FIGURE 1.

Sequences of riboswitch k-junctions and DUF-3268. (A) The sequence of Haloarcula marismortui Kt-7, a standard k-turn. The nucleotide positions are colored in our normal scheme and labeled with the normal k-turn nomenclature (Liu and Lilley 2007). Both coloring and nomenclature have been applied to the k-junctions, and used throughout. The blue arrows show the two cross-strand hydrogen bonds from L1 O2′ to A1n N1 and L-1n to A2b N1 or 3 (this varies between k-turns). (B,C) The sequences of the Arabidopsis (B) and Escherichia coli (C) TPP riboswitch k-junctions are shown on the left. The main differences from the simple k-turns are the presence of a bulge between G1b and A2b, and the connecting sequence (c1 and c2) and T-helix on the lower strand. (D) The secondary structure of the DUF-3268 RNA, with the sequence of the putative k-junction.