In Silico Analysis of Toehold-Aptamer Sequences Targeting the SARS-CoV-2 Nucleocapsid Protein Gene for Biosensor Development †
Abstract
:1. Introduction
2. Computational Methods
2.1. Structure Retrieval
2.2. Multiple Sequence Alignment Analysis
2.3. Aptamers’ 2D-Structure Prediction
2.4. Aptamers’ 3D Modeling
2.5. Molecular Docking
3. Results and Discussion
3.1. Multiple Sequence Alignment Results
3.2. Aptamers’ 2D Structure and Free Energy
3.3. Aptamers’ 3D Modeling
3.4. Molecular Docking
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
ID | Trigger | Length | Location |
---|---|---|---|
v1 | 5′- TCTTGGTTCACCGCTCTCACTCAA -3′ | 24 | 28,424–28,447 |
v2 | 5′- CGCTCTCACTCAACATGGCAAGG -3′ | 23 | 28,435–28,457 |
v3 | 5′- CTACGCAGAAGGGAGCAGAGGCGG -3′ | 24 | 28,786–28,809 |
C(+) | 3′- GCAAATCTAGGCTTGCTGTTTGGG -5′ | 24 | |
C(−) | 3′- TGCAGAAAAAAACCATGGGTTGGG -5′ | 24 |
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Esquivel-Ortiz, K.M.; Antonio-Pérez, A.; Torres-Huerta, A.L. In Silico Analysis of Toehold-Aptamer Sequences Targeting the SARS-CoV-2 Nucleocapsid Protein Gene for Biosensor Development. Eng. Proc. 2023, 35, 21. https://doi.org/10.3390/IECB2023-14718
Esquivel-Ortiz KM, Antonio-Pérez A, Torres-Huerta AL. In Silico Analysis of Toehold-Aptamer Sequences Targeting the SARS-CoV-2 Nucleocapsid Protein Gene for Biosensor Development. Engineering Proceedings. 2023; 35(1):21. https://doi.org/10.3390/IECB2023-14718
Chicago/Turabian StyleEsquivel-Ortiz, Karla M., Aurora Antonio-Pérez, and Ana L. Torres-Huerta. 2023. "In Silico Analysis of Toehold-Aptamer Sequences Targeting the SARS-CoV-2 Nucleocapsid Protein Gene for Biosensor Development" Engineering Proceedings 35, no. 1: 21. https://doi.org/10.3390/IECB2023-14718