Polyribonucleotides groups

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 the previous chapters the reactivity of metal ions with the monomer units of nucleic acids has been discussed. This section will deal with the binding of transition metals to the polynucleotides. There are also three types of complexes to be expected the metal-ring, the intermediate and the metal chain complex. The effect of the ribose or deoxyribose residue on the stability constants can be neglected since the reactivity of these sugars with cations is extremely low. However, as it will be seen later, the hydrolysis of polyribonucleotides is markedly facilitated by interaction of metal ions with the 2 —OH groups of the ribose. 

When RNA and other polyribonucleotides are heated with zinc ions a degradation of the polynucleotide chains occurs (12) within a 2 hrs period while DNA remains unaffected. This effect is similar to that obtained with La3+ (3, 23) and Cu2+ (12). According to this behavior it has to be emphasized that there must be a fourth type of metal nucleotide complex involving the 2 -0H group of the ribose moiety. It would be a valuable task to elucidate the precise structure of this type of complex... 

Narrower specificities have been obtained with antibodies to some unusual helical structures. Poly(dG)-poly(dC) induces antibodies specific for the immunogen and unreactive with other deoxyribonucleotide polymers, such as poly(dAT) or native DNA. Double-helical polyribonucleotides with modified furanoses, such as poly(A)-poly(2 -0-methylU), induce antibodies that react with a number of polymers bearing 2 -furanose substitutions (such as methyl or ethyl groups on either the purine or pyrimidine-containing strand). Poly(G)-poly(C) induced antibodies of narrow specificity in our studies, but Lacour and co-workers obtained anti-poly(G)-poly(C) that cross-reacted with several forms of viral RNA. ... 

It should be pointed out that these depolymerization reactions are carried out at elevated temperatures. At low temperatures RNA, like DNA, is stabilized by metal ions through the charge neutralization effect 18, 29). We have thus seen that coordination of metal ions with the phosphate group produces two strikingly different results with nucleic acid. At low temperatures the conformation of the macromolecules is stabilized by a charge neutralization mechanism, and at high temperatures RNA and the polyribonucleotides are depolymerized. 

It should be pointed out that the interferon inducers presented in Table 2 are widely different in activity, polyribonucleotide duplexes [such as poly(I) poly(C)] being superior to most other polynucleotides, especially those in which the 2 —OH group has been replaced by a 2 -H, 2 -F, 2 —Cl, 2 -N3, 2 -0-CH3 or 2 -0-CO-CH3 group (see Table 7). The interferon inducers listed in Table 2 also differ in the kinetics of interferon production poly-carboxylates (e.g. pyran copolymer, PAA, PMAA, COAM) and fluorenone... 

Alkaline phosphodiesterase 1 (EC 3.1.4.1) hydrolyses polyribonucleotides or oligodeoxyribonucleo-tides which have a free 3 -OH group, sequentiaUy U-berating 5 -nucleoside monophosphate (Khorana 1961). This enzyme has been recognised as a component of the plasma membrane of rabbit alveolar... 

It should be noted that even though the same metal can influence nucleic acid molecules in three different ways, these different influences take place under quite different conditions. The stabilization through neutralization of the charge on the phosphate occurs at relatively low temperature, in RNA below temperatures required for cleavage and in DNA below temperatures required for strand separation. The depolymerization occurs only with RNA, because of the requirement of the 2 -hydroxyl group, and the unwinding-rewinding phenomenon can occur only with molecules like DNA that have ordered structures that can be unwound. It is not confined to DNA, but works also with polyribonucleotides with helical properties. 

Both DNA and RNA are subject to metal ion-induced depolymerization. The presence of the 2 -hydroxyl group in RNA and polyribonucleotides makes possible direct metal-ion catalyzed cleavage of the internucleotide phosphodiester bonds. DNA and polydeoxynucleotides, lacking the 2 -hydroxyl group are not subject to such direct cleavage by metal ions, but can be attaeked by radical species formed by redox processes involving metal ions. 

The essentiality of an intact adenylyl end group for amino acid acceptor activity of soluble RNA from E. coU was also demonstrated by Preiss and co-workers (194) iu a number of ways. First, they showed that periodate, which splits cis-hydroxyls and hence, in a polyribonucleotide, can act only on the terminal nucleotide containing a free 3 -OH, completely inactivated their RNA. Second, snake venom diesterase, which degrades a polyribonucleotide chain starting from the end bearing the 3 -hydroxyl group caused complete loss of amino acid acceptor activity en approximately... 

In DNA the genetic code is found in the sequential bases, more precisely in the succession of groups of three nucleotides (triplets). As discussed in a latter section the genetic code was completely elucidated by comparing the template properties of synthetic polyribonucleotides in cell-free systems. However, first evidence that the c ing groups (codons) were triplets came from genetic studies. 

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