Self-assembly of large RNA structures: learning from DNA nanotechnology

Abstract

growth of other materials, and as drug delivery vectors. Both RNA and DNA have been successfully used to build scaffolds with rationally programmable features. RNA structures up to a few hundreds of nanometers large have been demonstrated to assemble in vitro as well as in vivo [2,3]. DNA has however been the polymer of choice to demonstrate 2D and 3D self-assembled structures with size ranging from 20 nm to several microns, due to its stability and the predictability of Watson-Crick base pair interactions [4][5][6].Although RNA and DNA share many general features, they also present many unique chemical and structural properties; Figure 1 summarizes some of the structural characteristics of DNA and RNA. These differences have prompted the development of distinct approaches to programmed self-assembly. Specifically, in silico sequence design to satisfy domain complementarity requirements combined with Holliday junction motifs dominates the field of DNA selfassembly [1]. In contrast, the exploitation of conserved, naturally evolved motifs with predictable tertiary structure (such as kissing loops) dominates RNA selfassembly methods [8].This brief review provides a comparison of existing approaches to the design of large, multi-component RNA and DNA nanostructures. For the reader's convenience, an abridged list of design methods and protocols is reported in Tables 1 and 2. We focus in particular on the problem of building large, multistranded RNA scaffolds with the potential of being stable or assembling in vivo. The construction of large RNA nanostructures presents significant challenges relative to small RNA nanoparticles [2], because of the higher likelihood of RNA strands to form undesired secondary structures. We suggest that methods developed for DNA tile systems may be viable to build large RNA assemblies which could be expressed and assemble in vivo; we highlight advantages, limitations, and challenges of this strategy. DOI 10.1515/rnan-2015-0002 Received September 8, 2015 accepted November 18, 2015 Abstract: Nucleic acid nanotechnology offers many methods to build self-assembled structures using RNA and DNA. These scaffolds are valuable in multiple applications, such as sensing, drug delivery and nanofabrication. Although RNA and DNA are similar molecules, they also have unique chemical and structural properties. RNA is generally less stable than DNA, but it folds into a variety of tertiary motifs that can be used to produce complex and functional nanostructures. Another advantage of using RNA over DNA is its ability to be encoded into genes and to be expressed in vivo. Here we review existing approaches for the self-assembly of RNA and DNA nanostructures and specifically methods to assemble large RNA structures. We describe de novo design approaches used in DNA nanotechnology that can be ported to RNA. Lastly, we discuss some of the challenges yet to be solved to build micron-scale, multi stranded RNA scaffolds.

Programmable RNA microstructures for coordinated delivery of siRNAs

“…Importing DNA nanotechnology design methods to RNA has the potential to yield increasingly complex and scalable nanostructures. Specifically, tile systems used in DNA nanotechnology could yield large RNA nanostructures, which may be useful in biomedical applications as delivery scaffolds for multiple nanoparticles 28 .…”

The Time Complexity of Self-Assembly

“…For example, virus assembly must be fast in order to produce many virus particles before the infected cell is eliminated by the host’s immune system [14, 22, 37]. Moreover, as larger and ever more complex nanostructures are to be realized for technological or medical applications, time efficiency in artificial self-assembly becomes vital [7, 30]. Designing self-assembly schemes that are fast and resource efficient is, however, challenging.…”

“…What kinds of schemes optimize the assembly time? Answers to these questions will enable assembly strategies to be identified that are optimally suited for the production of large, functionally complex macromolecular structures via artificial self-assembly, a major goal in nanotechnology [5, 7, 24, 27, 30]. Here, we address these questions by studying the time complexity (as opposed to structural complexity [1, 6, 10, 29]) of four prototypical self-assembly scenarios, using scaling arguments and in-silico modelling of the stochastic dynamics (see Methods).…”

The time complexity of self-assembly

“…For example, virus assembly must be fast to produce many virus particles before the infected cell is eliminated by the host’s immune system ( 1 – 3 ). Moreover, as larger and ever more complex nanostructures are to be realized for technological or medical applications, time efficiency in artificial self-assembly becomes vital ( 4 , 5 ). Designing self-assembly schemes that are fast and resource efficient is, however, challenging.…”

“…What kinds of schemes optimize the assembly time? Answers to these questions will enable assembly strategies to be identified that are optimally suited for the production of large, functionally complex macromolecular structures via artificial self-assembly, a major goal in nanotechnology ( 4 , 5 , 11 – 13 ). Here, we address these questions by studying the time complexity (as opposed to structural complexity) ( 14 – 17 ) of four prototypical self-assembly scenarios, using scaling arguments and in silico modeling of the stochastic dynamics.…”