A free-energy profile study of a bipedal single-stranded DNA nanowalker's walking gaits

DNA nanowalker is a class of dynamic DNA nanotechnology that exploits toehold mediated strand displacement and branch migration for movement. Speed is a key performance indicator of a good walker, and its threshold is determined by the walker's gait. Here, we conducted a systematic free energy profile study on a 15nt long ssDNA nanowalker on a dsDNA track using oxDNA, a coarse-grained DNA model. We identified all possible gaits for a ssDNA nanowalker, namely cartwheel, flip, prance and hop. The free energy profile of these gaits are sampled and studied in detail. The rate for a forward step is also estimated from the first passage time theory. Overall, we found that the local binding geometry affects the walking rate of each gaits. For cartwheel and flip, elongating the track will help increase the dissociation rate and decrease the first contact rate. The dissociation and first contact rate for a downhill prance walker decreases significantly on a longer track. Strategies to optimize the walking rate should therefore consider the gait of the bipedal walker.