Regulation of the structure of RNA assemblies through RNA tertiary interactions

We have previously shown that RNA building blocks containing two or three stem-loops based on the dimerization initiation site (DIS) connected by short linkers can be assembled into various one- and two-dimensional structures. Here, in an attempt to regulate the conformation of the RNA assemblies by adjusting the rigidity of the RNA building block, we have introduced the triple-helical scaffold (THS) into the linker region connecting two DIS-based stem-loops. As a result, linear and circular assemblies could be selectively formed with RNA building blocks containing the wild-type and mutant THS sequences, respectively. The results demonstrate how the conformation of RNA assemblies may be regulated by external factors, thereby expanding the utility of RNA-based nanostructures.