FET: Medium: Massively parallel DNA computation using DNA array synthesis, next generation sequencing and nanopore sensing

FET：中：使用 DNA 阵列合成、下一代测序和纳米孔传感进行大规模并行 DNA 计算

• 批准号: 1954665
• 负责人: Georg Seelig
• 金额: $ 100万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1954665&HistoricalAwards=false
• 关键词: FET; Medium; Massively; parallel; DNA

Computing with molecular components can enable innovations in a range of areas from health diagnostics and therapies to information technology. For example, molecular circuits that can process the information encoded in the levels and sequences of cellular molecules can be at the heart of embedded controllers for biomedical applications. However, the ability to build molecular controllers lags far behind the ability to engineer embedded control circuits for electromechanical devices. This project aims to develop new methods of writing and reading DNA circuits that will make it possible to scale up circuit complexity by at least an order of magnitude over the current state of the art and thus bring molecular controllers closer to practical applications. Furthermore, this project will accelerate training of students and professionals in the burgeoning field of molecular information systems. This area of research inherently increases the diversity of people, perspectives, and backgrounds in computing by bringing together the historically separated fields of computer science and biology. To increase participation of underrepresented persons in molecular programming research, the team of researchers will host summer interns from Rainier Scholars, an organization that supports students of color from low-income backgrounds in achieving academic success.This project introduces technological innovations that will increase the scalability of molecular circuitry. PIs will do this by taking advantage of massively parallel DNA synthesis technology and coupling it to high throughput readout methods, including next generation sequencing and nanopore sensing. These advances are significant because the scaling up of DNA circuitry is currently limited in two main ways: A first limitation is that the vast majority of DNA gates and similar computational elements are assembled from individually column-synthesized oligonucleotides because this technology provides low synthesis error rate and control over the concentration of individual strands. However, the cost of ordering individually synthesized oligos cannot scale. Array synthesized oligos provide a promising alternative because cost per oligo is orders of magnitude lower. But so far, array-synthesized oligos have not been used for molecular programming applications because of the lower synthesis quality, variation in concentration between oligos and the low yield of each individual oligo in the pool. A second limitation comes from the use of fluorescence-based reporters for reading out the results of a computation. That is, due to spectral overlap between fluorophores, only a very small number of outputs or variables can be monitored in a given computation (i.e. as many as there are independent fluorescence channels, typically no more than 4 and only a limited number of computations can be performed in parallel (i.e. as many as there are separate reaction chambers, typically no more than 96). Next generation DNA sequencing and nanopore sensing methods could theoretically be used to read out hundreds to millions of DNA sequences or barcodes in parallel. However, so far, DNA sequencing and nanopore sensing have not been widely used to read out DNA computations because current gate architectures are not compatible with these read out methods. This project directly addresses these limitations to the current state of the art.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.

使用分子成分进行计算可以实现从健康诊断和治疗到信息技术等一系列领域的创新。例如，可以处理细胞分子水平和序列中编码的信息的分子电路可以成为生物医学应用嵌入式控制器的核心。然而，构建分子控制器的能力远远落后于设计机电设备嵌入式控制电路的能力。该项目旨在开发写入和读取 DNA 电路的新方法，使电路复杂性比现有技术水平至少提高一个数量级，从而使分子控制器更接近实际应用。此外，该项目将加速分子信息系统这一新兴领域的学生和专业人员的培训。该研究领域通过将历史上分离的计算机科学和生物学领域结合在一起，从本质上增加了计算领域的人员、观点和背景的多样性。为了增加代表性不足的人群对分子编程研究的参与，研究人员团队将接待雷尼尔学者组织的暑期实习生，该组织旨在支持来自低收入背景的有色人种学生取得学术成功。该项目引入了技术创新，将提高可扩展性分子电路。 PI 将利用大规模并行 DNA 合成技术并将其与高通量读出方法（包括下一代测序和纳米孔传感）相结合来实现这一目标。这些进步意义重大，因为 DNA 电路的扩展目前主要在两个方面受到限制：第一个限制是绝大多数 DNA 门和类似的计算元件都是由单独的列合成寡核苷酸组装而成，因为该技术提供了较低的合成错误率并控制单条链的浓度。然而，订购单独合成的寡核苷酸的成本无法衡量。阵列合成的寡核苷酸提供了一种有前途的替代方案，因为每个寡核苷酸的成本要低几个数量级。但到目前为止，阵列合成的寡核苷酸尚未用于分子编程应用，因为合成质量较低、寡核苷酸之间的浓度存在差异以及池中每个寡核苷酸的产量较低。第二个限制来自于使用基于荧光的报告器来读出计算结果。也就是说，由于荧光团之间的光谱重叠，在给定的计算中只能监测非常少量的输出或变量（即与独立荧光通道一样多，通常不超过 4 个，并且只能进行有限数量的计算）可以并行执行（即，有多少个单独的反应室，通常不超过 96 个）。理论上，下一代 DNA 测序和纳米孔传感方法可用于并行读取数百至数百万个 DNA 序列或条形码。到目前为止，DNA 测序和纳米孔传感尚未广泛用于读取 DNA 计算，因为当前的门架构与这些读取方法不兼容。该项目直接解决了当前技术水平的这些限制。该奖项反映了 NSF 的法定规定。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。