Protein Labeling and Crosslinking by Covalent Aptamers

We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity‐driven electrophile at specific nucleotide sites. Using thrombin as a proof‐of‐concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease‐resistant enzyme inhibition. Nucleic acid aptamers were developed that are capable of covalently labeling their protein target with a functional molecule. Additionally, with little modification, the aptamer covalently crosslinked to its target instead, thereby inhibiting its function. Covalent aptamers offer a new tool for selective protein modification, detection, and inhibition.