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. Author manuscript; available in PMC: 2020 Feb 26.
Published in final edited form as: J Am Chem Soc. 2019 May 29;141(23):9365–9372. doi: 10.1021/jacs.9b03435

Scheme 2. Design of Self-Folding RNA from Ikawa et al.45 with Structural Elements Taken from the Tetrahymena Group I Ribozyme Indicated: GAAA Tetraloop and 11-nt Tetraloop Receptor and Triple Helical Scaffolda.

Scheme 2.

aThe 6 bp stem (grey) selected for stem replacement is indicated along with the site for insertion of a U-loop for bPNA binding. The resulting sequence and the simplified structural representation is shown to the right. (a) Cy3-(SK2M)3 and Cy5-(SK2M)3 were added sequentially to the RNA in a 1:1:1 ratio with a final concentration of 500 nM using a 20 min incubation time for each peptide addition step in 10× folding buffer (500 mM HEPES pH 7.5, 1M NaCl).