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. 2020 Feb 21;48(6):3134–3155. doi: 10.1093/nar/gkaa100

Figure 1.

Figure 1.

G/U pairs in different secondary structure contexts. (A) Case 0, G opposite U, sandwiched between canonical A/U or G/C WC base pairs. The abbreviation N stands for any RNA base, and N-bar for its WC complementary base. (B) Case 1, positions 1 and 6 are WC paired, representing the end of a helix, U is at the 3′ end of one helix strand, G is at the 5′ end of the other helix strand, positions 3 and 4 are WC base paired, and positions 3 and 4 are separated from 2 and 5 by a single-stranded region (red dashed lines) so that they enclose an internal loop. (C) Case 2, like Case 1, except that G is at the 3′ end of the helix strand and U is at the 5′ end, positions 3 and 4 are WC base paired, and positions 3 and 4 are separated from 2 and 5 by a single-stranded region (blue dashed lines) so that they enclose an internal loop.