Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization Concepts

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NSF 0726698 ? Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization ConceptsPI: Evgeny Katz, co-PI: Vladimir Privman AbstractThis research is directed towards the developments of new concepts in biochemical computing. Biocomputing shows promise of providing the mechanisms to better couple ordinary electronics with the signaling of biological organisms. On the conceptual level, it will further understanding of how living organisms manage to control extremely complex and coupled biochemical reactions, i.e., interpret metabolic pathways in the language of information theory. Biocomputing systems of even moderate complexity will allow effective interfacing between complex physiological processes and implantable biomedical devices and will be able to operate in nanobiorobotic and sensing systems. Great advances have been made in biocomputing research in recent years. However, to be practical, as well as compatible with ordinary electronics, biocomputing should be researched for ways to minimize/correct errors and develop "digitalization" concepts. This challenge is taken up in the present research program. Experimental exploration as well as theoretical modeling and optimization are performed for new systems based on encoded DNA sequences, enzymes and DNAzymes that show promise for digital biochemical computing, including the first attempt for an experimental realization of error correction. The experimental approach includes information processing using encoded DNA sequences, DNAzyme-biocatalyzed reactions and the use of DNA-functionalized magnetic nanoparticles. The error-free DNA sequences are purified using the hybridization procedure with the DNA-functionalized magnetic nanoparticles, amplified by a PCR technique and used as input signals for DNAzyme-based logic gates. Digital XOR and NAND logic gates, copying (fanout), error correction by utilizing redundancy, and signal rectification, are demonstrated. Electronic and optoelectronic probes of the encoded DNA sequences are used to read out the results.