DNA nanorobotics and sequence design

We briefly describe our hairpin-based DNA machines and the problem of designing DNA sequences of the machines. For designing such a machine, it is vital to predict conformational transition paths in the machine and reflect the prediction in the design of its DNA sequences. In particular, it is necessary to compute the energy barrier on transition paths between start and target conformations. For predicting conformational transition paths, the energy landscape consisting of conformations of a machine should be generated and analyzed. We have developed an efficient algorithm and its implementation for generating the energy landscape of a machine and computing the energy barrier between conformations. The algorithm not only computes the path that has the minimum energy barrier, but also the area around the path. This area is called the minimum basin because it consists of conformations whose energy is equal to or below the energy of any conformation on the path. The minimum basin is considered to contain various kinds of information for analyzing conformational transition.