RNA types

Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions (marginal figure). The different species of rRNA are generally referred to according to their sedimentation coefficients (see the Appendix to Chapter 5), which are a rough measure of their relative size (Table 11.2 and Figure 11.25). 

The genomic DNA is of necessity without design. All of the information contained within the strand in form of sequence variability comes to light through the code. One could state that the nearly limitless potential information hidden in the tons of nucleic acid of the DNA or RNA type, regardless of which code would be adapted, would inevitably lead to all the life forms on earth. The total variety of life forms on a particular planet under proper biogenesis conditions becomes a function of the total amount and variability of nucleic acids available. That gives us a biopotential theorem worthy of the new millennium. 

Know the properties of each RNA type. Be familiar with the anatomy of transfer RNA. 

You have isolated an RNA type of octanucleotide containing A, G, C, and U in a 1 1 1 1 ratio. Treatment with enzymes (consult Table 10.2 if you wish) produces the following compounds, among others ... 

Using more simple reagents and protocols, the GDS strategy has been used to successfully produce over twenty different families of dendrons/dendrimers based on classical repeat (monomer) units and branch cell reagents. Interestingly, these GDS strategies have been used recently by Damha (see Refs. 121-123) to produce dendritic DNA and RNA type structures. 

Hepatic protein synthesis proceeds via the subcellular stages of gene transcription (in the nucleus) and gene translation (in the cytoplasm). The DNA is transcribed into various types of RNA by the action of the different DNA-dependent RNA polymerases I (A), II (B) and III (C). RNA polymerase I is responsible for the transcription of ribosomal RNA, RNA polymerase II mediates the transcription of messenger RNA, and RNA polymerase III forms transcriptal RNA. These three different RNA types move out of the nucleus into the cytoplasm. Here the ribosomes acquire the genetic information needed for protein synthesis via mRNA, and tRNA transports the activated amino acids to the ribosomes, which are themselves activated (and if necessary replicated) by rRNA. (s. figs. 2.9, 2.17 3.5)... 

Clearly, the ultimate biological effect of an oligonucleotide will be influenced by the local concentration of the oligonucleotide at the target RNA, the concentration of the RNA, the rates of synthesis and degradation of the RNA, type of terminating mechanism, and the rates of the events that result in termination of the RNA s activity. At present, we understand essentially nothing about the interplay of these factors. 

Figure 1. Conformation of nucleotides in double-stranded helices of RNA (type A) and DNA (B type).

Small nuclear RNAs are found only in the nucleus of eukaryotic cells, and they are distinct from the other RNA types. They are involved in processing of initial mRNA transcription products to a mature form suitable for export from the nucleus to the cytoplasm for translation. Micro RNAs and small interfering RNAs are the most recent discoveries. SiRNAs are the main players in RNA interference (RNAi), a process that was first discovered in plants and later in mammals, including humans. RNAi causes the suppression of certain genes (see Chapter 11). It is also being used extensively by scientists who wish to eliminate the effect of a gene to help discover its function (see Chapter 13). Table 9.1 summarizes the types of RNA. 

Small nuclear RNA (snRNA) is found in the eukaryotic nucleus and is involved in splicing reactions of other RNA types. An snRNP is a small nuclear ribonucleoprotein particle. A complex of small nuclear RNA and protein catalyzes splicing of RNA. 

The sequence-dictated three-dimensional conformation of an RNA molecule is essential in the functionality of several RNA types The ribosomic RNAs fold into structures that scaffold the ribosomes, and the tRNAs fold into defined structures that allow their recognition by both amino-acyl tRNA synthetase and ribosomes. In both cases, some nucleotide sequences that remain single stranded are involved in the enzymatic processes performed by the molecules. Thus, the sequence of an RNA dictates its structure and allows it to perform its function. Both are strictly connected. One single mutation in a rRNA or a tRNA may completely change the favored three-dimensional structure of the molecule and totally impair the RNA s function (s). 

Ribonucleic Acid Ribonucleic acid (RNA) is a polymer consisting of nucleotides containing ribose and four different nucleotides adenine, guanine, cytosine, and uracil. Three main classes of RNA molecules are transcribed from DNA by three different types of RNA polymerases mRNA, tRNA and rRNA. Other RNA types are found in very small amounts including snRNAs, double-stranded RNA (dsRNA) and other non-coding RNAs such as the SRP RNAs. All RNA classes present in cells serve different functions. 

A hairpin-loop structure consists of a double-helical stem, bridged by a loop of n residues (n 2), see e.g. [85W1, 8701, 8702, 87R4]. An RNA-type hairpin-loop structure also has been investigated, see [84C1]. 

It is possible that the protein receptors which recognize the inducer substances and hormones and which determine the tissue competence are synthesized in this period, also. It is known, for instance, that in the differentiating embryonic and regenerating liver more RNA types are synthesized than are necessary for specialized mature cell. In the early period of the liver cell specialization there is a surplus of the RNA templates (Church and McCarthy, 1967). There are data that changing of the RNA amount is accompanied by the oscillation of the chromatin transcriptional activity (Thaler and Villee, 1967). Thus, the cell during development is as if... 

When a virus infects a cell, several events occur that are specific for the invader and hence offer opportunities for selective attack. First of all, there is the contact with the cell, then the penetration of the cell s plasma membrane and the (often simultaneous) rejection of the viral coating-protein. If the virus is of the RNA type, reverse transcriptase is soon in manufacture, but in any case the synthesis of nucleic acid polymerases dominates this early stage of invasion. Next follows the synthesis of viral nucleic acids, structural proteins, and yet more enzymes, followed by the assembly of these components to form the complete virus. Finally, some thousands of these virions are liberated from each cell. Apart from the possibilities for finding selective inhibitors for each of these stages, the patient could also be helped by other drugs to control the secondary (non-viral) symptoms, which are often of an inflammatory or anaphylaaic character. 

Methisazone inactivates a wide spectrum of tumour-causing viruses (RNA types) is tissue-culture (Levinson, Woodson, and Jackson, 1971). A simpler analogue, 5-hydroxy-2-formylpyridine thiosemicarbazone, was found to be highly active against several types of experimental cancer in mice, when given intraperitoneally (Blanz and French, 1968). 

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