Toward a DNA Nanoprocessor: Optimization of Tile-Associated DNA Circuits

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A nano-scale processor that uses individual molecules as operational units is a promising alternative to the modern computers that use semiconductor microprocessors. A computer built from molecules is potentially smaller and consumes less energy than its electronic counterpart. A long-term goal of this project is to construct a molecular scale processor from biological molecules, called DNA oligonucleotides. An additional advantage of such DNA-based computers is their biocompatibility, which is the ability to interact with biological molecules, cells and even organs in a controlled fashion. This property is crucial in application of molecular devices in living organisms for the control and corrections of metabolic functions, or in clinical tests for diagnosis of human genetic and infectious diseases. Recently, connectable logic units made of DNA oligonucleotides have been developed by implementing an original design that supports communication between logic gates made of DNA oligonucleotides. In the prior studies, a set of communicating AND, NOT and OR logic gates was designed and characterized. It was demonstrated that such logic gates have advantages over conventional technologies in the analysis of nucleic acid sequences of pathogenic bacteria, such as Mycobacterium tuberculosis. The communicating gates were attached to the DNA tiles to produce simple logic circuits, a counterpart of logic circuit used in modern computers. This project makes next three steps in the development of a DNA nanoprocessor. First, DNA circuits will be powered by chemical reactions to provide energy for continuous operation of the DNA computer. Next step is to achieve re-settable and re-usable mode of operation, such that the DNA computer can be used multiple times for logic operations. This will be achieved by using biocatalysts, such as enzymes and deoxyribozymes which digest DNA inputs, thus resetting the molecular devise in its original state. Third, larger-scale integration of DNA logic units will be achieved. More complex integrated circuits can solve more complex computational tasks. This will be achieved using most recent developments in DNA nanotechnology - controllable self-association of DNA strands in predesigned structures. To sum up, this project will solve three important problems of molecular computation on the way to the production of a first DNA nanoprocessor. This will lay a foundation for the future DNA nanoprocessors, a key component of smart medical molecular nanodevices of the future. The research will be integrated with education through introducing research topics into undergraduate teaching, research training of students at undergraduate and graduate levels, and the outreach program through partnerships with Central Florida high schools.