The k-turn structure in RNA. (A) The sequences of H. marismortui Kt-7 and A. fulgidus box C/D k-turns. The broken arrows colored in cyan indicate two critical cross-strand hydrogen bonds from the O2′ of L1 and −1n to the nucleobases of adenines 1n and 2b, respectively, that form the trans sugar–Hoogsteen G•A base pairs. The nomenclature of the nucleotide positions is shown on the Kt-7 sequence (left), and the various positions within the k-turn analyzed in this work are boxed on the box C/D sequence (right). In this view, the C-helix is on the left, while the NC-helix (that contains the G•A base pairs) is on the right side. (B) Parallel-eye stereoscopic image of the structure of the H. marismortui Kt-7 k-turn observed from the side of the non-bulged strand. The nucleotide positions that are studied and discussed in this work are identified. This image was prepared using PDB ID 4CS1, determined at 2.0 Å resolution (McPhee et al. 2014).
