Despite the existing variety of RNA (and DNA) nanoparticles (NPs) and computational tools for their design, the use of RNA NPs as modular building blocks for constructing RNA networks has never been systematically investigated. To address this need and thereby shift the existing paradigm, the goal of this project is to develop an RNA-based, programmable networking platform that simultaneously encodes targeted biophysical, mechanical, and biochemical properties through networks with multiple independently programmable architectural parameters.
Kirill Afonin (Chemistry; www.afoninlab.com)
The functionally-versatile RNA plays an essential role in living systems, and the new discipline of RNA nanotechnology studies how this intriguing biopolymer can be programmed to assemble into defined shapes and sizes with varying physicochemical and biological properties. These novel design principles address some fundamental problems relevant to the RNA structure-activity relationship, biophysics of folding, and chemical interactions with other biomolecules. They also allow RNA nanoparticles to be designed for applications in biosensors, circuits, and therapeutics. To advance current designs, this project seeks to incorporate multiple RNA nanoparticles into assembled networks in order to elucidate the critical parameters of this bottom-up assembly. By characterizing the physicochemical, mechanical, and biochemical properties of RNA networks, the results of this work will enable the establishment of assemblies with desired properties based upon the types of nanoparticles incorporated and their linking moieties.
REU Students’ Role
Students working in the Afonin lab will be involved in RNA nanoparticles preparation and extensive characterization using various in vitro techniques such as DLS, EMSA, FRET, etc. Students would learn about cutting-edge research on RNA nanotechnology, how RNA nanoasseblies can function inside cells, and how to engineer those nanoassemblies de novo. The summer program would be designed as an independent project (from start to finish) beginning with the computational design of RNA nanoassemblies to their use, for example, as programmable gene silencing inducers in human cancer cells. This course would be a huge asset to students entering the job force allowing them to put techniques on their CV’s that few other undergraduates or graduate students can claim.