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. 2020 Jan 24;48(5):2232–2245. doi: 10.1093/nar/gkaa036

Figure 4.

Figure 4.

(A) The sheared C·G pair with a C(O2)–G(H1) H-bond in the stable clamped triloop of CAG1 (Figure 1). (B) A side view of the CAG1 triloop with C3(blue), A4(orange) and G5(cyan). (C and D) Two long-lived loop conformations for CAG4 (Figure 1): (C) S(aa)-L(as)-G(a) (stable) and (D) S(as)-L(ss)-G(s) (kinetic trap). The cartoon only shows the residues from A3 to A12 with A6(blue), G7(orange), C8(red), A9(cyan) and A3–A12(green). (E) The strong stacking between the A–A mismatch in the tetraloop of CAG4 and the C–G Watson–Crick basepair immediately below: C5(yellow)/A6(blue) and A9(cyan)/G10(pink) in the S(aa)-L(as)-G(a) conformation (bases in the 5′-AGCA-3′ tetraloop in conformation anti–anti–anti–syn, with anti–anti conformation for the first mismatch closer to the loop, see text). (F) The two-stack loop in L(aa) (A–A in 5′-AGCA-3′ in anti-anti) for CAG2. Bases in colors: A3(blue), G4(orange), C5(red) and A6(cyan). (G) View for (F) of the stacking of A3(blue)/G4(orange) and C5(red)/A6(cyan).