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Peng C, Wang Y, Chen X, Wang X, Ding L, Xu X, Wei W, Yang L, Wu J, Sun M, Xu J. A Localized CRISPR Assay that Detects Short Nucleic Acid Fragments in Unamplified Genetically Modified Samples. ACS Sens 2023; 8:1054-1063. [PMID: 36802509 DOI: 10.1021/acssensors.2c01955] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Detecting short genetically modified (GM) nucleic acid fragments in GM crops and associated products is critically important for the global agriculture industry. Although nucleic acid amplification-based technologies have been widely used for genetically modified organism (GMO) detection, they still struggle to amplify and detect these ultra-short nucleic acid fragments in highly processed products. Here, we used a multiple-CRISPR-derived RNA (crRNA) strategy to detect ultra-short nucleic acid fragments. By combining confinement effects on local concentrations, an amplification-free CRISPR-based short nucleic acid (CRISPRsna) system was established to detect the cauliflower mosaic virus 35S promoter in GM samples. Moreover, we demonstrated assay sensitivity, specificity, and reliability by directly detecting nucleic acid samples from GM crops with a wide genomic range. The CRISPRsna assay avoided possible aerosol contamination from nucleic acid amplification and saved time due to an amplification-free approach. Given that our assay displayed distinct advantages over other technologies in detecting ultra-short nucleic acid fragments, it may have wide applications for detecting GM in highly processed products.
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Affiliation(s)
- Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuling Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Schwarz AP, Kovalenko AA, Zakharova MV, Zaitsev AV. The application of the self-probing primer PCR for quantitative expression analysis of R607Q (un)edited GluA2 AMPA receptor mRNA. Biochem Biophys Res Commun 2021; 569:174-178. [PMID: 34252589 DOI: 10.1016/j.bbrc.2021.07.020] [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: 06/17/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
Adenosine deaminase-dependent RNA editing is a widespread universal mechanism of posttranscriptional gene function modulation. Changes in RNA editing level may contribute to various physiological and pathological processes. In the α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) glutamate receptor GluA2 subunit, A-I editing in the Q607R site leads to dramatic changes in function, making the receptor channel calcium-impermeable. A standard approach for quantifying (un)edited RNAs is based on endpoint PCR (Sanger sequencing or restriction analysis), a time-consuming and semiquantitative method. We aimed to develop RT-qPCR assays to quantify rat Q607R (A-I) edited/unedited mRNA in samples in the present work. Based on self-probing PCR detection chemistry, described initially for detecting short DNA fragments, we designed and optimised RT-qPCR assays to quantify Q607R (un)edited mRNA. We used self-probing primer PCR technology for mRNA quantification for the first time. Using a novel assay, we confirmed that Q607R GluA2 mRNA editing was increased in 14-day- (P14) or 21-day-old (P21) postnatal brain tissue (hippocampus) compared to the embryonic brain (whole brains at E20) in Wistar rats. Q607R unedited GluA2 mRNA was detectable by our assay in the cDNA of mature brain tissue compared to that derived through classical methods. Thus, self-probing primer PCR detection chemistry is an easy-to-use approach for RT-qPCR analysis of RNA editing.
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Affiliation(s)
- Alexander P Schwarz
- Laboratory of Molecular Mechanisms of Neuronal Interactions, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Torez Avenue 44, 199223, St. Petersburg, Russia.
| | - Anna A Kovalenko
- Laboratory of Molecular Mechanisms of Neuronal Interactions, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Torez Avenue 44, 199223, St. Petersburg, Russia
| | - Maria V Zakharova
- Laboratory of Molecular Mechanisms of Neuronal Interactions, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Torez Avenue 44, 199223, St. Petersburg, Russia
| | - Aleksey V Zaitsev
- Laboratory of Molecular Mechanisms of Neuronal Interactions, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Torez Avenue 44, 199223, St. Petersburg, Russia
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Takabatake R, Onishi M, Minegishi Y, Futo S, Soga K, Nakamura K, Kondo K, Mano J, Kitta K. Development of a Novel Detection Method Targeting an Ultrashort 25 bp Sequence Found in Agrobacterium-Mediated Transformed GM Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15327-15334. [PMID: 33296196 DOI: 10.1021/acs.jafc.0c03864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Agrobacterium-mediated transformation is the most commonly used technique for plant genetic engineering. During the transformation, a T-DNA region, which is flanked by the right border (RB) and the left border, is transferred to plant nuclear chromosomes. Simultaneously, a sequence adjacent to the RB on T-DNA is frequently transferred to plant genomes together with the intentionally introduced recombinant DNA. We developed a novel polymerase chain reaction (PCR)-mediated detection method targeting this region. The conserved sequence of the region found in genetically modified (GM) crops is only 25 bp in length. To detect this ultrashort 25 bp sequence near the RB region, we designed a primer set consisting of a 12-base forward primer and a 13-base reverse primer. The predicted band was detected from GM crops by optimizing the PCR conditions. We used lateral flow DNA chromatography for rapid and inexpensive detection. The developed method would be applicable for screening the GM crops generated by Agrobacterium-mediated transformation.
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Affiliation(s)
- Reona Takabatake
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Mari Onishi
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Yasutaka Minegishi
- Nippon Gene Co., Ltd., 1-5, Kandanishiki-cho, Chiyoda-ku, Tokyo 101-0054, Japan
| | - Satoshi Futo
- FASMAC Co., Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Keisuke Soga
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Kosuke Nakamura
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Kazunari Kondo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Junichi Mano
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Kazumi Kitta
- Division of Analytical Science, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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