Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics

Poolsup, Suttinee; Zaripov, Emil; Hüttmann, Nico; Artyushenko, P. V.; Shchugoreva, Irina A.; Tomilin, Felix N.; Kichkailo, Anna S.; Berezovski, Maxim V.

doi:10.1016/j.omtn.2023.02.010

Cited by 12 publications

(6 citation statements)

References 72 publications

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“…However, to effectively minimize by-products and bias, optimizing the ePCR reaction condition is needed, and even with optimization, there have been reports of emerging PCR by-products. [38][39][40] Furthermore, the excessive preservation of rare aptamers with weak binding affinity may expand the pool of candidate aptamers, potentially complicating the identication of target aptamers. In addition to ePCR, the non-SELEX method, which involves sequential selections without amplication steps, represents another approach designed to address the PCR-related challenge of conventional SELEX.…”

Section: Discussionmentioning

confidence: 99%

A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen

Lin,

Chen,

et al. 2023

RSC Adv.

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Section: Discussionmentioning

confidence: 99%

A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen

Lin,

Chen,

et al. 2023

RSC Adv.

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“…This label-free aptamer-based BLI detected the SARS-CoV-2 N protein of the wild-type (WT) virus, as well as Delta and Omicron variants. This approach had an LOD of 4.5 nM for the N protein and successfully detected it in human saliva [ 91 ]. Another reported technique included a nanointerferometer sensor with aptamers as recognition elements, in which SARS-CoV-2 RBD-binding aptamer was incorporated into a nanostructured Fabry–Perot interference (nanoFPI) platform.…”

Section: Aptamersmentioning

confidence: 99%

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

Park,

Lee

et al. 2024

Biosensors

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The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

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“… 27 – 29 Regarding the target of the N protein in SARS-CoV-2, there have been some reports of N protein aptamers being used for virus detection. 30 , 31 However, there is still a lack of N protein-targeting aptamers for antiviral therapy.…”

Section: Introductionmentioning

confidence: 99%

Aptamers targeting SARS-CoV-2 nucleocapsid protein exhibit potential anti pan-coronavirus activity

Yang,

Li,

et al. 2024

Sig Transduct Target Ther

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Emerging and recurrent infectious diseases caused by human coronaviruses (HCoVs) continue to pose a significant threat to global public health security. In light of this ongoing threat, the development of a broad-spectrum drug to combat HCoVs is an urgently priority. Herein, we report a series of anti-pan-coronavirus ssDNA aptamers screened using Systematic Evolution of Ligands by Exponential Enrichment (SELEX). These aptamers have nanomolar affinity with the nucleocapsid protein (NP) of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and also show excellent binding efficiency to the N proteins of both SARS, MERS, HCoV-OC43 and -NL63 with affinity KD values of 1.31 to 135.36 nM. Such aptamer-based therapeutics exhibited potent antiviral activity against both the authentic SARS-CoV-2 prototype strain and the Omicron variant (BA.5) with EC50 values at 2.00 nM and 41.08 nM, respectively. The protein docking analysis also evidenced that these aptamers exhibit strong affinities for N proteins of pan-coronavirus and other HCoVs (−229E and -HKU1). In conclusion, we have identified six aptamers with a high pan-coronavirus antiviral activity, which could potentially serve as an effective strategy for preventing infections by unknown coronaviruses and addressing the ongoing global health threat.

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Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics

Cited by 12 publications

References 72 publications

A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen

A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

Aptamers targeting SARS-CoV-2 nucleocapsid protein exhibit potential anti pan-coronavirus activity

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