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Gudmundsson B, Thormar HG, Sigurdsson A, Dankers W, Steinarsdottir M, Hermanowicz S, Sigurdsson S, Olafsson D, Halldorsdottir AM, Meyn S, Jonsson JJ. Northern lights assay: a versatile method for comprehensive detection of DNA damage. Nucleic Acids Res 2018; 46:e118. [PMID: 30053193 PMCID: PMC6237810 DOI: 10.1093/nar/gky645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022] Open
Abstract
DNA damage assays have various limitations in types of lesions detected, sensitivity, specificity and samples that can be analyzed. The Northern Lights Assay (NLA) is based on 2D Strandness-Dependent Electrophoresis (2D-SDE), a technique that separates nucleic acids based on length, strandness, structure and conformation changes induced by damage. NLA is run on a microgel platform in 20-25 min. Each specimen is analyzed in pairs of non-digested DNA to detect single- and double-stranded breaks (DSBs) and Mbo I-digested DNA to detect other lesions. We used NLA to evaluate DNA in solution and isolated from human cells treated with various genotoxic agents. NLA detected and distinguished between single- and DSBs, interstrand and intrastrand DNA crosslinks, and denatured single-stranded DNA. NLA was sufficiently sensitive to detect biologically relevant amount of DNA damage. NLA is a versatile, sensitive and simple method for comprehensive and simultaneous analysis of multiple types of damage, both in purified DNA and in DNA isolated from cells and body fluids. NLA can be used to evaluate DNA quality in biosamples, monitor complex molecular procedures, assess genotoxicity, diagnose genome instability, facilitate cancer theranostics and in basic nucleic acids research.
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Affiliation(s)
- Bjarki Gudmundsson
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- Department of Genetics and Molecular Medicine, Landspitali–National University Hospital, Reykjavik IS-101, Iceland
- Lifeind ehf., Reykjavik IS-101, Iceland
| | - Hans G Thormar
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- Lifeind ehf., Reykjavik IS-101, Iceland
| | - Albert Sigurdsson
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
| | - Wendy Dankers
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
| | - Margret Steinarsdottir
- Department of Genetics and Molecular Medicine, Landspitali–National University Hospital, Reykjavik IS-101, Iceland
| | - Stefan Hermanowicz
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
| | - Stefan Sigurdsson
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
| | - David Olafsson
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- The Blood Bank, Landspitali–National University Hospital, Reykjavik IS-101, Iceland
| | | | - Stephen Meyn
- Department of Paediatrics, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- University of Toronto, Toronto, ON, M5S 1A8, Canada
- Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Jon J Jonsson
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik IS-101, Iceland
- Department of Genetics and Molecular Medicine, Landspitali–National University Hospital, Reykjavik IS-101, Iceland
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Abstract
We describe a system for horizontal 1D or 2D PAGE comprising an apparatus and microgels. There is no buffer outside the gel, making handling and sample loading easy. Specially designed electrodes on all four sides allow 2D electrophoresis without gel rotation. Electrophoresis is completed within 20 min and sensitivity is in the subnanogram range. The system is temperature controlled for speed, denaturation of nucleic acid molecules and maintaining molecules single-stranded. The system allows characterization of structure, conformation and damage in complex nucleic acid preparations. Besides quick 1D PAGE, 2D applications include characterization of efficiency of complex molecular procedures, checking quality of biosamples and detecting DNA damage in cells and body fluids. The system should also run protein gels.
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de Ruiter MV, Overeem NJ, Singhai G, Cornelissen JJLM. Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:184002. [PMID: 29512513 PMCID: PMC7104908 DOI: 10.1088/1361-648x/aab4a9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/16/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.
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Affiliation(s)
- Mark V de Ruiter
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
| | - Nico J Overeem
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
| | - Gaurav Singhai
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
- Flinders Centre for Nanoscale Science and Technology, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Jeroen J L M Cornelissen
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
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Felsani A, Gudmundsson B, Nanni S, Brini E, Moles A, Thormar HG, Estibeiro P, Gaetano C, Capogrossi M, Farsetti A, Jonsson JJ, Guffanti A. Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results. Brief Funct Genomics 2014; 14:156-62. [DOI: 10.1093/bfgp/elu001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Petkovic S, Müller S. RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA. FEBS Lett 2013; 587:2435-40. [PMID: 23796421 DOI: 10.1016/j.febslet.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/05/2013] [Accepted: 06/05/2013] [Indexed: 01/08/2023]
Abstract
We have engineered a self-processing RNA, derived from the hairpin ribozyme that runs through a cascade of cleavage and ligation reactions thereby changing its topology. The first two cleavage events leave the resulting RNA with a 5'-OH group and a 2',3'-cyclic phosphate. Thus, upon refolding, intramolecular ligation delivers a cyclic species. In addition, we demonstrate formation of concatemers resulting from multiple intermolecular ligations. Our results demonstrate the potential of RNA for self-supported topology changes and support the suggestion of 2',3'-cyclic phosphates being suitable activated building blocks for reversible phosphodiester bond formation in the RNA world.
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Affiliation(s)
- Sonja Petkovic
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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Thormar HG, Gudmundsson B, Eiriksdottir F, Kil S, Gunnarsson GH, Magnusson MK, Hsu JC, Jonsson JJ. Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis. Clin Chem 2013; 59:667-74. [PMID: 23378568 DOI: 10.1373/clinchem.2012.193839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. METHODS We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription-based microarray expression analysis. RESULTS The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P < 0.05) when the dsDNA percentage was between 12% and 35%. In contrast, only 3% of probes showed between-sample variation when the dsDNA percentage was 69% and 72%. Replication experiments of the 35% dsDNA and 72% dsDNA samples were used to separate sample variation from probe replication variation. The estimated SD of the sample-to-sample variation and of the probe replicates was lower in 72% dsDNA samples than in 35% dsDNA samples. CONCLUSIONS Variation in the relative amount of double-stranded cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase-based microarray expression analysis.
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Affiliation(s)
- Hans G Thormar
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik, Iceland
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Hegedüs E, Kókai E, Kotlyar A, Dombrádi V, Szabó G. Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis. Nucleic Acids Res 2009; 37:e112. [PMID: 19553189 PMCID: PMC2761254 DOI: 10.1093/nar/gkp539] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.
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Affiliation(s)
- Eva Hegedüs
- Department of Biophysics and Cell Biology, University of Debrecen, 4012 Debrecen, Nagyerdei krt. 98, Hungary
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