Deoxyribozyme-Based Molecular Computation - DNA Nanotechnology: From Structure to Function - page 342

Chapter 17
Deoxyribozyme-Based Molecular Computation

Renjun Pei

Abstract Nucleic acids are ideal for molecular computation. A full set of molecular
logic gates have been constructed using deoxyribozymes, nucleic acid catalysts
made of DNA. These gates have been combined to form various molecular circuits,
including molecular automata which perform complex game-playing tasks. Our
newest molecular automaton uses reconfigurable deoxyribozyme-based logic gates
to build a multipurpose reprogrammable device that can be taught by example
to play a game. Herein the design and progress on deoxyribozyme-based molec-
ular computation is described, especially for MAYA-III, our newest molecular
automaton.

Keywords Deoxyribozyme • Logic gates • Molecular circuits • Game playing •
Molecular automaton • Molecular computation

17.1 Introduction

The progress in molecular computation has resulted in rapid development of various
programmable molecular automata and complex molecular networks [ 1 - 34 ]. Over
the past several years, using deoxyribozymes, Stojanovic group at Columbia
University constructed a full set of molecular logic gates, which analyze sets of
oligonucleotides or proteins as inputs and produce cleaved oligonucleotides as
outputs [ 35 - 40 ]. These basic logic gates enabled to establish simple molecular
circuits such as half and full adders for performing basic arithmetical operations
[ 41 , 42 ]. They were also integrated into molecular automata for performing complex
computational tasks such as game playing as an unbiased test of the complexity that

R. Pei ( )
Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics,
Chinese Academy of Sciences, Suzhou 215123, China
e-mail: [e-mail]