RNA Junction Motifs as Scaffolds for Construction of Multifunctional RNA Nanoparticles (2013)

Bottom-up approach in RNA nanotechnology has recently emerged as an important means to construct RNA nanoparticles via self-assembly with desired structure and stoichiometry. The approach relies on the intrinsic nanoscale attributes of RNA as a construction material (Guo, 2010). Structurally, RNA can fold into incredibly diverse structures, displaying single-stranded bulges, hairpins, internal loops, and pseudoknots, which makes it distinct from DNA (Zuker, 1989; Pleij and Bosch, 1989; Guo, 2005; Isambert, 2009). In addition to canonical Watson-Crick (W-C) base pairing, RNA exhibits noncanonical W-C base pairing (such as, G-U wobble base pairs), base stacking and tertiary interactions (Searle and Williams, 1993; Sugimoto et al., 1995; Ikawa et al., 2004; Leontis et al., 2006; Li et al., 2006; Matsumura et al., 2009; Schroeder et al., 2010). Furthermore, RNA/RNA helices areCONTENTS6.1 Introduction ........................................................................................................................ 121 6.2 3WJ Motifs ........................................................................................................................... 1236.2.1 Classifications and Occurrences .......................................................................... 123 6.2.2 Application of 3WJ in Nanotechnology .............................................................. 124 6.2.3 Construction of 3WJ-Based RNA Nanoparticles Harboring FunctionalModules ................................................................................................................... 126 6.2.4 Evaluation of Functional Modules Incorporated in 3WJ RNA Nanoparticles ... 126 6.2.5 Construction of 3WJ-Based Square-Shaped and Triangular RNANanoparticles ......................................................................................................... 129 6.3 4WJ Motifs ........................................................................................................................... 1306.3.1 Classifications and Occurrences .......................................................................... 130 6.3.2 Application of 4WJ Motifs in Nanotechnology ................................................. 1326.4 Future Outlook and Perspectives .................................................................................... 132 6.4.1 Mutations to Increase Thermodynamic Stability .............................................. 133 6.4.2 Chemical Modifications to Increase Serum Stability ....................................... 133 6.4.3 Computational Approaches to Guide Nanoparticle Assembly ...................... 134 6.4.4 Evaluation of Functionality of Modules Incorporated into 3WJ or 4WJScaffold .................................................................................................................... 134 Acknowledgments ...................................................................................................................... 134 References ..................................................................................................................................... 134thermodynamically more stable than DNA/DNA equivalents (Searle et al., 1993; Sugimoto et al., 1995), which makes it particularly attractive for in vivo delivery. Functionally, RNA is versatile, as evidenced by the existence of several functionally active molecules in vivo, such as short interfering RNA (siRNA) (Fire et al., 1998; Li et al., 2002), micro RNA (miRNA) (Fabian et al., 2010), RNA apatmer (Ellington and Szostak, 1990; Tuerk and Gold, 1990), ribozyme (Kruger et al., 1982; Guerrier-Takada et al., 1983), and riboswitches (Sudarsan et al., 2008).