Aptamer-Guided Site-Specific Bioconjugation Enables Ultra-Efficient Covalent Coupling of a Nucleic Acid with an Intact Protein

Specific bioconjugation of a nucleic acid to a protein is not only used to identify, manipulate and functionalize the native protein but also provides a programmable linker that can interconnect the active protein with other functional molecules. Currently, most bioconjugation methods apply random modification, thereby disrupting the integrity of the protein structures and functions; otherwise, genetically engineered proteins are required for site-specific modification, significantly increasing its complexity and costs. Site-specific bioconjugation of intact proteins with functional nucleic acids has been an unmet need while fully securing the activity of the conjugated proteins. In this work, we propose the engineered aptamer-guided covalent conjugation of a nucleic acid to an unmodified protein as the guanine analogue, formed by nitrosation of guanine, can mediate activation-free crosslinking with nearby natural proteins. By inventing a synthetic way to prepare the reactive base-containing aptamer, we demonstrate that the newly synthesized aptamers targeting many different proteins can form a covalent linkage to the aimed location of the target proteins with exceptionally high specificity and efficiency.