Deoxyribozyme Logic Gates for Molecular Computation

1. Playing to win at DNA computation Jeffrey J. Tabor, Andrew D. Ellington Nature Biotechnology 21(9), 1013-1015 (2003) presented by Ki-Roo Shin

2. Deoxyribozyme-Based Logic Gates • Stojanovic,M.N.1, Mitchell,T.E.1, and Stefanovic,D.2J.AM.CHEM.SOC.124,3555-3561 (2002) • 1Department of Medicine, Columbia University, NewYork • 2Department of Computer Science University of New Mexico, Albuquerque, New Mexico • They incorporated two modular allosteric domains into an RNA-cleaving deoxyribozyme (E6) that were capable of activating or inhibiting the enzyme in the presence of complementary oligonucleotide effectors.

3. A deoxiribozyme-based molecular automaton • Stojanovic, M.N., Stefanovic, D. Nat. Biotechnol. 21, 1069-1074 (2003). • 3×3 tic-tac-toe • An automaton built with DNA enzymes plays tic-tac-toe against human players • 9 wells corresponding the 9 squares signifies the moves • The human player responds by adding a DNA oligonucleotide effector to all 9 wells • 23 different deoxyribozymes, 8 different oligonucleotide effectors

4. Tic-tac-toe

5. Summary • They suggest htat their biological logic gates might be refashioned as intracellular sentinels, capable of recognizing multiple disease signals and responding with a single functional output, such as the release of cytotoxic factors. • It may be possible to similarly reengineer signal transduction pathways using the same sorts of techniques. • Molecular computers can be used to directly mimic and even solve problems that occur within the provenance of biology: that is, inside of a cell.