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    Comparison of Six Aptamer-Aptamer Pairs on Rapid Detection of SARS-CoV-2 by Lateral Flow Assay
    (Oxford Univ Press Inc, 2024) Derin, Dilek Cam; Gultekin, Enes; Gunduz, Elif; Otlu, Baris
    Background SARS-CoV-2 is a threat to humanity. Both the spike (S) protein and its receptor binding domain (sRBD) are extensively used for rapid detection. Although real-time reverse transcription polymerase chain reaction (rRT-PCR) is mostly used method for the molecular detection of SARS-CoV-2, rapid assays for antigenic detection are always needed. Lateral flow assays (LFAs) are the most commonly used tests for this purpose, and aptamers having stability and long shelf life are used as capture reagents.Objective This study aimed to develop the LFAs based on the aptamer pairs for the antigenic detection of SARS-CoV-2 with the naked eye.Method Gold nanoparticles (AuNPs) were used as labels, and six sandwich models by three different aptamers were prepared using 4 mu M and 8 mu M probes and two kinds of membranes for developing the LFAs.Results The 8 mu M probe concentration and M2 membrane showed the best recognition of both the synthetic sRBD and SARS-CoV-2 coming from the naso/oropharingeal swabs by designed LFAs as 100% sensitivity and 93.3% specificity compared to the antibody-detecting LFAs.Conclusions Our developed strip assays based on aptamer pairs recognized the target directly in 5-6 min with the naked eye. It was also concluded that aptamer pairs, membrane types, assay buffers, and probe concentrations have a significant role in the detection of SARS-CoV-2 by LFAs.Highlights The detection of SARS-CoV-2 in clinical samples was demonstrated with the best aptamer pairs, sensitively and selectively among the designed six aptamer pairs for LFAs. Developed LFAs can be an alternative method to the conventional antibody-based LFAs for SARS-CoV-2 detection.
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    Designing of rapid assay for the detection of RdRp/Orf1ab specific to SARS-CoV-2
    (Elsevier, 2023) Derin, Dilek Cam; Gultekin, Enes; Taskin, Irmak Icen; Otlu, Baris; Oktem, Huseyin Avni
    SARS-CoV-2 is still threat and mostly used detection method is real time reverse transcriptase polymerase chain reaction (rRT-PCR) for the open reading frame (Orf1ab), RNA-dependent RNA polymerase (RdRp), nucleocapsid (N) and envelope (E) genes of virus. However, rRT-PCR may have false negative rate for the nucleic acid detection. Since the RdRp/Orf1ab has high sensitivity for the molecular detection, two sandwich models, Model 1A-Model 1B, based on hybridization on lateral flow assay (LFA) were designed here and applied with the synthetic and clinical samples of RdRp/Orf1ab. In this purpose colloidal gold nanoparticles (AuNPs) were used as label. Membranes having different flow rate, three oligonucleotide probe concentrations and running buffers were used. Although synthetic target sequence was recognized by all the LFAs, PCR products obtained from either the synthetic plasmid DNA or oro/nasopharyngeal swabs were detected by Model 1 A using W12 mem-brane. Designed strip assays detected the RdRp/Orf1ab of the clinical samples as 100% sensitivity and specifity. It means that they might be used for the detection of virus and can be modified for the recognition of mutant genes of virus. These findings also demonstrated the importance of membranes, sandwich models, probe con-centrations and sample contents for developing LFAs for viral detection.
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    Development of nucleic acid based lateral flow assays for SARS-CoV-2 detection
    (Soc Bioscience Bioengineering Japan, 2023) Derin, Dilek Cam; Gultekin, Enes; Taskin, Irmak Icen; Yakupogullari, Yusuf
    SARS-CoV-2 is still threat for humanity and its detection is crucial. Although real time reverse transcriptase poly-merase chain reaction is the most reliable method for detection of N protein genes, alternative methods for molecular detection are still needed. Thus, lateral flow assay models for 2019-nCoV_ N3 were developed for molecular detection. Briefly, gold nanoparticles were used as label and three sandwich models (1A, 1B, and 1.2) were designed. Prob con-centrations on gold nanoparticles, types of sandwich model and membrane, limit of detection of target gene and buffer efficiency were studied. Model 1B has shown the best results with M170 membrane. Lower limit of detection was achieved by model 1.2 as 5 pM. All parameters have significant role for molecular detection of SARS-CoV-2 by lateral flow assays, and these results will be useful for nucleic acid based lateral flow assays for viral detection or multiple detection of mutated forms in various detection systems.(c) 2022, The Society for Biotechnology, Japan. All rights reserved.