Читать книгу Chemistry and Biology of Non-canonical Nucleic Acids - Naoki Sugimoto - Страница 38

Kissing-loop interaction is a basic type loop-loop interaction that causes cross-linkage between different helices, which are located in intrastrand or interstrand (Figure 2.15). The basic interaction of the kissing loop is formation of base pairing by complementary sequences in the apical loops of two hairpins. Intramolecular kissing complexes have been found in many RNA structures, ranging from transfer RNA (tRNA), in which length is shorter than 100 nucleotides, to ribosomal RNA (rRNA) with more than 1000 nucleotides [31]. The kissing-loop complex is usually stabilized by coaxial stacking of nucleobases included in the interhelical duplex (Figure 2.15) [32]. On the other hand, even if the sequence in the loop forms only two G·C base pairs without the coaxial stacking, a simplest kissing interaction is observed between hairpins each with a GACG tetraloop [33]. In that case, kissing base pairs are stabilized through cross-strand interactions caused by adjacent adenines in the loop [33].

Figure 2.14 T-loop motifs. (a) General secondary structure of T-loop motif consisting of neighboring stem loop and single-stranded regions. (b) Sequence and tertiary structures of yeast phenylalanine-tRNA containing T-loop motif (PDB ID: 1EHZ). Solid lines show sequence connectivity of different RNA regions involved in T-loop motif. Dashed lines show interaction between nucleobases. Enlarged image of T-loop motif surrounded by dashed circle at the overall structure is shown on right.

Figure 2.15 Kissing-loop interaction. (a) General secondary structure of kissing-loop interaction. (b) Sequence and tertiary structure of typical kissing-loop interaction (PDB ID: 1XPE). The RNA sequence is derived from dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1). Nucleobases forming base pairs in kissing-loop region are emphasized dark. Hydrogen bonds between the nucleobases in the kissing-loop region are shown in dashed lines. Mismatched base pairs are shown with black circles in the secondary structure.