Phosphodiesterase exonuclease

Second, the efficiency of exonucleases and endonucleases in hydrolysing DNA is greatly affected by modification of the bases (Dizdaroglu et /., 1978 Breimer, 1991). For example, Maccubbin et al. (1991) reported that the presence of 8-OH-Gua severely inhibits digestion of dinucleotides by phosphodiesterase. Thus it is not always certain that modified bases are completely hydrolysed from DNA, especially when published hydrolysis techniques are transplanted from one laboratory to another and not revalidated. 

Using phosphotriester methods, dinucleoside (3 - 50-monophosphates containing 6-methyl-2,-deoxyuridine at the 3 - or 5 -end have been prepared.44 N.m.r. spectroscopy indicates that this nucleoside possesses the syn conformation in these compounds, and, on treatment with snake venom phosphodiesterase, d(m6UpT) is degraded, while d(Apm6U) is not, indicating that this enzyme, a 3 -exonuclease, requires the anti conformation to be present in the substrate. Two modified nucleo-side-5 -monophosphates, (20) and (21), which are resistant to 5 -nucleotidase, have been isolated from tRNA snake venom hydrolysates.45 A synthesis of (20) has been reported.46... 

Venom exonuclease [EC 3.1.15.1], also known as venom phosphodiesterase, catalyzes the exonucleolytic cleavage of RNA or DNA (preferring single-stranded substrates) in the 3 to 5 direction to yield 5 -phosphomononucleo-tides. Similar enzymes include hog kidney phosphodiesterase and the Lactobacillus exonuclease. See also specific phosphodiesterase J. A. Gerit (1992) The Enzymes, 3rd ed., 20, 95. 

Velocity-modulated allosteric regulation, V, ,-TYPE ALLOSTERIC SYSTEM VENOM EXONUCLEASE Venom phosphodiesterase, PHOSPHODIESTERASES VESICLE TRANSPORT IN CELLS Vibrational bond stretching mode,... 

Most phosphodiesterases catalyze transfer of the phosphoryl group to water with retention of configuration. Again, in keeping with other evidence for phosphorylenzyme intermediates, these probably represent double displacement reactions. One exception occurs with the 3 — 5 exonuclease of T4 DNA polymerase (Chapter 14) its reactions proceed with inversion.49... 

First, exonuclease (phosphodiesterase), endonuclease (8, 10-12), 5 -nucleotidase (13), and nonspecific phosphatase (13) are present in all venoms that have been analyzed. Therefore, nature did not provide these materials as sources of any one of these enzymes free from undesirable contaminants which may be represented by the others. 

The terms venom exonuclease and venom phosphodiesterase are at present used interchangeably to designate the same enzyme. The reviewer prefers the first, because he would like to see phosphodiesterase restored to it original meaning as the general name for all enzymes attacking diesterified phosphate. During the recent past, venom exonuclease has been reviewed several times (15-21). Three books (22-24) devoted to nucleases discuss venom exonuclease. 

Other substrates for spleen exonuclease are the p-nitrophenyl esters of nucleoside-3 -phosphates and bis(p-nitrophenyl) phosphate, which is split only very slowly. These substrates are also split by enzymes having quite different natural substrates (Table I) (80-87). In fact, not only phosphodiesterases, in a broad sense, such as acid DNase, micrococcal nuclease, spleen and venom exonucleases, and cyclic phosphodiesterase but also enzymes such as nucleoside phosphoacyl hydrolase and nucleoside polyphosphatase split these substrates. As pointed out by Spahr and Gesteland (86), this may be explained by the fact that these substrates are not true diesters but rather mixed phosphoanhydrides because of the acidic character of the phenolic OH. It is evident that the use of the synthetic substrates, advocated by Razzell (3) as specific substrates for exonucleases, may be very misleading. Table II shows the distinctive characters of three spleen enzymes active on bis(p-nitrophenyl) phosphate which are present in the crude extracts from which acid exonuclease is prepared. 

When the Tg lesions is opened by ammonolysis, the resulting product (ureidoisobutyric acid) inhibits snake venom phosphodiesterase, A exonuclease and the Klenow (exo ) fragment (Matray et al. 1995 see also Greenberg and Matray 1997). It is, however, removed by E. coli Fpg and Nth proteins (Jurado et al. 1998). 

Snake Venom Phosphodiesterase An exonuclease is an enzyme that sequentially cleaves nucleotides from the end of a polynucleotide strand. Snake venom phosphodiesterase, which hydrolyzes nucleotides from the 3 end of any oligonucleotide with a free 3 -hydroxyl group, cleaves between the 3 hydroxyl of the ribose or deoxyribose and the phosphoryl group of the next nucleotide. It acts on single-stranded DNA or RNA and has no base specificity. This enzyme was used in sequence... 

Preparation of partial exonuclease digests (i) Venom phosphodiesterase... 

The mutagenic ribonucleotide rPTP (87) has been used in an in vitro retroviral replication model. After four rounds of replication the mutation frequency was raised to 3.8 x 10 per nucleotide, with C U and U C mutations observed. It was suggested that such an analogue could induce mutations in a retroviral target beyond its error threshold. The tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine (g-clamp, see (141)) have been incorporated into ODNs to study their effect with exonuclease. It was found that a single substitution at the 3 -terminus afforded complete protection of the ODN with snake venom phosphodiesterase. ... 

This final acid phosphatase preparation had a specific activity of 468 and represented an approximately 1900-fold purification of the acid phosphatase in the starting crude spleen nuclease II. It contained no acid deoxyribonuclease, acid ribonuclease, exonuclease, and phosphodiesterase activities that could be detected in a 0.1-ml sample after 2 hours of incubation with the appropriate substrate. The relative rates of hydrolysis of various substrates were as follows p-nitrophenyl phosphate, 100 5 -AMP, 63 j8-glycerophosphate, 60 ATP, 0. With p-nitrophenyl phosphate as substrate, the pH optimum was broad and lay between pH 3.0 and pH 4.8. The Michaelis constant at 37°C was 7.25 X 10" mM. Phosphate and chloride ions acted as competitive inhibitors. 

There are 11 different PDE families (PDEl-11) with different substrate specificity, affinity, sensitivity to inhibitors, and tissue localization. In addition, there are exonucleases such as 5 -nucleotide phosphodiesterase (PDE 1) and 3 -nucleotide phosphodiesterase (PDE 11) that hydrolyze phosphodi-ester bounds. These enzymes have several known functions in nucleic acids. By using all these enzymes in a sensor surface and by measuring changes in fluorescence polarization it was concluded that YTX binds to cyclic nucleotide PDEl, with a calcium-dependent effect, PDE3, and PDE4, and shows high affinity by exonuclease PDE 1 [15,16]. 

The ohgonucleotide of Exercise 11.9 is digested with a 5 -acting exonuclease calf serum phosphodiesterase. What m/z values of the ions will be observed in the MALDI mass spectrum ... 

An oligonucleotide was digested with a S -actmg exonuclease calf serum phosphodiesterase. The MALDI mass spectrum contains ions of m/z values of 1775.37, 1471.30, 1182.20, 869.22, 540.12, and 227.10. What is the sequence of the oligonucleotide ... 

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. 

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