Catalytic RNA nano-objects formed by self-assembly of group I ribozyme dimers serving as unit structures

An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers

“…We substituted two RzMs in 1-K-1 to prepare a trio of Urds (3-K-2 , 2-K-4 and 4-K-3 ) for triblock-type kUrd copolymer. For this purpose, we introduced three RzM:RzM interactions 2:2 , 3:3 and 4:4 (Figure 3A and Figure S1D), which were designed to be orthogonal to one another in their recognition specificity [28]. In a similar manner, a pair of Urds (1-K-5 and 5-K-1 ) were also designed for diblock-type kUrd copolymer (Figure 3A and Figure S1D), which would selectively yield a closed dimer.…”

“…A pair of symmetrical ∆P5-P5abc interfaces yielding RzM:RzM homodimer was then engineered to asymmetrical recognition interfaces, such as RzM:RzM interface 1:1′, yielding RzM:RzM heterodimers (Figure 1). We then connected a pair of RzM monomers in a tail-to-tail manner at their P6b region, enabling the resulting covalent dimer (termed unit ribozyme dimer and abbreviated as Urd) to homooligomerize in a directional manner (Figure 1) [28]. Unit ribozyme dimers (Urds) homooligomerized to form an open chain assembly (Figure 1).…”

“…Unit ribozyme dimers (Urds) homooligomerized to form an open chain assembly (Figure 1). The extents of oligomerization were programmable by designing the specificity of the assembly interfaces between two ribozyme modules (RzMs) in Urds [28]. We also expected that the parent Urds could be modified to produce closed forms of symmetrical oligomers if we used a bent P6b-P6b linker.…”