FIGURE 1.

Examples of a GNRA “U-turn” and a UNCG “Z-turn” along with their U_SH-turn and Z_anti-turn variants (1–4 bp and relevant nucleobase–phosphate hydrogen bonds are shown in the insets). In all panels, the cyan dashed lines mark contact distances between the OP/O4′ atoms—emphasized as yellow spheres—and the stacked nucleobase that are associated with oxygen-π contacts ≤3.5 Å (see Materials and Methods and insets of panels A and C). For clarity, all nonrelevant OP atoms were hidden. The C = G closing base pairs are shown in white. For all secondary structures, symbols according to the Leontis and Westhof nomenclature were used (Leontis and Westhof 2001; Nasalean et al. 2009). (A) G₂₆₅₉AAA tetraloop (chain A) adopting a classical U-turn (symbolized by a circled “U”). The first G and the phosphate of the third nucleotide involved in an OP–π contact are marked in red as well as the oxygen atoms of the phosphate involved in the 1–4 base–phosphate hydrogen bond. The three stacked A nucleotides are colored in wheat. (B) U₂₅₃CAC tetraloop (chain 0) adopting the rare U_SH-turn variant (symbolized by a circled “U”). The first U and the phosphate of the third nucleotide are marked in red. The three stacked CAC nucleobases and part of their backbone are colored in wheat. (C) U₂₁₄₄CCG tetraloop (chain B) adopting a Z-turn (symbolized by a circled “Z”). The CpG step forming a Z-RNA motif is shown in red. The two ribose O4′ atoms of the CpG step are shown in yellow to mark the characteristic head-to-tail orientation of the sugars. The fourth nucleotide adopts a syn conformation. The UpC step is colored in wheat. (D) C₃₁₉₄UUGu pentaloop (chain 1) adopting a rare Z_anti-turn variant (symbolized by a circled “Z”). The UpG step forming a Z-RNA motif, with the G adopting an anti instead of a syn conformation, is shown in red. The two ribose O4′ atoms of the CpG step are shown in yellow to mark the characteristic head-to-tail orientation of the sugars. The CpU step is colored in wheat and the bulged “u” in blue.