Phosphodiester, hydrolytic cleavage

Extant ribozymes generally promote one of two types of reactions hydrolytic cleavage of phosphodiester bonds or phosphoryl transfers (Chapter 26). In both cases, the substrates of the reactions are also RNA molecules. The ribosomal RNAs provide an important expansion of the catalytic range of known ribozymes. Coupled to the laboratory exploration of potential RNA catalytic function (see Box 26-3), the idea of an RNA world as a precursor to current life forms becomes increasingly attractive. 

DNAse Deoxyribonuclease, catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone... 

The selectivities of enzymes that catalyze reactions involving high molecular weight substrates have been found to change when these enzymes are immobilized, because the diffusion of macromolecular substrates is slower, and because steric factors lower the activity of the enzyme by preventing free access of substrate to the enzyme s active site. For example, the enzyme ribonuclease (RNase) catalyzes the hydrolytic cleavage of phosphodiester bonds linking the nucleotides of polymeric RNA (Eq. 4.20) ... 

C. Hydrolytic Cleavage of RNA, DNA, and Simple Phosphodiesters by Metal Complexes... 

Nucleases a group of hydrolytic enzymes which cleave nucleic acids. Exonucleases attack the nucleic acid molecule at its terminus, whereas endonucleases are able to catalyse a hydrolytic cleavage within the polynucleotide chain. Deoxyribonucleases (DNAases) are specific for DNA, ribonucleases (RNAases) for RNA. All N. are Phosphodiesterases (see) they catalyse the hydrolysis of either the 3 or 5 bond of the 3, 5 -phosphodiester linkage. Ribonuclease (see) has been extensively studied. 

The extremely high resistance of DNA towards hydrolysis makes it very difficult to study the mechanism of the hydrolysis reaction. Therefore, DNA is replaced in many studies by more reactive compounds with a phosphodiester bond (chart 1). Bis-(p-nitrophenyl)phosphate (BNPP) is a very popular model compound for the study of the hydrolytic cleavage by nucleases. Hydrolysis of the diphosphate ester yields two equivalents of a yellow nitrophe-nolate product, the formation of which can be monitored by spectrophotometry (kmax =... 

The apparent usefulness of the modeling approach suggested that possible active site interactions important in understanding the mode of action of the well-characterized enzymes, ribonuclease (16) and staphylococcal nuclease (17). may be revealed. Both have been the subject of extensive crystallographic studies (18,19) with suitable inactive substrates in place. We considered the first step of hydrolytic action of ribonuclease (RNase) on the dinucleotide substrate uridylyl-(3 -5 )-adenosine(UpA). Our results (20) on the enzyme mechanism were consistent with the main features summarized by Roberts et al (21). The first step is a transphosphorylation leading to cleavage "oT the phosphodiester... 

The Co(m)-complex of cyden, Co(m)Cyc, is one of the most effedive synthetic catalysts discovered so far for the hydrolysis of supercoiled DNAs [59]. The hydrolytic nature of DNA cleavage by the Co(m) complexes of polyamines including cyden has been well documented [57, 58]. The mechanism illustrated in 25 has been proposed [57] for the catalytic action of the Co(m) complexes. Given the remarkable enhancement of proteolytic activity of Cu(n)Cyc upon attachment to PCD [49], we tested the activity of Co(m)Cyc in phosphodiester hydrolysis to see if it is also enhanced greatly upon attachment to PCD derivatives [61, 62]. 

In a given phosphodiester bond, hydrolytic enzymatic cleavage can occur at two locations, indicated by p and d in Figure 10.16. The former is proximal with respect to the 3 -OH group the latter is distal with respect to the 3 -OH. Enzymes that catalyze the hydrolysis of nucleic acids are nucleases (see Table 10.2). Exonucleases remove nucleotides (or nucleosides) from either the 5 or the 3 end of the polynucleotide. These are specific for either the p or the d bond. Thus, an exo-... 

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