Ni aptamer: DNA mimic of His-tag to recognize Ni-NTA

We introduced Ni Apt as the first aptamer with a characterized dissociation constant for recognizing Ni-NTA. Serving as a nucleic acid analog of the His-tag commonly employed for protein purification using Ni-NTA resin, Ni Apt displays a remarkable binding affinity (Kd = 106 nM) towards Ni-NTA. Furthermore, it can be eluted from the resin using imidazole or EDTA, similar to the removal of His-tag from Ni-NTA resin. The versatile capabilities of Ni Apt make it a valuable molecular tool in nucleic acid purification and recognition applications.

DNA aptamers inhibit SARS-CoV-2 spike-protein binding to hACE2 by an RBD- independent or dependent approach

Objective: Nobody knows when the COVID-19 pandemic will end or when and where the next coronavirus will outbreak. Therefore, it is still necessary to develop SARS-CoV-2 inhibitors for different variants or even the new coronavirus. Since SARS-CoV-2 uses its surface spike-protein to recognize hACE2, mediating its entry into cells, ligands that can specifically recognize the spike-protein have the potential to prevent infection. Methods: We have recently discovered DNA aptamers against the S2-domain of the WT spike-protein by exploiting the selection process called SELEX. After optimization, among all candidates, the aptamer S2A2C1 has the shortest sequence and the best binding affinity toward the S2-protein. More importantly, the S2A2C1 aptamer does not bind to the RBD of the spike-protein, but it efficiently blocks the spike-protein/hACE2 interaction, suggesting an RBD-independent inhibition approach. To further improve its performance, we conjugated the S2A2C1 aptamer with a reported anti-RBD aptamer, S1B6C3, using various linkers and constructed hetero-bivalent fusion aptamers. Binding affinities of mono and fusion aptamers against the spike-proteins were measured. The inhibition efficacies of mono and fusion aptamers to prevent the hACE2/spike-protein interaction were determined using ELISA. Results: Anti-spike-protein aptamers, including S2A2C1 and S1B6C3-A5-S2A2C1, maintained high binding affinity toward the WT, Delta, and Omicron spike-proteins and high inhibition efficacies to prevent them from binding to hACE2, rendering them well-suited as diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants. Conclusions: Overall, we discovered the anti-S2 aptamer, S2A2C1, which inhibits the hACE2/spike-protein interaction via an RBD-independent approach. The anti-S2 and anti-RBD aptamers were conjugated to obtain the fusion aptamer, S1B6C3-A5-S2A2C1, which recognizes the spike-protein by an RBD-dependent approach. Our strategies, which discovered aptamer inhibitors targeting the highly conserved S2-protein, as well as the design of fusion aptamers, can be used to target new coronaviruses as they emerge.

A universal DNA aptamer as an efficient inhibitor against spike-protein/hACE2 interactions

A universal aptamer against spike-proteins of diverse SARS-CoV-2 variants was discovered via DNA SELEX towards the wild-type (WT) spike-protein. This aptamer, A1C1, binds to the WT spike-protein or other variants of concern such as Delta and Omicron with low nanomolar affinities. A1C1 inhibited the interaction between hACE2 and various spike-proteins by 85-89%. This universal A1C1 aptamer can be used to design diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants.