RNA Tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology

Abstract

RNA molecules are versatile biomaterials that act not only as DNA-like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence-specific hybridization. This feature allows the design of RNA-based artificial gene regulators (riboregulators). RNA can also build complex two-dimensional (2D) and 3D nanostructures, which afford protein-like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self-assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells.

Stable RNA nanoparticles as potential new generation drugs for cancer therapy

“…Since Westhof et al proposed the concept of RNA tectonics [191], a variety of RNA 2D and 3D nano-constructs (TectoRNAs) have been constructed (for review, see reference [64]). These constructs follow the principle that natural or artificially designed RNA motifs can serve as building blocks for assembly of RNA architectures by coordinating RNA motifs with certain lengths of base pairing, specific angles, and tertiary interactions, such as tetraloop/receptor interactions and kissing loop interactions.…”

“…The accumulated information regarding the modularity of RNA architectures also allows use of small RNA modules for bottom-up design and assembly of artificial RNA structures (RNA tectonics) [38]. RNA motifs [43,44,56] and RNA inter-/intra-molecular interactions [33,55,64] have been used to build up diverse RNA nano-particles, such as squares [62], jigsaw puzzles [40], filaments [65], cubic scaffolds [61], and polyhedrons [63]. RNA folding and structural computation is essential for directing RNA motifs in RNA nanoparticle assembly.…”

Modeling of RNA nanotubes using molecular dynamics simulation

“…These nucleobases are connected to the sugar ring and then to the phosphate backbone to construct a complete strand. There are several structural derivatives of RNA modeled in literature in the nanoscale range (Holbrook 2005;Ishikawa et al 2013;Jaeger et al 2001). One of the most significant developments of RNA nanostructures is in the design of RNA nanorings, nanotubes (Grabow et al 2011;Afonin et al 2012;Badu et al 2014), and other nanostructures of different geometrical structures.…”

Diverse self-association properties within a family of phage packaging RNAs

“…In addition, because both naturally occurring and "designed" self-associating and self-assembling RNAs hold promise as ways to generate higher-order nanostructures (Westhof et al 1996;Yan 2004;Ko et al 2010;Dibrov et al 2011;Lee et al 2012;Ishikawa et al 2013), the insight gained by studying pRNA can inform these efforts. Most published research on pRNA has focused on the phi29 strain, in particular the kissing hairpin interaction, the molecularity of the multimer (dimer, trimer, etc.…”