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

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.