A quantitative model of temperature actuated DNA origami nanocaliper constructs*

Manipulation of temperature can be used to actuate gold nanoparticle incorporated into DNA origami nanocalipers. We develop a physical model of this system that uses partition function analysis of the interaction between the nanocaliper and nanoparticle to predict the probability that the nanocaliper is open at a given temperature. The model agrees well with experimental data, and the comparison between model and experiment reveals surprising insights into the nanocaliper-nanoparticle system. For instance, geometric constraints on the system are suggested. Additionally, the model predicts experimental conditions that allow the actuation temperature of the nanocaliper to be tuned over a wide range of temperatures from 20^oC to 60^oC. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.