Mechanistic Model Study of Surface Based DNA Walkers

DNA walkers are engineered nanostructures that can migrate on prescriptive landscape based on various mechanisms including strand displacement and enzymatic reaction. Over the years, the focus on DNA walker studies have been on improving speed and processivity, where models analyzing walker behaviors are vital for improving the designs. Here, we introduce a comprehensive model for an enzyme-powered DNA walker that moves autonomously on 2D surfaces. Our analysis show that the walkers have multiple modes - ballistic, Lévy, self-avoiding, and diffusive. These different modes show distinct step time and velocity distributions. To understand the dynamics, we adopt a random walk model bridging the scaling of mean-squared displacement and statistical features of various movements. Coherence between the model and experimental results are demonstrated. Mechanistic studies were performed experimentally to investigate the effects of key parameters that govern walker behaviors. These include cargo types and sizes, strand lengths and sequences, design of walkers, and environmental conditions. The parameters influence the statistical features of motions and lead to walkers with various velocities and processivity. Finally, a set of design principles are proposed for future walker designs.