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

设计的核酸序列(DNA或RNA)可以自组装成纳米级的结构和设备，在诊断、治疗和纳米级制造中具有广阔的应用前景。链置换是动态DNA纳米技术中的一个关键过程，即入侵者的单链取代与互补底物结合的现有链。虽然DNA链置换电路已被证明能够进行复杂的计算，但它们与生物系统(如CRISPR)的接口不像RNA那样自然。与此同时，RNA电路并没有取得同样程度的成功。这项研究旨在更丰富地理解和精确控制杂交DNA：RNA置换，这可能导致能够与生物系统互操作的分子电路中的全新复杂水平。灵活、用户友好的序列设计工具将显著降低非专家实施的障碍。教育和外联活动将扩大对计算机的参与，并通过跨越学科界限对学生进行多学科交叉培训。研究人员将收集实验数据，以对DNA-RNA杂交系统的新粗粒度模型进行参数化，包括能够快速进行计算机模拟以确定动力学反应速率的马尔可夫链模型。这些混合模型还将对置换过程中错配的创建和修复进行参数化，从而使使用DNA和RNA进行精确动力学控制的链置换反应的设计成为可能，从而允许复杂的计算级联与生物信号的自然接口。将开发一个通用的DNA和RNA序列设计工具，专注于四项任务：算法/效率的改进，新模型的开发以增强可表达为约束的行为，与现有工具的集成，以及混合DNA：RNA置换系统的设计和实验演示，该系统实现了一个自我稳定的时钟，能够在固定的时间段产生RNA链。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.