A Rationally Designed Connector for Assembly of Protein-Functionalized DNA Nanostructures

We report on the rational engineering of the binding interface of the self‐ligating HaloTag protein to generate an optimized linker for DNA nanostructures. Five amino acids positioned around the active‐site entry channel for the chlorohexyl ligand (CH) of the HaloTag protein were exchanged for positively charged lysine amino acids to produce the HOB (halo‐based oligonucleotide binder) protein. HOB was genetically fused with the enzyme cytochrome P450 BM3, as well as with BMR, the separated reductase domain of BM3. The resulting HOB‐fusion proteins revealed significantly improved rates in ligation with CH‐modified oligonucleotides and DNA origami nanostructures. These results suggest that the efficient self‐assembly of protein‐decorated DNA structures can be greatly improved by fine‐tuning of the electrostatic interactions between proteins and the negatively charged nucleic acid nanostructures. HOBbing proteins with DNA: Halo‐based oligonucleotide binder (HOB, right) is an oligonucleotide‐binder protein in which positively charged amino acids (blue) were incorporated around the active‐site entry channel for the chlorohexyl ligand (green) of the self‐ligating HaloTag protein (left). HOB fusion proteins bind to oligonucleotides and DNA origami with significantly improved reaction rates.