Читать книгу Chemistry and Biology of Non-canonical Nucleic Acids - Naoki Sugimoto - Страница 33

An internal loop is formed when single-stranded loops on two strands are enclosed by adjacent two stems (Figure 2.10). Internal loops can be symmetrical or asymmetrical with respect to the number of loop residues on each strand. In the symmetrical internal loops, there is high possibility of forming the unusual base pairs, which are described above, between the nucleobases present at opposite positions. Fully paired and stacked internal loops consisting of eight unusual base pairs have been structurally observed (Figure 2.10) [22]. In contrast, asymmetric internal loops often become motifs that shape a three-dimensional RNA structures by bringing large changes in the helical structure such as bends and turns. Certain asymmetric internal loop motifs, such as kink-turn (K-turn) and reverse K-turn, have been identified and characterized as resulting in sharp turns important for tertiary structure formation (Figure 2.10) [23]. By considering the possible internal loops diversities, relatively few experimental data are available for stabilities of internal loops.

Figure 2.10 Internal loop structure. (a) General secondary structure of internal loop. (b) Sequence and tertiary structure of RNA hairpin containing internal loop forming consecutive mismatched base pairs (PDB ID: 1MNX). RNA sequence is derived from loop E region of 5S ribosomal RNA. Nucleobases forming mismatched base pairs in the internal loop, in which base pairs are shown with black circles in the secondary structure, are emphasized dark. Sequences and structures of typical kink-turn (c; PDB ID: 5FJ1) and reverse kink-turn (d; PDB ID: 1ZZN) motifs. Mismatched base pairs are shown with black circles in the secondary structures.