Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning
Name:
Publisher version
View Source
Access full-text PDFOpen Access
View Source
Check access options
Check access options
Author
Moitra, ParikshitChaichi, Ardalan
Abid Hasan, Syed Mohammad
Dighe, Ketan
Alafeef, Maha
Prasad, Alisha
Gartia, Manas Ranjan
Pan, Dipanjan
Date
2022-03-22Journal
Biosensors & BioelectronicsType
Article
Metadata
Show full item recordAbstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has been characterized by the emergence of sets of mutations impacting the virus characteristics, such as transmissibility and antigenicity, presumably in response to the changing immune profile of the human population. The presence of mutations in the SARS-CoV-2 virus can potentially impact therapeutic and diagnostic test performances. We design and develop here a unique set of DNA probes i.e., antisense oligonucleotides (ASOs) which can interact with genetic sequences of the virus irrespective of its ongoing mutations. The probes, developed herein, target a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency which do not mutate among the known variants. Further probing into the interaction profile of the ASOs reveals that the ASO-RNA hybridization remains unaltered even for a hypothetical single point mutation at the target RNA site and diminished only in case of the hypothetical double or triple point mutations. The mechanism of interaction among the ASOs and SARS-CoV-2 RNA is then explored with a combination of surface-enhanced Raman scattering (SERS) and machine learning techniques. It has been observed that the technique, described herein, could efficiently discriminate between clinically positive and negative samples with ∼100% sensitivity and ∼90% specificity up to 63 copies/mL of SARS-CoV-2 RNA concentration. Thus, this study establishes N gene targeted ASOs as the fundamental machinery to efficiently detect all the current SARS-CoV-2 variants regardless of their mutations.Rights/Terms
Copyright © 2022 Elsevier B.V. All rights reserved.Keyword
SARS-CoV-2 variantssurface-enhanced Raman scattering
selective and ultrasensitive diagnosis
mutation resistant probe
Oligonucleotides, Antisense
Identifier to cite or link to this item
http://hdl.handle.net/10713/18539ae974a485f413a2113503eed53cd6c53
10.1016/j.bios.2022.114200
Scopus Count
Related articles
- Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19).
- Authors: Aleem A, Akbar Samad AB, Slenker AK
- Issue date: 2022 Jan
- SARS-CoV-2 detection by targeting four loci of viral genome using graphene oxide and gold nanoparticle DNA biosensor.
- Authors: Babadi AA, Rahmati S, Fakhlaei R, Heidari R, Baradaran S, Akbariqomi M, Wang S, Tavoosidana G, Doherty W, Ostrikov K
- Issue date: 2022 Nov 12
- Model of the SARS-CoV-2 Virus for Development of a DNA-Modified, Surface-Enhanced Raman Spectroscopy Sensor with a Novel Hybrid Plasmonic Platform in Sandwich Mode.
- Authors: Samodelova MV, Kapitanova OO, Meshcheryakova NF, Novikov SM, Yarenkov NR, Streletskii OA, Yakubovsky DI, Grabovenko FI, Zhdanov GA, Arsenin AV, Volkov VS, Zavyalova EG, Veselova IA, Zvereva MI
- Issue date: 2022 Sep 19
- Non-enzymatic signal amplification-powered point-of-care SERS sensor for rapid and ultra-sensitive assay of SARS-CoV-2 RNA.
- Authors: Zhang J, Miao X, Song C, Chen N, Xiong J, Gan H, Ni J, Zhu Y, Cheng K, Wang L
- Issue date: 2022 Sep 15
- Plasmonic nanostructure-enhanced Raman scattering for detection of SARS-CoV-2 nucleocapsid protein and spike protein variants.
- Authors: Yeh YJ, Le TN, Hsiao WW, Tung KL, Ostrikov KK, Chiang WH
- Issue date: 2023 Jan 25