Demonstration of a Scalable DNA Computing Platform: Writing and Selection

Abstract

High value data like historical or health records, seismic or satellite images, particle collision events or original recordings, requires a long-term storage medium that is resilient, scalable, secure, and computable. DNA has been proposed as a solution and storage has been demonstrated using basewise synthesis. Separately, DNA computing demonstrations have shown complex programs executed on small datasets. Here, we demonstrate a new unified approach to DNA-based data storage and computing. We describe a novel combinatorial assembly approach to writing data into DNA. We define a trie-like DNA data structure and use it to write data in key-value form. We demonstrate our approach by writing The Complete Works of William Shakespeare - about 1 million words of text - into DNA with raw error rates rivaling conventional media. Leveraging our DNA data structure, we define two new computing instructions - select and quotient - and using them, demonstrate how DNA-encoded text could be searched for exact or approximate matches to a query word. Our search demonstrations achieve perfect recall and high precision. Our approach is more scalable in cost and throughput that previous approaches and our platform is extensible to more powerful computing instructions applicable to a variety of applications.