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. Author manuscript; available in PMC: 2016 Nov 6.
Published in final edited form as: J Mol Biol. 2015 May 27;427(22):3501–3515. doi: 10.1016/j.jmb.2015.05.018

Figure 4.

Figure 4

Activation of PKR by the trp 5’-UTR in the presence and absence of a known longdistance tertiary interactions. (a) Model of the full-length (1–206) trp 5’-UTR in the TRAP-free form. (Left) RNA-fold with long-distance tertiary interaction between residues 36–60 and both the 5’- and 3’- regions of the downstream internal loop. (Right) Addition of either a 5’- or 3’-chimeric DNA/LNA blocking oligonucleotide (5’-BO and 3’-BO) disrupts these tertiary interactions. (b–d) Percent PKR activation as a function of RNA concentration for trp 5’-UTR constructs (b) FL (1–206), (c) LH (61–188), and (d) T + tails (89–159) with and without 5’- or 3’-BOs (legends provided in figures). Blocking oligonucleotides are in two-fold excess over the trp 5’-UTR. The average of three independent trials is plotted, connected by trend lines. The average standard deviation was ~20%PKR activation.