Living cells constantly monitor their surroundings for physical and chemical changes and respond by controlling genetic and biochemical processes inside the cell. These processes involve sophisticated sensing and information processing that are very different from the conventional silicon-based counterparts. The investigators will develop novel biologically-inspired systems capable of sophisticated molecular sensing and elementary computations in cell-free conditions. The cell-fee gene switches and circuits could be used as a part of larger systems or devices that use biological elements to achieve complex functions, such as biosensors and diagnostic devices. Additionally, the project will enable deeper understanding of how RNAs control gene expression in living cells, which will further enhance our ability to engineer synthetic gene circuits with complex functions.
The research will focus on the development of RNA-based molecular sensors and gene circuits that function in cell-free conditions. The investigators will develop new techniques to isolate RNA switches and circuits from a large pool of mutants in the laboratory. Complex circuits will be built using the simpler parts generated by the techniques. The gene switches and logic gates that will be developed during the project period will be reusable as parts in other biomolecular devices and systems, thus they will be deposited in a public database. The proposed educational component of the project will provide an exceptional opportunity for undergraduate students to engage in real problem solving activities in small teams, both in the classroom and in the laboratory at University of California, Davis.
The goal of the NSF project was to develop and analyze novel methods to control gene expression reactions based on a naturally observed mechanism called riboswitches found in bacteria. Riboswitches are gene "switches" that turn ON or OFF the production of proteins encoded in DNA by using RNA as a sensor for specific molecular triggers such as vitamins, amino acids, and sugars. By learning from the natural riboswitches, we sought to design artificial gene switches capable of controlling gene expression in response to various molecules. Such riboswitches have potential uses in biotechnology to produce useful chemicals, drugs, and fuels more efficiently. Furthermore, we expected to gain fundamental insights into how riboswitches function in general. Through the project, we developed novel methods to develop artificial riboswitches by cell-free selection. Furthermore, we developed several strategies to integrate multiple riboswitches to create a complex "circuit" called "band-pass filter". We have also analyzed the molecular structure changes that are responsible for the function of an artificial riboswitch. Overall, these outcomes have significantly advanced our ability to engineer riboswitches and deepened our understanding of their molecular mechanisms. Six reearch articles have been published based on the project to date. In addition, the project engaged high school and undergraduate students through summer research programs and internships. An undergraduate laboratory module directly related to the project was developed and taught at University of California, Davis.
