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. Author manuscript; available in PMC: 2018 Sep 19.
Published in final edited form as: Biochemistry. 2017 Sep 6;56(37):4972–4984. doi: 10.1021/acs.biochem.7b00573

Figure 5.

Figure 5

Structural probing of the 3′-end RNA by the lr-AID NMR approach. (A) Proposed secondary structure of the 3′-end open conformation in which 3′X folds into the 2SL conformation. The lr-AID cassette was engineered into the top SL2/3 stem in 3′-endop-lrAID. (B) Proposed secondary structure of the kissing-loop conformation of the 3′-end. The lr-AID cassette was introduced into the kissing-loop base pairs of 3′-endK-lrAID to probe the long-range interaction. Lowercase letters denote non-native nucleotides added to the RNA constructs to promote in vitro RNA synthesis by T7 polymerase. (C) One-dimensional NOESY spectra of 3′-end (black), 3′-endop-lrAID (blue), 3′-endK-lrAID in low-ionic strength buffer (green), and 3′-endK-lrAID in PI buffer (orange).