A novel RNA motif was identified based on its
sequence by computational structure modeling. The RNA
molecule was reported to be a substrate for the structurally
specific endoribonuclease, Dicer, which cleaves doublestranded
RNA and cuts out 20−25 nucleotide fragments.
This enzymatic property was essential for the potential
utilization of the motif in the nanoparticle design of
further biological experiments. Herein, the protocol for the
prediction of the structure of this motif in-silico is presented,
starting from its primary sequence and proceeding
through secondary and tertiary structure predictions.
Applying RNA architectonics, this novel structural motif,
3wj-nRA, was used for rational RNA nanoparticle design.
The molecules, which are based on this three-way junction
fold, may assemble into more complex, triangular shaped
nano-objects. This trimeric nanoparticle containing
3wj-nRA motif can be further utilized for functionalization