Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation

Abstract

Whiplash PCR (WPCR), due to Hagiya et al. [1], is a novel technique for autonomous molecular computation where a state machine is implemented with a single stranded DNA molecule and state transition is driven by polymerase and thermal cycles. The significance of WPCR computation lies in the fact that while other forms of autonomous molecular computing such as tiling assembly [2] or Benenson automata [3] operate based on global rules, it is possible to execute multiple WPCR machines, each holding its own distinct program, in parallel. However, since each transition requires a thermal cycle, multi-step WPCR machines are laborious and time-consuming. Hence they limit program execution to only a few steps. To date, no WPCR protocol has been developed which is both autocatalytic (self-executing) and isothermal (with no change in temperature). Here we describe such a protocol for computing with WPCR which uses a combination of strand displacement and DNA polymerization. Our designs include (1) a protocol where transition rules cannot be reused in subsequent computing, a feature that is crucial for reducing back-hybridization (2) a protocol where rules can be reused using an auxiliary strand displacement event, (3) a reusable rule protocol that prevents back-hybridization [1]. We also compute its state transition likelihood and rate and present a DNA sequence design of a 3-state machine and an experimental verification plan.