CAREER: Deoxyribozyme-Deoxyribozyme Logic, a New Computational Substrate

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EIA-0243796Darko StefanovicUniversity of New MexicoDeoxyribozyme-deoxyribozyme Logic, a new computational substrateDeoxyribozymes (nucleic acid enzymes) are the basis for a family of molecular-scale elementary logic gates which have input and output signals of the same kind, as concentrations of oligonucleotides, and which operate in solution. Chemical-kinetic properties of these gates are being studied through collaborative experiments, analytical modelling, and computer simulation. Dynamic properties of larger circuits composed of elementary gates and capable of autonomously carrying out complex Boolean functions (decision-making) as well as other computational tasks are being studied, including the reliability of communication between gates, in order to characterize the functional behavior and performance of such circuits. Analysis and synthesis tools tailored to deoxyribozyme-based logic are being developed.Through this work, the state of knowledge about large-scale chemical kinetics modelling, oligonucleotide library design and other combinatorial problems is being advanced, and interdisciplinary collaborations between computer science and biochemistry and nanotechnology are being established. Through involvement in research and through curriculum development, undergraduate and graduate students are being trained in the emerging area of bioinformatics. Finally, foundations are being laid for diagnostic and therapeutic applications in which individual cells can be analyzed according to Boolean criteria, so that diseased cells can be reliably distinguished from healthy ones and specifically treated.