Cloverleaf structure

Fig. 13 Cloverleaf structure of yeast tRNAP. Reprinted from [214] with permission from Elsevier...

Figure 5-30 Schematic cloverleaf structure of a phenylalanine-specific transfer RNA (tRNA he) of yeast. The dots represent pairs or triplets of hydrogen bonds. Nucleosides common to almost all tRNA molecules are circled. Other features common to most tRNA molecules are also marked. The manner in which the anticodon may be matched to a codon of mRNA is indicated at the bottom.

The processing steps of E. coli tyrosine tRNATyr are diagrammed in figure 28.15. The initial transcript has, in addition to the 85 nucleotide residues of the final product, 41 residues at the 5 end and 225 residues at the 3 end it probably folds to form the typical cloverleaf structure of the mature tRNA prior to processing. Processing begins when a specific endonuclease called RNaseF cleaves the precursor... 

The general structure of a tRNA molecule, (a) Representation in the form of a cloverleaf, which is the simplest way of observing the secondary structure, (b) A more realistic drawing of the three-dimensional folded structure. Color coding shows how the various loops in the cloverleaf structure correspond to the parts of the folded... 

While RNA molecules usually exist as single chains, they often form hairpin loops consisting of double helices in the A conformation (Moore, 1999). The best-known forms of RNA are the low-molecular-weight tRNA molecules. In all of them the bases can be paired to form a cloverleaf structure with three hairpin loops and sometimes a fourth. The cloverleaf structure of tRNA is further folded into an T-shape conformation with the anticodon triplet and the aminoacyl attachment CCA forming the two ends. 

This non-canonical fold, established according to chemical and enzymatic structure probing, includes an extended amino acid acceptor stem, an extra large loop instead of the T-stem and loop, and an anticodon-like domain. Hence, one or several of the six modified nucleosides are required and are responsible for its cloverleaf structure. In a further study a chimeric tRNA with the sole modification of 1-methyladenosine in position 9 was synthesized it was demonstrated that this chimeric RNA folds correctly [27]. Thus, because of Watson-Crick base-pair disruption, a single methyl group is sufficient to induce the cloverleaf folding of this unusual tRNA sequence. 

Fig. 15 a M-[7]H forms at 95% of the saturated monolayer CW-rotated pinwheels (top, left) while CCW-rotated pinwheels are observed via STM for P-[7H] (top, right) [44]. At full ML opposite tilt angles of cloverleaf clusters with respect to the adlattice are observed (bottom). Images 10 nm x 10 nm. Reprinted with permission from Wiley, b Model for the M-[7]H cloverleaf structure obtained from MMC. Minimal repulsion is achieved for certain relative azimuthal orientations... 

The base-pairing of complementary nucleotides gives the secondary structure of a nucleic acid. In a double-stranded DNA or RNA, this refers to the Watson-Crick pairing of complementary strands. In a single-stranded RNA or DNA, the intramolecular base pairs between complementary base pairs determines the secondary structure of the molecule. For example, the cloverleaf structure of Figure 8-2a gives the secondary structure of transfer RNAs. 

The program looks first for cloverleaf structure and then, if required, for conserved bases. The sizes of the loops, the number of base pairs in the stems and the required conserved bases may all be specified by the user. The process of looking for the presence of conserved bases can reduce the number of potential structures found considerably and we refer to this process as filtering . The user may also specify that an intron may be present in the anticodon loop. The level of the similarities of the tRNA s were assessed by studying the compilation of their sequences contained in reference [8]. 

Transfer RNA (tRNA) has the lowest molecular weight, that is, near 28,000. Its function is to activate amino acids for protein biosynthesis. It has a unique cloverleaf structure (Figure 10.29), and there are sections of double-helix, bulges, and hairpin turns. Of all RNAs, it has the highest number of unusual bases (10-15%). Thus, the hairpin arm pointing east contains pseudouridine W and is... 

Figure 17-7 is a diagrammatic representation of tRNA folded into the typical cloverleaf structure, containing a number of stems (base-paired) and loops. While the sequences of the different tRNAs are different, there are regions that remain invariant. Most of these are in the loops, within which the unusual bases are concentrated, and at the 3 end of the molecule contained within the acceptor stem. The sequence at this end is always CCA, and it is to the 3 OH that the appropriate amino acid is attached through its carboxyl group. The three nucleotides complementary to the codon for the amino acid make up what is known as the anticodon (shaded part of Fig. 17-7). The three-dimensional structure of tRNA is known. In this structure, there are additional H bonds, which stabilize the cloverleaf in a more elongated L-shaped structure, with the acceptor sequence at one end and the anticodon loop at the other.

Fig. 17-7 A diagrammatic representation of the folded cloverleaf structure of tRNA.

Transfer RNA (tRNA) forms a cloverleaf structure that contains many unusual nucleotides and an anticodon. 

Transfer RNA (tRNA) has a cloverleaf structure and contains modified nucleotides. Transfer RNA molecules are relatively small, containing about 80 nucleotides. 

Figure 3-12. The cloverleaf structure of tRNA. Bases that commonly occur in a particular position are indicated by letters. Base-pairing in stem regions is indicated by lines between strands, xy = pseudouridine T = ribothymi-dine D = dihydrouridine.

Fig. 4.1 The cloverleaf structure of transfer RNA is shown. The main features of the arms are colored the anticodon arm in green that pairs with messenger RNA during translation, The acceptor stem (red) with the protruding CCA-end to which the activated amino acids are attached...

Figure 4.1 depicts the cloverleaf structure of a tRNA the bars represent base pairs in the stems. There are four arms and three loops - the acceptor, D, T pseudouridine C, and anticodon arms, and D, T pseudouridine C, and anticodon loops. Sometimes tRNA molecules have an extra or variable loop (shown in yellow in Fig. 4.1). The synthesis of transfer RNA proceeds in two steps. The body of the tRNA is transcribed from a tRNA gene. The acceptor stem is the same for all tRNA molecules and added after the synthesis of the main body. It is replaced often during lifetime of a tRNA molecule. The 3-D structure of a yeast tRNA molecule, which can code for the amino acid serine, shows how the molecule is folded with the...

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... 

What is the role of transfer RNA in protein synthesis Transfer RNA is relatively small, about 80 nucleotides long. It exhibits extensive intrachain hydrogen bonding, represented in two dimensions by a cloverleaf structure. Amino acids are brought to the site of protein synthesis bonded to transfer RNAs. 

Recall Sketch a typical cloverleaf structure for transfer RNA. Point out any similarities between the cloverleaf pattern and the proposed structures of ribosomal RNA. 

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. 

Eukaryotic pre-tRNA processing Many eukaryotic tRNA transcripts contain small introns, which do not dismpt the cloverleaf structure and are excised. Eukaryotic tRNA transcripts lack the obligatory -CCA sequence at their 3 end. This sequence is appended stepwise by the action of tRNA nucleotidyltransferase using CTP and ATP as substrates. 

There is less information about the secondary structures of RNAs. It is known that the RNA molecules are lower in molecular weight than are the DNA molecules. In addition, it is known that there are three main types of RNAs in living cells. These are ribosomal RNA (r-RNA), rran crRNA (t-RNA), and messenger RNA (m-RNA). The molecular weight of the three forms on the average are about 1,000,000,25,000, and 500,000, respectively. RNA molecules, with the help of hydrogen bonding, take three-dimensional cloverleaf structures. The molecules s three-dimensional shape also assumes an L-shape, into which the cloverleaf is bent. 

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