Computational protocol: RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications

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Protocol publication

[…] The first step in RNA nanoparticle construction is the consideration of the blueprint []. This requires an understanding of the assembly and folding mechanism in the bottom-up assembly. Designing the sequence of the building block is critical for successful RNA nanostructure assembly, which can be achieved by experience and brainstorming taking into consideration of RNA folding, complementation, hand-in-hand interaction, foot-to-foot interaction, and the use of thermostable motifs, kissing loops, sticky ends, helices, stem loops, etc. All RNA nanoparticles constructed based on phi29 motor pRNA was achieved via experience and brainstorming without computer algorithm besides the traditional RNA folding program developed by Zuker 30 years ago []. It is expected that computer algorithms will facilitate RNA nanoparticle construction. A variety of computer programs such as NanoFolder, NanoTiler and RNA2D3D are available to facilitate the in silico design of RNA sequences (these sequences may contain inter-strand and intra-strand pseudoknot-like interactions) capable of self-assembly into multi-sequence RNA nanostructures and the 3D modeling of such structures [–]. For example, by utilizing computational modeling and sequence optimization, three-dimensional cubic RNA-based scaffolds can be successfully designed and engineered with precise control over their shape, size and composition []. Moreover, online RNA structure databases such as RNAJunction database also provides useful RNA structures for designing RNA nanostructures []. […]

Pipeline specifications

Software tools NanoFolder, NanoTiler, RNA2D3D
Databases RNAJunction
Application RNA structure analysis
Chemicals RNA