Chemistry and Biology of Non-canonical Nucleic Acids. Naoki Sugimoto

Chemistry and Biology of Non-canonical Nucleic Acids - Naoki Sugimoto


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form the hairpin structure. Stability of RNA hairpin depends on the length of loop size. Stability decreases with increasing loop length, and four or five nucleotides in the loop form the most stable hairpin [14]. Closing base pair, which is a base pair located at the boundary between the stem and loop region, also affects the stability. G·C and C·G base pairs are preferred to make stable and robust hairpin structures [15]. Some specific loop sequence, which is typified by UNCG, in which N is any nucleobase, can drastically stabilize the loop region [16]. For example, 5′-UUCG-3′ loop with C·G closing base pair forms one of the most stable hairpin loops, which can be often seen in natural RNAs [17]. NMR structure of 5′-GGACUUCGGUCC-3′ demonstrated that the hairpin loop structure is stabilized by unusual base pairing between uracil and guanine in the loop, in which glycosidic bond angle of guanine is in syn conformation. The structure is also stabilized by a cytosine-phosphate contact and extensive base stacking on the crossing base pair (Figure 2.8) [18].

      2.6.2.2 Bulge Loop

Schematic illustration of the hairpin structure. (a) General secondary structure of hairpin. (b) Sequence and tertiary structure of typical RNA hairpin with stable UUCG tetraloop sequence. Top view of UUCG tetraloop sequence is shown on right side of the structure. Hydrogen bonds formed within the UUCG tetraloop are shown as dashed lines. Schematic illustration of the bulge structure. (a) General secondary structure of bulge. (b) Sequence and tertiary structure of RNA hairpin containing single nucleotide bulges, which is derived from an RNA element responsible for dynein-mediated localization of Drosophila mRNA. Bulged nucleobases are emphasized dark. Secondary structure and side view of the region forming single nucleotide bulges are shown in right boxes surrounded by solid and dashed lines.

      2.6.2.3 Internal Loop

      2.6.3 Elements in Tertiary Interactions of RNA

Schematic illustration of A-minor interactions. Examples of hydrogen bonding patterns of consecutive A-minor interactions observed in 23S ribosomal RNA of H. marismortui 50S ribosome (a) and that between 23S and 5S ribosomal RNAs (b) (PDBID: 1FFK). Alphabets and numbers show nucleotide positions in the ribosomal RNAs. Hydrogen bonds are shown in <hr><noindex><a href=Скачать книгу