Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold-mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold-mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold-mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one-to-many and many-to-one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold-mediated DNA strand displacement.