Bio-QuBIC: Engineering Molecular Logic Gates Using Nucleic Acids

Yale University, New Haven CT

Investigators

Abstract

EIA-0129939 Ronald Breaker Yale University Title: Engineering Molecular Logic Gates Using Nucleic Acids Under this project, test tube evolution is used to create molecular switches that serve as logic gates, and these chemically triggered switches are assembled into first-generation biomolecular computing devices. This project is creating new functional RNA and DNA molecules that perform as distinct types of logic gates. This advance in "molecular hardware" design is adding to the repertoire of molecular computing infrastructure and permitting the construction of more advanced molecular computing devices. As a demonstration of utility, these logic gates are assembled into molecular computing systems that can be used to add any two numbers. A combination of modular rational design and in vitro evolution is being used to create nucleic acid molecular switches that are analogous to electronic logic gates. This design strategy employs the process of Darwinian evolution, where molecular "survival-of-the-fittest" is used to identify unique RNA switches that have AND gate function. The kinetic characteristics of the selected RNAs are examined to identify robust constructs that can be altered to produce up to 1 trillion different AND gate species. To demonstrate the utility of these logic gates, they are assembled to create a functional architecture for a molecular computer that can add any two numbers. The result of the molecular computation is reported as pixels on a chip-like surface using radioisotope signaling. In addition, other RNA and DNA switches are created using similar strategies that perform as representatives of the remaining common logic gates.