Polymerization of mononucleotides

The problem here is to accept the idea that a self-replicating RNA family formed spontaneously by itself—an assumption which, at the state of our knowledge on the prebiotic biosynthesis of mononucleotides and their polymerization, comes close to blind faith. It is possible that the research of the next future will show that the spontaneous formation of a RNA self-replicating family has some scientific basis. At the present time, instead of waiting, it is perhaps right to look for other alternatives. 

Template-induced polymerization of nucleotides. The idea is to have one single-stranded polynucleotide (e.g. poly A) as guest in reverse micelles, as well as an excess of mononucleotide (e. g. U or of short oligomers thereof). The binding A=U should produce an array of U lined up to the poly A matrix, and the polymerization should then take place by chemical activation. The process, if successful, can lead to any series of block copolymers or random copolymers. 

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. 

In a physicochemical study of oligo- or polynucleotides, it has been reported that Hypochromicity, depends on the degree of polymerization [61]. The value of native DNA is about 60%, which corresponds to the Hypochromicity, of the absorption of its mononucleotides [60]. The present result indicates that the purine rings may intramolecularly stack by themselves in an aqueous solution... 

The stability of the unsaturated furanuronate 159 at room temperature is limited spontaneous polymerization occurs within several days, resulting in a white solid that is insoluble in most organic solvents. The instability may be attributable to its acrylic ester structure, involved in the furanoid system. Nevertheless, other 3,4-unsaturated 3-deoxyfuranu-ronate conjugates obtained from divers mononucleotides did not prove to be unstable. 

Flavin mononucleotide (FMN) is an anion at pH 7 therefore it can be doped into poly(pyrrole) by growing films in the presence of the ion. Absorption spectra confirm the presence of FMN within films, and cyclic voltammery shows that entrapped flavin can be oxidized and reduced. It appears that entrapped reduced flavin is oxidized before the polymer backbone while the reduction of FMN and the backbone coincide. Electrochemistry of the entrapped material is shifted from that for the solution species, as we expect, due to the difference in the environment. The FMN has also been incorporated into poly(pyrrole-alkylammonium) films by ion exchange of the anion into the polymerized film. Reversible voltammetry for incorporated FMN was observed with a slight shift in potential with respect to the solution species, and it was attributed to microenvironmental effects. These films were shown to catalyze oxygen reduction. 

The polymeric DNA chain is elongated at the 5 end with a radioactive nucleoside triphosphate. Hydrolytic enzymes which break the phosphodiester bond between P and C-5 of deoxyribose are then used to give a mixture of mononucleoside monophosphates (mononucleotides). The radioactive mononucleotide can then be readily identified (14.28). Similar methods can be used to identify the other end of the chain, using an enzyme which hydrolyses from the 3 end. 

This series of calculations [20][21][6] on the conformational dependence of chemical shifts Illustrates the need of a continuously more precise determination of the conformation of the mononucleotides and of the contribution of the "rearrangement effect" to the polymerization shift, 1f one wants to be able to fully Interpret the NMR measurements of polymers In solution. 

The nucleic acids are polymers of a large number of appropriate mononucleotide residues (base-sugar-phosphate) joined by internucleotidic ribose phosphate esterifications the polymeric linkage is the phosphate ester bond. Their biological importance is evident from the fact that two types, called RNA and DNA, are found in all cells and some viruses. Although DNA appears to exist exclusively within the cell nucleus, RNA (though more abundant in the cytoplasm) also occurs to some extent in the nucleus. RNA represents the sole nucleic acid type associated with the plant viruses 156) whereas the bacterial viruses, which are rich in DNA, apparently lack RNA 157). (For histochemical identification, see Chapter XI.)... 

Narang and Michniewicz (87) reported successful application of Avicel-cellulose plates for the rapid and efficient fractionation of complex chemically polymerized thymidine 5 -phosphate reaction mixtures, in situ quantitative analysis of the oligonucleotides on TLC plate by reflectant spectrophotometry, in situ identiflcation of the common mononucleosides and mononucleotides by double-scanning technique and fractionation of oligonucleotides on thick-layer Avicel-cellulose plates on a preparative scale. 

The mononucleotides in DNA are connected by phosphodiester bonds as shown in Figure 1.2a. This polymeric chain is commonly called single stranded DNA (abbreviated as ssDNA). Based on the numerical labeling of the carbon atoms in ribose, links exist between the third and fifth carbons of successive riboses hence, 3 5 bridges or links are said to exist. Also, based on this numbering scheme, practitioners note that a strand has either a free 3 or 5 hydroxyl end. ... 

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