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A deoxyribozyme-based molecular automaton Milan N Stojanovic & Darko Stefanovic

A deoxyribozyme-based molecular automaton Milan N Stojanovic & Darko Stefanovic Nature Biotechnology, Sept. 2003. 인지과학 협동과정 이 은 석 2004. 11. 20. Tic-Tac-Toe. X. O. X. X. O. O. X. MAYA Implementation. M olecular A rray of Y ES and A NDANDNOT Gates

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A deoxyribozyme-based molecular automaton Milan N Stojanovic & Darko Stefanovic

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  1. A deoxyribozyme-based molecular automaton Milan N Stojanovic & Darko Stefanovic Nature Biotechnology, Sept. 2003 인지과학 협동과정 이 은 석 2004. 11. 20.

  2. Tic-Tac-Toe X O X X O O X

  3. MAYA Implementation • Molecular Array of YES and ANDANDNOT Gates • 3x3 wells, 24 deoxyribozymes in 9 wells • Automata: 2 YES gates, 2 AND gates, 19ANDANDNOT gates • E6: an RNA-cleaving deoxyribozyme (activating or inhibiting the enzyme) • Logic gate = Enzyme : Output = Fluorescent product

  4. Basic concept of deoxyribozyme-based logic gate M. N. Stojanovic, et al. JACS 2002, 124, 3555

  5. YES gate M. N. Stojanovic, et al. JACS 2002, 124, 3555

  6. NOT gate M. N. Stojanovic, et al. JACS 2002, 124, 3555

  7. M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  8. Input Oligonucleotides i1-i4, i6-i9 M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  9. Game Tree for TTT M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  10. Corresponding Boolean Formulas M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  11. Schematic Representation M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  12. Representative Game Board J. J. Tabor & A. D. Ellington Nat. BioT.Sept. 2003

  13. M. N. Stojanovic & D. Stefanovic, Nat. BioT.Sept. 2003

  14. Features • An analogy: digital logic circuits in computers, or enzymes in metabolic circuits • No autonomous play dynamic game before the present work (without human controlling) • Not in massively parallel fashion: a substrate of one gate can be the input of another • Not necessarily in one tube for all • Shed light on?: genetic, regulatory and metabolic systems networks or in vivo computation networks and cells with engineered properties (using stem loops)

  15. References • Milan N Stojanovic & Darko Stefanovic, A deoxyribozme-based molecular automaton, Nature Biotechnology, vol.21 no.9 Sept. 2003. • Milan N. Stojanovic, Tiffany Elizabeth Mitchell, & Darko Stefanovic, Deoxyribozyme-Based Logic Gates, JACS, 124, 3555, 2002. • Jeffrey J Tabor & Andres D Ellington, Playing to win at DNA computation, Nature Biotechnology, vol.21 no.9 Sept. 2003.

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