A Hexameric Ribozyme Nanostructure Formed by Double‐Decker Assembly of a Pair of Triangular Ribozyme Trimers

Abstract

The modular architecture of naturally occurring ribozymes makes them a promising class of structural platform for the design and assembly of three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahy-mena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.

Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes

“…We also installed orthogonality into substrate recognition to distinguish the activities of Rz-α and Rz-β. While the ribozyme oligomers derived from RNase P ribozymes were open-forms in this study, polygonal and three-dimensional nanostructures could be designed and constructed using RNase P ribozymes by following the design strategy for ribozyme-based nanostructures using the Tetrahymena group I ribozyme [ 18 , 20 , 21 , 22 ]. The development of polygonal-shaped oligomers of RNase P ribozymes is feasible through tuning the KL interacting motifs because these interactions have been used as vertices to assemble RNA duplexes to form RNA oligomers with polygonal shapes [ 33 ].…”

“…To expand structural design of ribozyme-based RNA oligomers and its reliability, it is important to eliminate undesired interactions and assemblies, which were often formed when additional elements were introduced to the parent ribozymes ( Figure 2 D, lanes 7 and 10) [ 21 , 22 ]. Because they cannot be predicted easily by secondary structure prediction, steady effort may be most effective for optimization of the structural elements to be added.…”

“…To complement the limited number of naturally occurring RNAs that assemble with geometrical shapes, we have developed artificial RNA assemblies by using modular group I ribozymes [ 18 , 19 , 20 , 21 , 22 ]. We reorganized the catalytic module and structural module composing the Tetrahymena group I ribozyme to achieve intermolecular assembly [ 18 , 19 ].…”