Secondary structure of tRNA

RNA molecules form secondary structure by folding their polynucleotide chains via hydrogen bond formations between AU pairs and GC pairs. The thermochemical stability of forming such hydrogen bonds provides useful criterion for deducing the cloverleaf secondary structure of tRNAs that is, tRNA molecules are folded into DFI... 

You can see the common structural features of tRNAs at both the secondary and tertiary levels. Only a few sequences or bases are common to all tRNAs. The common secondary structure of tRNAs is the cloverleaf pattern, where the 5 and 3 sequences are base-paired, and then the other three stem-loops of the cloverleaf are formed by... 

Figure 5 Protein-RNA interactions of aaRSs. The cloverleaf secondary structure of tRNA " folds into an L-shaped tertiary molecule. The tRNA can bind in an aminoacylation complex, where the 3 end is located in the canonical Class I or Class II core as shown in the upper right for the P. horikoshii LeuRS-tRNA - aminoacylation complex. In aaRSs that edit, a second complex can be formed, where the 3 end interacts with a separate domain such as the connective polypeptide insertion (CPI) that contains a hydrolytic active site as shown in the lower right for the T. thermophilus LeuRS-tRNA - editing complex. (Table (1) PDB files 1WZ2 and 2BYT).

Figure 29.6. Helix Stacking in tRNA. The four helices of the secondary structure of tRNA (see Figure 29,4) stack to form an L-shaped structure.

The structure of t (transfer) and r(ribosomal) RNA consists of multiple, single stranded, stem-loop structures. The stems consist of helices formed by base pairing of complementary regions within the RNA. The secondary structure of tRNA and rRNA are important for their biological functions, mRNA also assumes some degree of secondary structure but not to the same extent as tRNA and rRNA. 

Intrachain hydrogen bonding occurs in tRNA, forming A-U and G-G base pairs similar to those that occur in DNA except for the substitution of uracil for thymine. The duplexes thus formed have the A-helical form, rather than the B-helical form, which is the predominant form in DNA (Section 9.3). The molecule can be drawn as a cloverleaf structure, which can be considered the secondary structure of tRNA because it shows the hydrogen bonding between... 

The primary and secondary structure of tRNA molecules are often depicted as a cloverleaf pattern containing double-stranded stems and stems connected to single stranded loops, two recurring elements of RNA secondary structure. Each A-form... 

Helical stacking Helical stacking is one strategy for packing RNA helices into a tertiary structure. The secondary structure of tRNA consists of four short helices that radiate from the center in a cloverleaf-like shape. In its three-dimensional structure, two pairs of helices coaxially stack and perpendicularly align to yield the L-shaped tertiary structure. Coaxial stacking of helices is observed in ribozymes leading to extensive tertiary interactions between helical subdomains. 

It soon became obvious that the sequence Holley revealed for L-alanine RNA could not fit Zubay s simple model. Furthermore, it was also established that the low molecular weight material whose study had led to the elaboration of the Zubay model was most likely to be fragments of degraded ribosomal RNA (which in fact has a highly ordered tertiary structure). The secondary structure of tRNA is important because... 

The base sequence and the cloverleaf representation of the secondary structure of tRNAs is presented in Fig. 1, p. 426, for tRNA" (yeast), and the folded (tertiary) structure for tRNA (yeast) is presented in Fig. 2, p. 426. Base sequences of particular tRNAs can be found in the compilation by Sprinzl et al. [85S3]. 

The base sequence and the cloverleaf representation of the secondary structure of tRNAs is presented ... 

The secondary structure of tRNA is usually presented in two dimensions as a cloverleaf to highlight the regions of base-pairing (Fig. 5a). X-ray crystallography reveals that additional hydrogen bonds give rise to an L-shaped tertiary structure (Fig. 5b). The CCA sequence carrying the amino acid is located distal to the anticodon. 

Figure I. The secondary structures of tRNA -ribozymes, as predicted by computer folding analysis. The sequence of the hammerhead ribozyme was ligated downstream of that of a seven-base-deleted tRNA (capital letters) with linker sequences (lowercase letters). The sequences that correspond to the internal promoter of tRNA , namely the A and B boxes, are indicated by shaded boxes. The recognition arms of ribozymes are indicated by underlining. The predicted secondary structure of human placental tRNA is shown in the right panel. The tRNA is processed at three sites (arrowheads) to yield the mature tRNA (capital letters). Rz-CBPl through Rz-CBP3 are ribozymes targeted to CBP mRNA.

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

RNA consists of long strings of ribonucleotides, polymerised in a similar way to DNA, but the chains are considerably shorter than those of DNA. RNA contains ribose rather than deoxyribose and also contains uracil instead of thymidine. This has important connotations in the secondary structure of RNA which does not form the long helices found in DNA. RNA is usually much more abundant than DNA in the cell and its concentration varies according to cell activity and growth. This is because RNA has several roles in protein synthesis. There are three major classes messenger RNA (mRNA) ribosomal RNA (rRNA) and transfer RNA (tRNA). 

The three dimensional structure of tRNA (Fig. lb) is even more complex because of additional interactions between the various units of secondary structure. 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

The secondary clover-leaf structure of tRNA is stabilized by Watson-Crick base pairs. The tRNA s are a large family of molecules consisting of 71 to 76 nucleotides, with about 10% of rare bases (Fig. 15.2). The known nucleotide sequences of over 200 tRNA s [695J can be arranged in a characteristic clover-leaf model with four double helical stems and three loop regions. In some of the positions, the same nucleotide occurs, called invariant, in others only the type is conserved, i.e.,... 

Hatfield DL, Gladyshev VN. How selenium has altered our understanding of the genetic code. Mol. CeU. Biol. 2002 22 3565-3576. Wu XQ, Gross HJ. The length and the secondary structure of the D-stem of human selenocysteine tRNA are the major identity determinants for serine phosphorylation. EMBO J. 1994 13 241-248. Hubert N, Sturchler C, Westhof E, Carbon P, Krol A. The 9/4 secondary structure of eukaryotic selenocysteine tRNA more pieces of evidence. Rna 1998 4 1029-1033. 

Fig. 21. Secondary structure of the aminoglycoside-binding region of tRNA °. Dashes indicate neomycin and dimeric neomycin interactions. Reprinted with permission, Copyright 2001 Nature Publishing Group (http //www.nature.com/).

The task of assigning a plausible pattern of base pairing is greatly simplified if sequences are available for different species of RNA known to possess similar structures and functions. For example, the cloverleaf structure and the L-shaped fold have served as good approximations for modeling the secondary and tertiary structures of tRNA respectively. DNA and RNA sequences can be submitted to respective DNA mfold (http //bioinfo.math.rpi.edu/ nnfold/dna) and RNA mfold (http //bioinfo.math.rpi.edu/ mfold/ma) for fold predictions. 

Because of their small size, a number of tRNAs have been studied extensively. > Figure 11.14 shows a representation of the secondary structure of a typical tRNA. This tRNA molecule, like all others, has regions where there is hydrogen bonding between complementary bases, and regions (loops) where there is no hydrogen bonding. 

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