Evolution on a Chip: Microfluidic-Based Evolution of RNA Enzymes

The Scripps Research Institute, La Jolla CA

Investigators

Abstract

Processes of Darwinian evolution are fundamental to understanding biological form and function, but are difficult to appreciate on the human timescale. Over the past two decades, methods have been developed for evolving biological macromolecules under controlled laboratory conditions. The most powerful of these methods operate in a continuous manner, allowing one to maintain "cultures" of functional molecules, analogous to the way one cultures bacterial or eukaryotic cells. During the previous period of NSF support, new methods were devised for carrying out "evolution on a chip", employing microfluidic technology to bring about the continuous evolution of RNA enzymes in a highly precise and automated manner. The current project is expanding upon those efforts by implementing novel approaches for evolution within "cellular" compartments. Evolution is being made to occur within hundreds of millions of water-in-oil droplets of uniform size, generated by a high-throughput microfluidic device. This system will be used to study genetic drift through the accumulation of neutral mutations, to investigate competition between two different "species" of coevolving enzymes, and to examine the maximum frequency of mutation that can be tolerated by an evolving population. A special case involves RNA enzymes that catalyze their own replication and can evolve in a self-sustained manner. These enzymes are being used to construct compartmented synthetic genetic systems, for which replication will be made contingent upon the sensing of particular molecules within the local environment. The broader impact of this research derives from its ability to make Darwinian evolution a tangible process that one can witness in real time. The recent demonstration of evolution on a chip has had an impact on students by showing them how one can "run" molecular evolution experiments just as one runs a computer program. The work on self-sustained Darwinian evolution, especially when carried out within individual compartments, will bring these studies to the edge of synthesizing life in the laboratory. This research offers a reductionist but complete view of Darwinian evolution, and helps to demystify Darwinian evolution by presenting it as a biochemical process. Microfluidic-based evolution in particular allows students and investigators to see how Darwinian evolution can solve complex biochemical problems, while providing a detailed account of the genotypic and phenotypic changes that occur throughout the process of evolutionary adaptation. This project is jointly supported by the Molecular Genetics and the Molecular Biochemistry Programs in the Division of Molecular and Cellular Biosciences and Chemistry of Life Processes in the Division of Chemistry.