Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics
The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This stud...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253123000306 |
| _version_ | 1811155491420635136 |
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| author | Suttinee Poolsup Emil Zaripov Nico Hüttmann Zoran Minic Polina V. Artyushenko Irina A. Shchugoreva Felix N. Tomilin Anna S. Kichkailo Maxim V. Berezovski |
| author_facet | Suttinee Poolsup Emil Zaripov Nico Hüttmann Zoran Minic Polina V. Artyushenko Irina A. Shchugoreva Felix N. Tomilin Anna S. Kichkailo Maxim V. Berezovski |
| author_sort | Suttinee Poolsup |
| collection | DOAJ |
| description | The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis. |
| first_indexed | 2024-04-10T04:35:12Z |
| format | Article |
| id | doaj.art-6e6e8578da604e78a7b6a2ab97f84687 |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-04-10T04:35:12Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-6e6e8578da604e78a7b6a2ab97f846872023-03-10T04:34:50ZengElsevierMolecular Therapy: Nucleic Acids2162-25312023-03-0131731743Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnosticsSuttinee Poolsup0Emil Zaripov1Nico Hüttmann2Zoran Minic3Polina V. Artyushenko4Irina A. Shchugoreva5Felix N. Tomilin6Anna S. Kichkailo7Maxim V. Berezovski8Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, CanadaDepartment of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, CanadaJohn L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, CanadaJohn L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, CanadaLaboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, RussiaLaboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, RussiaDepartment of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia; Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, RussiaLaboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, RussiaDepartment of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Corresponding author: Maxim V. Berezovski, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.http://www.sciencedirect.com/science/article/pii/S2162253123000306MT: Oligonucleotides: Diagnostics and BiosensorsCOVID-19 diagnosisSARS-CoV-2 nucleocapsid detectionlabel-free optical aptasensoraptamer selectionbiolayer interferometry |
| spellingShingle | Suttinee Poolsup Emil Zaripov Nico Hüttmann Zoran Minic Polina V. Artyushenko Irina A. Shchugoreva Felix N. Tomilin Anna S. Kichkailo Maxim V. Berezovski Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics Molecular Therapy: Nucleic Acids MT: Oligonucleotides: Diagnostics and Biosensors COVID-19 diagnosis SARS-CoV-2 nucleocapsid detection label-free optical aptasensor aptamer selection biolayer interferometry |
| title | Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics |
| title_full | Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics |
| title_fullStr | Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics |
| title_full_unstemmed | Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics |
| title_short | Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics |
| title_sort | discovery of dna aptamers targeting sars cov 2 nucleocapsid protein and protein binding epitopes for label free covid 19 diagnostics |
| topic | MT: Oligonucleotides: Diagnostics and Biosensors COVID-19 diagnosis SARS-CoV-2 nucleocapsid detection label-free optical aptasensor aptamer selection biolayer interferometry |
| url | http://www.sciencedirect.com/science/article/pii/S2162253123000306 |
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