-translation system. Functional activity of soluble PfTopoII from the translation lysates was confirmed through both a plasmid relaxation and a DNA decatenation activity that was dependent on magnesium and ATP. To facilitate future drug discovery, a convenient and sensitive fluorescence assay was established to follow DNA decatenation, and a stable, truncated PfTopoII was engineered for high level enzyme production. PfTopoII was purified using a DNA affinity column. Existing TopoII inhibitors previously developed for other non-malaria indications inhibited PfTopoII, as well as malaria parasites in culture at submicromolar concentrations. Even before optimization, inhibitors of bacterial gyrase, GSK299423, ciprofloxacin, and etoposide exhibited 15-, 57-, and 3-fold selectivity for the malarial enzyme over human TopoII. Finally, it was possible to use the purified PfTopoII to dissect the different modes by which these varying classes of TopoII inhibitors could trap partially processed DNA. The present biochemical advancements will allow high throughput chemical screening of compound libraries and lead optimization to develop new lines of antimalarials.
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Affiliation(s)
- Devaraja G Mudeppa
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Shiva Kumar
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Sreekanth Kokkonda
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - John White
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Pradipsinh K Rathod
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
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Novel angular furoquinolinones bearing flexible chain as antitumor agent: Design, synthesis, cytotoxic evaluation, and DNA-binding studies. Bioorg Med Chem 2008; 16:8713-8. [DOI: 10.1016/j.bmc.2008.07.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/27/2008] [Accepted: 07/29/2008] [Indexed: 11/18/2022]
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Hwang LC, Wohland T. Recent Advances in Fluorescence Cross-correlation Spectroscopy. Cell Biochem Biophys 2007; 49:1-13. [PMID: 17873335 DOI: 10.1007/s12013-007-0042-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 11/30/1999] [Accepted: 05/21/2007] [Indexed: 12/14/2022]
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a method that measures the temporal fluorescence fluctuations coming from two differently labeled molecules diffusing through a small sample volume. Cross-correlation analysis of the fluorescence signals from separate detection channels extracts information of the dynamics of the dual-labeled molecules. FCCS has become an essential tool for the characterization of diffusion coefficients, binding constants, kinetic rates of binding, and determining molecular interactions in solutions and cells. By cross-correlating between two focal spots, flow properties could also be measured. Recent developments in FCCS have been targeted at using different experimental schemes to improve on the sensitivity and address their limitations such as cross-talk and alignment issues. This review presents an overview of the different excitation and detection methodologies used in FCCS and their biological applications. This is followed by a description of the fluorescent probes currently available for the different methods. This will introduce biological readers to FCCS and its related techniques and provide a starting point to selecting which experimental scheme is suitable for their type of biological study.
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Affiliation(s)
- Ling Chin Hwang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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Abstract
Cell biologists strive to characterize molecular interactions directly in the intracellular environment. The intrinsic resolution of optical microscopy, however, allows visualization of only coarse subcellular localization. By extracting information from molecular dynamics, fluorescence cross-correlation spectroscopy (FCCS) grants access to processes on a molecular scale, such as diffusion, binding, enzymatic reactions and codiffusion, and has become a valuable tool for studies in living cells. Here we review basic principles of FCCS and focus on seminal applications, including examples of intracellular signaling and trafficking. We consider FCCS in the context of fluorescence resonance energy transfer and multicolor imaging techniques and discuss application strategies and recent technical advances.
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Affiliation(s)
- Kirsten Bacia
- Institute of Biophysics, Dresden University of Technology, Tatzberg 47-51, D-01307 Dresden, Germany
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