AAWSAP DIRD, Quantum Computing and Utilizing Organic Molecules in Automation Technology, December 2010

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Deoxyribozyme-based Boolean Automata
The deoxyribozyme logic gates were applied to the construction of the first DNA-based
Boolean automata capable of autonomously responding to human inputs: "MAYAs" are
automata playing a game of tic-tac-toe against a human player. In tic-tac-toe there are a
maximum of 4 moves by the human player when MAYA has the first move. The initial MAYA
automaton played a simplified game, always claiming the center first, and the first human
move is symmetry-restricted to one corner or one side move. These simplifications led to a
representation of the game as a series of Boolean formulae that compute the automaton's
output in each well, based on the human inputs present in all wells. These formulae were
mapped to 23 deoxyribozyme-based logic gates by arranging gates in the individual wells
around a common substrate. These "hard-wired" automata give the human no chance to win
(Figure 22, Figure 23). (120, 122) One, two and three input deoxyribozyme-based logic
gates are allosterically modulated by 32 human-operated input oligonucleotides: 97 logic
gates distributed across 9 wells which calculate automaton moves, and 32 gates (boxed)
display human moves by implementation of a two-color fluorogenic output system.
Even
though this mechanism is simplistic in nature, it has performed flawless Boolean calculations.
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Figure 22. Basic gate structures, derived from allosterically regulated deoxyribozyme E6, for playing tic-tac­
toe against a human opponent. The truth tables constructed are sufficient to ensure the human player cannot
win the game. (120)
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