Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds

Dynamic DNA nanotechnology creates programmable reaction networks and nanodevices by using DNA strands. The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, achieved through three- and four-way strand exchange reactions. While both reactions have been widely used, the four-way exchange reaction has traditionally been slower and less efficient than the three-way reaction. In this paper, we describe a new mechanism to optimize the kinetics of the four-way strand exchange reaction by adding bulges to the toeholds of the four-way DNA complexes involved in the reaction. These bulges facilitate an alternative branch migration mechanism and destabilize the four-way DNA junction, increasing the four-way strand exchange rate by an order of magnitude. This advancement has the potential to expand the field of dynamic DNA nanotechnology by enabling efficient four-way strand exchange reactions for in vivo applications.