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Juma KM, Morimoto K, Sharma V, Sharma K, Biyani R, Biyani M, Takita T, Yasukawa K. Detection of SARS-CoV-2 spike protein D614G mutation using μTGGE. Mol Biol Rep 2024; 51:289. [PMID: 38329653 DOI: 10.1007/s11033-023-09065-1] [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: 06/12/2023] [Accepted: 11/02/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The accurate and expeditious detection of SARS-CoV-2 mutations is critical for monitoring viral evolution, assessing its impact on transmission, virulence, and vaccine efficacy, and formulating public health interventions. In this study, a detection system utilizing micro temperature gradient gel electrophoresis (μTGGE) was developed for the identification of the D614 and G614 variants of the SARS-CoV-2 spike protein. METHODS The in vitro synthesized D614 and G614 gene fragments of the SARS-CoV-2 spike protein were amplified via polymerase chain reaction and subjected to μTGGE analysis. RESULTS The migration patterns exhibited by the D614 and G614 variants on the polyacrylamide gel were distinctly dissimilar and readily discernible by μTGGE. In particular, the mid-melting pattern of D614 was shorter than that of G614. CONCLUSIONS Our results demonstrate the capability of μTGGE for the rapid, precise, and cost-effective detection of SARS-CoV-2 spike protein D614 and G614 variants without the need for sequencing. Therefore, this approach holds considerable potential for use in point-of-care mutation assays for SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Vishnu Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
- Biyani BioSolutions Pvt. Ltd., R-4, Sector 3, Vidhyadharnagar, Jaipur, 302023, India
| | - Kirti Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Radhika Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Manish Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan.
- Biyani BioSolutions Pvt. Ltd., R-4, Sector 3, Vidhyadharnagar, Jaipur, 302023, India.
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan.
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.
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Kojima K, Baba M, Tsukiashi M, Nishimura T, Yasukawa K. RNA/DNA structures recognized by RNase H2. Brief Funct Genomics 2018; 18:169-173. [DOI: 10.1093/bfgp/ely024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Ribonuclease H (RNase H) [EC 3.1.26.4] is an enzyme that specifically degrades RNA from RNA/DNA hybrids. Since its discovery in 1969, the enzyme has been extensively studied for its catalytic mechanism and physiological role. RNase H has been classified into two major families, Type 1 and Type 2. Type 1 enzymes are designated RNase HI in prokaryotes and RNase H1 in eukaryotes, while Type 2 enzymes are designated RNase HII in prokaryotes and RNase H2 in eukaryotes. Type 2 enzymes are able to cleave the 5′-phosphodiester bond of one ribonucleotide embedded in a DNA double strand. Recent studies have shown that RNase H2 is involved in excision of a single ribonucleotide embedded in genomic DNA and removal of an R-loop formed in cells. It is also involved in double-strand break of DNA and its repair. In this review, we aim to outline the structures recognized by RNase H2.
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Affiliation(s)
- Kenji Kojima
- Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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