Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes
Abstract We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy...
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43004-9 |
| _version_ | 1797557921819656192 |
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| author | Ren Ren Shenglin Cai Xiaona Fang Xiaoyi Wang Zheng Zhang Micol Damiani Charlotte Hudlerova Annachiara Rosa Joshua Hope Nicola J. Cook Peter Gorelkin Alexander Erofeev Pavel Novak Anjna Badhan Michael Crone Paul Freemont Graham P. Taylor Longhua Tang Christopher Edwards Andrew Shevchuk Peter Cherepanov Zhaofeng Luo Weihong Tan Yuri Korchev Aleksandar P. Ivanov Joshua B. Edel |
| author_facet | Ren Ren Shenglin Cai Xiaona Fang Xiaoyi Wang Zheng Zhang Micol Damiani Charlotte Hudlerova Annachiara Rosa Joshua Hope Nicola J. Cook Peter Gorelkin Alexander Erofeev Pavel Novak Anjna Badhan Michael Crone Paul Freemont Graham P. Taylor Longhua Tang Christopher Edwards Andrew Shevchuk Peter Cherepanov Zhaofeng Luo Weihong Tan Yuri Korchev Aleksandar P. Ivanov Joshua B. Edel |
| author_sort | Ren Ren |
| collection | DOAJ |
| description | Abstract We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required. |
| first_indexed | 2024-03-10T17:23:06Z |
| format | Article |
| id | doaj.art-1aeae1396aa84739853d9656c3d758c3 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-10T17:23:06Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-1aeae1396aa84739853d9656c3d758c32023-11-20T10:14:57ZengNature PortfolioNature Communications2041-17232023-11-0114111610.1038/s41467-023-43004-9Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probesRen Ren0Shenglin Cai1Xiaona Fang2Xiaoyi Wang3Zheng Zhang4Micol Damiani5Charlotte Hudlerova6Annachiara Rosa7Joshua Hope8Nicola J. Cook9Peter Gorelkin10Alexander Erofeev11Pavel Novak12Anjna Badhan13Michael Crone14Paul Freemont15Graham P. Taylor16Longhua Tang17Christopher Edwards18Andrew Shevchuk19Peter Cherepanov20Zhaofeng Luo21Weihong Tan22Yuri Korchev23Aleksandar P. Ivanov24Joshua B. Edel25Department of Chemistry, Imperial College London, Molecular Sciences Research HubDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubThe Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubThe Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubThe Chromatin Structure and Mobile DNA Laboratory, The Francis Crick InstituteThe Chromatin Structure and Mobile DNA Laboratory, The Francis Crick InstituteThe Chromatin Structure and Mobile DNA Laboratory, The Francis Crick InstituteNational University of Science and Technology “MISIS”National University of Science and Technology “MISIS”ICAPPIC LimitedMolecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonSection of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonSection of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonMolecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonState Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang UniversityDepartment of Metabolism, Digestion and Reproduction, Imperial College LondonDepartment of Metabolism, Digestion and Reproduction, Imperial College LondonThe Chromatin Structure and Mobile DNA Laboratory, The Francis Crick InstituteThe Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesThe Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesDepartment of Metabolism, Digestion and Reproduction, Imperial College LondonDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubDepartment of Chemistry, Imperial College London, Molecular Sciences Research HubAbstract We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.https://doi.org/10.1038/s41467-023-43004-9 |
| spellingShingle | Ren Ren Shenglin Cai Xiaona Fang Xiaoyi Wang Zheng Zhang Micol Damiani Charlotte Hudlerova Annachiara Rosa Joshua Hope Nicola J. Cook Peter Gorelkin Alexander Erofeev Pavel Novak Anjna Badhan Michael Crone Paul Freemont Graham P. Taylor Longhua Tang Christopher Edwards Andrew Shevchuk Peter Cherepanov Zhaofeng Luo Weihong Tan Yuri Korchev Aleksandar P. Ivanov Joshua B. Edel Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes Nature Communications |
| title | Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes |
| title_full | Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes |
| title_fullStr | Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes |
| title_full_unstemmed | Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes |
| title_short | Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes |
| title_sort | multiplexed detection of viral antigen and rna using nanopore sensing and encoded molecular probes |
| url | https://doi.org/10.1038/s41467-023-43004-9 |
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