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. 2018 May;24(5):656–672. doi: 10.1261/rna.064527.117

FIGURE 2.

FIGURE 2.

Base-pairings of studied sequences. (A) Canonical cis-Watson–Crick/Watson–Crick GC pair closing the NMR conformation of (5′-GAGC-3′)2 internal loop. (B) Canonical cis-Watson–Crick/Watson–Crick AU pair closing the NMR conformation of (5′-AAGU-3′)2 internal loop. (C) Canonical cis-Watson–Crick/Watson–Crick (wobble) GU pair closing the NMR conformation of (5′-UAGG-3′)2 internal loop and alternative maximally H-bonded conformation of (5′-GAGU-3′)2. (D) trans-Watson–Crick/Hoogsteen GG pair in the loop of (5′-GAGU-3′)2 NMR (bulged) conformation; both G′s are syn. (E) cis-Watson–Crick/Watson–Crick (imino) AG pair in the loop of alternative (maximally H-bonded) conformation of (5′-GAGU-3′)2 and NMR conformations of (5′-GAGC-3′)2, (5′-AAGU-3′)2, and (5′-UAGG-3′)2. (F) cis-Watson–Crick/Sugar edge GU pair stabilizing the centroid of simulation observed starting with (5′-GAGU-3′)2 alternative (maximally H-bonded) structure.