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Anantharaj A, Das SJ, Sharanabasava P, Lodha R, Kabra SK, Sharma TK, Medigeshi GR. Visual Detection of SARS-CoV-2 RNA by Conventional PCR-Induced Generation of DNAzyme Sensor. Front Mol Biosci 2020; 7:586254. [PMID: 33425988 PMCID: PMC7793695 DOI: 10.3389/fmolb.2020.586254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
The gold standard for the diagnosis of SARS-CoV-2, the causative agent of COVID-19, is real-time polymerase chain reaction (PCR), which is labor-intensive, expensive, and not widely available in resource-poor settings. Therefore, it is imperative to develop novel, accurate, affordable, and easily accessible assays/sensors to diagnose and isolate COVID-19 cases. To address this unmet need, we utilized the catalytic potential of peroxidase-like DNAzyme and developed a simple visual detection assay for SARS-CoV-2 RNA using a conventional thermal cycler by the PCR-induced generation of DNAzyme sensor. The performance of RT-PCR DNAzyme-based sensor was comparable to that of real-time PCR. The pilot scale validation of RT-PCR DNAzyme-based sensor has shown ~100% sensitivity and specificity in clinical specimens (nasopharyngeal swab, n = 34), with a good correlation (Spearman r = 0.799) with the Ct-value of fluorescence probe-based real-time PCR. These findings clearly indicate the potential of this inexpensive, sensitive, and specific molecular diagnostic test to extend our testing capabilities for the detection of SARS-CoV-2 to curtail COVID-19 transmission.
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Affiliation(s)
- Anbalagan Anantharaj
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Soon Jyoti Das
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Patil Sharanabasava
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil K. Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Tarun Kumar Sharma
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Guruprasad R. Medigeshi
- National Capital Region - Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Safarpour H, Dehghani S, Nosrati R, Zebardast N, Alibolandi M, Mokhtarzadeh A, Ramezani M. Optical and electrochemical-based nano-aptasensing approaches for the detection of circulating tumor cells (CTCs). Biosens Bioelectron 2019; 148:111833. [PMID: 31733465 DOI: 10.1016/j.bios.2019.111833] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
More recently, detection of circulating tumor cells (CTCs) has been considered as an appealing prognostic and diagnostic approach for cancer patients. CTCs as a type of tumor-derived cells are secreted by the tumor and released into the blood circulation. Since the migration of CTCs is an early event in cancer progression, patients who still have tumor-free lymph nodes have to be well examined for the CTCs presence in their blood circulation. Nowadays, there is a broad range of detection methods available to identify CTCs. As artificial RNA oligonucleotides or single-stranded DNA with receptor and catalytic characteristics, aptamers have been standing out, owing to their target-induced conformational modifications, elevated stability, and target specificity to be implemented in biosensing techniques. To date, several sensitivity-enhancement methods alongside smart nanomaterials have been used for the creation of new aptasensors to address the limit of detection (LOD), and improve the sensitivity of numerous analyte identification methods. The present review article supports a focused overview of the recent studies in the identification and quantitative determination of CTCs by aptamer-based biosensors and nanobiosensors.
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Affiliation(s)
- Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Sadegh Dehghani
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nozhat Zebardast
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Zhang W, Li J, Salena B, Li Y. A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions. Chemistry 2019; 26:592-596. [PMID: 31475757 DOI: 10.1002/chem.201903536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/28/2019] [Indexed: 01/24/2023]
Abstract
DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.
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Affiliation(s)
- Wenqing Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Bruno Salena
- Department of Medicine, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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Yamashige R, Kimoto M, Okumura R, Hirao I. Visual Detection of Amplified DNA by Polymerase Chain Reaction Using a Genetic Alphabet Expansion System. J Am Chem Soc 2018; 140:14038-14041. [PMID: 30336010 DOI: 10.1021/jacs.8b08121] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Visual DNA amplification using a simple polymerase chain reaction (PCR) device is useful for field tests to detect target DNA and RNA. We hereby describe a detection system involving PCR amplification visualized with the naked eye, by genetic alphabet expansion. The system employs fluorescence resonance energy transfer (FRET) between unnatural base combinations: self-quenched dinucleotides of 2-amino-6-(2-thienyl)purine (s) as a donor and Cy3-conjugated 2-nitro-4-propynylpyrrole (Cy3-hx-Px) as an acceptor. During PCR, the triphosphate substrate of Cy3-hx-Px (Cy3-hx-dPxTP) is incorporated into DNA opposite its pairing partner, 7-(2-thienyl)-imidazo[4,5- b]pyridine (Ds), in the primer, which also contains the dinucleotides of s. Thus, the amplified DNA can be visualized by the Cy3 fluorescence resulting from the FRET between the s-dinucleotides and the incorporated Cy3-hx-Px upon 365 nm irradiation. Using this system, we demonstrated the visual single nucleotide polymorphism detection of a series of quinolone-resistant bacteria genes.
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Affiliation(s)
- Rie Yamashige
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Michiko Kimoto
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, #07-01 , Singapore 138669 , Singapore
| | - Ryo Okumura
- Rare Disease Laboratories, Group I, R&D Division , Daiichi Sankyo Co. Ltd. , 1-2-58 Hiromachi , Shinagawa-ku , Tokyo 140-8710 Japan
| | - Ichiro Hirao
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, #07-01 , Singapore 138669 , Singapore
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Kim SU, Batule BS, Mun H, Shim WB, Kim MG. Ultrasensitive colorimetric detection of Salmonella enterica Typhimurium on lettuce leaves by HRPzyme-Integrated polymerase chain reaction. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ford Carleton P, Schachter S, Parrish JA, Collins JM, Crocker JB, Dixon RF, Edgman-Levitan S, Lewandrowski KB, Stahl JE, Klapperich C, Cabodi M, Gaydos CA, Rompalo AM, Manabe Y, Wang TH, Rothman R, Geddes CD, Widdice L, Jackman J, Mathura RA, Lash TB. National Institute of Biomedical Imaging and Bioengineering Point-of-Care Technology Research Network: Advancing Precision Medicine. IEEE JOURNAL OF TRANSLATIONAL ENGINEERING IN HEALTH AND MEDICINE 2016; 4:2800614. [PMID: 27730014 PMCID: PMC5052024 DOI: 10.1109/jtehm.2016.2598837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 12/28/2022]
Abstract
To advance the development of point-of-care technology (POCT), the National Institute of Biomedical Imaging and Bioengineering established the POCT Research Network (POCTRN), comprised of Centers that emphasize multidisciplinary partnerships and close facilitation to move technologies from an early stage of development into clinical testing and patient use. This paper describes the POCTRN and the three currently funded Centers as examples of academic-based organizations that support collaborations across disciplines, institutions, and geographic regions to successfully drive innovative solutions from concept to patient care.
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K+-responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment. Biochem Biophys Res Commun 2015; 468:27-31. [DOI: 10.1016/j.bbrc.2015.10.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/31/2015] [Indexed: 11/23/2022]
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Wang S, Liu Y, Sun X, Tian Y, Zhou N. Ultrasensitive electrochemical detection of dual DNA targets based on G-quadruplex-mediated amplification. RSC Adv 2015. [DOI: 10.1039/c5ra08084c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dual DNA targets were ligated to a long strand containing a G-quadruplex forming sequence and detected on a capture probe modified electrode.
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Affiliation(s)
- Shuling Wang
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Yong Liu
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Xiaofan Sun
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Yaping Tian
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Nandi Zhou
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
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