Discovering and Assembling RNA Architectures for Materials, Therapeutics and Diagnostics

The 2017 GRC in RNA Nanotechnology will draw on the success of the first conference on this topic, held in 2015, to foster collaborations between scientists and engineers working in the diverse fields of chemistry, biochemistry, structural biology, microbiology, cancer biology, cell biology, biophysics, pharmacy, materials, and nanotechnology, with the purpose of promoting transformative advances that will enable the monitoring and improvement of human health and the diagnosis and treatment of diseases utilizing the unique modality provided by RNA-based nanoparticles.

RNA Nanotechnology has emerged from a series of important discoveries over the past 30 years, showing that: 1) RNA molecules, like proteins, can form complex and compact folded structures; 2) RNA molecules can function as enzymes, just like proteins, to catalyze important reactions in living cells macromolecules; 3) most RNA molecules in human cells are non-protein coding RNA (ncRNA) and play important roles in regulating gene expression; 4) most of the genome is transcribed and most of RNA produced is functional; 5) RNA is capable of self-assembly into complex quaternary structures, in association with other RNA molecules, proteins, or even DNA; and 6) RNA is capable of specifically binding small molecules and changing its structure in response to binding. Like proteins, RNA molecules form complex, hierarchically organized structures, that span several orders of magnitude.

In parallel with these discoveries, powerful new experimental methods have been developed to rapidly probe the solution structures of RNA with chemical and enzymatic probes, to establish atomic resolution structures by crystallography, NMR, and increasingly high-resolution cryo-electron microscopy (EM) and to evolve RNA molecules with new functionalities. Advances in computational analysis and 3D modeling of RNA have occurred in parallel, which have greatly improved our ability to 1) predict the 2D and 3D structures of RNA molecules based on sequence and 2) to design RNA molecules to fold into a desired 3D structure capable of self-assembling into a target supra-molecular assembly. Analysis of new 3D structures of large RNA molecules, beginning with catalytic Group I ribozymes and culminating with the ribosome revealed recurrent, modular 3D motifs and folds that can be reassembled to create novel architectures for constructing homogeneous nanostructures having defined size, shape, and stoichiometry; this pioneering concept demonstrated over 15 years ago by Prof. Peixuan Guo, Chair of the 2015 RNA Nanotechnology GRC and Prof. Neocles Leontis, Chair of the upcoming 2017 meeting.

The field has developed rapidly since then. The use of RNA as a medium for nanotechnology follows on the successful use of DNA, for this purpose pioneered by Nadrian Seeman and his many co-workers. RNA has recently catapulted as a nanotechnology platform due to its diversity in both structure and function. RNA is unique in comparison to DNA by virtue of its high thermodynamic stability, the formation of both canonical and non-canonical base pairings, the stabilization by base stacking, and distinctive in vivo attributes. (3) RNA nanotechnology is a unique field that is distinct from the classical studies of native RNA structure and folding that are decades old. In addition to intra-molecular (within a molecule) interactions that facilitate folding, special knowledge of inter-molecular interactions that enable supra-molecular self-assembly is required. (4) RNA nanoparticles can be purified to homogeneity and can be characterized or visualized by chemical, physical, biophysical, and optical methods. (5) Previously, the sensitivity of RNA to RNase degradation had been the biggest hurdle in the production of RNA for use as a construction material. Recently, simple chemical modifications, such as incorporation of 2'-fluorinated nucleosides, have provided resistance to enzymatic degradation, with little perturbation of folding properties and overall retention of biological function in certain cases. (6) Finally, RNA nanotechnology transcends conjugation of functional RNA modules to gold, liposome, dendrimer or polymer based nanoparticles, and more broadly encompasses application of bottom-up approaches to assemble nanometer scale particles composed primarily of RNA.