Fig. 1
From: Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules
Design and screening strategy for RNA-DNA hybrid nanoshapes. a Secondary structure of an internal loop RNA from the genome of the hepatitis C virus which adopts a bent fold similar to motifs previously used for the design of all-RNA nanoshapes23. b Self-assembling all-RNA nanoshapes which were designed from crystal structures of bent internal loop motifs18,19. c Design of polygonal RNA-DNA hybrid nanoshapes that contain bent RNA motifs as architectural joints and straight DNA modules as connectors. Length variation of single-stranded regions (y) for interaction between the building blocks, length of the double-stranded core (x) of the DNA modules, and choice of a bent RNA motif give rise to a complex screening library of RNA and DNA components. d Screening for stable hybrid complexes of RNA and DNA module combinations by native polyacrylamide gel electrophoresis (PAGE). Stable polygonal nanostructures that self-assemble from a given combination of RNA and DNA modules are expected to give rise to a small number of discrete bands with negligible background and without nucleic acid material retained in the gel pocket. Here, the internal loop RNA shown in a with single-stranded overhangs of 6 nucleotides (y) was combined with different DNA modules carrying 9–13 base pairs (bp) in the double-stranded core (x). For each combination, the DNA module alone (left lane) and together with the RNA motif (right lane) is shown. M is a linear double-stranded RNA size marker. Sq is an all-RNA square comprised of 100 nucleotides which self-assembles from four internal loop RNA modules similar to the one shown in a and for which a crystal structure has been determined previously. The three distinct bands observed for the combination of the bent RNA motif with a DNA module containing a core of 11 bp indicate the formation of polygonal nanoshapes (RNA-DNA-11) whose size is consistent with triangles, squares and pentagons. e Composition of the RNA-DNA-11 hybrid nanoshapes discovered by screening, including triangle (201 nucleotides), square (268 nucleotides) and pentagon (335 nucleotides). Source data are provided as a Source Data file
