A single-stranded architecture for cotranscriptional folding of RNA nanostructures
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.
© 2014 American Association for the Advancement of Science. Received for publication 25 March 2014. Accepted for publication 16 June 2014. The authors thank E. Winfree and M. Dong for use of their AFM facilities. We acknowledge financial support from the Danish Council for Independent Research (Sapere Aude Starting Grant DFF-0602-01772), the Danish National Research Foundation funding Centre for DNA Nanotechnology (grant DNRF81, http://cdna.au.dk/), the U.S. National Science Foundation for Expeditions in Computing funding for the Molecular Programming Project (grant nos. 0832824 and 1317694, http://molecular-programming.org), and Army Research Office award W911NF-11-1-0117. C.G., P.W.K.R., and E.S.A planned experiments and wrote the paper together. C.G. performed all experiments. The authors declare no competing financial interests.
Supplemental Material - Geary.SM.pdf