GOALI: SemiSynBio-III: Moving Millions of Droplets at Megahertz Speeds: DNA Computing, DNA Storage, and Synthetic Biology on an Industrial Platform for Digital Microfluidics

自从沃森和克里克首次描述了DNA的分子结构，它承载信息的潜力对计算机科学家来说就显而易见了。对于从A、T、C和G的四值字母表中提取的序列中的每个核苷酸，具有n个核苷酸的DNA分子存储4的n次幂的数据。原则上，DNA可以提供一种比传统介质密度高许多个数量级的存储介质。在生物技术和制药工业的推动下，DNA测序（阅读）和合成（写入）技术都取得了迅速发展。然而，在阅读/写速度方面的理论可能性与实践中所证明的速度之间仍然存在很大差距。这项研究的工业合作伙伴希捷正在开发一种电子平台来缩小差距。学术团队的目标是探索Seagate正在开发的技术的替代应用。这些方法包括对存储在DNA中的数据进行计算的新方法，操纵合成细胞，以及工程生物反应器。在整个过程中，学术团队将努力争取高水平的公众参与。计划开展的活动包括发起政策讨论，特别是关于人工生命和生物安全的讨论，以及让高中生参与生物化学“制造者”文化。该提案涉及基于数字微流体的DNA存储的最先进的系统。这种技术通过电荷操纵网格上的小液滴。电子设备执行各种复杂的操作来组装DNA：合并，分裂，加热，冷却，混合和纯化。学术团队将探索一种方案，用于计算存储在DNA核苷酸序列中的数据，而是存储在DNA链的拓扑修饰中：DNA磷酸二酯骨架中的断裂称为“切口”，缺口称为“立足点”。在先前的工作中，这种计算已经通过用酶系统如CRISPR/Cas9切割DNA来证明。在这项工作中，带有必要缺口和支点的DNA将直接在电子网格上组装。学术团队还将探索合成生物学的应用，包括无细胞蛋白质表达、脂质体封装和直接在电子网格上进行RNA工程。该项目由生物科学局分子和细胞生物科学处、计算机和信息科学与工程局计算和通信基础处、电气部，通信和网络系统（ECCS）在工程局（ENG）和材料研究部（DMR）在数学和物理科学局（该奖项反映了NSF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。

Ever since Watson and Crick first described the molecular structure of DNA, its information-bearing potential has been apparent to computer scientists. With each nucleotide in the sequence drawn from the four-valued alphabet of A, T, C, and G, a molecule of DNA with n nucleotides stores 4 to the power of n bits of data. In principle, DNA could provide a storage medium that is many orders of magnitude denser than conventional media. Spurred by the biotech and pharma industries, the technology for both sequencing (reading) and synthesizing (writing) DNA has progressed rapidly. Nevertheless, a large gap remains between what is theoretically possible in terms of reading/writing speed and what has been demonstrated in practice. The industrial partner in this research, Seagate, is developing an electronic platform to close the gap. The goal of the academic team is to explore alternate applications of the technology that Seagate is developing. These range from novel ways of performing computation on data stored in DNA, to manipulating synthetic cells, to engineering bioreactors. Throughout, the academic team will strive for a high level of public engagement. Planned activities include initiating policy discussions, particularly regarding artificial life and biosafety, and engaging high-school students in biochem "maker" culture. This proposal pertains to a state-of-the-art system for DNA storage based on digital microfluidics. Such technology manipulates small droplets on a grid via electric charge. The electronics perform a variety of complex operations to assemble DNA: merging, splitting, heating, cooling, mixing, and purifying. The academic team will explore a scheme for computing on data stored not in the sequence of nucleotides of the DNA but rather in topological modifications to the strands: breaks in the phosphodiester backbone of DNA called "nicks" and gaps called "toeholds". In prior work, such computation has been demonstrated by nicking DNA with enzymatic systems such as CRISPR/Cas9. In this work, DNA with the requisite nicks and toeholds will be assembled directly on the electronic grid. The academic team will also explore applications in synthetic biology, including cell-free protein expression, liposome encapsulation, and RNA engineering directly on the electronic grid. The project was jointly funded by the Division of Molecular and Cellular Biosciences (MCB) in the Directorate for Biological Sciences (BIO); Division of Computing and Communication Foundations (CCF) in the Directorate for Computer and Information Science and Engineering (CISE); Division of Electrical, Communications and Cyber Systems (ECCS) in the Directorate for Engineering (ENG) and the Division of Materials Research (DMR) in the Directorate for Mathematical and Physical Sciences (MPS).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.