Reaction with phosphate groups

The reactivity of metal ions is not always the same with DNA and RNA. One reaction that is exclusive to RNA is depolymerization of the polynucleotide structure by the cleavage of the phosphodiester bonds. This depolymerization reaction, as with other RNA hydrolyses, can be induced by metal hydroxides, Zn being one of the most effective. A simple mechanism is that the Zn" chelates to the phosphate group and the 2 -hydroxyl group of ribose (the 2 -group is absent in DNA). Electron withdrawal by the Zn ion then weakens the phosphodiester linkage. Such a mechanism, however, does not take into account the observed influence of the nature of the adjacent base and the formation of metal-dependent products. Pb is also an effective catalyst in site-specific depolymerization of tRNA. In this case the metal has been shown to bind to the bases with only weak interactions with phosphate groups. The catalytic action has been interpreted in terms of nucleophilic attack by a metal-bonded hydroxide ion.134 This may have implications for the mechanisms of other metal ions active in this reaction. 

Dihydroxy alcohols and amino alcohols in which the functional groups are not separated by more than four carbon atoms are effective acceptors. There is a general difference in the behavior of these compounds, however, in that hydroxyl alcohols decrease the rate of formation of p-nitro-phenol from p-nitrophenyl phosphate and amino alcohols increase the rate. Amino alcohols are relatively good nucleophiles in reaction with phosphate esters, perhaps because the amino group serves as a general base catalyst (143, 144)-... 

The mechanism of HDEHP radiolysis has been investigated by ESR spectroscopy after y-irradiation (74,159). The formation of the radical C4H9-C (CH3)C2H5 formed by the removal of a hydrogen atom from the alkyl chain of HDEHP has been proposed (159). A large G-value (about 6 molecuels/100 eV) for the formation of this latter radical indicated that the ester bond of HDEHP is likely to crack at the C-0 position by radiolytic excitation. However, the split alkyl radicals are liable to recombine with phosphate groups and reform HDEHP (159). The following reactions (Equations 8.5 and 8.6), were proposed to explain the formation of 1-methyl-l-ethylpentyl radical. 

At this point, it is clear that aluminum can interact with phosphate groups of nucleotides or in enzyme catalytic structures, thus it is probable that many other enzymatic reactions not discussed here could be damaged by aluminum. 

The natural-template method was developed in 1974. It can produce porous HA powders. A suitable template was found to be the calcium carbonate (CaC03) skeleton of reef-building corals, such as those found in the South Pacific. The reaction to produce HA involves a hydrothermal exchange reaction of carbonate groups with phosphate groups, which can occur via the following chemical reaction ... 

In the first reaction, a phosphate group from ATP (adenosin triphosphate) is transferred to the substrate with the formation of ADP. 

Lead immobilization by phosphates arises from the low solubility of pyromorphite (Pb5(P04)3Cl). As stated, lead members of the apatite group minerals are much less soluble than their calcium congeners. Nriagu [39], as early as 1974, proposed the removal of lead from wastewaters and the stabilization of lead in contaminated soils and sediments by reaction with phosphate ions to precipitate pyromorphite. 

In E. coli GTP cyclohydrolase catalyzes the conversion of GTP (33) into 7,8-dihydroneoptetin triphosphate (34) via a three-step sequence. Hydrolysis of the triphosphate group of (34) is achieved by a nonspecific pyrophosphatase to afford dihydroneopterin (35) (65). The free alcohol (36) is obtained by the removal of residual phosphate by an unknown phosphomonoesterase. The dihydroneoptetin undergoes a retro-aldol reaction with the elimination of a hydroxy acetaldehyde moiety. Addition of a pyrophosphate group affords hydroxymethyl-7,8-dihydroptetin pyrophosphate (37). Dihydropteroate synthase catalyzes the condensation of hydroxymethyl-7,8-dihydropteroate pyrophosphate with PABA to furnish 7,8-dihydropteroate (38). Finally, L-glutamic acid is condensed with 7,8-dihydropteroate in the presence of dihydrofolate synthetase. 

The disadvantage of this method is that the dichloridites and monochloridites are sensitive to water and thus could not be used readily in automated oligonucleotide synthesis. This problem was overcome by Beaucage and Caruthers, who developed the phosphoramidite approach. In this method, derivatives of the form R 0P(NR2)2 react with one equivalent of an alcohol (catalyzed by species such as l//-tetrazole) to form diesters, R OP(OR")NR2, which usually are stable, easily handled solids. These phosphoroamidites are easily converted to phosphite triesters by reaction with a second alcohol (catalyzed by l//-tetrazole). Here, again, oxidation of the phosphite triester with aqueous iodine affords the phosphate triester. Over the years, numerous protective groups and amines have been examined for use in this approach. Much of the work has been reviewed. ... 

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