Cleavage of a phosphodiester bond

Fig. 3 Possible catalytic functions of metal ions in the cleavage of a phosphodiester bond. Metal ions can act as (a) a general acid catalyst, (b) a general base catalyst, (c) a Lewis acid that stabilizes the leaving group, (d) a Lewis acid that enhances the deprotonation of the attacking nucleophile, and (e) an electrophilic catalyst that increases the electrophilicity of the phosphorus atom...

Fig. 5.2.6. Mechanism of the reversible cleavage of a phosphodiester bond catalyzed by the hairpin ribozyme.

DNA ligase relaxes supercoiled DNA by catalyzing the cleavage of a phosphodiester bond in a DNA strand. The... 

Polysaccharides composed of D-mannosyl and phosphate residues (5 1) have been isolated and purified from cells of Candida intermedia and Torulopsis famata. D-Mannose 6-phosphate was released on mild hydrolysis with acid, possibly by cleavage of a phosphodiester bond linking it to C-1 of an adjacent D-mannosyl residue. 

This enzyme (also known as DNA-(apurmic or apyrimid-inic site) lyase, AP endonuclease class I, E. coli endonuclease III, Phage-T4 UV endonuclease, and Micrococcus luteus UV endonuclease) catalyzes the cleavage of the phosphodiester bond in a lyase-type reaction, not hydro-... 

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. 

The order of preference of RNase T2 for various bonds in RNA is ApN > UpN > GpN > CpN (55), so no general rule can be stated for the preference for purine or pyrimidine, or for keto or amino substituent. Recently, it was found that RNase T2 gave complete cleavage of the phosphodiester bonds of 4-thiouridylate in tRNA (55) and of 6-thio-guanylyl-(3 -5 )-cytidine (27). This shows that the substitution of sulfur at the 4 position of pyrimidine base or at the 6 position of purine base does not effect the action of RNase T2. Furthermore, the phosphodiester bonds of the nucleotides with a large substituent at the 6 position of purine base such as A6-isopentenyladenosine (57), 2-methyl thio-N6-(A2-... 

RNA molecules are structurally and metabolically distinct from DNA molecules. First of all, the sugar present on the nucleotide is ribose and not deoxyribose. This has the consequence that an RNA chain is less stable than the corresponding DNA because the 2 -OH group makes the 3, 5 phosphodiester chain of RNA hydrolyzable in alkaline solution. In an alkaline solution, OH" ions in the solution remove a proton from the 2 -OH of ribose the 2 -0" then is attracted to the central, relatively positive, phosphorus. The resulting intermediate can be resolved by the cleavage of the phosphodiester bond and the breaking off of the next nucleotide in the chain as shown in Figure 10-1. 

Figure 6 Detection ofthe 8-oxoGua/formylamine tandem lesions in isolated DNA exposed to gamma radiation in aerated aqueous solution. DNA was digested by a mild enzymatic treatment in order to release the lesions without cleavage of the phosphodiester bond. The sample was then injected onto a reverse phase HPLC column. The detection was provided by a mass spectrometer monitoring the main fragmentation ofthe two tandem base lesions.

Until recently, all enzymes that catalyze the cleavage of phosphate ester bonds were assumed to be phosphohydrolases, i.e., the cleavage reaction occurs by hydrolysis of a phosphodiester bond to generate ends containing a phosphate monoester and a hydroxyl group. This assumption has now been shown to be incorrect for enzymes that introduce strand breaks on the 3 -side of aldehydic abasic sites (also referred to as apurinic, apyrimidinic, or simply AP sites) during DNA repair. Despite the title of this chapter, the mechanism of the strand cleavage reaction will be briefly described. 

Merrifieid, J. Am. Chem. Soc. 91, 501 (1969) Denkewalter, Hirschmann et at, Ibid. 502. Series of articles describing the total synthesis of a protein having the full enzymic activity of bovine pancreatic RNase N. Fujii, H. Yajima, J. Chem. Soc. Perkin Trans. I 1981, 789-841. Specifically catalyzes the cleavage of the phosphodiester bond between the 3 and 5 positions of the ribose moieties in RNA with the formation of oligonucleotides terminating in 2, 3 -cyclic phos-... 

A structure-related disadvantage of the duplex drugs is that upon enzymatic cleavage of the phosphodiester bonds, a 1-to-l ratio of nucleoside to nucleotide is obtained (see Figure 7.7-6). Thus, the desired 5 -phosphorylated nucleotide is only formed at maximally 50%. Additionally, one of the two nucleosides has to be transformed into a lipophilic derivative without loss of antitumor or antiviral activity. On the other hand, it was shown that the lipophilic derivatization of nucleosides can result in enhanced activity and modulation of cell specificity [106]. 

New DNA strands are synthesized in the 5 —>3 direction. This means that new deoxyribonucleotide triphosphates (dNTPs) are added onto the 3 -OH of the growing chain in a template-directed maimer by DNA polymerase. The polymerization involves the formation of a phosphodiester bond between the a-phosphate of the incoming nucleotide and the 3 -OH of the nascent chain. Only the deoxyribonucleotide monophosphate (dNMP) is incorporated into the growing chain the pyrophosphate (PPi) is cleaved off during polymerization. The cleavage of the phosphodiester bond provides the energy for the polymerization reaction. The resulting pyrophosphate ion is rapidly hydrolyzed to two phosphate ions by the ubiquitous and abundant enzyme pyrophosphatase, and this reaction drives the polymerization in the direction of polymer formation (Fig. 8-1). 

Fig. 1. Chemical reactions catalyzed by DNA topoisomerases. An initial transesterilication involves the attack of the nucleotide phosphorus by the tyrosine of the enzyme active site. This reaction produces cleavage of the phosphodiester bond and formation of a covalent link between the tyrosine and the DNA end (in the example, the 5 end). A second transesterilication, the attack of the phosphorus by the free hydroxyl DNA end, reverses the reaction, resealing the phosphodiester bond and liberating the tyrosine.

Mikkola S, Stenman E, Nurmi K, Yousefi-Salakdeh E, Stromberg R, Lormberg H The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of... 

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