Interfacing Synthetic DNA Logic Operations with Protein Outputs†
This work was supported by the University of Pittsburgh. We acknowledge Dr. Chungjung Chou for assistance in developing protein expression conditions and Dr. Indraneel Ghosh (University of Arizona) for the expression constructs.
Graphical Abstract
Gated Proteins: By using zinc-finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs by activating or deactivating a split-luciferase enzyme. The gate designs are simple and modular, thus enabling integration with larger multigate circuits and providing flexibility in the choice of protein outputs. Response to microRNA inputs was achieved through the use of translator circuits.
Abstract
DNA logic gates are devices composed entirely of DNA that perform Boolean logic operations on one or more oligonucleotide inputs. Typical outputs of DNA logic gates are oligonucleotides or fluorescent signals. Direct activation of protein function has not been engineered as an output of a DNA-based computational circuit. Explicit control of protein activation enables the immediate triggering of enzyme function and could yield DNA computation outputs that are otherwise difficult to generate. By using zinc-finger proteins, AND, OR, and NOR logic gates were created that respond to short oligonucleotide inputs and lead to the activation or deactivation of a split-luciferase enzyme. The gate designs are simple and modular, thus enabling integration with larger multigate circuits, and the modular structure gives flexibility in the choice of protein output. The gates were also modified with translator circuits to provide protein activation in response to microRNA inputs as potential cellular cancer markers.
