Mismatch-Induced Toehold-Free Strand Displacement Used to Control a DNA Nanodevice

Dynamic DNA structures are controlled through toehold-based strand displacement, a method in which a DNA or RNA strand can bind to a single-stranded extension, cause branch migration, and result in the displacement of previously bound DNA. Here, we developed a toehold-free strand displacement method utilizing mismatched base pairs and stability differences between DNA complexes to control the reconfiguration of DNA nanostructures. We demonstrate this method using simple DNA duplexes and apply the strategy to reconfigure a paranemic crossover (PX) DNA based nanodevice into its topoisomer juxtaposed (JX) DNA. While the mismatch-induced toehold-free strand displacement was efficient in a simple double-stranded DNA model, the efficiency of strand displacement was lower in complex nanostructures. Increasing the number of mismatches increased the efficiency of the PX-JX conversion, and the process could be further controlled by tuning the number of mismatches. This device can be useful in stimuli-responsive mechanisms that have applications in biosensing, drug delivery, and molecular computation.