Collaborative Research: FET: Small: Algorithmic Self-Assembly with Crisscross Slats

合作研究：FET：小型：十字交叉板条的算法自组装

• 批准号: 2329909
• 负责人: David Doty
• 金额: $ 6.32万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-05-15 至 2027-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2329909&HistoricalAwards=false
• 关键词: Collaborative; Research; FET; Small; Algorithmic

This project utilizes DNA, the fundamental genetic material of all living organisms, as a construction material for nano-scale structures. The potential impact of this research spans multiple fields, including healthcare, where it could lead to breakthroughs in disease detection and treatment, and nano-engineering, offering new methods for manufacturing at the nanoscale. Leveraging the inherent base-pairing properties of DNA, the project employs a novel strategy known as slat assembly, where DNA sequences are designed to fold into elongated slats that then piece together to form complex geometries. This approach aims to circumvent the limitations of previous DNA assembly methods—specifically, the high costs and error rates associated with constructing larger structures. Slat assembly stands to substantially lower these barriers, enabling the creation of more intricate and vast nanostructures. Furthermore, by integrating these advancements into academic curricula, the project also seeks to equip a new generation of scientists with the interdisciplinary skills necessary to push the boundaries of what is scientifically possible.The focus of this project is to refine and advance slat-based DNA assembly as a solution to the challenges currently faced in DNA nanotechnology, specifically the errors associated with algorithmic self-assembly and the scalability issues of hard-coded approaches. The research team will engage in a systematic exploration of slat assembly, starting with computer simulations to design DNA-based slat systems that promise to mitigate growth errors. These theoretical designs will be brought to empirical testing through a series of incremental experiments. Initial phases will replicate and then simplify existing slat-based motifs, progressing to the development of motifs capable of arbitrary size expansion. This sets the groundwork for implementing algorithmic growth patterns within these scalable platforms, a novel endeavor within the field. The project includes designing slats of variable lengths and shapes, a technique that requires precise control and innovation beyond current methodologies. Successful implementation of these strategies will demonstrate the feasibility of algorithmic growth using slats, exemplified by constructing a discrete version of the Sierpinski triangle. This project represents a pivotal step towards achieving scalable, error-minimized assembly of DNA nanostructures, with significant implications for the future of nanotechnology and its applications across various disciplines.This project is jointly funded by the Foundations of Emerging Technologies program in the Division of Computing and Communication Foundations and the Established Program to Stimulate Competitive Research (EPSCoR).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.

该项目利用所有生物体的基本遗传物质 DNA 作为纳米级结构的构建材料，这项研究的潜在影响涵盖多个领域，包括医疗保健，它可能会在疾病检测和治疗方面取得突破。纳米工程，利用 DNA 固有的碱基配对特性，提供了新的纳米级制造方法，采用了一种称为板条组装的新策略，其中 DNA 序列被设计成折叠成细长的板条，然后拼凑在一起形成。这种方法旨在规避以前 DNA 组装方法的局限性，特别是与构建更大结构相关的高成本和错误率，可以大大降低这些障碍，从而能够创建更复杂和更大的纳米结构。通过将这些进步整合到学术课程中，该项目还寻求为新一代科学家提供必要的跨学科技能，以突破科学上可能的界限。该项目的重点是完善和推进基于板条的 DNA 组装，一个解决目前 DNA 纳米技术面临的挑战，特别是与算法自组装相关的错误和硬编码方法的可扩展性问题，研究团队将进行板条组装的系统探索，从计算机模拟开始设计 DNA-。基于板条的系统有望减少生长误差。这些理论设计将通过一系列增量实验进行实证测试，初始阶段将复制并简化现有的基于板条的图案，进而开发出具有任意尺寸的图案。这为在这些可扩展平台中实现算法增长模式奠定了基础，该项目是该领域的一项新颖尝试，包括设计可变长度和形状的板条，这是一种需要超越当前方法的精确控制和创新的技术。策略将证明使用板条进行算法增长的可行性，以构建离散版本的谢尔宾斯基三角形为例，该项目代表了实现可扩展、误差最小化的 DNA 纳米结构组装的关键一步。对纳米技术及其跨学科应用的未来具有重大影响。该项目由计算和通信基础部新兴技术项目基金会和刺激竞争性研究既定项目 (EPSCoR) 联合资助。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Proceedings of the 29th International Conference on DNA Computing and Molecular Programming (DNA 29)

第 29 届国际 DNA 计算和分子编程会议论文集 (DNA 29)

• DOI: 10.4230/lipics.dna.29.7
• 发表时间: 2023-01
• 期刊: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
• 作者: Doty, David;Fleming, Hunter;Hader, Daniel;Patitz, Matthew J.;Vaughan, Lukas A.
• 通讯作者: Vaughan, Lukas A.