Exonuclease resistance

Povirk LF, Goldberg IH (1985a) Detection of neocarzinostatin chromophore-deoxyribose adducts as exonuclease-resistant sites in defined-sequence DNA. Biochemistry 24 4035-4040 Povirk LF, Goldberg IH (1985b) Endonuclease-resistant apyrimidinic sites formed by neocarzinostatin at cytosine residues in DNA evidence for a possible role in mutagenesis. Proc Natl Acad Sci USA 82 3182-3186... 

Instead of specific amplification of one target to improve sensitivity, methods that amplify all genomic DNA or mRNAs are useful when the target is in short supply. For example, multiple-displacement amplification uses exonuclease-resistant random hexamers and a highly pro-cessive polymerase to amplify DNA nonspecificaily. Initial DNA denaturation is not necessary and the reaction proceeds isothermally. Similarly, messenger RNA can be generi-caUy amplified with a poly(T) primer modified with an RNA polymerase promoter. After reverse transcription, second-strand DNA synthesis, and transcription, antisense RNA is produced. Both whole genome and antisense RNA amplification are also useful as nucleic acid purification methods before amplification or detection. 

Griffey, R.H. et al, 2 -0-aminopropyl ribonucleotides a zwitterionic modification that enhances the exonuclease resistance and biological activity of antisense oligonucleotides, /. Med. Chem., 39, 5100,1996. 

The boranophosphate internucleotide linkage in dimer 2 is quite stable toward cleavage by exonucleases. Enzymatic hydrolysis studies were performed on TpT in vitro (normal dinucleotide), and a mixture of R and S boronated diastereomers of TpBT 2 to ascertain the in vitro exonuclease resistance of the intemucleotide linkage (12). Under conditions where normal dithymidylyl phosphate is >97% cleaved, dimer 2 is >92% stable to both calf spleen and snake venom phosphodiesterase. The boronation confers considerable resistance to these two particular exonucleases. The extent of protection shows that both the R and S chiral forms exhibit nuclease resistance. These experiments are now being repeated for the R and S stereoisomers of the dimer, which we have separated by HPLC. In summary, the P—BH3 group possesses sufficient hydrolytic stability to survive use in biological systems. 

Table 2 Exonuclease resistance and serum stability of single-stranded oligonucleotides...

To test exonuclease resistance, the oligonucleotides were incubated with venom exonuclease phosphodiesterase I from Crotalus adamanteus (0.2 mU) in a total volume of 180 pL for 15 min. To test serum stability, oligonucleotides were incubated in 10% bovine serum for 30 min... 

The phosphorodithioates DNA derivatives have been shown to bind specifically to complementary DNA or ENA sequences to form stable adducts. Because they are also highly resistant to degradation by cellular exonucleases, these derivatives can be useful both for appHcations in research and as therapeutic dmgs. Phosphorodithioate DNA has been shown to stimulate Rnase H activity in nuclear cell extracts and is a potent inhibitor of HIV type-1 reverse transcriptase (56). 

The HPLC-MS/MS assay was also successfully applied to the measurement of UV-induced dimeric pyrimidine photoproducts [123, 124]. The latter lesions were released from DNA as modified dinucleoside monophosphates due to resistance of the intra-dimer phosphodiester group to the exonuclease activity during the hydrolysis step [125, 126]. The hydrolyzed photoproducts exhibit mass spectrometry and chromatographic features that allow simultaneous quantification of the three main classes of photolesions, namely cyclobutane dimers, (6-4) photoproducts, and Dewar valence isomers, for each of the four possible bipyrimidine sequences. It may be added that these analyses are coupled to UV detection of normal nucleosides in order to correct for the amount of DNA in the sample and obtain a precise ratio of oxidized bases or dimeric photoproducts to normal nucleosides. 

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... 

Utilising a reversion assay in Salmonella enterica, Prieto et al reported an increased frequency of point mutations following bile-salt exposure. Mutations were predominantly nucleotide substitutions (GC to AT transitions) and -1 frameshift mutations.The frameshifts were dependent on SOS induction and linked to the activity of DinB polymerase (Pol IV). The authors proposed that the GC to AT transitions stimulated by bile, could have arisen from oxidative processes giving rise to oxidised cytosine residues. Consistent with this hypothesis, the authors demonstrated that strains of S. enterica-lacking enzymes required for base-excision repair (endonuclease III and exonuclease IV) and the removal of oxidised bases, demonstrated increased bile-acid sensitivity compared with competent strains. In another study using E. coli, resistance to the DNA-damaging effects of bile was associated with Dam-directed mismatch repair, a pathway also involved with the repair of oxidative DNA lesions. ... 

Unmodified siRNA in this context is restricted to the 19 base pairing nucleotides of siRNA duplexes. Most siRNAs are synthesized with two nucleotide 3 overhangs. The last or the last two nucleotides are often desoxy-thymidines in order to increase the resistance of the siRNAs against exonucleases and because of technical reasons in RNA synthesis. siRNAs modified with 3 desoxy-thymidines are classified as unmodified in the context of this chapter. 

With RNA as substrate the results are conflicting. Cousin (52) observed that poly I, poly U, and poly C were rapidly and completely hydrolyzed, whereas under identical conditions poly I -f- poly C was hydrolyzed slowly and incompletely. Native rRNA and tRNA were resistant to 60 jug/ml of commercial exonuclease, but after heat de-naturation rRNA was readily and tRNA partly digested (52). Nihei and Cantoni (53) digested tRNA to completion, as did Keller (54) who observed a two-phase reaction. In agreement with the last two authors (53, 54) but contrary to the results of Cousin (52), Hadjiolov et al. 

It has been known for many years (15-24) that venom exonuclease is capable of hydrolyzing both DNA and RNA. Gray and Lane (56) showed that naturally occurring 2 -0-methyl-substituted ribose derivatives are also hydrolyzed, even though the rate of hydrolysis is slower than with the unsubstituted ribose. Interestingly, the 2 -0-methylated derivatives are totally resistant to 5 -nucleotidase (57, 58). 

The action of venom exonuclease is also blocked by thymine dimers produced as a result of UV irradiation of DNA at 280 nm. Setlow et al. (66) subjected irradiated DNA to exhaustive digestion by venom exonuclease. They isolated and identified the products of the reaction, which were composed of large amounts of all four 5 -mononucleotides and of small amounts of trinucleotides of the type d-pNpTpT where N was any of four common nucleosides and TpT was the irradiation-induced dimer of thymidine. These trinucleotides were totally resistant to further digestion with venom exonuclease but became partially susceptible after UV irradiation at 240 nm, known to reverse dimerization. The authors picture the action of venom exonuclease as proceeding linearly from the internal bond one base beyond the dimer. From there on conventional hydrolysis is resumed until the next block. This experiment touches upon one of the most pressing problems connected with venom exonuclease. Is the endonucleolytic activity an intrinsic property of the enzyme ... 

Derivatives bearing a 3 -monopbosphoryl group were originally classified as totally resistant to venom exonuclease. As the quality of the enzyme preparation improved, these compounds were found susceptible but required 1000-fold more enzyme than was needed to hydrolyze 5 -monophosphate-bearing compounds. This unusual resistance led to another erroneous conclusion, that the polarity of exonuclease changes (20). The basis for this belief were the experiments in which a mixture of tri-, tetra-, and pentanucleotides of the type d-N pNPpN pN p were used as substrates. The early products were nucleosides and nucleotides, whereas 3, 5 -mononucleoside diphosphates appeared considerably later. It is clear now that the mixture was contaminated with a small amount of dephosphorylated chains which were rapidly hydrolyzed to completion. 

The mechanism of action of spleen exonuclease is similar to that seen for venom exonuclease (19-21) but different from the processive type of attack exhibited by E. coli RNase II, sheep kidney exonuclease, and polynucleotide phosphorylase (22, 23), in which cases each polynucleotide molecule is completely degraded before the enzymes attack a new molecule. The results of Bernardi and Cantoni (12) contradict the previous beliefs that the enzyme has an intrinsic, though weak, endonucleolytic activity (5) and that a phosphate group in a terminal 5 position makes a polynucleotide chain completely resistant to the enzyme (15, 24, 25). 

The enzyme is very sensitive to the secondary structure of the substrate. Native calf thymus DNA is quite resistant to enzymic attack by spleen exonuclease, being split at less than 4% the rate at which alkali-denatured DNA is split (11). Long deoxyribonucleotides (average chain length 20-50), which still have complementary double-stranded structure, are rather resistant to the enzyme (26). Some limited results obtained with synthetic polyribonucleotides (11) are rather puzzling since poly C was found to be completely resistant, whereas poly A, poly I, and poly U were degraded at comparable rates. In the solvent used (0.15 M acetate buffer-0.01 M EDTA, pH 5.0), poly A and poly C are believed to have... 

Glucosylated oligonucleotides obtained from T4 phage DNA by acid DNase digestion are resistant to spleen exonuclease (28). It has been reported that acetylation of the 2 -OH groups of tRNA completely inhibits the action of the enzyme, whereas venom exonuclease is not affected (29). The naturally occurring methylation of sugars and bases in tRNA does not seem to hinder the action of spleen exonuclease. 

Figure 7.5 Example of a chimeric oligonucleic acid and its modification. Chimeric RNA-DNA hybrids are used for correction of point mutations in target genes. One strand of this oligonucleic acid is composed of O-methyl-RNA (outline) with an interruption of 5 bases of deoxyribonucleic acid. X and Y are target residues for correction. In the complementary strand, there is a DNA nick, and T residues loop both ends. 3 -exonuclease and FEN-1 may act on the nick, PARP-1 possibly binds to and is activated by the nick, resulting in activation of damage response pathways. In the modified version, the 3 end is replaced by ribonucleic acids. The 5 end is extended, and the flipped back RNA tail is added. Thus, the nick is expected to be resistant to 3 -exonuclease and FEN-1. In addition, PARP-1 may not be activated by such a nick.

Fig. 10. Incremental truncation libraries (Ostermeier et al., 1999b). Plasmid DNA is digested with two restriction enzymes one that produces a 3 recessed end (A which is susceptible to Exo III digestion) and the other that produces a 5 recessed end (B which is resistant to Exo III digestion). Digestion with Exonuclease III proceeds under conditions in which the digestion rate is slow enough so that the removal of aliquots at frequent intervals results in a library of deletions of all possible lengths from one end of the fragment. The ends of the DNA can be blunted by treatment with SI nuclease and Klenow so that unimolecular ligation results in the desired incremental truncation library.

---