Organization of Enzyme Proximity Controlled By Strand Displacement

Structural DNA nanotechnology utilizes the predictive capabilities of DNA hybridization for the creation of distinct, self-assembling nucleic acid complexes. Employing strand displacement technology, certain DNA complex conformations and assemblies can be controlled by some distinct input strand(s). Taking advantage of strand displacement potentiality, we have created a switchable DNA assembly for the particular organization of proteins via DNA-protein conjugates. The design shows high potential for easy manipulation and control of enzyme co-localization and delocalization.

Utilizing the ligand binding capabilities of HaloTag protein we covalently linked fluorescent proteins to DNA with high efficiency and employed a simple purification regime by means of an elastin like polypeptide tag. We use CFP/YFP FRET to examine and validate the ability to create switchable protein-protein proximity from protein-DNA conjugates. The kinetic analysis, via FRET, confirms that our protein-DNA strand displacement design is highly effective.  The platform of our fusion protein design allows for replacement of the fluorescent proteins with any proteins of interest for studying or exploiting the effects of enzyme co-localization.