Preliminary experiments on hairpin structure dissociation for constructing robust DNA machines

Our group has constructed several hairpin-based DNA machines that have multiple transition states (M. Hagiya et al., 1999)-(M. Kubota et al., 2003). In these studies, we have conducted technical design of a single sequence or multiple sequences forming an artificial DNA nanomachine, based on prediction of free energy of secondary structures in silico. In this study, rather than relying on the free energy prediction in silico, we verified some fundamental behaviors of hairpin-based machines in vitro. In particular, we conducted some fundamental experiments about how a hairpin structure is opened when its opener sequence is added with or without the existence of a blocking sequence which prevents the opener from annealing with the hairpin structure. This paper reports on the new experimental results, and also discusses some new ideas based on the new results.