ITR/SY(CISE): Biomolecular Computing by DNA/Enzyme Systems

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EIA-0113443Winfree, ErikCalifornia Institute of TechnologyTitle: Biomolecular Computing by DNA/Enzyme SystemsDr. Erik Winfree and Dr. Hideo Mabuchi are working together to develop techniques and instruments for high-precision quantitative analysis of the DNA molecular devices. These are being designed, characterized and optimized to investigate issues such as robustness and error-tolerance of these DNA molecular devices. The technical objectives being achieved in this project are: development of spFRET instrument capable of counting individual photons from single molecules; characterization of conformal states, kinetics, and thermodynamics of DNA switches; characterization of the activities of two enzymes, RNAP and RNase, on the DNA switches; development of stochastic models of in vitro transcriptional circuits; and investigation of robust algorithms and error-control for transcriptional circuits.Through this project, the PIs are establishing a set of experimental systems and techniques for exploring computation by biological molecules. This will provide fundamental knowledge and principles for nanoscale computation, such as models of computation, molecular algorithms, physical limits, sources of error and error correction strategies. Thus the aim is to leverage the advanced control over biochemical systems to begin establishing a broader foundation for reliable molecular computing.