DNA Computation in Cells

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DNA logic gates are powerful computation devices because the outputs are chemically equivalent to the inputs, and the output of one gate can act as the input for a subsequent gate - similar to electronic gates. This enables serial connections of gates, generating signaling cascades that can be assembled into complex molecular circuits based on nucleic acid hybridization where both the encoded program and the machinery that runs the program are composed of DNA. The use of synthetic DNA as a material for biocomputing in human cells has several advantages: DNA circuits rely on fully programmable Watson-Crick base-pairing interactions and thus can be rationally designed at the molecular level, delivering a high degree of control. New components, such as gates, amplifiers, and sub-networks can be readily encoded in DNA sequences, which provides modularity and adaptability. The completion of the research objectives will lead to broadly applicable approaches to programmable biological computation devices that are functional in human cells. The developed methodologies will be of interest to scientists who are developing or applying DNA-programmable algorithms or assemblies to biological systems; furthermore, they will facilitate interactions with the field of microRNA biology. The outputs of the DNA computation process can be readily interfaced with cellular and organismal systems, thus extending the impact of this methodology into broader applications. In addition, the proposed biocomputing circuitry is inexpensive to manufacture and easy to assemble - in contrast to traditional techniques for the analysis of microRNA patterns. Due to its multidisciplinary nature, this project will train the next generation of students in the programming in oligonucleotides, oligonucleotide chemistry, and cell biology. Based on developed expertise, outreach activities with museums and schools will be conducted in order to excite children at a young age (and their parents) about STEM, specifically at the interface of computer science, biology, and chemistry.This research will test if cellular microRNA pattern detection, analysis, and response functions of devices can be combined in DNA-based computation circuitry. This will represent an innovative approach to the analysis of microRNA patterns directly inside of live cells. Output signals of DNA-based circuits are not restricted to electrical or optical outputs (as in case of traditional detection and analysis methods), but can be designed as oligonucleotides, fluorophores, dyes, and other molecules. An innovative DNA-analog based biocomputing system will be developed in order to protect the encoded oligonucleotide programs from biological environments and highly specific self-assembly capabilities will provide flexible designs for next-generation molecular computation devices in living systems. The following research objectives will be pursued: (1) demonstrate DNA computing of increasing complexity in live cells, (2) interface cellular DNA computing with signal amplification, (3) engineer cellular DNA computing to provide molecular outputs, and (4) use new materials to encode oligonucleotide programs in order to protect the DNA devices from cellular environments.