Calibrating catalytic DNA nanostructures for site-selective protein modification

Many biomedical fields rely on proteins that are selectively modified with novel chemical entities. These are often attached using reactive or catalytic moieties, but the position where these moieties are attached is often poorly controlled. In this work, we assess how catalyst position affects the efficiency and selectivity of protein modification. For this, we anchored a template DNA strand to the active site of three different proteins, which were subsequently hybridized to DNA strands that contained catalysts at different positions. We found that catalysts operating via a covalently bound reactant intermediate show a strong correlation between their distance to the protein surface and their efficiency and that the site-selectivity of the modification is affected by the position of the catalyst. Our results are rationalized using computational simulations, showing that one-point anchoring of the DNA construct leads to notable differences in the site of modification.