CSCE Seminar: PNA-Mediated Whiplash PCR: Massively Parallel Autonomous Molecular Computation

The University of Tokyo 3:30 PM Friday April 27 Rm. 304 ENGR

Computers implemented in DNA have the potential for massively parallel computational operations and vast amounts of storage capacity. In the Whiplash PCR architecture, finite automata are implemented in the form of template-directed, recursive polymerase extension of a mixture of DNA molecular hairpins, appropriately encoded with finite state transitions. Autonomous parallel computation on a massive scale is achieved by iterating the reaction temperature through a 3-step thermal cycle appropriate for enforcing the parallel hybridization, extension, and denaturation of all hairpin species. Although the autonomous nature of the WPCR architecture shows great promise from a computational point of view, a serious barrier which confronts the efficient implementation of various forms of recursive-PCR-based computation is a systematic tendency for computational molecules towards a simple form of self-inhibition. In this talk, modifications to the protocol based on PNA are discussed that might make massively parallel autonomous computation achievable in practice. In addition, an evolutionary algorithm based on WPCR is proposed.