Collaborative Research: FET: Medium: Engineering DNA and RNA computation through simulation, sequence design, and experimental verification

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Designed nucleic acid sequences (DNA or RNA) can self-assemble into nanoscale structures and devices with promising applications in diagnostics, therapeutics, and nanoscale manufacturing. Strand displacement, where an invader single strand displaces an incumbent strand bound to a complementary substrate, is a key process in dynamic DNA nanotechnology. While DNA strand displacement circuits have proven to be capable of complex computation, they do not interface as naturally to biological systems (e.g., CRISPR) as RNA. Meanwhile, RNA circuits have not achieved the same level of success. This research aims to develop a richer understanding and precise control of hybrid DNA:RNA displacement that may lead to entirely new levels of sophistication in molecular circuits capable of inter-operation with biological systems. A flexible, user-friendly sequence design tool will significantly reduce the barrier to implementation for non-experts. Education and outreach activities will broaden participation in computing and cross-train students in multiple disciplines by reaching across subject boundaries. The investigators will collect experimental data to parameterize new coarse-grained models of DNA-RNA hybrid systems, including Markov chain models capable of rapid in-silico simulation to determine kinetic reaction rates. These hybrid models will also parameterize mismatch creation and repair during displacement making possible the design of strand displacement reactions with precise kinetic control using both DNA and RNA, and thus allowing a natural interface of complex computational cascades with biological signals. A general-purpose DNA and RNA sequence design tool will be developed that focuses on four tasks: algorithmic/efficiency improvements, development of new models to enhance the behaviors expressible as constraints, integration with existing tools, and the design and experimental demonstration of a hybrid DNA:RNA displacement system that implements a self-stabilizing clock, capable of producing RNA strands at a fixed period.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.