Gene Expression as Output Detection for Bio-molecular Computing

1. Scitech 2010 Jason Albalah and Debra Linfield Mentor: Sivan Shoshani The Schulich Faculty of Chemistry The Interdisciplinary Program for Biotechnology The Technion- Israel Institute of Technology Gene Expression as Output Detection for Bio-molecular Computing Computation Process: Figure 1: Mathematical Model: Figure 1: Transition Rules- For example, for automaton 1, if the automaton is originally in state S0 and FokI cuts symbol ‘a’, then the automaton will remain in state S0. However, if FokI cuts symbol ‘b’, then the automaton changes to S1. For automaton 2, in state S1, the automaton will remain in state S1 if FokI cuts symbol ‘a’, and will switch to state S0, if it cuts symbol ‘b’. Figure 2: Transition Molecules Abstract: This research concentrates on constructing a two-symbol-two-state finite automaton made entirely of molecular components. The output contains a gene for a fluorescent protein, which can be expressed in plant cells. This research demonstrates the potential of bio-molecular computers to directly interact with organisms and expands the applications of autonomous molecular computing devices. Figure 2: Transition molecules. A list of transition molecules comprising each automaton. Each transition molecule has a different sticky end and spacer and therefore can only bond to a specific processed input molecule. Discussion: The project was designed to advance the usage of molecular computers in biological applications. A successful design created allowed for the implementation and direct interaction of a bio-computer with a eukaryotic cell, a task unpracticed previously. The next step in the research is to continue to narrow the barrier between bio-technology and biology, to close the gap between bio-computers and organic life. Additional practical applications would truly exhibit a critical juncture in molecular computer advancement. Conclusion: This project shows boundless opportunities in the field of bio-molecular computing. Because of the molecules direct interaction with the cell, there are many possible medical prospects, like its potential to respond and treat diseases autonomously. It could monitor levels of chemicals, hormones, or sugars in the human body, and then respond accordingly. Additionally, bio-computers store abundant amounts of information and perform synchronized computations, both major advances in computer technology. This project shows that bio-molecular computing devices are capable of interacting directly with a cell. The future of bio-molecular computing devices is optimistic, and maybe one day they will replace silicon computers. Acknowledgements: We thank our mentor Sivan who taught, directed, and enabled us to complete everything on time and correctly. Sivan, thanks for introducing us to some awesome research and making us excited about science. We'd also like to thank the SciTech staff for their constant encouragement and making our summers stupendous. We thank the Schulich Faculty of Chemistry for letting us use their facilities. We thank our parents for sending us to the program and for their participation in the program and project. Thanks guys! Figure 4: Input molecules. Each input molecule consists of TTT sticky ends, spacers (in black), a FokI recognition site (in pink), symbol ‘a’ (in blue), symbol ‘b’ (in green), and a terminator (in red). In addition there is a PstI recognition site (CTGCAG) in the last spacer for later use.