1
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Tuo LJ, Zhang T, Chen GQ, Liu Y, Zhao C, Jiang SW. Proper application of DNA dyes in agarose gel electrophoresis. Electrophoresis 2024. [PMID: 39091179 DOI: 10.1002/elps.202400082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/11/2024] [Accepted: 07/14/2024] [Indexed: 08/04/2024]
Abstract
Various dyes are used to visualize DNA bands in agarose gel electrophoresis (AGE) by the methods of pre- or post-staining. The DNA dye user's guides generally state that the binding of the dye to DNA will affect DNA mobility in electrophoresis, thus recommending post-staining for accurate measurement of DNA size. However, many AGE performers prefer pre-staining procedures for reasons such as convenience, real-time observation of DNA bands, and/or the use of a minimal amount of dye. The detrimental effect of the dye on DNA mobility and the associated risk for inaccurate measurement of DNA size are often overlooked by AGE performers. Here we quantitatively determine the impact on DNA migration imposed by frequently used dyes, including GelRed, ethidium bromide (EB), and Gold View. It was observed that pre-staining with GelRed and EB significantly slowed down DNA migration to cause as much as 39.1% overestimation on the size of sample DNA, whereas Gold View had little effect. The slowdown of DNA migration increased with dye concentration until it plateaued when the dye concentration reached a saturated level. Thus, to take advantage of pre-staining, saturated levels of DNA dyes should always be applied for both DNA samples and DNA markers to ensure a fair comparison of DNA sizes. In addition, GelRed and EB display much higher sensitivity than Gold View in the detection of DNA bands in post-staining. The saturated concentrations, cost considerations, and other useful features of these frequently used dyes are summarized for the information of AGE performers.
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Affiliation(s)
- Ling-Jin Tuo
- Lianyungang Research Institute for Women's and Children's Health, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Teng Zhang
- Department of Obstetrics, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Guo-Qing Chen
- Department of Outpatient, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yuan Liu
- Scientific Research Department, Lianyungang Maternal and Child Health Hospital Lianyungang, Lianyungang, Jiangsu, China
| | - Cheng Zhao
- Lianyungang Research Institute for Women's and Children's Health, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shi-Wen Jiang
- Lianyungang Research Institute for Women's and Children's Health, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
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2
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Faikhruea K, Supabowornsathit K, Angsujinda K, Aonbangkhen C, Chaikeeratisak V, Palaga T, Assavalapsakul W, Wagenknecht HA, Vilaivan T. Nucleic Acid-Templated Synthesis of Cationic Styryl Dyes in Vitro and in Living Cells. Chemistry 2024; 30:e202400913. [PMID: 38563862 DOI: 10.1002/chem.202400913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A novel method for synthesizing cationic styryl dyes through a nucleic acid-templated reaction has been developed. This approach overcomes issues associated with traditional synthesis methods, such as harsh conditions, low throughput, and wasteful chemicals. The presence of a nucleic acid template accelerated the styryl dye formation from quaternized heteroaromatic and cationic aldehyde substrates. These styryl dyes show remarkable optical properties change when bound to nucleic acids, hence the success of the synthesis could be readily monitored in situ by UV-Vis and fluorescence spectroscopy and the optical properties data were also observable at the same time. This method provides the desired products from a broad range of coupling partners. By employing different substrates and templates, it is possible to identify new dyes that can bind to a specific type of nucleic acid such as a G-quadruplex. The templated dye synthesis is also successfully demonstrated in live HeLa cells. This approach is a powerful tool for the rapid synthesis and screening of dyes specific for diverse types of nucleic acids or cellular organelles, facilitating new biological discoveries.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Kitipong Angsujinda
- Aquatic Resources Research Institute, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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3
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Madden I, Taylor D, Mitchell N, Goray M, Henry J. Predicting probative levels of touch DNA on tapelifts using Diamond™ Nucleic Acid Dye. Forensic Sci Int Genet 2024; 70:103024. [PMID: 38335775 DOI: 10.1016/j.fsigen.2024.103024] [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] [Received: 08/22/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Tapelifting is a common strategy to recover touch DNA deposits from porous exhibits in forensic DNA casework. However, it is known that only about 30 % of tapelifts submitted for DNA analysis in operational forensic laboratories yield profiles suitable for comparison or upload to a searchable database. A reliable means to identify and remove non-probative tapelifts from the workflow would reduce sample backlogs and provide significant cost savings. We investigated whether the amount of macroscopic or microscopic fluorescence on a tapelift following staining with Diamond Nucleic Acid Dye (DD), determined using a Polilight and Dino Lite microscope respectively, could predict the DNA yield and/or the DNA profiling outcome using controlled (saliva), semi-controlled (finger mark) and uncontrolled (clothing) samples. Both macroscopic and microscopic DD fluorescence could predict DNA yield and profiling outcome for all sample types, however the predictive power deteriorated as the samples became less controlled. For tapelifts of clothing, which are operationally relevant, Polilight fluorescence scores were significantly impacted by clothing fibres and other non-cellular debris and could not be used to identify non-probative samples. The presence of less than 500 cells on a clothing tapelift using microscopic counting of stained corneocytes was identified as a potential threshold for a non-probative DNA profiling outcome. A broader examination of the reliability of this threshold using a casework trial is recommended. Due to the labour intensiveness of microscopic cell counting, and the increased risk of inadvertent contamination, automation of this process using image software in conjunction with artificial neural networks (ANN) should be explored.
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Affiliation(s)
- Isla Madden
- College of Science and Engineering, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia
| | - Duncan Taylor
- College of Science and Engineering, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia; Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia
| | - Natasha Mitchell
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia
| | - Mariya Goray
- College of Science and Engineering, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia
| | - Julianne Henry
- College of Science and Engineering, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia; Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia.
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4
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Bennett HA, McAdorey A, Yan H. Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA. J Fluoresc 2024; 34:1193-1205. [PMID: 37505363 DOI: 10.1007/s10895-023-03343-8] [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] [Received: 06/03/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.
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Affiliation(s)
- Hayley-Ann Bennett
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Alyssa McAdorey
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada.
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5
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Franck N, Vera Candioti L, Gerlero GS, Urteaga R, Kler PA. A simple method for the assessment of electrophoretic mobility in porous media. Electrophoresis 2024; 45:589-598. [PMID: 37853649 DOI: 10.1002/elps.202300180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Developing paper-based electrophoretic methods involve dealing with significant uncertainty levels when compared to their capillary counterparts. Critical information for developing these kinds of methods are the electrophoretic mobility of background electrolytes and samples. This work presents the design and characterization of a device for measuring the electrophoretic mobilities of dyes in porous media. The device was developed with the aim of validating a previously presented model and also proposing a protocol for the straightforward determination of electrophoretic mobilities in porous media when open-channel values are already known. Whatman #1 paper was used as a model substrate as far as it is the most common porous medium substrate for paper-based electrophoresis. The device was designed using a numerical simulation-assisted approach, utilizing OpenFOAM® and specific solvers for capillary transport and electromigration, namely porousMicroTransport and electroMicroTransport, respectively. The electrophoretic mobilities of five dyes were analyzed experimentally with the proposed device. To establish appropriate comparative values at different pHs, experiments in fused silica capillaries were also performed. An effective parameter model for describing the electrophoretic behavior of dyes in porous media, that is, the constriction factor, was found consistent with previous reports for the Whatman #1 paper. This consistency was found after considering (via direct measurements) the chromatographic effect of the medium over each dye. Consequently, the recorded values hold significant worth due to their potential for direct application in designing new experiments or devices in Whatman #1 paper. With the validation of the model through the experiments with the proposed device, those researchers interested on developing electrophoretic methods in porous substrates can make use of the open-channel electrophoretic mobilities reported in the literature, or in the well-known software databases, and correct them for the media of interest just by performing two simple characterization steps.
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Affiliation(s)
- Nicolás Franck
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Instituto de Física del Litoral (IFIS Litoral, UNL-CONICET), Santa Fe, Argentina
| | - Luciana Vera Candioti
- Departamento de Ciencias Biológicas, Cátedra de Bromatología y Nutrición-(FBCB,UNL-CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - Gabriel S Gerlero
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Universidad Nacional de Rafaela, Rafaela, Santa Fe, Argentina
| | - Raúl Urteaga
- Instituto de Física del Litoral (IFIS Litoral, UNL-CONICET), Santa Fe, Argentina
| | - Pablo A Kler
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Departamento de Ingeniería en Sistemas de Información, FRSF-UTN, Lavaise, Santa Fe, Argentina
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6
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Trinh E, Batt LJ, Yue Q, Du R, Jones ST, Fielding LA. Bridging Flocculation of a Sterically Stabilized Cationic Latex as a Biosensor for the Detection of Microbial DNA after Amplification via PCR. Biomacromolecules 2024; 25:1629-1636. [PMID: 38361251 PMCID: PMC10934273 DOI: 10.1021/acs.biomac.3c01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
There is a high demand for rapid, sensitive, and accurate detection methods for pathogens. This paper demonstrates a method of detecting the presence of amplified DNA from a range of pathogens associated with serious infections including Gram-negative bacteria, Gram-positive bacteria, and viruses. DNA is amplified using a polymerase chain reaction (PCR) and consequently detected using a sterically stabilized, cationic polymer latex. The DNA induces flocculation of this cationic latex, which consequently leads to rapid sedimentation and a visible change from a milky-white dispersion to one with a transparent supernatant, presenting a clear visible change, indicating the presence of amplified DNA. Specifically, a number of different pathogens were amplified using conventional or qPCR, including Staphylococcus aureus, Escherichia coli, and Herpes Simplex Virus (HSV-2). This method was demonstrated to detect the presence of bacteria in suspension concentrations greater than 380 CFU mL-1 and diagnose the presence of specific genomes through primer selection, as exemplified using methicillin resistant and methicillin susceptible Staphylococcus aureus. The versatility of this methodology was further demonstrated by showing that false positive results do not occur when a PCR of fungal DNA from C. albicans is conducted using bacterial universal primers.
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Affiliation(s)
- Elisabeth Trinh
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
| | - Lauren J. Batt
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
- Henry
Royce Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Qi Yue
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
- Henry
Royce Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Ruiling Du
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
- Henry
Royce Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Samuel T. Jones
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
- Henry
Royce Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- School
of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Lee A. Fielding
- Department
of Materials, School of Natural Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, United
Kingdom
- Henry
Royce Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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7
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Bawane H, Kadam K, Mahale V, Kulkarni R. Comprehensive assessment of 12 commercial DNA-binding dyes as alternatives to ethidium bromide for agarose gel electrophoresis. Electrophoresis 2024; 45:442-450. [PMID: 37933673 DOI: 10.1002/elps.202300154] [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] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Staining and visualization of the nucleic acid bands on agarose gels using ethidium bromide (EB) has been a widely used technique in molecular biology. Although it is an efficient dye for this purpose, EB is known to be mutagenic and genotoxic in humans. This led to the emergence of various alternative dyes, which were claimed to be safer and more efficient than EB. However, these dyes portray varied sensitivity and interference with the electrophoretic mobility of nucleic acids. This work aimed at assessing ten nucleic acid-binding dyes and two prestained dyes for these properties by three staining techniques, such as precasting, preloading, and poststaining. Of these, preloading was not suitable for any of the dye while poststaining worked optimal for most of them. Precasting was suitable for only four dyes viz. DNA Stain G, SYBR™ safe, EZ-Vision® in-gel, and LabSafe™. Poststaining was, in general, a costlier method than precasting. The work gives a comprehensive understanding of the performance of nucleic acid-binding dyes for routine molecular biology experiments.
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Affiliation(s)
- Hemangi Bawane
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Komal Kadam
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Vinit Mahale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
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8
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Day EC, Chittari SS, Bogen MP, Knight AS. Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows. ACS POLYMERS AU 2023; 3:406-427. [PMID: 38107416 PMCID: PMC10722570 DOI: 10.1021/acspolymersau.3c00025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023]
Abstract
Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.
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Affiliation(s)
| | | | - Matthew P. Bogen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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9
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Nolan M, Handt O, Linacre A. Persistence of cellular material after exposure to water. J Forensic Sci 2023; 68:2128-2137. [PMID: 37356058 DOI: 10.1111/1556-4029.15316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
Disposing of items of forensic relevance in bodies of water is one countermeasure offenders can use to avoid detection. The impact of immersion in water has been explored for blood, saliva, and semen; however, few studies have assessed touch DNA. Here we report on the effect of exposure to water on the persistence of touch DNA over prolonged periods of time. To evaluate the persistence of cells from touch DNA, after water exposure, three substrates and two water types were tested: plastic, metal, and ceramic, submerged into seawater or tap water. Diamond™ Nucleic Acid Dye was used to stain cells deposited by touch. Cell counts before and after water exposure were compared to investigate cell loss over time, ranging from 6 hours to 5 days. A logarithmic increase in the percent of cells lost was observed over time when the data for substrate and water type conditions were combined. Substrate type influenced the persistence of cells, with the metal substrate retaining cells longer than plastic or ceramic. The influence of water type appeared dependent on the substrate, with varied cell persistence on metal whereas plastic and ceramic recorded similar cell loss over time between water types. The ability to visualize cells after exposure to water could assist in triaging evidence within operational forensic laboratories and allow for targeted sampling. This proof-of-concept study demonstrated that greater than 50% of cells can persist on various items submerged in aqueous environments for at least 5 days, highlighting the possibility for downstream DNA testing.
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Affiliation(s)
- Madison Nolan
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Oliva Handt
- College of Science and Engineering, Flinders University, Adelaide, Australia
- Forensic Science South Australia, Adelaide, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, Australia
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10
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Linacre A, Petcharoen P. Detection of Latent DNA Using a DNA Binding Dye. Methods Mol Biol 2023; 2685:359-366. [PMID: 37439993 DOI: 10.1007/978-1-0716-3295-6_22] [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: 07/14/2023]
Abstract
Latent DNA can be deposited every time a person holds or touches an item. This "touch DNA" can be crucial evidence if the item is of forensic significance. Until very recently, there were no means to visualize this DNA. The advent of using a dye that binds to DNA has opened up this possibility. The application of the dye is simple to perform, and a mobile microscope allows rapid visualization of the cellular material, even in ambient light. The dye can be applied in a solution of either 75% ethanol or water. As this is a solution-based dye, the application works best on non-absorbent surfaces.DNA within cellular material, such as dead skin cells, appears as green dots under 50X magnification; zooming to 220X magnification confirms that these are cells. The location and number of these cells can be photographed allowing a record of the presence of otherwise latent DNA.This chapter details the processes involved in the detection of latent DNA using Diamond™ Nucleic Acid Dye with both control samples (that act as very effective training samples) and the staining of evidential items. By developing skills in determining cell locations, a targeted approach to crime scene collection is now possible.
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Affiliation(s)
- Adrian Linacre
- Forensic DNA Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
| | - Piyamas Petcharoen
- Forensic Technology and Innovation Module, School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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11
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Yaneva Z, Ivanova D, Nikolova N, Toneva M. Organic dyes in contemporary medicinal chemistry and biomedicine. I. From the chromophore to the bioimaging/bioassay agent. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2039077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zvezdelina Yaneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Donika Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nevena Nikolova
- Ecology Unit, Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Monika Toneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
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12
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Liu Y, Chen J, Cheng Y, Li Y, Li X, Zhang Z, Xu X, Lin Y, Xu J, Li Z. A simple and rapid technique of template preparation for PCR. Front Microbiol 2022; 13:1024827. [PMID: 36439815 PMCID: PMC9686307 DOI: 10.3389/fmicb.2022.1024827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Many techniques have been developed for extracting DNA, but most are often complex, time-consuming, and/or expensive. In this study, we describe a simple, rapid and cost-effective technique for preparing DNA template for PCR. This technique involves 0.1 M potassium hydroxide treatment at 100°C for 10 min followed by centrifugation. The suspended centrifuged sediments were shown as excellent templates for PCR. Templates prepared using this technique worked for diverse microorganisms belonging to bacteria, fungi and oomycetes and their amplification efficiencies were comparable to/better than those prepared using common but relatively more complex, time-consuming, and/or expensive methods, including commercial DNA extraction kits. Furthermore, this technology is suitable for high-throughput batch processing and for amplifications of long DNA fragments. Flow cytometry and scanning electronic microscopy analyzes showed that this technique generated primarily damaged cells and cell-bound DNA, not free naked DNA. This technique provides a great convenience for simple PCR template preparation.
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Affiliation(s)
- Yunyun Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yi Li
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha, China
| | - Xinwen Li
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha, China
| | - Zhengbing Zhang
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha, China
| | - Xiumei Xu
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha, China
| | - Yufeng Lin
- Plant Protection and Inspection Station, Agriculture and Rural Department of Hunan Province, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
- Jianping Xu,
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Zhimin Li,
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13
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Liu W, Wang Y, Sheng F, Wan B, Tang G, Xu S. A nucleic acid dye-enhanced electrochemical biosensor for the label-free detection of Hg 2+ based on a gold nanoparticle-modified disposable screen-printed electrode. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3451-3457. [PMID: 36000503 DOI: 10.1039/d2ay00548d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this paper, a nucleic acid dye-enhanced electrochemical biosensor based on a screen-printed carbon electrode (SPCE) modified with Au nanoparticles (AuNPs) was designed for the detection of Hg2+ in water. AuNPs were modified on the surface of the disposable SPCE through the electrodeposition of HAuCl4. Subsequently, thiolated DNA probes were immobilized on the AuNP-modified electrode surface by Au-S reaction. After Hg2+ was bound with a DNA probe by thymine (T)-Hg2+-thymine (T) mismatch, the DNA probe was folded into a hairpin structure where positively charged GelRed molecules were embedded into the double-stranded part of the hairpin. Thus, the current of [Fe(CN)6]3-/4- increased significantly on account of the decreased electrostatic repulsion at the electrode surface. Under the optimized experimental conditions, the peak current of [Fe(CN)6]3-/4- exhibited a good linear relationship with lgCHg2+ in the concentration of Hg2+ linear range of 0.1 nM to 500 nM, and the limit of detection (S/N = 3) was calculated as 0.04 nM. The electrochemical sensor also exhibited excellent selectivity for Hg2+ in the presence of nine interfering ions, including Na+, Fe3+, Ni2+, Mg2+, Co2+, Pb2+, K+, Al3+ and Cu2+. Meanwhile, the developed electrochemical sensor was tested in the analysis of Hg2+ in tap water and river water samples, and the recoveries ranged from 81.0 to 114%. Therefore, this nucleic acid dye-enhanced electrochemical biosensor provided the advantages of simplicity, sensitivity, and specificity and is expected to be an alternative for Hg2+ detection in actual environmental samples.
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Affiliation(s)
- Wei Liu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Yunqi Wang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Fangfang Sheng
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Bing Wan
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Gangxu Tang
- College of Material and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, P. R. China
| | - Shuxia Xu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, P. R. China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu University of Technology, Chengdu 610059, P. R. China
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14
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Supabowornsathit K, Faikhruea K, Ditmangklo B, Jaroenchuensiri T, Wongsuwan S, Junpra-Ob S, Choopara I, Palaga T, Aonbangkhen C, Somboonna N, Taechalertpaisarn J, Vilaivan T. Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids. Sci Rep 2022; 12:14250. [PMID: 35995925 PMCID: PMC9395382 DOI: 10.1038/s41598-022-18460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.
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Affiliation(s)
- Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Theeranuch Jaroenchuensiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sutthida Wongsuwan
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sirikarn Junpra-Ob
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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15
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Hussein Ali T, Mousa Mandal A, Alhasan A, Dehaen W. Surface fabrication of magnetic core-shell silica nanoparticles with perylene diimide as a fluorescent dye for nucleic acid visualization. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Wittmeier P, Hummel S. Agarose gel electrophoresis to assess PCR product yield: comparison with spectrophotometry, fluorometry and qPCR. Biotechniques 2022; 72:155-158. [PMID: 35311378 DOI: 10.2144/btn-2021-0094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Agarose gel electrophoresis is a relatively easy to use method, commonly applied to evaluate PCR reaction success. Intercalating agents or dyes are used to visualize the amplified fragments. However, it is uncertain to what extent the brightness of bands is informative about the concentration of the amplicons. To more closely examine the suitability of agarose gel electrophoresis to assess PCR product yield, we quantified the brightness of bands on a gel and compared these data with the results from spectrophotometry, fluorometry and qPCR. Evaluation of the results suggests that assessment of the relative quantity of amplicons by band brightness is precise enough even for post-PCR analysis steps requiring PCR product concentrations within a certain range to function properly.
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Affiliation(s)
- Patrick Wittmeier
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Susanne Hummel
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
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17
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DNA dyes: toxicity, remediation strategies and alternatives. Folia Microbiol (Praha) 2022; 67:555-571. [PMID: 35292916 DOI: 10.1007/s12223-022-00963-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/08/2022] [Indexed: 11/04/2022]
Abstract
Release of untreated effluent from processing or manufacturing industries and other commercial premises into water bodies is a major threat to environment and human health. In this regard, the effluent generated from laboratories and other research facilities is of great concern. Among other harmful chemicals, the effluent is rich in toxic organic dyes, which get exposed to the environment and pose serious health risk. The dyes used in nucleic acid analysis specially the DNA dyes are known for their teratogenicity and mutagenic potential, which mainly depends upon the organism and circumstances under which it is exposed. Among animals and humans, exposure to theses dyes may lead to irritation in mouth, eyes and respiratory tract and many other possible effects which are yet to be explored. To overcome these problems, dyes present in the effluents from laboratories must be degraded to non-toxic forms. Various strategies have been proposed and investigated for degradation and remediation of contaminated laboratory effluent. As a modern and cost-effective technique, biodegradation using microbes and plants is potentially eco-friendly and sustainable technique for detoxifying these dyes. In this article, we have discussed and reviewed the structure, properties and toxicity profile of prominent nucleic acid dyes, along with the strategies of remediation of laboratory effluents contaminated with these dyes. In addition, we have also discussed the feasibility and limitations of these remediation strategies and identified research gaps that can help researchers to explore more effective solutions to manage this area of great concern. We have also reviewed various less toxic alternatives of these common as safer options of these dyes.
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18
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Single-staining flow cytometry approach using SYTOX™ green to describe electroporation effects on Escherichia coli. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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20
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Maurye P, Basu A, Kumari K, Dey P, Sen S, Devi MS. A unified quartet DNA gel electrophoresis instrument with integrated agarose gel casting, electrophoresis, staining, and imaging facilities. SEPARATION SCIENCE PLUS 2021. [DOI: 10.1002/sscp.202100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Praveen Maurye
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
| | - Arpita Basu
- Biotechnology Kendriya Vidyalaya Ministry of Human Resource Development Bhubaneswar Orissa India
| | - Kavita Kumari
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
| | | | - Sohini Sen
- School of Bioscience and Engineering Jadavpur Universty Kolkata West Bengal India
| | - Manoharmayum Shaya Devi
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
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21
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Cook R, Mitchell N, Henry J. Assessment of Diamond™ Nucleic Acid Dye for the identification and targeted sampling of latent DNA in operational casework. Forensic Sci Int Genet 2021; 55:102579. [PMID: 34455366 DOI: 10.1016/j.fsigen.2021.102579] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Accepted: 08/15/2021] [Indexed: 12/19/2022]
Abstract
Recovery and DNA profiling of latent touch DNA deposits is a ubiquitous practice by operational forensic laboratories that provides critical evidence in many criminal investigations. Despite recent improvements in the sensitivity of contemporary DNA profiling kits, the inability to localise and visually quantify touch DNA deposits on an exhibit means that ineffective or unwarranted sampling is often performed leading to poor success. Diamond™ Nucleic Acid Dye (DD) is a fluorescent DNA binding dye which has recently been shown to bind to corneocytes enabling visualisation and targeted sampling of touch DNA deposits under controlled conditions. The ability to translate these findings to operational casework, where a diverse range of substrates is encountered and the amount and distribution of touch DNA is uncontrolled, is currently unknown. Here, we provide the first report on the use of DD in an operational context. Spraying items with DD was shown to have no impact on downstream immunological testing, DNA extraction, or DNA profiling with the GlobalFiler™ PCR amplification kit. DD was shown to effectively locate areas of touch DNA on select exhibits using the Polilight. Issues with background fluorescence, non-specific staining, interference from fingerprint enhancement reagents, or absorbance of the excitation light by black surfaces demonstrated that DD is not compatible with all exhibits. Background fluorescence also prevented the use of DD to screen for the presence of cellular material on IsoHelix swabs post-sampling but it was suitable for screening Lovell DNA tapelifts. A casework trial of 49 plastic bag and tape exhibits showed limited application of DD to triage out negative items as DNA was recovered from items where DD fluorescence was not detected. Where DD fluorescence was detected, its broad distribution prevented targeted sampling and any correlation to be made between the amount observed and DNA yield or profiling outcome. The DD procedure also increased the time taken to search exhibits and risk of inadvertent contamination. Our study suggests that DD is not suited as a generalised screening technique across all touch casework exhibits but further investigation is warranted to determine its applicability to specific exhibit types.
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Affiliation(s)
- Russell Cook
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia
| | - Natasha Mitchell
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia
| | - Julianne Henry
- Forensic Science SA, GPO Box 2790, Adelaide, South Australia 5001, Australia; College of Science and Engineering, Flinders University of South Australia, Bedford Park, South Australia 5042, Australia.
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22
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Saarnio VK, Alaranta JM, Lahtinen TM. Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference. J Mater Chem B 2021; 9:3484-3488. [PMID: 33909740 DOI: 10.1039/d1tb00312g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Five nucleic acid binding cyanine dyes were synthesized and their photophysical properties were evaluated. Changing a single heteroatom in the chromophore causes major differences both in brightness and photostability between the dyes. With such alteration, the brightness of the chromophore increased two-fold compared to the one found in SYBR Green I.
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Affiliation(s)
- Ville K Saarnio
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
| | - Johanna M Alaranta
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
| | - Tanja M Lahtinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
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23
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Zand E, Schottroff F, Steinacker E, Mae-Gano J, Schoenher C, Wimberger T, Wassermann KJ, Jaeger H. Advantages and limitations of various treatment chamber designs for reversible and irreversible electroporation in life sciences. Bioelectrochemistry 2021; 141:107841. [PMID: 34098460 DOI: 10.1016/j.bioelechem.2021.107841] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 01/25/2023]
Abstract
The fundamental mechanisms of pulsed electric fields on biological cells are not yet fully elucidated, though it is apparent that membrane electroporation plays a crucial role. Little is known about treatment-chamber-specific effects, and systematic studies are scarce. Thus, the present study evaluates the (dis-)advantages of various treatment chamber designs for liquid applications at differing scales. Three chambers, namely parallel plate microfluidic (V̇: 0.1 ml/min; titanium electrodes), co-linear meso (V̇: 5.0 ml/min; stainless steel electrodes), and co-linear macro (V̇: 83.3 ml/min; stainless steel electrodes) chambers, were studied. Electroporation effects on Escherichia coli in media with 0.1-10.0 mS/cm were evaluated by plate counts and flow cytometry at 8, 16, and 20 kV/cm. For the microfluidic chamber, predominantly irreversible electroporation (2.5 logs10 reductions) was seen at 0.1 mS/cm, while high irreversible electroporation (4.2 logs10 reductions) at 10.0 mS/cm was observed for the macro chamber. The meso chamber indicated a similar trend towards increased conductivity, even though only low inactivation levels were present. Variation in conductivity and electrode configuration or area likely induces effects resulting in distinct electroporation levels, as observed for the micro and macro chamber. Suitable application scenarios, depending on targeted electroporation effects, were suggested.
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Affiliation(s)
- Elena Zand
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Felix Schottroff
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; BOKU Core Facility Food & Bio Processing, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Elisabeth Steinacker
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Jennifer Mae-Gano
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Terje Wimberger
- Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Klemens J Wassermann
- Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Henry Jaeger
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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24
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Champion J, Kanokwongnuwut P, van Oorschot RAH, Taylor D, Linacre A. Evaluation of a fluorescent dye to visualize touch DNA on various substrates. J Forensic Sci 2021; 66:1435-1442. [PMID: 33629435 DOI: 10.1111/1556-4029.14695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
A wide variety of items are submitted as evidence in a forensic investigation. Identifying the location of DNA on such items is central to maximizing DNA profiling success and thus the ability to link a person of interest to a particular item or crime. Recent publications describe a fluorescent staining method using Diamond™ Dye (DD) to visualize cellular material on the surface of non-porous items (e.g., glass, plastic). However, substrates of varying porosity and background color have not yet been examined. Varying porous substrates (i.e., paper bank note, stamp, cigarette, wooden matchstick, and fabric) and non-porous substrates (i.e., enamel tooth and plastic bank note) were examined for their suitability with the use of DD. To improve the visualization of cellular material on the porous substrates, we also explored two DD diluents and adjusting image contrast. The results suggest the optimal diluent depends on the absorbent nature of the substrate. For example, ethanol was sufficient for visualization on the non-porous substrates, whereas water was better for the porous substrates. While cellular material was detected on the paper bank note, tooth, and stamp, background fluorescence or autofluorescence and surface type of matchstick prevented clear visualization on this substrate. It was also determined that by adjusting the contrast of images for tooth, paper bank note and matchstick aided in the detection of cellular material. Overall, this study extends the use of DD for latent DNA detection to absorbent substrates, highlights the limitations associated with these substrate types, and suggests modifications to improve visualization on these challenging substrates.
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Affiliation(s)
- Jessica Champion
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Vic., Australia.,School of Molecular Sciences, La Trobe University, Bundoora, Vic., Australia
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia.,Forensic Science South Australia, Adelaide, SA, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia
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25
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Nouwairi RL, O'Connell KC, Gunnoe LM, Landers JP. Microchip Electrophoresis for Fluorescence-Based Measurement of Polynucleic Acids: Recent Developments. Anal Chem 2020; 93:367-387. [PMID: 33351599 DOI: 10.1021/acs.analchem.0c04596] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Renna L Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Killian C O'Connell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Leah M Gunnoe
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22903, United States
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26
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Alkhamis O, Yang W, Farhana R, Yu H, Xiao Y. Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease. Nucleic Acids Res 2020; 48:e120. [PMID: 33053182 PMCID: PMC7672472 DOI: 10.1093/nar/gkaa849] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
In vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Weijuan Yang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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27
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Wang Y, Zhou R, Liu W, Liu C, Wu P. Comparison of benzothiazole-based dyes for sensitive DNA detection. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.01.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Cunha EN, de Souza MFB, Lanza DCF, Lima JPMS. A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum. PLoS One 2020; 15:e0240536. [PMID: 33057447 PMCID: PMC7561130 DOI: 10.1371/journal.pone.0240536] [Citation(s) in RCA: 4] [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: 04/30/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.
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Affiliation(s)
- Eduardo Nogueira Cunha
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
| | - Maria Fernanda Bezerra de Souza
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - Daniel Carlos Ferreira Lanza
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - João Paulo Matos Santos Lima
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Natal, Brazil
- * E-mail:
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Olsen A, Miller M, Yadavalli VK, Ehrhardt CJ. Open source software tool for the automated detection and characterization of epithelial cells from trace biological samples. Forensic Sci Int 2020; 312:110300. [PMID: 32371282 DOI: 10.1016/j.forsciint.2020.110300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 11/25/2022]
Abstract
This paper presents a strategy for an unsupervised workflow for identifying epithelial cells in microscopic images and characterizing their morphological and/or optical properties. The proposed method can be used on cells that have been stained with fluorescent dyes and imaged using conventional optical microscopes. The workflow was tested on cell populations that were imaged directly on touch/contact surfaces and stained with nucleic acid dyes to visualize genetic content. Our results show that this approach could be a useful strategy for characterizing differences in staining efficiency and/or morphological properties of individual cells or aggregate populations within a biological sample. Further, they can potentially reduce the laborious nature of microscopic analysis and increase throughput and reproducibility of similar studies.
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Affiliation(s)
- Anita Olsen
- Department of Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Mekhi Miller
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vamsi K Yadavalli
- Department of Chemical and Life Sciences Engineering, Virginia Commonwealth University, Richmond, VA, United States
| | - Christopher J Ehrhardt
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, United States.
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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31
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Motohashi K. Development of highly sensitive and low-cost DNA agarose gel electrophoresis detection systems, and evaluation of non-mutagenic and loading dye-type DNA-staining reagents. PLoS One 2019; 14:e0222209. [PMID: 31498824 PMCID: PMC6733488 DOI: 10.1371/journal.pone.0222209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/23/2019] [Indexed: 11/18/2022] Open
Abstract
Highly sensitive and low-cost DNA agarose gel detection systems were developed using non-mutagenic and loading dye-type DNA-staining reagents. The DNA detection system that used Midori Green Direct and Safelook Load-Green, both with an optimum excitation wavelength at ~490 nm, could detect DNA-fragments at the same sensitivity to that of the UV (312 nm)-transilluminator system combined with ethidium bromide, after it was excited by a combination of cyan LED light and a shortpass filter (510 nm). The cyan LED system can be also applied to SYBR Safe that is widely used as a non-toxic dye for post-DNA-staining. Another DNA-detection system excited by black light was also developed. Black light used in this system had a peak emission at 360 nm and caused less damage to DNA due to lower energy of UV rays with longer wavelength when compared to those of short UV rays. Moreover, hardware costs of the black light system were ~$100, less than 1/10 of the commercially available UV (365 nm) transilluminator (>$1,000). EZ-Vision and Safelook Load-White can be used as non-mutagenic and loading dye-type DNA-staining reagents in this system. The black light system had a greater detection sensitivity for DNA fragments stained by EZ-Vision and Safelook Load-White compared with the commercially available imaging system using UV (365 nm) transilluminator.
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Affiliation(s)
- Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo Motoyama, Kita-Ku, Kyoto, Japan
- * E-mail:
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32
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Karimi F, Dabbagh S. Gel green fluorescence ssDNA aptasensor based on carbon nanotubes for detection of anthrax protective antigen. Int J Biol Macromol 2019; 140:842-850. [PMID: 31470050 DOI: 10.1016/j.ijbiomac.2019.08.219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/09/2023]
Abstract
Bacillus anthracis, the causative agent of anthrax, is a harmful pathogen with potential ability as a biological weapon which persuades scientists to develop novel methods to detect anthrax from infected resources. In this study, a multi-walled carbon nanotube (MWCNTs)-based fluorescence aptasensor was fabricated to detect the recombinant protective antigen domain 4 (rPAD4) of Bacillus anthracis as the most important key factor in development of anthrax. First, PAD4 was recombinant expressed in E. coli and purified by Ni-NTA column. Second, the affinity of aptamer to rPAD4 was confirmed by ELAA assay. In aptasensor design, the aptamer was labeled with Gel Green and immobilized on MWCNTs. Upon the adsorption of labeled aptamer on MWCNTs, fluorescence emission was quenched. In contrast, by adding rPAD4 to hybridization reaction and incubation for 10 min, the fluorescence emission was significantly recovered to 85% compared to the control. Detection limit for the sensitivity and specificity of the aptasensor was determined 20 ng/ml and 62.5 ng/ml purified and unpurified rPAD4 protein, respectively. Also, applicability of aptasensor was showed in mouse serum sample. Finally, results indicated that nanosensor has the potential to be developed as a high-sensitive, cost-effective and fast-acting system for measuring of PA in anthrax diagnostic tests.
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Affiliation(s)
- Farrokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, P.O. Box 55181-83111, Maragheh, Iran.
| | - Somayyeh Dabbagh
- Department of Biotechnology, Faculty of Science, University of Maragheh, P.O. Box 55181-83111, Maragheh, Iran
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33
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Improved STR profiles from improvised explosive device (IED): fluorescence latent DNA detection and direct PCR. Forensic Sci Int Genet 2019; 41:168-176. [DOI: 10.1016/j.fsigen.2019.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/27/2019] [Accepted: 05/14/2019] [Indexed: 11/30/2022]
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34
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Enhancement of fingermarks and visualizing DNA. Forensic Sci Int 2019; 300:99-105. [DOI: 10.1016/j.forsciint.2019.04.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 01/26/2023]
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35
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Sun N, Wang Y, Yao X, Chen F, Gao D, Wang W, Li X. Visual signal generation for the detection of influenza viruses by duplex recombinase polymerase amplification with lateral flow dipsticks. Anal Bioanal Chem 2019; 411:3591-3602. [PMID: 31079175 DOI: 10.1007/s00216-019-01840-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
We present a detailed study on visual detection of influenza viruses by duplex recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFDs). The LFD consisted of two test lines and a control line, on which anti-fluorescein isothiocyanate antibodies, anti-digoxigenin antibodies, and biotinylated bovine serum albumin were immobilized, respectively. The performance of the LFD was evaluated with dual-labeled DNA amplicons. The results indicate that the detection of DNA amplicons by LFDs is specific and sensitive, with detection limits of 5.80 fmol for fluorescein isothiocyanate-labeled amplicons and 8.39 fmol for digoxigenin-labeled amplicons. We next developed a duplex RPA-LFD assay for simultaneous detection of influenza A virus and influenza B virus, and then optimized the parameters, including the reaction temperature, reaction time, and concentrations of primers and probes. Assessment of the specificity and sensitivity indicated that this assay is sensitive and specific for simultaneous detection of influenza viruses, with detection limits of 50 copies per reaction for influenza B virus and 500 copies per reaction for influenza A virus, without cross-reactivity with other pathogens. Compared with real-time PCR as a reference method to detect influenza viruses in clinical samples, the clinical sensitivity of the duplex RPA-LFD assay was 78.57% for influenza A virus and 87.50% for influenza B virus, with 100% specificity. In conclusion, the duplex RPA-LFD assay is a rapid, cost-effective, and sensitive method for the identification of influenza viruses.
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Affiliation(s)
- Ning Sun
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Ying Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xinyue Yao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Fangfang Chen
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Deyu Gao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Weiping Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xiaojun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China. .,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, 210002, Jiangsu, China.
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36
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Han X, Wang E, Cui Y, Lin Y, Chen H, An R, Liang X, Komiyama M. The staining efficiency of cyanine dyes for single-stranded DNA is enormously dependent on nucleotide composition. Electrophoresis 2019; 40:1708-1714. [PMID: 31004446 DOI: 10.1002/elps.201800445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/21/2019] [Accepted: 04/15/2019] [Indexed: 11/12/2022]
Abstract
The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson-Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.
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Affiliation(s)
- Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Erchi Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yikai Lin
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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37
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Oluwadare O, Highsmith M, Cheng J. An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data. Biol Proced Online 2019; 21:7. [PMID: 31049033 PMCID: PMC6482566 DOI: 10.1186/s12575-019-0094-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/01/2019] [Indexed: 01/08/2023] Open
Abstract
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.
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Affiliation(s)
- Oluwatosin Oluwadare
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
| | - Max Highsmith
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
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38
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Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
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Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
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39
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Kanokwongnuwut P, Kirkbride KP, Linacre A. Detection of latent DNA. Forensic Sci Int Genet 2018; 37:95-101. [DOI: 10.1016/j.fsigen.2018.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/13/2018] [Accepted: 08/07/2018] [Indexed: 11/29/2022]
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40
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Kanokwongnuwut P, Kirkbride P, Linacre A. Visualising latent DNA on swabs. Forensic Sci Int 2018; 291:115-123. [DOI: 10.1016/j.forsciint.2018.08.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 01/23/2023]
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41
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GelRed/[G3T]5/Tb3+ hybrid: A novel label-free ratiometric fluorescent probe for H2O2 and oxidase-based visual biosensing. Biosens Bioelectron 2018; 100:526-532. [DOI: 10.1016/j.bios.2017.09.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/26/2017] [Accepted: 09/26/2017] [Indexed: 11/18/2022]
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42
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Choi YJ, Zhu J, Chung S, Siddiqui N, Feng Q, Stathopulos PB. Targeting Cysteine Thiols for in Vitro Site-specific Glycosylation of Recombinant Proteins. J Vis Exp 2017. [PMID: 29053695 DOI: 10.3791/56302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Stromal interaction molecule-1 (STIM1) is a type-I transmembrane protein located on the endoplasmic reticulum (ER) and plasma membranes (PM). ER-resident STIM1 regulates the activity of PM Orai1 channels in a process known as store operated calcium (Ca2+) entry which is the principal Ca2+ signaling process that drives the immune response. STIM1 undergoes post-translational N-glycosylation at two luminal Asn sites within the Ca2+ sensing domain of the molecule. However, the biochemical, biophysical, and structure biological effects of N-glycosylated STIM1 were poorly understood until recently due to an inability to readily obtain high levels of homogeneous N-glycosylated protein. Here, we describe the implementation of an in vitro chemical approach which attaches glucose moieties to specific protein sites applicable to understanding the underlying effects of N-glycosylation on protein structure and mechanism. Using solution nuclear magnetic resonance spectroscopy we assess both efficiency of the modification as well as the structural consequences of the glucose attachment with a single sample. This approach can readily be adapted to study the myriad glycosylated proteins found in nature.
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Affiliation(s)
- Yoo Jung Choi
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario
| | - Jinhui Zhu
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario
| | - Steve Chung
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario
| | - Naveed Siddiqui
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario
| | - Qingping Feng
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario;
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Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments. PLoS One 2017; 12:e0169554. [PMID: 28056074 PMCID: PMC5215936 DOI: 10.1371/journal.pone.0169554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
In this study, GelGreen™ was investigated as a replacement for SYBR® Safe to stain DNA in cesium chloride (CsCl) density gradients for DNA-stable isotope probing (SIP) experiments. Using environmental DNA, the usage of GelGreen™ was optimized for sensitivity compared to SYBR® Safe, its optimal concentration, detection limit for environmental DNA and its application in environmental DNA-SIP assay. Results showed that GelGreen™ was more sensitive than SYBR® Safe, while the optimal dosage (15X concentration) needed was approximately one-third of SYBR® Safe, suggesting that its sensitivity was three times more superior than SYBR® Safe. At these optimal parameters, the detection limit of GelGreen™-stained environmental DNA was as low as 0.2 μg, but the usage of 0.5 μg environmental DNA was recommended to produce a more consistent DNA band. In addition, a modified needle extraction procedure was developed to withdraw DNA effectively by fractionating CsCl density gradients into four or five fractions. The successful application of GelGreen™ staining with 13C-labeled DNA from enriched activated sludge suggests that this stain was an excellent alternative of SYBR® Safe in CsCl density gradients for DNA-SIP assays.
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44
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Optimization of Diamond Nucleic Acid Dye for quantitative PCR. Biotechniques 2016; 61:183-189. [DOI: 10.2144/000114458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/19/2016] [Indexed: 11/23/2022] Open
Abstract
Here, we evaluate Diamond Nucleic Acid Dye (DD) for use in quantitative PCR (qPCR) applications. Although DD is a commercially available stain for detection of DNA separated by gel electrophoresis, its use as a detection dye in qPCR has yet to be described. To determine if DD can be used in qPCR, we investigated its inhibitory effects on qPCR at concentrations ranging 0.1–2.5×. Serial dilution of DNA was used to determine the efficiency, sensitivity, and linearity of DD-generated qPCR data in comparison to other commonly used fluorescent dyes such as SYBR Green (SG), EvaGreen (EG), and BRYT Green (BG). DD was found to be comparable with other dyes for qPCR applications, with an R2 value >0.9 and an efficiency of 0.83. Mitochondrial DNA (mtDNA) target signals were successfully produced by DD over a DNA dilution range of ∼28 ng— 0.28 pg, demonstrating comparable sensitivity to the other dyes investigated. Cq values obtained using DD were lower than those using EG by almost 7 cycles. We conclude that Diamond Nucleic Acid Dye is a cheaper, less toxic alternative for qPCR applications.
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45
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Fluorescent cyanine dyes for the quantification of low amounts of dsDNA. Anal Biochem 2016; 511:74-9. [DOI: 10.1016/j.ab.2016.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/21/2022]
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46
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Examination of tryptamine-squaraine complexes as both colorimetric and fluorometric stains in gel electrophoresis. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Haines AM, Linacre A. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling. Forensic Sci Int 2016; 262:190-5. [DOI: 10.1016/j.forsciint.2016.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/16/2016] [Accepted: 03/12/2016] [Indexed: 12/24/2022]
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Haines AM, Tobe SS, Kobus H, Linacre A. Finding DNA: Using fluorescent in situ detection. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.198] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Haines AM, Tobe SS, Kobus HJ, Linacre A. Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing. Electrophoresis 2015. [DOI: 10.1002/elps.201500170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alicia M. Haines
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Shanan S. Tobe
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Hilton J. Kobus
- School of Chemical and Physical Sciences; Flinders University; Adelaide South Australia
| | - Adrian Linacre
- School of Biological Sciences; Flinders University; Adelaide South Australia
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