A single-stranded architecture for cotranscriptional folding of RNA nanostructures

TLDR

Artificial DNA and RNA scaffolds are used for nanoscale devices, but RNA structures are smaller yet can fold cotranscriptionally, enabling genetic encoding and cellular expression. The study proposes a single‑strand RNA architecture that arranges antiparallel helices via tertiary motifs and a novel crossover pattern. This architecture uses RNA tertiary motifs and a new crossover pattern to precisely organize antiparallel helices in a single‑strand design. RNA tiles assembled into hexagonal lattices via annealing or cotranscriptional folding, and tiles up to 660 nucleotides were achieved, comparable to large natural ribozymes.

Abstract

Artificial DNA and RNA structures have been used as scaffolds for a variety of nanoscale devices. In comparison to DNA structures, RNA structures have been limited in size, but they also have advantages: RNA can fold during transcription and thus can be genetically encoded and expressed in cells. We introduce an architecture for designing artificial RNA structures that fold from a single strand, in which arrays of antiparallel RNA helices are precisely organized by RNA tertiary motifs and a new type of crossover pattern. We constructed RNA tiles that assemble into hexagonal lattices and demonstrated that lattices can be made by annealing and/or cotranscriptional folding. Tiles can be scaled up to 660 nucleotides in length, reaching a size comparable to that of large natural ribozymes