Polyribonucleotides

Polynucleotides. Polynucleotides are potent interferon inducers. A mismatched, double-stranded synthetic polyribonucleotide ampligen and the double-stranded acids, polyadenylic-polyuridylic acid and polyinosinic-polycytidylic acids have been widely studied for cancer therapy(ii). Although these materials elicit excellent activity with murine rodents, therapeutic effects are dramatically decreased within primates. 

Ampligen Polyribonucleotide Toll receptor agonist Cancer... 

A binding has also been observed with the RNA of virus [117] and bacteria [ 118 ] as well as in several synthetic polyribonucleotides [119, 120], giving rise to effects on physical properties. 

If polyribonucleotides are treated simultaneously with methoxylamine and bisulphite, cytidine residues are converted into 5,6-dihydro-7V4-methoxycytidine-6-sulphonate,154 and uridine into 5,6-dihydrouridine-6-sulphonate.155 Treatment with dilute ammonia regenerates the uridine residues, leaving the dihydrocytidine derivatives unaffected. When only the cytidine residues have been derivatized, pancreatic ribonuclease becomes uridyl ribonuclease, since it is unable to cleave the chain on the 3 -side of the modified cytidine.154 This allows the isolation of blocks of modified cytidine residues. T2 ribonuclease may also be used. Alternatively, a ribonuclease from Physarum polycephalum has been found to hydrolyse CpX links very slowly, allowing the isolation of cytidine blocks.156 If both uridine and cytidine residues are modified, T2 ribonuclease acts as puryl ribonuclease, allowing the isolation of cumulative blocks of pyrimidines.155 This ability to alter the specificity of nuclease cleavage is a useful tool in sequence analysis. 

Bratcher SC, Sikka HC. 1982. Binding of 3,3 -dichlorobenzidine to DNA and polyribonucleotides in vitro. Chem Biol Interactions 38 369-375. 

This enzyme [EC 6.5.1.3], also known as polyribonucleotide synthase (ATP), catalyzes the reaction of ATP with [ribonucleotide] and [ribonucleotide], to produce [ribonucleotide]( + m), AMP, and pyrophosphate (or, diphosphate). This enzyme converts linear RNA to a circular form by the transfer of the 5 -phosphate to the 3 -hydroxyl terminus. 

SORBITOL DEHYDROGENASE POLYPHOSPHATE GLUCOKINASE POLYPHOSPHATE KINASE Polypodal attachment, BIOMINERALIZATION Polyribonucleotide synthase (ATP),... 

Spatial Configurations of Polynucleotide Chains. I. Steric Interactions in Polyribonucleotides A Virtual Bond Model ... 

N 110 "Spatial Configurations of Polynucteotide Chains. II. Conformational Energies and the Average Dimensions of Polyribonucleotides"... 

The reaction catalyzed by polynucleotide phosphorylase differs fundamentally from the polymerase activities discussed so far in that it is not template-dependent. The enzyme uses the 5 -diphosphates of ribonucleosides as substrates and cannot act on the homologous 5 -triphos-phates or on deoxyribonucleoside 5 -diphosphates. The RNA polymer formed by polynucleotide phosphorylase contains the usual 3, 5 -phosphodiester linkages, which can be hydrolyzed by ribonuclease. The reaction is readily reversible and can be pushed in the direction of breakdown of the polyribonucleotide by increasing the phosphate concentration. The probable function of this enzyme in the cell is the degradation of mRNAs to nucleoside diphosphates. 

For example, a functional 17-bp gene for the 53-residue human epidermal growth factor was synthesized by joining ten oligonucleotides of lengths 11-59 bp.575 DNA is often synthesized enzymatically using methods described in Chapter 26. Cloned sequences of synthetic DNA can also be transcribed to produce polyribonucleotides of any desired sequence.583 New nonenzymatic methods for RNA synthesis have also been devised.583-587... 

A recent discovery in biochemistry is that RNA can act as an enzyme in chemical reactions, usually reactions involving RNA hydrolysis. Discuss the features of RNA structure that might favor evolution of enzymes composed entirely of a single polyribonucleotide chain, and describe a proposed mechanism for RNA-catalyzed hydrolysis of RNA molecules. 

Vibrational circular dichroism involves IR absorption bands. The technique has been applied to sugars,110 oligosaccharides,111 proteins,112 and nucleic acids.113 The related vibrational Raman optical activity has also been applied to polyribonucleotides.114... 

Inhibitors and Primers. Two other adjunct substances are the inhibitors, which retard or block enzyme action and the primers, which enhance, or in some cases, are essential to it. An example is the priming nT polyribonucleotide phosphotransferase by short ribonucleotide polymers. See also Enzyme Inhibitors. 

The base specificity has been extensively investigated by the 3 -terminal analysis of digestion products of RNA and polyribonucleotides and by the studies on the susceptibility of dinucleoside monophosphates or nucleoside 2, 3 -cyclic phosphates to the enzyme. The results are summarized in Table V (24-87). From the base specificity study, the es-... 

Although the specific cleavage of RNA has to be further confirmed in different conditions, it is suggested that the enzyme will hydrolyze polyribonucleotides as shown below in appropriate experimental conditions. This degradation has the advantage that 3 and 5 terminals in the digests may be easily distinguished by alkaline hydrolysis as nucleosides and nucleoside diphosphates, respectively. 

The existence of a deoxyribonuclease in E. coli bound to an inhibitory RNA was first suggested by Kozloff (3< ) who found that the DNase activity of freshly prepared extracts could be markedly enhanced by pretreatment with ribonuclease. The enzyme was subsequently purified and freed of inhibitor (39). The purified enzyme termed endonuclease I could, in turn, be competitively inhibited by a variety of RNA s including transfer RNA, and Ri values as low as 10-8 M (nucleotide) have been observed (40). Examination of various purified RNA species and synthetic polyribonucleotides for their inhibitory activity has led... 

The enzyme is very sensitive to the secondary structure of the substrate. Native calf thymus DNA is quite resistant to enzymic attack by spleen exonuclease, being split at less than 4% the rate at which alkali-denatured DNA is split (11). Long deoxyribonucleotides (average chain length 20-50), which still have complementary double-stranded structure, are rather resistant to the enzyme (26). Some limited results obtained with synthetic polyribonucleotides (11) are rather puzzling since poly C was found to be completely resistant, whereas poly A, poly I, and poly U were degraded at comparable rates. In the solvent used (0.15 M acetate buffer-0.01 M EDTA, pH 5.0), poly A and poly C are believed to have... 

The enzyme degrades polyribonucleotides to 3 P mononucleosides these are inhibitory. 

None of the detailed mechanisms to be discussed considers the macro-molecular association that may be involved in the action of RNase on high molecular weight polyribonucleotides. Preiss reported from light scattering studies that very large RNA-enzyme aggregates may be formed (393). Their significance for the catalytic mechanism is unknown. 

Nucleotides are the building blocks of nucleic acids their structures and biochemistry were discussed in chapter 23. When a 5 -phosphomononucleotide is joined by a phosphodiester bond to the 3 -OH group of another mononucleotide, a dinucleotide is formed. The 3 -5 -linked phosphodiester intemucleotide structure of nucleic acids was firmly established by Lord Alexander Todd in 1951. Repetition of this linkage leads to the formation of polydeoxyribonucleotides in DNA or polyribonucleotides in RNA. The structure of a short polydeoxyribonucleotide is shown in figure 25.3. The polymeric structure consists of a sugar phosphate diester backbone with bases attached as distinctive side chains to the sugars. 

The first enzyme discovered that could catalyze polynucleotide synthesis was a bacterial enzyme called polynucleotide phosphorylase. This enzyme, isolated by Severo Ochoa and Marianne Grunberg-Manago in 1955, could make long chains of 5 -3 -linked polyribonucleotides starting from nucleoside diphosphates. However, there was no template requirement for this synthesis, and the sequence was uncontrollable except in a crude way by adjusting the relative concentrations of different nucleotides in the starting materials. 

In addition to the cellular enzyme(s) that catalyzes DNA-directed RNA synthesis, cellular enzymes are involved in polyribonucleotide synthesis that do not use a template. Some of the properties of these enzymes are summarized in table 28.5. We have already mentioned polynucleotide phosphorylase in this chapter, and in chapter 26 we discussed the importance of DNA primase to DNA synthesis. 

Nirenberg, M. W., and J. H. Mattaei, The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc. Natl. Acad. Sci. 

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