Secondary structure of RNA

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. 

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... 

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). 

Nucleic acid structures also involve assembly events determined by differential solubilities of different molecular constituents. The stacking of purine and pyrimidine bases in the helical structures of DNA relies on hydrophobic effects, whereas the positioning of phosphate groups in contact with solvent reflects their hydrophilic nature. Secondary structures of RNA likewise are influenced by differential solubilities of polar and nonpolar constituents. 

RNA The secondary structure of RNA consists of a single polynucleotide. RNA can fold so that base pairing occurs between complementary regions. RNA molecules often contain both single- and double-stranded regions. The strands are antiparallel and assume a helical shape. The helices are of the A-form (see above). 

Northern blotting was not named for its inventor, but as a companion technique that uses RNA rather than DNA as the test nucleic acid. RNA is transferred from the gel after electrophoresis onto a solid support followed by hybridization with a specific labeled probe. Because RNA molecules have defined lengths and are much shorter than genomic DNA, it is not necessary to cleave RNA before electrophoresis. However, because of the secondary structure of RNA, it is necessary to perform electrophoresis under denaturing... 

Ribonucleic Acid. RNA yeast nucleic acid. Polynucleotide directly involved in protein synthesis found in both the nucleus and the cytoplasm oi cells. Description of components of RNA see Nucleic Acids. The Four primary nucleosides are adenosine, guanosine, cytidine and uridine minor nucleosides are also found. The nucleosides are linked by phosphate diester bonds from the 3 -hydroxyl of one D -ribose to the 5 -hydroxyl of the next. The secondary structure of RNA is that of an incompletely Organized single-stranded polynucleotide consisting of some areas with helical structure alternating with non helical lengths. Compere Deoxyribonucleic Acid (DNA). Structure Brown,... 

Nonenzymatic hydrolysis of RNA assisted by metals (312-316) as well as by some ribozymes (317, 318) presumably follows the mechanism described above. Metals may be involved in the deprotonation of the 2 -OH group (319). Ribozymes, now recognized as metalloenz5mies (318,320,321), correspond to selected sequences of RNA able to cleave the same strand (intramolecular process) or an RNA sequence on a different strand (intermolecular process). Metal ions are necessary to ribozymal activity (318). They promote the folding of the secondary structure of RNA into an active tertiary structure, and it is difficult to discriminate between their structural and/or catalytic role (322, 323). 

Side chain placement In proteins, the a-helix and P-sheet places the chemical groups of amino acid side chains on the surface of the secondary structures, optimally positioned for tertiary structural interactions, whereas the secondary structure of RNA places the chemical groups of nucleotides in the interior of the A-form duplex largely inaccessible for tertiary strueture formation. 

In this chapter, we first discuss the primary and secondary structure of RNA in Section 15.2. Next, we present RNA tertiary structure as well as some discussion of RNA folding in Section 15.3. 

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. 

In any case, the results show that the amount of the stacking interaction is less in the intraribosomal RNA than in the isolated RNA molecules. If we assume that the difference is essentially due to a difference in the helical content, our analysis based oh Eq.l indicates that the RNA inside the ribosome has a lower amount of A U and G-C base pairs than the isolated RNA, the average decrease in f and f being of 7 2% and 6 2%, respectively. This result suggests that proteins may play a role in determining the secondary structure of RNA inside the ribosome. 

Table 16b. EfTects on secondary structure of RNAs other than tRNAs. ...

G. (2011). 6. Predicting parasite-host networks with Markov Entropy measures for secondary structures of RNA phylogenetic biomarkers. In... 

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