Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS‐CoV‐2 Variants

Abstract

Many DNA aptamers have been reported to target the spike protein (S‐protein) of SARS‐CoV‐2. These aptamers display different affinities or recognize different epitopes of the S‐protein. We conducted a comparative study of 9 DNA aptamers for binding to several variants of the S‐protein and pseudoviruses using the same testing methods, including dot‐blot assays and enzyme‐linked aptamer binding assays, to evaluate their affinity ranking and analytical utility. Moreover, the binding sites of these aptamers on the S‐protein were examined using aptamer competition assays to understand the effect of S‐protein mutations on aptamer affinity and the degree of overlapping of the binding sites by these aptamers.

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

“…In this regard, we set out to test the binding characteristics of the different aptamers using complementary analysis platforms. A recent cross-comparative study assessed the affinity of different aptamers binding to the SARS-CoV-2 spike protein through filter retention analysis and showed consistent binding of all tested aptamers [20]. In contrast, our comparative study reveals clear differences and suggests that the specificity for some of the aptamers might be influenced by the experimental conditions and that their binding is primarily directed to associated purification tags rather than to the spike protein.…”

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

“…Utilizing this ELASA, Li et al [ 79 ] achieved sensitive detection of pseudo-lentiviruses with a limit of detection (LOD) of 400 fM in 50% saliva. Furthermore, Zhang et al [ 117 ] utilized nine previously discovered SARS-CoV-2 aptamer sequences to detect several variants of the S protein of pseudoviruses and determine the performance of these aptamers for variants of concern (VOCs) recognition ( Figure 3 ). Other colorimetric strategies used absorbance and color change methods.…”

“…( C ) The data show color changes by detection outcomes for pseudoviruses using various aptamers. Reprinted from [ 117 ].…”

“…This sensor exploits the yellow-to-pink transition of phenol due to urease activity enhanced by RCA, achieving an LOD of 3.2 × 10 3 copies/mL for pseudovirus. Reprinted from [117].…”

“…Nine aptamers were utilized in sandwich assays to detect pseudoviruses expressing S proteins from the SARS-CoV-2 wild-type (WT), P.1, B.1.617.2, and B.1.1.529 variants. (C) The data show color changes by detection outcomes for pseudoviruses using various aptamers.Reprinted from[117].…”