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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

Figure 4.

Figure 4.

(A) Illustration of FRET-sensitive RNA kissing complex formation enabled by Cy3 (green) and Cy5 (red) labeled (SK2M)3 bPNA+ (blue strands) that complex with RNA1 and RNA2 ColE1-derived hairpins containing U6 domains (red lines). RNA1-U6: 5′-GGCAGCUUUUUUUUGGUAGUUUUUUGCUGCC-3′; RNA2-U6: 5′-GGCACCGUUUUUUCUACCAAUUUUUUCGGUGCC-3′. (B) Polyacrylamide gel under kissing complex conditions with the following in each lane from left to right: [RNA2-U6·Cy3-(SK2M)] alone; at 1:1 ratio, [RNA2-U6·Cy3-(SK2M)], [RNA1-U6·Cy5-(SK2M)]; at 1:1:1 ratio [RNA2-U6·Cy3-(SK2M)], [RNA1-U6·Cy5-(SK2M)], Rop. As indicated, gel was imaged by Cy3 excitation and emission (Cy3), Cy5 excitation and emission (Cy5), Cy3 excitation and Cy5 emission (FRET), and the merged channels (Merged). (C) With Cy3 excitation only, Cy3 fluorescence (570 nm, ■) from [RNA2-U6·Cy3-(SK2M)] decreases upon addition of [RNA1-U6·Cy5-(SK2M)] complex, while Cy5 emission (670 nm, -●-) increases.