DNA-based data storage via combinatorial assembly

Persistent data storage is the basis of all modern information systems. The long-term value and volume of data are growing at an accelerating rate and pushing extant storage systems to their limits. DNA offers exciting potential as a storage medium, but no practical scheme has been proposed to date that can scale beyond narrow-band write rates. Here, we demonstrate a combinatorial DNA data encoding scheme capable of megabits per second write speeds. The system relies on rapid, combinatorial assembly of multiple smaller DNA parts that are dispensed through inkjet printing. To demonstrate this approach, we wrote approximately 25 kB of information into DNA using our system and read the information back out with commercially available nanopore sequencing. Moreover, we demonstrate the ability to replicate and selectively access the information while it is in DNA, opening up the possibility of more sophisticated DNA computation.

Photochemical NOT Gate for DNA Computing

DNA-based Boolean logic gates (AND, OR and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. We developed a novel DNA gate design utilizing photocaging groups that prevents gate function until irradiation at a certain time-point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA inputs. We further demonstrate the utility of the NOT gate within multi-layer circuits in response to a specific pattern of four microRNAs.