FET: Small: DNA Storage and Computation with Strand Displacement Cascades

FET：小型：具有链位移级联的 DNA 存储和计算

• 批准号: 2200290
• 负责人: David Soloveichik
• 金额: $ 60万
• 依托单位: University of Texas at Austin
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2200290&HistoricalAwards=false
• 关键词: FET; Small; DNA; Storage; Computation

DNA is incredibly information-dense (up to 6 orders of magnitude denser than optical or magnetic media) and stable (readable over millennia). Storage and retrieval of up to gigabytes of digital information in the form of text, images, and movies has already been successfully demonstrated. DNA storage is typically viewed as a form of passive storage (“cold storage”) and performing computation on the stored data currently involves sequencing the DNA, electronically computing the desired transformation, and synthesizing new DNA, which is an expensive and slow loop. This project seeks to make the next generation of dynamic DNA storage, where chemical interactions can manipulate the stored information “in memory.” Investigators will develop molecular versions of important algorithms for computation on digital data and implement them using programmable DNA-DNA interactions. The project will also contribute to undergraduate and graduate education and support undergraduate hands-on research, as well as provide training of students in applying the principles of computer science and electrical engineering to traditionally incompatible domains of biology and chemistry.This project will develop the SIMD-DNA (Single-Instruction Multiple-Data DNA) paradigm for using DNA strand displacement reactions to manipulate digital information recorded in the topological modification of the DNA substrate (location of strand breaks). Using the inherent parallelism of chemistry, this data processing scheme will be capable of parallel, in-memory computation, eliminating the need for sequencing and synthesizing new DNA on each data update. More specifically, the award will fund the development of the theoretical foundation of SIMD-DNA computation, including strand displacement programs to simulate various data-processing algorithms, as well as the experimental demonstration of the molecular algorithms and methodology. Further, software to simulate and verify SIMD-DNA programs will be developed. Theoretical and experimental studies on strand displacement on DNA of biological origin and sequence (native DNA) will be used to understand and decrease the spurious interactions that can occur in the absence of conventional sequence design. Native DNA has the potential to improve fidelity and significantly decrease cost compared to chemically synthesized DNA. Finally, new methods to improve the speed and efficiency of large strand displacement cascades will be explored, which may generalize beyond DNA storage.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.

DNA具有令人难以置信的信息密度（比光学或磁性介质密度高达6个数量级）和稳定性（数千年可读）。存储和检索高达千兆字节的文本、图像和电影形式的数字信息已经被成功地证明。DNA存储通常被视为被动存储（“冷存储”）的一种形式，对存储的数据进行计算目前涉及DNA测序，电子计算所需的转换，以及合成新的DNA，这是一个昂贵且缓慢的循环。该项目旨在制造下一代动态DNA存储，其中化学相互作用可以操纵存储在“内存”中的信息。研究人员将开发用于数字数据计算的重要算法的分子版本，并使用可编程DNA-DNA相互作用来实现它们。该项目还将为本科生和研究生教育做出贡献，支持本科生的动手研究，并为学生提供将计算机科学和电气工程原理应用于传统上不兼容的生物和化学领域的培训。该项目将开发SIMD-DNA（单指令多数据DNA）范例，用于使用DNA链位移反应来操作记录在DNA底物拓扑修饰中的数字信息（链断裂的位置）。利用化学固有的并行性，该数据处理方案将能够在内存中并行计算，从而消除了每次数据更新时测序和合成新DNA的需要。更具体地说，该奖项将资助SIMD-DNA计算理论基础的发展，包括模拟各种数据处理算法的链位移程序，以及分子算法和方法的实验演示。此外，将开发模拟和验证SIMD-DNA程序的软件。生物起源和序列（天然DNA）的DNA链位移的理论和实验研究将用于理解和减少在没有常规序列设计时可能发生的虚假相互作用。与化学合成的DNA相比，天然DNA具有提高保真度和显著降低成本的潜力。最后，将探索提高大链位移级联的速度和效率的新方法，这可能会推广到DNA存储之外。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。