Clover-leaf structures

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. 

In all tRNAs the bases can be paired to form "clover-leaf" structures with three hairpin loops and sometimes a fourth as is indicated in Fig. 5-30.329 331 This structure can be folded into the L-shape shown in Fig. 5-31. The structure of a phenylalanine-carrying tRNA of yeast, the first tRNA whose structure was determined to atomic resolution by X-ray diffraction, is shown.170/332 334 An aspartic acid-specific tRNA from yeast,335 and an E. coli chain-initiating tRNA, which places N-formyl-methionine into the N-terminal position of proteins,336,337 have similar structures. These molecules are irregular bodies as complex in conformation as globular proteins. Numerous NMR studies show that the basic... 

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.,... 

Guanine cytosine, G.C, (11 to 13 ppm) and adenine uracil, A.U, (13 to 15 ppm) NH resonances are shifted by the ring currents of nearby bases, and calculations [42] indicate that the solid-state clover leaf structure is appropriate in solution. NH Resonances disappear when the helices melt and Mg helix stabilisation is readily observed by NMR [43] but optical melting points are higher than the temperature range over which NH resonances broaden and disappear [44]. for the double helix of d(A-A-C-A-A) with d(T-T-G-T-T), for example, is 28°C but resonances have disappeared by 9°C T is thymine. 

Figure 4.31 General structure of an aminoacyl-tRNA. The amino acid Is attached at the 3 end of ihe RNA. The anticodon is the template-recognition site. Notice that the tRNA has a clover leaf structure with many hydrogen bonds (green dots) between bases.

Figure 22. Clover leaf structure of yeast t-KNAphe...

Fig. 4. Example of combination of caRNAc and Mfold. The first two structures (A,B) are the best two results given by Mfold alone for the third tRNA sequence of Fig. 1. The last structure (C) is obtained with Mfold using constraint information produced by caRNAc (file C in Fig. 2). In this case, Mfold correctly completes the structure and identifies the fourth stem that is missing in caRNAc output. This leads to the typical clover leaf structure (the acceptor stem is on the top).

The sequence of the approximately 75 nucleotide residues has been determined for many different tRNA molecules. In all of them there are the same four sequences of complementary pairs A=U or G=C, as shown in Figure 15-25. The existence of these sequences permitted the inference to be drawn that the molecule has the clover-leaf structure shown in Figure 15-25. This structure has been verified by an x-ray-diffraction study of crystals of yeast phenylalanine tRNA, with the result shown in Figure 15-26. 

In the crystalline state the tRNA exists in clover-leaf structure.>,What is its shape when it... 

The distances that thqr calculated from observed transfer efficiencies were as follows a was separated from F by 24, b fi-om f by 38, c from e by 36, d finm f by more than 65, and e fi om f by 55 amstrong units. The distances that were determined ciystallographically are 25, 41, 23. 74, and 53 amstrong units respectively. Thus, except for the distance between c and e where the two data do not agree well, all other distances are very close. The conclusion that Yang and Soil reached was that even in solutions tRNA adopts a clover leaf structure, (see Figure 8.29). 

Figure 8,29. Clover leaf structure of tRNA. The diagram shows the positions at which fluorescent labels were introduced as well as the positions of unusual bases on the basts of which each arm is given a name.

They are relatively small molecules containing about 80 nucleotides. Less common purines and pyrimidines occur quite often among the base building blocks but we do not need to bother with their formulae here. In all probability certain regions of the RNA strand are paired with each other, leading to the postulated clover leaf structure. All known tRNA molecules terminate at one end with the nucleotide sequence—CCA. In 1965, Holley and his colleagues succeeded in elucidating the nucleotide sequence of a tRNA specific for the amino acid alanine. Since then the nucleotide sequence of other kinds of tRNA has also become known (Fig. 10). 

Fig. 10. Structural model of serine tRNA. Many rare bases are conspicuous in the clover leaf structure, e.g. I = inosine or IPA (page 205) directly adjacent to the anticodon (modified from Zachau et al. 1966).

Fig. 5.15. The charging of t-RNA. The diagram shows the selection of phenylalanine by t-RNA (phenylalanine t-RNA) from a group of activated amino acids. ENZ, amino acid activating enzyme PHE, phenlyalanine VAL, valine MET, methionine ASP, aspartic acid. The diagram of t-RNA " illustrates the anticodon loop and a double stranded helical portion of the molecule. The full clover leaf structure is not represented. The black square adjacent to the anticodon illustrates the position occupied by isopenteny-aminopurine in some plant t-RNAs (see p. 299).

Fig. 76. A skeletal drawing of the large supercage of the framework structure showing the clover-leaf-shaped windows and the pockets at the corners of the cage [471]...

The clover-leaf pattern of Figure 25-26 shows the general structure of tRNA. There are regions of the chain where the bases are complementary to one another, which causes it to fold into two double-helical regions. The chain has three bends or loops separating the helical regions. 

Fig. 2.4. The flow reactor as a device for RNA structure optimization. RNA molecules with different shapes are produced through replication and mutation. New sequences obtained by mutation are folded into minimum free energy secondary structures. Replication rate constants are computed from structures by means of predefined rules (see text). For example, the replication rate is a function of the distance to a target structure, which was chosen to be the clover leaf shaped tRNA shown above (white shape) in the reactor. Input parameters of an evolution experiment in silico are the population size N, the chain length X of the RNA molecules as well as the mutation rate p.

Fig. 2.7. RNA secondary structures. The nucleotide sequence oftRNAphe (shown in the upper string) is presented together with the secondary structure of minimal free energy and the symbolic notation (lower string). The sequence contains several modified nucleotides (D, M, P, T, Y) in addition to the conventional bases (A, U, C, C). Individual nucleotides in the secondary structure are shown as light gray (single bases), dark gray and black pearls (base pairs). ThetRNA structure is a clover leaf with three hairpin loops (adjacent stacks are shown in black) and a closing stack...

Fig. 2.15 Diagram of the liver lobule and the acinus arranged like a clover leaf around the portal field according to the acinar structure (modified from D. Sasse, t986) central hepatic vein (CV) or terminal hepatic vein, periportal field (P). Circulatory and meta-bolically different zones zone t (periportal), zone 2 (intermediate), zone 3 (perivenous)...

The sequences of several other tRNA molecules were determined a short time later, thousands of sequences are now known. The striking finding is that all of them can be arranged in a clover leaf pattern in which about half the residues are base-paired (Figure 30.3). Hence, tRNA molecules have many common structural features. This finding is not unexpected, because all tRNA molecules must be able to interact in nearly the same way with the ribosomes, mRNAs, and protein factors that participate in translation. 

Work on tRNA yields a of 23-2.5 nm by X-ray scattering. Many of the earliest studies predated the crystal structure determination of tRNA in 1974 [347-355] and thus attempted to elucidate its overall shape on the basis of the clover-leaf base-pairing model from sequence data. Open structures were discarded in favour of more compact schemes. Many folded structures were, however, compatible with the experimental data, while a simple triaxial body was not. The observation of two distinct i xs values led to the development in 1970 of a model with one large and two small ellipsoids whose main axes are parallel to one another and are arranged in an L-shape [353], and which anticipated the L-shape determined by crystallography (Fig. 26). Other studies on tRNA have investigated its melting... 

Samples of r-RNA tend to have a spherical random-coil configuration and m-RNA is usually single stranded. The clover leaf-type structure (Figure 10.50) has been found to be common to most species of t-RNA, and in many cases the complete base sequence has been worked out. Samples of r-RNA tend to have a spherical random-coil configuration and m-RNA is usually single stranded. The clover leaf-type structure (Figure 10.46) has been found to be common to most species of t-RNA, and in many cases the complete base sequence has been worked out. 

The key to translating the message carried by the codons on mRNA into amino acids is transfer RNA (tRNA). There are 56 different types (species) of tRNA in the cell. They all have the same general structure, RNA twisted into a clover-leaf shape, and consisting of some 70—90 nucleotides. About half the bases in tRNA are paired by hydrogen bonding, which maintains of the shape of the molecule. The 3 and 5 ends of the molecule are adjacent to each other as a result of this folding. 

The structure of tRNA has been estabUshed in greater detail. These naturally occurring nucleic acids are the smallest so far isolated and in many cases the sequence has been determined. The clover leaf model, first proposed by Holley et al. (1965) is now generally accepted as a description of secondary structure in these biologically important nucleic acids. The tertiary structure has not been completely elucidated but it is clear that the molecule is extremely compact and is composed of double-helical regions with hairpin loops containing five to seven nucleotides. The structure is quite stable and is probably more compact than that of rRNA. 

There have been several reviews on the thermodynamics of DNA unfolding [ 1, 2,3] so that the overall stability and the melting behaviour of any given B-DNA duplex structure can be predicted from its known primary sequence [4]. In this overview I will rather concentrate on non-inear nucleic acids/structures. Several non-linear, but nevertheless highly helical structures have been found. In these cases apparently random sequences find complementary sequences with which they pair generally in the standard Watson-Crick base pairing mode. There have been cases of local three-strandedness, and even G-quartet structures have been reported. The best known and most widely studied non-linear structures are the transfer RNAs (tRNAs). Here a two-dimensional set of stem-loop structures are arranged in a clover-leaf in the absence of which folds into a three-... 

---