A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern

Abstract

What is the most significant result of this study?This study reports on au nique DNA aptamer,d enoted MSA52, that displays auniversally high affinityfor the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta, and Omicron variants. This aptamer also recognizes pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS-CoV-2 with K d values between 20-50 pM. It was integrated into as imple colorimetric assay for the detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of asingle protein, including emerging variants, making them well-suited for molecular recognition of rapidly evolving targets such as those found in SARS-CoV-2.

Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer

“…The aptamer used for this work is MSA52, a monomeric DNA aptamer (Figure B) discovered by us through selection with variant S proteins . Impressively, MSA52 was found to universally recognize variants that were not analyzed in the original selection experiment, demonstrating that the aptamer is insensitive to emerging S protein mutations . Hence, MSA52 is an ideal candidate for COVID-19 recognition, and the trimerization of this MRE should enhance its complementarity to and affinity for the S protein.…”

“…The choice of a T15 linker was made for the following reasons. First, MSA52 has been shown to bind to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. , Second, it has been demonstrated that the distance between RBD subunits on the spike protein trimer ranges from 2.7 to 7.4 nm, considering the “closed” and “open” conformational states of the RBD. Third, our calculations indicate that each arm of the trebler-linked trimeric aptamer with a 15-thymine linker has a persistence length of 6.9 nm .…”

SCORe: SARS-CoV-2 Omicron Variant RBD-Binding DNA Aptamer for Multiplexed Rapid Detection and Pseudovirus Neutralization

“…We compared the sequence of SCORe to other aptamers reported to bind the SARS-CoV-2 S protein at the RBD (CoV-2-RBD-1C, CoV-2-RBD-4C, CoV-2-6C3, nCoV-S1-Apt1, MSA5, and MSA52-T5) ,, and found no similarity between SCORe and the other sequences when compared with local alignment (Figure S4). …”

“… 15 Most of the currently reported aptamers were selected against wild-type or alpha variant S protein. 13 , 16 − 19 To the best of our knowledge, only the Li group has reported a DNA aptamer that binds to BA.1 S protein 20 that does not also bind nonspecifically to His-tag-containing proteins ( Figure S1A ). We tested literature-reported S-binding aptamers (SP6.51, 18 SNAP1, 13 SNAP4.74, 14 CoV-2-4C, 19 CoV-2-6C3 21 ), including two discovered by our group, but none of these aptamers show specific binding to BA.1 NTD or S1 protein ( Figure S1 ) in our testing conditions.…”

“…DNA aptamers against SARS-CoV-2 S protein have been identified using a library selection process called the systematic evolution of ligands by exponential enrichment (SELEX) . Most of the currently reported aptamers were selected against wild-type or alpha variant S protein. ,− To the best of our knowledge, only the Li group has reported a DNA aptamer that binds to BA.1 S protein that does not also bind nonspecifically to His-tag-containing proteins (Figure S1A). We tested literature-reported S-binding aptamers (SP6.51, SNAP1, SNAP4.74, CoV-2-4C, CoV-2-6C3), including two discovered by our group, but none of these aptamers show specific binding to BA.1 NTD or S1 protein (Figure S1) in our testing conditions. ,, While the CoV-2-4C and CoV-2-6C3 aptamers showed binding to BA.1 NTD, S1, and RBD proteins, they also showed binding to a control, His-tagged protein (Figure S1A), an observation also noted by Schmitz et.…”