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Abid HA, Ong JW, Lin ES, Song Z, Liew OW, Ng TW. Low-cost Imaging of Fluorescent DNA in Agarose Gel Electrophoresis using Raspberry Pi cameras. J Fluoresc 2022; 32:443-448. [PMID: 35064858 PMCID: PMC8888377 DOI: 10.1007/s10895-021-02884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/27/2021] [Indexed: 01/13/2023]
Abstract
Low-cost analytical solutions built around microcomputers like the Raspberry Pi help to facilitate laboratory investigations in resource limited venues. Here, three camera modules (V1.3 with and without filter, as well as NoIR) that work with this microcomputer were assessed for their suitability in imaging fluorescent DNA following agarose gel electrophoresis. Evaluation of their utility was based on signal-to-noise (SNR) and noise variance metrics that were developed. Experiments conducted with samples were subjected to Polymerase Chain Reaction (PCR), and the amplified products were separated using gel electrophoresis and stained with Midori green. Image analysis revealed the NoIR camera performed the best with SNR and noise variance values of 21.7 and 0.222 respectively. In experiments conducted using UV LED lighting to simulate ethidium bromide (EtBr) excitation, the NoIR and V1.3 with filter removed cameras showed comparable SNR values.
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Affiliation(s)
- Hassan Ali Abid
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Jian Wern Ong
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Eric Shen Lin
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Zhixiong Song
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Oi Wah Liew
- Centre for Translational Medicine, Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, 117599, Singapore
| | - Tuck Wah Ng
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia.
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Qamar AZ, Asefifeyzabadi N, Taki M, Naphade S, Ellerby LM, Shamsi MH. Characterization and application of fluidic properties of trinucleotide repeat sequences by wax-on-plastic microfluidics. J Mater Chem B 2020; 8:743-751. [PMID: 31894829 DOI: 10.1039/c9tb02208b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trinucleotide repeat (TNR) sequences introduce sequence-directed flexibility in the genomic makeup of all living species leading to unique non-canonical structure formation. In humans, the expansions of TNR sequences are responsible for almost 24 neurodegenerative and neuromuscular diseases because their unique structures disrupt cell functions. The biophysical studies of these sequences affect their electrophoretic mobility and spectroscopic signatures. Here, we demonstrate a novel strategy to characterize and discriminate the TNR sequences by monitoring their capillary flow in the absence of an external driving force using wax-on-plastic microchannels. The wax-on-plastic microfluidic system translates the sequence-directed flexibility of TNR into differential flow dynamics. Several variables were used to characterize sequences including concentration, single- vs. double-stranded samples, type of repeat sequence, length of the repeat sequence, presence of mismatches in duplex, and presence of metal ion. All these variables were found to influence the flow velocities of TNR sequences as these factors directly affect the structural flexibility of TNR at the molecular level. An overall trend was observed as the higher flexibility in the TNR structure leads to lower capillary flow. After testing samples derived from relevant cells harboring expanded TNR sequences, it is concluded that this approach may transform into a reagent-free and pump-free biosensing platform to detect microsatellite expansion diseases.
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Affiliation(s)
- Ahmad Zaman Qamar
- Department of Chemistry & Biochemistry, Southern Illinois University at Carbondale, 1245 Lincoln Dr, Carbondale, IL 62901, USA.
| | - Narges Asefifeyzabadi
- Department of Chemistry & Biochemistry, Southern Illinois University at Carbondale, 1245 Lincoln Dr, Carbondale, IL 62901, USA.
| | - Motahareh Taki
- Department of Chemistry & Biochemistry, Southern Illinois University at Carbondale, 1245 Lincoln Dr, Carbondale, IL 62901, USA.
| | - Swati Naphade
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, USA
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, USA
| | - Mohtashim Hassan Shamsi
- Department of Chemistry & Biochemistry, Southern Illinois University at Carbondale, 1245 Lincoln Dr, Carbondale, IL 62901, USA.
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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Abstract
Trinucleotide repeats are a peculiar class of microsatellites involved in many neurological as well as developmental disorders. Their propensity to generate very large expansions over time is supposedly due to their capacity to form specific secondary structures, such as imperfect hairpins, triple helices, or G-quadruplexes. These unusual structures were proposed to trigger expansions in vivo. Here, I review known technical issues linked to these structures, such as slippage during polymerase chain reaction and aberrant migration of long trinucleotide repeats during agarose gel electrophoresis. Our current understanding of interactions between trinucleotide repeat secondary structures and the mismatch-repair machinery is also quickly reviewed, and critical questions relevant to these interactions are addressed.
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Affiliation(s)
- Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS UMR3525, Paris, France.
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The flash-small-pool PCR: how to transform blotting and numerous hybridization steps into a simple denatured PCR. Biotechniques 2019; 64:262-265. [PMID: 29939093 DOI: 10.2144/btn-2018-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Numerous human diseases are associated with abnormal expansion of unstable trinucleotide repeats (TNRs). TNR instability mechanisms are complex, and remain only partially understood. Small-pool-PCR (SP-PCR) is the reference method to assess TNR instability. SP-PCR amplifies a low number of DNA molecules and is followed by Southern blot. However, SP-PCR remains expensive and time consuming. Here, we describe an optimized SP-PCR that can be done in a day, which reduces cost and experimental biases: the flash-small-pool PCR (FSP-PCR). This method consists of a fluorescent PCR on a few DNA molecules, followed by an alkaline gel electrophoresis revealed with a near infra-red detector system. With reduced experimental steps, cost, and time consumption, microsatellite analysis will become more accessible due to FSP-PCR.
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Cumming SA, Hamilton MJ, Robb Y, Gregory H, McWilliam C, Cooper A, Adam B, McGhie J, Hamilton G, Herzyk P, Tschannen MR, Worthey E, Petty R, Ballantyne B, Warner J, Farrugia ME, Longman C, Monckton DG. De novo repeat interruptions are associated with reduced somatic instability and mild or absent clinical features in myotonic dystrophy type 1. Eur J Hum Genet 2018; 26:1635-1647. [PMID: 29967337 PMCID: PMC6189127 DOI: 10.1038/s41431-018-0156-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/23/2018] [Accepted: 03/30/2018] [Indexed: 01/10/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystem disorder, caused by expansion of a CTG trinucleotide repeat in the 3'-untranslated region of the DMPK gene. The repeat expansion is somatically unstable and tends to increase in length with time, contributing to disease progression. In some individuals, the repeat array is interrupted by variant repeats such as CCG and CGG, stabilising the expansion and often leading to milder symptoms. We have characterised three families, each including one person with variant repeats that had arisen de novo on paternal transmission of the repeat expansion. Two individuals were identified for screening due to an unusual result in the laboratory diagnostic test, and the third due to exceptionally mild symptoms. The presence of variant repeats in all three expanded alleles was confirmed by restriction digestion of small pool PCR products, and allele structures were determined by PacBio sequencing. Each was different, but all contained CCG repeats close to the 3'-end of the repeat expansion. All other family members had inherited pure CTG repeats. The variant repeat-containing alleles were more stable in the blood than pure alleles of similar length, which may in part account for the mild symptoms observed in all three individuals. This emphasises the importance of somatic instability as a disease mechanism in DM1. Further, since patients with variant repeats may have unusually mild symptoms, identification of these individuals has important implications for genetic counselling and for patient stratification in DM1 clinical trials.
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Affiliation(s)
- Sarah A Cumming
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mark J Hamilton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK.
| | - Yvonne Robb
- Clinical Genetics Service, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Helen Gregory
- Department of Clinical Genetics, Aberdeen Royal Hospital, Aberdeen, AB25 2ZA, UK
| | | | - Anneli Cooper
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Berit Adam
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Josephine McGhie
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Graham Hamilton
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Pawel Herzyk
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Michael R Tschannen
- Human and Molecular Genetics Center, Medical College Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Elizabeth Worthey
- Human and Molecular Genetics Center, Medical College Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, NW, Huntsville, AL, 35806, USA
| | - Richard Petty
- Department of Neurology, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Bob Ballantyne
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Jon Warner
- Molecular Genetics Service, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Maria Elena Farrugia
- Department of Neurology, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Cheryl Longman
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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