I seek to utilize RNA’s unique structural properties to design new nanomachines for therapeutic and biosensor applications.
RNAMake removes difficulties plaguing RNA 3D design. I have developed the RNAMake software suite for the design and analysis of RNA 3D structure (rnamake.stanford.edu). RNAMake codifies and automates decades of learned rules of 3D design, removing the requirement for painstaking manual modeling and time-consuming selection experiments that previously hampered the generation RNA nanostructures. With RNAMake, I rapidly designed a host of 3D nanostructures to near-atomic accuracy, as confirmed by X-ray crystallography. Furthermore, I used RNAMake to design complex RNA machines; I designed a single-stranded ribosome and increased the affinity and stability of the ATP and GFP analog (spinach) RNA aptamers.
Problems in RNA nanotechnology solved by RNAMake
(a) ‘miniTTRs’ require two strands (green, purple between tetraloop (orange) and tetraloop-receptor (blue); (b) tethered ribosomes require two strands (green, purple) to link the small subunit (orange) to the large subunit (blue). c) ‘Locking’ a small-molecule binding aptamer (cyan; ATP molecule in pink spheres) by designing four strands (green, purple, teal, magenta) to a peripheral tertiary contact(orange, blue). d) Demonstration of RNAMake design algorithm, which builds an RNA path via the successive addition of motifs and helices from a starting base pair to the ending base pair.
Develop RNA-based therapeutic and biosensors with RNAMake. Taking advantage of the automated design algorithms I designed with RNAMake, I will design therapeutic and biosensing RNA machines that harness RNAs ability to detect, bind and recruit other molecules. Here, I present the first three nanomachines my laboratory will design and produce: (1) ultra-high-affinity chemical sensors, (2) tertiary structure detectors for non-coding RNA discovery and (3) therapeutic inhibitors and stabilizers of protein-protein interactions. Each represents a milestone in RNA nanotechnology and, in conjunction with developing novel methods, will permit the generation of numerous complex RNA-based machines.
Long term goals. In the long term, my lab will be able to build revolutionary RNA-based devices, such as custom ribosomes that decode light pulses instead of mRNA, next-generation RNA drugs that treat a wide range of diseases, and RNA guide strands that can perform complex computations for CRISPR-based gene editing and other applications.