Photochemical NOT Gate for DNA Computing

Abstract

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.