Tertiary base pairings

Figure 4.16 The structure of yeast tRNAplle (a) the cloverleaf form of the base sequence tertiary base-pairing interactions are represented by thin red lines connecting the participating bases. Bases that are conserved in all tRNAs are circled by solid and dashed lines, respectively. The different parts of the structure are colour-coded, (b) The X-ray structure showing how the different base-paired stems are arranged to form an L-shaped molecule. The sugar-phosphate backbone is represented as a ribbon with the same colour scheme as in (a). (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

C) Schematic representation of L form of E. coli. tRNAcys. Some tertiary base pairings are indicated by dashed lines. No modified bases are shown. See Hou et al,180... 

This site shows only at shorter times, disappears with longer exposure. Binding causes shift of G15 base with possible disruption of G15-C48 tertiary base pair (see Table 18a, No. 38). 

Fig. 9. Stmctures of tRNA (a) secondary stmcture of tRNA, where conserved base pairs are indicated by lines and (b) tertiary stmcture.

A problem with employment of ASON in a larger clinical setting is their poor uptake and inappropriate intracellular compartmentalization, e.g., sequestration in endosomal or lysosomal complexes. In addition, there is a need for a very careful selection of the ASON-mRNA pair sequences that would most efficiently hybridize. To date, several computer programs are used to predict the secondary and tertiary structures of the target mRNA and, in turn, which of the mRNA sequences are most accessible to the ASON. However, even with this sophisticated techniques, the choice of base-pairing partners still usually includes a component of empiricism. Despite these principal limitations, it has become clear that ASON can penetrate into cells and mediate their specific inhibitory effect of the protein synthesis in various circumstances. 

Fig. 3. The hepatitis delta virus ribozyme. A Secondary structure of the genomic HDV ribo-zyme RNA used for the determination of the crystal structure [37]. The color code is reflected In the three dimensional structure B of this ribozyme. PI to P4 indicate the base-paired regions. Nucleotides in small letters indicate the U1 A binding site that was engineered into the ribozyme without affecting the overall tertiary structure. The yellow region indicates close contacts between the RNA and the U1 A protein...

To say that RNA molecules are single-stranded molecules is not the same as saying that they have no higher-order structures, hi fact they have several. The formation of Watson-Crick complementary base pairs is a driving force for formation of higher-order structures. These include the stem-loop and hairpin secondary structures, as well as more complex tertiary structures. Of particular note, are the complex structures for transfer RNAs, tRNAs. Examples are provided in figure 12.5 (note that there are several nnnsnal bases in these structnres this is typical of tRNAs but not of RNA molecnles in general). These strnctures are intimately related to the function of these molecnles as adaptors in the process of protein synthesis, as developed in the next chapter. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

Messenger RNAs (mRNAs) transfer genetic information from the cell nucleus to the cytoplasm. The primary transcripts are substantially modified while still in the nucleus (mRNA maturation see p.246). Since mRNAs have to be read codon by codon in the ribosome, they must not form a stable tertiary structure. This is ensured in part by the attachment of RNA-binding proteins, which prevent base pairing. Due to the varying amounts of information that they carry, the lengths of mRNAs also vary widely. Their lifespan is usually short, as they are quickly broken down after translation. 

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

RNA molecules are unable to form extended double helices, and are therefore less highly ordered than DNA molecules. Nevertheless, they have defined secondary and tertiary structures, and a large proportion of the nucleotide components enter into base pairings with other nucleotides. The examples shown here are 5S-rRNA (see p. 242), which occurs as a structural component in ribosomes, and a tRNA molecule from yeast (see p.82) that is specific for phenylalanine. 

The use of compounds with activated methylene protons (doubly activated) enables the use of a mild base during the Neber reaction to 277-azirines. Using ketoxime 4-toluenesulfonates of 3-oxocarboxylic esters 539 as starting materials and a catalytic quantity of chiral tertiary base for the reaction, moderate to high enantioselectivity (44-82% ee) was achieved (equation 240). This asymmetric conversion was observed for the three pairs of Cinchona alkaloids (Cinchonine/Cinchonidine, Quinine/Quinidine and Dihydro-quinine/Dihydroquinidine). When the pseudoenantiomers of the alkaloid bases were used, opposite enantioselectivity was observed in the reaction. This fact shows that the absolute configuration of the predominant azirine can be controlled by base selection. 

E. coli has a specific three-dimensional conformation featuring extensive intrachain base pairing. The predicted secondary structure of the rRNAs (Fig. 27-10) has largely been confirmed in the high-resolution models, but fails to convey the extensive network of tertiary interactions evident in the complete structure. 

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