Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design

A bimolecular ribozyme consisting of a core ribozyme (Delta P5 RNA) and an activator module (P5abc RNA) has been used as a platform to design assembled RNA nanostructures. The tight and specific assembly between the P5abc and Delta P5 modules depends on two sets of intermodule interactions. The interface between P5abc and Delta P5 must be controlled when designing RNA nanostructures. To expand the repertoire of molecular recognition in the P5abc/Delta P5 interface, we modified the interface by replacing the parent tertiary interactions in the interface with artificial interactions. The engineered P5abc/Delta P5 interfaces were characterized biochemically to identify those suitable for nanostructure design. The new interfaces were used to construct 2D-square and 1D-array RNA nanostructures.