Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus
Background/Introduction: The havoc wrought by COVID-19 pandemic across the globe has pushed the frontiers in science, creating many opportunities and advancements in the diagnostic and therapeutic. One such positive impact is the effort to synthesize highly contagious SARS-CoV-2 virus, virus-like pa...
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Elsevier
2025-03-01
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| Series: | International Journal of Infectious Diseases |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971224006593 |
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| author | Dr Siti Farah Nawi Mr Amir Muhaimin Akmal Shukri Assoc Prof Dr Wang Seok Mui Assoc Prof Dr Chia Suet Lin Dr Citartan Marimuthu |
| author_facet | Dr Siti Farah Nawi Mr Amir Muhaimin Akmal Shukri Assoc Prof Dr Wang Seok Mui Assoc Prof Dr Chia Suet Lin Dr Citartan Marimuthu |
| author_sort | Dr Siti Farah Nawi |
| collection | DOAJ |
| description | Background/Introduction: The havoc wrought by COVID-19 pandemic across the globe has pushed the frontiers in science, creating many opportunities and advancements in the diagnostic and therapeutic. One such positive impact is the effort to synthesize highly contagious SARS-CoV-2 virus, virus-like particles (VLPs) that mimics the actual virus albeit much safer. We previously developed a SARS CoV-2 Delta variant VLPs (SDV-VLPs) which is a safe alternative to the SARS-CoV-2 virus and mimics the morphology of the virus. On the other hand, aptamers are increasingly emerging as the alternative molecular recognition element to antibodies. Aptamers are single-stranded nucleic acids that can bind to various target molecules with high specificity and affinity. Their production is cheaper, faster, and simpler with ease of chemical modifications with no batch-to-batch variation. The existing aptamers can be further improved by rational design approach, such as multimerization. In this study, we aim to evaluate the performance of the multimerized aptamers in the detection of SDV-VLPs. Methods & Materials: Oligonucleotide sequences (Apt25 & Apt27) were retrieved from the study by Mironov et al.. Each parent aptamer was modified through truncation followed by multimerization (HMApt25 & HMApt27). The resulting secondary structures of the modified aptamers were verified using the mFold webserver to ensure that the core secondary structural motifs as in the parent aptamers were retained. All the four aptamers including the first-generation aptamers were subjected to direct enzyme-linked aptasorbent assay (ELASA) against the SDV-VLPs and recombinant spike protein (RS). Results: Based on the direct ELASA assay against SDV-VLPs and RS, both the modified aptamers HMApt25 and HMApt27 have higher OD readings compared to the full-length Apt25 and Apt27. There is an increase of 1.39-fold and 1.1-fold in OD450 value obtained between HMApt25 and HMApt27 and their respective parents against the SDV-VLPs. Discussion: In this study, we found that the HMApt27 showed improved binding toward the SDV-VLPs compared to the HMApt25 despite both having similar secondary structures. This could be due to the steric hindrance-induced electrostatic attraction is alleviated in HMApt27. Higher OD450 values obtained by multimerized aptamers that have multivalency properties also suggest that having more binding sites against the target protein gives improved binding than their parent aptamers. The same observation occurred with aptamers tested against the SDV-VLPs compared to RS, which was possibly due to the SDV-VLPs harbouring many copies of spike proteins on its surface as compared to the RS. Conclusion: The increase in the binding strength following the multimerization of aptamers as a refinement strategy with its biological stability could potentially improve diagnostic performance and therapeutic activities. Future investigations involving computational methods such as rigid docking and molecular dynamic simulation are recommended to validate its use and applications. |
| format | Article |
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| institution | OA Journals |
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| language | English |
| publishDate | 2025-03-01 |
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| series | International Journal of Infectious Diseases |
| spelling | doaj-art-21177ac6aa684d6a9f8d2aae5d80fecc2025-08-20T02:10:57ZengElsevierInternational Journal of Infectious Diseases1201-97122025-03-0115210758410.1016/j.ijid.2024.107584Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 VirusDr Siti Farah Nawi0Mr Amir Muhaimin Akmal Shukri1Assoc Prof Dr Wang Seok Mui2Assoc Prof Dr Chia Suet Lin3Dr Citartan Marimuthu4Department of Medical Microbiology and Parasitology, Faculty of Medicine,Universiti Teknologi MARA (UiTM)Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARADepartment of Medical Microbiology and Parasitology, Faculty of Medicine,Universiti Teknologi MARA (UiTM); Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA; Non-Destructive Biomedical and Pharmaceutical Research Center, Smart Manufacturing Research Institute (SMRI), Universiti Teknologi MARADepartment of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia; UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra MalaysiaAdvanced Medical & Dental Institute (AMDI), Universiti Sains MalaysiaBackground/Introduction: The havoc wrought by COVID-19 pandemic across the globe has pushed the frontiers in science, creating many opportunities and advancements in the diagnostic and therapeutic. One such positive impact is the effort to synthesize highly contagious SARS-CoV-2 virus, virus-like particles (VLPs) that mimics the actual virus albeit much safer. We previously developed a SARS CoV-2 Delta variant VLPs (SDV-VLPs) which is a safe alternative to the SARS-CoV-2 virus and mimics the morphology of the virus. On the other hand, aptamers are increasingly emerging as the alternative molecular recognition element to antibodies. Aptamers are single-stranded nucleic acids that can bind to various target molecules with high specificity and affinity. Their production is cheaper, faster, and simpler with ease of chemical modifications with no batch-to-batch variation. The existing aptamers can be further improved by rational design approach, such as multimerization. In this study, we aim to evaluate the performance of the multimerized aptamers in the detection of SDV-VLPs. Methods & Materials: Oligonucleotide sequences (Apt25 & Apt27) were retrieved from the study by Mironov et al.. Each parent aptamer was modified through truncation followed by multimerization (HMApt25 & HMApt27). The resulting secondary structures of the modified aptamers were verified using the mFold webserver to ensure that the core secondary structural motifs as in the parent aptamers were retained. All the four aptamers including the first-generation aptamers were subjected to direct enzyme-linked aptasorbent assay (ELASA) against the SDV-VLPs and recombinant spike protein (RS). Results: Based on the direct ELASA assay against SDV-VLPs and RS, both the modified aptamers HMApt25 and HMApt27 have higher OD readings compared to the full-length Apt25 and Apt27. There is an increase of 1.39-fold and 1.1-fold in OD450 value obtained between HMApt25 and HMApt27 and their respective parents against the SDV-VLPs. Discussion: In this study, we found that the HMApt27 showed improved binding toward the SDV-VLPs compared to the HMApt25 despite both having similar secondary structures. This could be due to the steric hindrance-induced electrostatic attraction is alleviated in HMApt27. Higher OD450 values obtained by multimerized aptamers that have multivalency properties also suggest that having more binding sites against the target protein gives improved binding than their parent aptamers. The same observation occurred with aptamers tested against the SDV-VLPs compared to RS, which was possibly due to the SDV-VLPs harbouring many copies of spike proteins on its surface as compared to the RS. Conclusion: The increase in the binding strength following the multimerization of aptamers as a refinement strategy with its biological stability could potentially improve diagnostic performance and therapeutic activities. Future investigations involving computational methods such as rigid docking and molecular dynamic simulation are recommended to validate its use and applications.http://www.sciencedirect.com/science/article/pii/S1201971224006593 |
| spellingShingle | Dr Siti Farah Nawi Mr Amir Muhaimin Akmal Shukri Assoc Prof Dr Wang Seok Mui Assoc Prof Dr Chia Suet Lin Dr Citartan Marimuthu Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus International Journal of Infectious Diseases |
| title | Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus |
| title_full | Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus |
| title_fullStr | Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus |
| title_full_unstemmed | Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus |
| title_short | Evaluation of Multimerization of Aptamers against SARS-CoV-2 Delta Variant VLP as A Refinement Strategy in The Detection of the SARS-CoV-2 Virus |
| title_sort | evaluation of multimerization of aptamers against sars cov 2 delta variant vlp as a refinement strategy in the detection of the sars cov 2 virus |
| url | http://www.sciencedirect.com/science/article/pii/S1201971224006593 |
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