Another realization of aqueous computing with peptide nucleic acid

Abstract

Head proposed a framework of aqueous computing as a code design free molecular computing. Aqueous computing handles an aqueous solution of general-purpose memory molecules with a small set of elementary laboratory operations. It fits to solve a certain pattern of NP complete problems. We focus upon scaling the address space up and propose another biomolecular realization. Peptide nucleic acid (PNA) is an artificial analogue of DNA. Since PNA-DNA hybrid has higher melting temperature than DNA-DNA case, PNA will take over hydrogen bonds and displace itself into a double strand DNA. This phenomenon can be regarded as an irreversible write-once operation on a memory molecule. PNA brings a much larger address space than natural enzymes can provide. In this paper, we propose elementary operations for aqueous computing with PNA and realize one bit memory for a feasibility study to confirm strand displacement by PNA. We also propose an idea to copy a memory state upon a DNA sequence by using whiplash PCR.