Towards an autonomous multistate biomolecular devices built on DNA

Abstract

A major challenge in DNA computing area is to design autonomous and programmable biomolecular devices built on DNA. The significant achievement in the field of DNA nanodevices was a laboratory implementation of the 2-state biomolecular finite automaton based on one restriction enzyme FokI [3]. Although this practical implementation represents a proof of concept for autonomous computing with DNA molecules, it has a limited computational power. The restriction enzyme FokI enables construction an automata with at most 3-states. We propose to use several restriction enzymes (instead of one) which act autonomously in a test tube to construct more powerful finite state machines. It enables to build any finite nondeterministic automata or even push-down automata. The autonomous operation of the automaton is based on alternating cleavages of DNA molecules by several restriction enzymes. We illustrate this new idea by presenting a laboratory implementation of a particular case of finite automata. In this experiment two restriction endonucleases act autonomously on DNA in one test tube. This approach may be used (in the future) to build nanomachines, even push-down automata (made of DNA molecules) which may be applied in medicine, pharmacy or biotechnology.