Structures of RNA

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

Ribonucleic acid (RNA) Molecules including messenger RNA, transfer RNA, ribosomal RNA, or small RNA. RNA serves as a template for protein synthesis and other biochemical processes of the cell. The structure of RNA is similar to that of DNA except for the base thymidine being replaced by uracil. 

U snRNPs) Sm proteins and trimethylguanosine Gap structure of RNA Importin /3/Snurportin... 

DNA is one type of nucleic acid. The other type of nucleic acid is called RNA (short for ribonucleic acid). RNA is present throughout a cell. It works closely with DNA to produce the proteins in the body. Table 2.3, on the next page, shows the structures of RNA and DNA. 

Abstract The last few years have seen a considerable increase in our understanding of catalysis by naturally occurring RNA molecules, called ribozymes. The biological functions of RNA molecules depend upon their adoption of appropriate three-dimensional structures. The structure of RNA has a very important electrostatic component, which results from the presence of charged phosphodiester bonds. Metal ions are usually required to stabilize the folded structures and/or catalysis. Some ribozymes utilize metal ions as catalysts while others use the metal ions to maintain appropriate three-dimensional structures. In the latter case, the correct folding of the RNA structures can perturb the pKa values of the nucleo-tide(s) within a catalytic pocket such that they act as general acid/base catalysts. The various types of ribozyme exploit different cleavage mechanisms, which depend upon the architecture of the individual ribozyme. 

It is generally accepted that the tertiary structures of RNA molecules are stabihzed by metal ions. The roles of metal ions in ribozyme-catalyzed reactions fall into two distinct types the metal ions can act as catalysts during the chemical cleavage step, as shown in Fig. 3, and they can also stabilize the conformation of the ribozyme-substrate complex. 

Base pairings of this type are only possible, however, when the polarity of the two strands differs—i. e., when they run in opposite directions (see p.80). In addition, the two strands have to be intertwined to form a double helix. Due to steric hindrance by the 2 -OH groups of the ribose residues, RNA is unable to form a double helix. The structure of RNA is therefore less regular than that of DNA (see p. 82). 

NMR is a powerful and versatile tool for structural studies of biological RNAs and complexes they form with other nucleic acids, proteins, and small molecules. The goal of these studies is to determine the role that structure and dynamics play in biological function. NMR has the capacity to determine high-resolution structures, as well as to map RNAiligand interfaces at low resolution. Most structures of RNA and RNA-ligand complexes are under 20 KDa in size however, recent advances allow for determination of solution structures of complexes up to 40 kDa. NMR can also probe dynamic motions in RNA on micro- to millisecond time scales. A number of biologically relevant internal motions such as... 

Fig. 1.54 Principle of negative control of translation initiation by protein binding to mRNA. Proteins can negatively effect translation by binding to the sequences in the 5 non-translated region of their own or other mRNAs. The participating proteins are sequence-specific RNA binding proteins and recognize RNA sequences in hairpin structures or other secondary structures of RNA. The protein binding interferes with the scanning of ribosomes and prevents the translation of mRNA.

FIGURE 8-26 Secondary structure of RNAs (a) Bulge, internal loop, and hairpin loop, (b) The paired regions generally have an A-form right-handed helix, as shown for a hairpin. 

The structure of RNA polymerase, the signals that control transcription, and the varieties of modification that RNA transcripts can undergo dffer among organisms, and particularly from prokaryotes to eukaryotes. Therefore, in this chapter, the discussions of prokaryotic and eukaryotic transcription are presented separately. 

Related methods are being applied to the determination of the secondary structure of RNA molecules665 666 and to the study of interactions with proteins. For example, treatment with dimethyl sulfate under appropriate conditions methylates bases that are not paired, giving largely 1-methyladenosine and 3-methyl-cytidine.667... 

Figure 28-4 (A) Hypothetical structure of a "transcription bubble" formed by an RNA polymerase. Shown is a double-stranded length of DNA with the unwound bubble in the center. This contains a short DNA-RNA hybrid helix formed by the growing mRNA. The DNA double helix is undergoing separation at point A as is the hybrid helix at point B. NTP is the ribonucleotide triphosphate substrate. See Yager and von Hippel.71 (B) Stereoscopic view of the structure of RNA polymerase from Thermus aquaticus in a complex with a promoter DNA. Included are the al, all, (0, (3, P, and a subunits. However, the a C-terminal domains have been omitted. The template (t) strand passes through a tunnel, which is formed by the P and P subunits and two of the structural domains of the a subunit. The nontemplate (nt) strand follows a different path. The position of the -10, -35, and UP elements of the DNA are marked. From Murakami et al.33d Courtesy of Seth A. Darst.

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Like most trace elements, nickel can activate various enzymes in vitro, but no enzyme has been shown to require nickel, specifically, to be activated. Howevei, mease has been shown to be a nickel metalloenzyme and has been found to contain 6 to 8 atoms of nickel per mole of enzyme (Fishbein et al.. 1976). RNA (ribonucleic add) preparations from diverse sources consistently contain nickel in concentrations many times higher than those found in native materials from which the RNA ts isolated (Wacker-Vallee, 1959 Sunderman, 1965). Nickel may serve to stabilize the ordered structure of RNA. Nickel may have a role in maintaining ribosomal structure (Tal, 1968, 1969). These studies and other information have led to the suggestion that nickel may play a role in nucleic acid and/or protein metabolism. 

The other important feature of the primary structure of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the helical conformations accessible to double-stranded RNA. 

As the discoverers of the enzyme suggest (129), RNase III of E. coli will be an important tool in studies of the function and structure of RNA ... 

The studies during the 1940 s and 1950 s on the specificity of RNase were closely connected with the elucidation of the structure of RNA itself. 

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). 

Solution structures of RNA and DNA are more difficult to determine, compared to those of proteins, due to the lack of medium and long range NOEs. Long range constraints can be provided by the pseudocontact shifts obtained in the presence... 

Fig. 33.1. Structure of DNA aptamers for recognition fibrinogen (A) [15,29] and heparin binding sites (B) [17] of thrombin. The non-canonical hydrogen bonds between guanines are shown by dotted lines. In the case of structure (A), the spacer composed of 15 T chain terminated by thiol group at the end of hydrophobic spacer is shown [34]. (C) Structure of RNA aptamer against fibrinogen binding site of thrombin [23].

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