Supersecondary Structure Code for RNA: Trace of Conformational Change on the <i>Mycoplasma pneumoniae</i> Ribosome and the R-Loop Formation of Cas9

The shape of motifs is important for RNA functions and deeply reflects the structure of RNA at the supersecondary level, an intermediate level between secondary and spatial structure. However, there is currently no standardized classification system for the RNA supersecondary structures. Primary and secondary occupied conformations, accounting for 73% of the nucleic acid backbone units, were found by extending the concept of protein supersecondary structure code (SSSC) combined with the conformational code for organic molecules. The supersecondary structure code for RNA (SSCR) was introduced as a conformational term for each unit of the nucleic acid backbone using the letters P, S, T, and D, denoting respectively the primary occupied conformation (P), the secondary occupied conformation (S), the set of other conformations (T), and disordered residues (D). The alignment of SSCR sequences was used to compare with the different nucleic acid base sequences, depending on the species. SSCR can also trace the conformational change of motifs in RNA molecules such as ribosomal RNA (rRNA) and single-molecule guide RNA (sgRNA) in the R-loop formation process of Cas9. The assignment of supersecondary structure code T using the fuzzy search technique of structural code homology is an effective and quick detection method for motifs with conformational wobbling, such as the relatively rigid TTT motifs of sgRNA with Cas9, streptomycin-binding RNA aptamer, 23S rRNA, 2'-dG-II riboswitch, and human hepatitis B virus ε pregenomic RNA, which work as the scaffold for protein and RNA molecules or as the support stand for small external substrates.