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PubMed2002

Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors.

DNA nucleases catalyze the cleavage of phosphodiester bonds. These enzymes play crucial roles in various DNA repair processes, which involve DNA replication, base excision repair, nucleotide excision repair, mismatch repair, and double strand break repair. In recent years, new nucleases involved in various DNA repair processes have been reported, including the Mus81 : Mms4 (Eme1) complex, which functions during the meiotic phase and the Artemis : DNA-PK complex, which processes a V(D)J recombination intermediate. Defects of these nucleases cause genetic instability or severe immunodeficiency. Thus, structural biology on various nuclease actions is essential for the elucidation of the molecular mechanism of complex DNA repair machinery. Three-dimensional structural information of nucleases is also rapidly accumulating, thus providing important insights into the molecular architectures, as well as the DNA recognition and cleavage mechanisms. This review focuses on the three-dimensional structure-function relationships of nucleases crucial for DNA repair processes.

Animals↗
PubMed1988

Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences.

A long A+T-rich sequence in supercoiled pBR322 DNA is hypersensitive to single-strand-specific nucleases at 37 degrees C but not at reduced temperature. The basis for the nuclease hypersensitivity is stable DNA unwinding as revealed by (i) the same temperature dependence for hypersensitivity and for stable unwinding of plasmid topoisomers after two-dimensional gel electrophoresis, (ii) preferential nuclease digestion of stably unwound topoisomers, and (iii) quantitative nicking of stably unwound topoisomers in the A+T-rich region. Nuclease hypersensitivity of A+T-rich sequences is hierarchical, and either deletion of the primary site or a sufficient increase in the free energy of supercoiling leads to enhanced nicking at an alternative A+T-rich site. The hierarchy of nuclease hypersensitivity reflects a hierarchy in the free energy required for unwinding naturally occurring sequences in supercoiled DNA. This finding, along with the known hypersensitivity of replication origins and transcriptional regulatory regions, has important implications for using single-strand-specific nucleases in DNA structure-function studies.

Base Sequence↗
PubMed2000

A single nuclease active site of the Escherichia coli RecBCD enzyme catalyzes single-stranded DNA degradation in both directions.

The RecBCD enzyme of Escherichia coli is an ATP-dependent DNA exonuclease and a helicase. Its exonuclease activity is subject to regulation by an octameric nucleotide sequence called chi. In this study, site-directed mutations were made in the carboxyl-terminal nuclease domain of the RecB subunit, and their effects on RecBCD's enzymatic activities were investigated. Mutation of two amino acid residues, Asp(1067) and Lys(1082), abolished nuclease activity on both single- and double-stranded DNA. Together with Asp(1080), these residues compose a motif that is similar to one shown to form the active site of several restriction endonucleases. The nuclease reactions catalyzed by the RecBCD enzyme should therefore follow the same mechanism as these restriction endonucleases. Furthermore, the mutant enzymes were unable to produce chi-specific fragments that are thought to result from the 3'-5' and 5'-3' single-stranded exonuclease activities of the enzyme during its reaction with chi-containing double-stranded DNA. The results show that the nuclease active site in the RecB C-terminal 30-kDa domain is the universal nuclease active site of RecBCD that is responsible for DNA degradation in both directions during the reaction with double-stranded DNA. A novel explanation for the observed nuclease polarity switch and RecBCD-DNA interaction is offered.

Amino Acid Sequence↗
PubMed1991

Nuclease S1-mediated enhancement of the 32P-postlabeling assay for aromatic carcinogen-DNA adducts.

Treatment of DNA digests with nuclease P1 prior to 32P-labeling of adducts has previously been shown to enhance the sensitivity of the 32P-postlabeling assay for the detection of aromatic carcinogen-DNA adducts. The enhancement was based on the ability of nuclease P1 to remove the 3'-phosphate from normal nucleotides but not the corresponding phosphate from most aromatic adducted nucleotides. We investigated the utility of another 3'-dephosphorylating enzyme, nuclease S1, for this purpose, and found it to be as effective as nuclease P1. The recovery of DNA adducts derived from benzo[a]-pyrene (B[a]P), benzoquinone (BQ) and 2-acetylaminofluorene (AAF) was comparable after enhancement with either enzyme. Some differences were, however, observed. Recovery of a minor B[a]P adduct was 1.5 times higher by the S1 procedure. Among minor adducts of BQ, two showed higher values (2.8- and 6.1-fold) by the S1 procedure and one by the P1 procedure (2.4-fold). The major AAF adduct, deoxyguanosine-C8-AF, exhibited poorer recovery (1-11%) by either procedure, while the minor adducts, deoxyguanosine-N2-AAF and deoxyguanosine-C8-AAF, showed better recovery (2-3 times) than by the enhancement procedure involving extraction of adducts into butanol. Our results show that the nuclease S1 assay can complement the nuclease P1 assay, with improved recoveries for some adducts. Considering the complexity of the postlabeling assay, this additional variant may prove useful in unequivocal detection of DNA adducts.

2-Acetylaminofluorene↗
PubMed1995

Detection of deoxyadenosine-4-aminobiphenyl adduct in DNA of human uroepithelial cells treated with N-hydroxy-4-aminobiphenyl following nuclease P1 enrichment and 32P-postlabeling analysis.

To characterize the DNA adducts in human uroepithelial cells (HUC) exposed to 4-aminobiphenyl and its proximate N-hydroxy metabolites, we used 32P-postlabeling analyses following butanol extraction of the DNA hydrolysates. Using this method, we identified N-(deoxyguanosin-3',5'-bisphospho-8-yl)-4-aminobiphenyl (pdGp-ABP) as a major adduct and N-(deoxyadenosin-3',5'-bisphospho-8-yl)-4-aminobiphenyl (pdAp-ABP) as a minor adduct in an immortalized non-tumorigenic cell line of HUC following exposure to N-hydroxy-4-aminobiphenyl (N-OH-ABP). Towards characterization of pdAp-ABP, we postlabeled the synthetic N-(deoxyadenosin-3'-phospho-8-yl)-4-aminobiphenyl (dAp-ABP) adduct to generate pdAp-ABP and determined its chromatographic (TLC and HPLC) properties and sensitivity to nuclease P1 digestion. In contrast to pdGp-ABP, which was cleaved to the corresponding 5'-monophosphate by nuclease P1, the pdAp-ABP adduct was unaffected when incubated with nuclease P1 under similar conditions. To test whether nuclease P1 digestion could be adopted for enrichment of the dAp-ABP adduct in HUC samples, postlabeling analyses were carried out after butanol extraction following nuclease P1 digestion of the DNA hydrolysate. Under these conditions, the pdAp-ABP adduct was detected in DNA from HUC E7 cells treated with N-OH-ABP and in calf thymus DNA reacted with N-OH-ABP under acidic (pH 5.0) conditions. These data indicate that pdGp-ABP and pdAp-ABP adducts are generated in HUC E7 on treatment with N-OH-ABP and that nuclease P1 enrichment may provide a method for qualitative and quantitative analyses of the pdAp-ABP adduct in DNA.

Aminobiphenyl Compounds↗
PubMed1985

Studies on the herpes simplex virus alkaline nuclease: detection of type-common and type-specific epitopes on the enzyme.

Five monoclonal antibodies to the alkaline nuclease of herpes simplex virus (HSV) types 1 and 2 have been used in immunoperoxidase tests to demonstrate the nuclear localization of the enzyme within HSV-1- and HSV-2-infected cells and to purify the enzyme from cells infected with either virus by immunoadsorbant chromatography. Affinity chromatography with a 32P-labelled extract of HSV-2-infected cells has enabled us to demonstrate that the nuclease eluting from the immunoadsorbant is a phosphoprotein, hence confirming the nuclease to be identical to the phosphorylated polypeptide previously referred to as ICSP 22 (HSV-2) or ICP 19 (HSV-1). In addition, the results clearly demonstrate that monoclonal antibodies Q1, CC1 and CH2 are directed against HSV type-common epitopes while V1 and T2T1 antibodies are against HSV-2-specific epitopes on the enzyme. Using the type-specific monoclonal antibodies in an immunoperoxidase test, the enzyme specified in cells infected with intertypic recombinants has been typed; correlation of these data with restriction endonuclease maps of the recombinants has enabled us to map the position of the active site of the nuclease gene to map units 0.168 to 0.184 on the genomes of both HSV-1 and HSV-2. Taken with the data mapping the mRNA encoding this enzyme, the nuclease active site can be mapped to 0.168 to 0.175 on the genome. Finally, the use of monoclonal antibodies in immunofluorescence tests on infected cells has demonstrated that the nuclease is synthesized within 2 h post-infection.

Antibodies, Monoclonal↗
PubMed1975

Nuclease digestion of synthetase x tRNA complexes.

Phenylalanyl-tRNA and seryl-tRNA synthetase protect strongly though not completely their cognate tRNAs against nuclease attack, as had been shown previously. In an investigation of the mechanism of protection it was demonstrated that the low susceptibility of phenylalanyl-tRNA-synthetase x tRNA-Phe complexes to nucleases is due to free tRNA present in equilibrium with synthetase. The equilibrium can be shifted by an excess of synthetase or by dilution of the complex. It therefore appears that synthetase competes with the nuclease for free tRNA. Degradation of the complex is low, however, because under the conditions of partial digestion the synthetase has a greater affinity for the tRNA than does the nuclease. Fragmented tRNAs, as they are formed during partial nuclease digestion, bind to synthetase to different degrees. tRNA-Phe with a lesion in the dihydrouridine loop binds very poorly whereas a nick in the anticodon loop reduces the strength of binding to a much lesser extent. In a systematic study of the stoichiometry of protection it was confirmed that under standard conditions one phenylalanyl-tRNA synthetase protects one tRNA-Phe and one seryl-tRNA synthetase two tRNA-Ser molecules against nuclease attack. Under certain conditions, however, (concentration of the complex higher than 10 mu-M, or alternately in buffers of low ionic strength) it is observed that phenylalanyl-tRNA synthetase binds up to 1.6 molecules tRNA-Phe. In the serine system, these special conditions do not affect the binding properties of seryl-tRNA synthetase.

Amino Acyl-tRNA Synthetases↗
PubMed2003

Single-strand-specific nucleases.

Single-strand-specific nucleases are multifunctional enzymes and widespread in distribution. Their ability to act selectively on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids has led to their extensive application as probes for the structural determination of nucleic acids. Intracellularly, they have been implicated in recombination, repair and replication, whereas extracellular enzymes have a role in nutrition. Although more than 30 single-strand-specific nucleases from various sources have been isolated till now, only a few enzymes (S1 nuclease from Aspergillus oryzae, P1 nuclease from Penicillium citrinum and nucleases from Alteromonas espejiana, Neurospora crassa, Ustilago maydis and mung bean) have been characterized to a significant extent. Recently, some of these enzymes have been cloned, their crystal structures solved and their interactions with different substrates have been established. The detection, purification, characteristics, structure-function correlations, biological role and applications of single-strand-specific nucleases are reviewed.

DNA, Single-Stranded↗
PubMed1979

Transformation in pneumococcus: nuclease resistance of deoxyribonucleic acid in the eclipse complex.

Donor deoxyribonucleic acid strands in the eclipse phase of genetic transformation of pnuemococcus (Streptococcus pneumoniae) are purified as a complex with a cf the deoxyribonucleic acid strand in this complex to digestion by nucleases was shown to be 50- to 1,000-fold less than that of uncomplexed single strands of deoxyribonucleic acid. Deoxyribonuclease I, micrococcal nuclease, Neurospora endonuclease, nuclease P1, and the major endogenous nuclease of cell-free extracts were studied. Sensitivity to nuclease attack was not uniform along the deoxyribonucleic acid strand; sequences of strongly protected bases were separated by more sensitive regions. The minimum size of protected fragments was about 70 bases. A complex of protein with the protected deoxyribonucleic acid segments was obtained after partial digestion. The sizes of these complexes, of the protected deoxyribonucleic acid segments, and of the protein subunit released by complete nuclease digestion, are all approximately identical, as determined by gel exclusion chromatography. Deoxyribonucleic acid strands of eclipse complex were also shown to be particularly well protected from attack by the major pneumococcal endonuclease in cell extracts.

Bacterial Proteins↗
PubMed2006

Comparison of culture and a novel 5' Taq nuclease assay for direct detection of Campylobacter fetus subsp. venerealis in clinical specimens from cattle.

A Campylobacter fetus subsp. venerealis-specific 5' Taq nuclease PCR assay using a 3' minor groove binder-DNA probe (TaqMan MGB) was developed based on a subspecies-specific fragment of unknown identity (S. Hum, K. Quinn, J. Brunner, and S. L. On, Aust. Vet. J. 75:827-831, 1997). The assay specifically detected four C. fetus subsp. venerealis strains with no observed cross-reaction with C. fetus subsp. fetus-related Campylobacter species or other bovine venereal microflora. The 5' Taq nuclease assay detected approximately one single cell compared to 100 and 10 cells in the conventional PCR assay and 2,500 and 25,000 cells from selective culture from inoculated smegma and mucus, respectively. The respective detection limits following the enrichments from smegma and mucus were 5,000 and 50 cells/inoculum for the conventional PCR compared to 500 and 50 cells/inoculum for the 5' Taq nuclease assay. Field sampling confirmed the sensitivity and the specificity of the 5' Taq nuclease assay by detecting an additional 40 bulls that were not detected by culture. Urine-inoculated samples demonstrated comparable detection of C. fetus subsp. venerealis by both culture and the 5' Taq nuclease assay; however, urine was found to be less effective than smegma for bull sampling. Three infected bulls were tested repetitively to compare sampling tools, and the bull rasper proved to be the most suitable, as evidenced by the improved ease of specimen collection and the consistent detection of higher levels of C. fetus subsp. venerealis. The 5' Taq nuclease assay demonstrates a statistically significant association with culture (chi2 = 29.8; P < 0.001) and significant improvements for the detection of C. fetus subsp. venerealis-infected animals from crude clinical extracts following prolonged transport.

Animals↗
PubMed2004

The Mre11 nuclease is not required for 5' to 3' resection at multiple HO-induced double-strand breaks.

Current hypotheses suggest the Mre11 nuclease activity could be directly involved in double-strand break (DSB) resection in the presence of a large number of DSBs or limited to processing abnormal DNA ends. To distinguish between these possibilities, we used two methods to create large numbers of DSBs in Saccharomyces cerevisiae chromosomes, without introducing other substrates for the Mre11 nuclease. Multiple DSBs were created either by expressing the HO endonuclease in strains containing several HO cut sites embedded within randomly dispersed Ty1 elements or by phleomycin treatment. Analysis of resection by single-strand DNA formation in these systems showed no difference between strains containing MRE11 or the mre11-D56N nuclease defective allele, suggesting that the Mre11 nuclease is not involved in the extensive 5' to 3' resection of DSBs. We postulate that the ionizing radiation (IR) sensitivity of mre11 nuclease-defective mutants results from the accumulation of IR-induced DNA damage that is normally processed by the Mre11 nuclease. We also report that the processivity of 5' to 3' DSB resection and the yield of repaired products are affected by the number of DSBs in a dose-dependent manner. Finally, we show that the exonuclease Exo1 is involved in the processivity of 5' to 3' resection of an HO-induced DSB at the MAT locus.

Chromosomes, Fungal↗
PubMed1980

Extracellular nucleases of Lysobacter enzymogenes: production of the enzymes and purification and characterization of an endonuclease.

Lysobacter enzymogenes produced a nonspecific extracellular nuclease and an extracellular RNAase when grown in tryptone broth. Both enzyme activities appeared after the exponential growth phase of the organism. The addition of RNA to the medium specifically inhibited the production of the nuclease and the addition of phosphate prevented the synthesis of the RNAase. DNA had no effect on the enzyme production. The Lysobacter nuclease was purified 274-fold and its molecular weight was estimated to be between 22 000 and 28 000. Freshly purified nuclease showed one major protein band and one major activity band on polyacrylamide gels, whereas two major bands were seen after prolonged storage of the enzyme. The nuclease was most active at pH 8.0 and required Mg2+ or Mn2+. Little activity was obtained in the presence of Ca2+. The enzyme degraded double-stranded DNA more rapidly than single-stranded DNA or RNA and was essentially inactive with poly(A) or poly(C) as the substrate. Extensive hydrolysis of double-stranded DNA by the enzyme yielded oligodeoxyribonucleotides with terminal 5'-phosphate groups. The Lysobacter RNAase appeared to have a molecular weight approximately twice that of the nuclease and was specific for ribonucleotide polymers.

Bacteria↗
PubMed1994

dsRNA degrading nucleases are differentially expressed in tobacco anthers.

Nucleases, capable of digesting double-stranded RNAs are mainly confined to extracellular fractions of tobacco anthers and diffusate of mature pollen. dsRNAse activity is about 150-fold higher in anther fractions than in crude nuclease extracts from tobacco leaves. The level of dsRNAse activity varies during pollen development from the microspore stage to maturity. In the anther soluble fraction, dsRNAse activity reached a maximum (approx. 50 units/anther) at the end of microspore mitosis and then decreased continuously until the stage of almost mature anthers. In contrast, the nuclease activity associated with pollen increased continuously reaching a maximum (5 units/anther), during subsequent stages of pollen maturation. Gel electrophoretic analysis revealed four slowly migrating sugar-unspecific nucleases (active against DNA and RNA) and three faster migrating RNases which were all able to digest dsRNA. Competition experiments showed that the sugar-unspecific nucleases accounted for 95% of the total dsRNAse activity. Anther extracellular nucleases were further characterized after partial purification on NADP-agarose: dsRNAse activity had a pH optimum at 5.5, was strongly inhibited by NaCl and by 1 mM Zn2+ and was insensitive to EDTA which could stimulate activity in crude preparations. Analysis of the activity with defined substrates showed that ssRNA is more readily degraded than dsRNA and that both, endo- and exonucleolytic activities are detected.

Centrifugation, Density Gradient↗
PubMed2004

Mutation detection using Surveyor nuclease.

We have developed a simple and flexible mutation detection technology for the discovery and mapping of both known and unknown mutations. This technology is based on a new mismatch-specific DNA endonuclease from celery, Surveyor nuclease, which is a member of the CEL nuclease family of plant DNA endonucleases. Surveyor nuclease cleaves with high specificity at the 3' side of any mismatch site in both DNA strands, including all base substitutions and insertion/deletions up to at least 12 nucleotides. Surveyor nuclease technology involves four steps: (i) PCR to amplify target DNA from both mutant and wild-type reference DNA; (ii) hybridization to form heteroduplexes between mutant and wild-type reference DNA; (iii) treatment of annealed DNA with Surveyor nuclease to cleave heteroduplexes; and (iv) analysis of digested DNA products using the detection/separation platform of choice. The technology is highly sensitive, detecting rare mutants present at as low as 1 in 32 copies. Unlabeled Surveyor nuclease digestion products can be analyzed using conventional gel electrophoresis or high-performance liquid chromatography (HPLC), while end labeled digestion products are suitable for analysis by automated gel or capillary electrophoresis. The entire protocol can be performed in less than a day and is suitable for automated and high-throughput procedures.

Base Sequence↗
PubMed2000

Potential nuclease-based strategies for HIV gene therapy.

Gene therapy for HIV (human immunodeficiency virus) involves the introduction of a therapeutic gene into the infected individual for the purposes of reducing viral load and ultimately reconstituting a healthy immune system. Clinical trials for HIV gene therapy have not yet reported therapeutic benefit. In addition to improving the efficiency of gene delivery and the maintenance of gene expression, better therapeutic genes must be designed before this therapy becomes available to patients. A new class of therapeutic genes expressing nucleases may be designed. These nucleases may be classified into three categories based on their mode of action: (i) 'targeted nucleases' for specifically cleaving HIV RNA within the cell, (ii) 'colocalized nucleases' for cleaving HIV genomic DNA or RNA present within the cell or progeny virus, and (iii) 'cytotoxic nucleases' for conferring selective toxicity to HIV-infected cells. The focus of this review is on the design and application of these nucleases for HIV gene therapy.

Deoxyribonucleases↗
PubMed2002

Detection of rodent Helicobacter spp. by use of fluorogenic nuclease polymerase chain reaction assays.

Polymerase chain reaction (PCR) analysis is the standard method for detection of Helicobacter spp. infections in laboratory rodents, with H. hepaticus, H. bilis, and H. typhlonius considered primary pathogens. Fluorogenic nuclease PCR assays that detect all known rodent Helicobacter spp., or that specifically detect H. hepaticus, H. bilis, or H. typhlonius were developed to eliminate post-PCR processing, enhance specificity, and provide quantitative data on starting template concentration. Each fluorogenic PCR assay detected a minimum of 10 copies of target template, had comparable or greater sensitivity when compared directly with corollary gel detection PCR assays, and detected only targeted species when numerous Helicobacter spp. and other enteric bacteria were analyzed. Fluorogenic nuclease PCR analysis of fecal DNA samples obtained from numerous laboratory mice sources detected all samples with positive results by use of Helicobacter spp., H. hepaticus, H. bilis, and/or H. typhlonius gel detection PCR analysis, except for one sample that had positive results by H. typhlonius gel detection PCR but negative results by H. typhlonius fluorogenic nuclease PCR analysis. Among fecal DNA samples that were Helicobacter spp. negative by use of all gel detection PCR assays, the fluorogenic nuclease PCR assays detected target template in only one sample that was positive by use of the Helicobacter spp. and the H. bilis fluorogenic nuclease PCR assays. In conclusion, fluorogenic nuclease PCR assays provide sensitive, specific, and high-throughput diagnostic assays for detection of Helicobacter spp., H. hepaticus, H. bilis, and H. typhlonius in laboratory rodents, and the quantitative data generated by these assays make them potentially useful for bacterial load determination.

Animals↗
PubMed1975

A guanosine 3':5'-monophosphate-sensitive nuclease from Bacillus brevis.

In toluene-treated cells of Bacillus brevis, newly synthesized RNA is rapidly degraded in a reaction that is inhibited by cyclic guanosine 3':5'-monophosphate (cGMP) and by 1,10-phenanthroline. This appears to be due to a ribonuclease found in cell-free extracts of B. brevis which is inhibited by cGMP and related compounds as well as by 1,10-phenanthroline. The cGMP-sensitive nuclease hydrolyzes synthetic polynucleotides, yielding nucleoside 5'-monophosphates as the sole products, even during the early stages of hydrolysis. Synthetic polynucleotides terminated by a 3'-phosphate are resistant to hydrolysis. While with 3'-hydrolysis of the polymer. The enzyme is therefore an exonuclease that degrades polynucleotides from the 3' end to product 5'-mononucleotides. It also acts on denatured but not on native DNA. Activity is greatest in the presence of Mn2+ and is not affected by the presence of monovalent cations. 1,10-Phenanthroline, but not 1,7-phenanthroline, inhibits the nuclease even when Mn2+ is present in excess. The inhibition of the enzyme by cGMP is noncompetitive, and cGMP itself is not hydrolyzed. The sensitivity of the nuclease to inhibition depends strikingly on the nature of the substrate and is lost when the enzyme is assayed at high pH. These observations suggest that cGMP inhibits the nuclease by combining with an allosteric site on the enzyme. Although cGMP was found to be the most effective inhibitor, other nucleoside 3':5'-monophosphates and derivatives of 5'-GMP can also inhibit the nuclease. Since measurements of cGMP in B. brevis have not revealed detectable amounts (less than 5 times 10-8 M), the substance that modulates the activity of the nuclease under physiological conditions remains to be identified.

Bacillus↗
PubMed1990

[The identification of Ca2+-dependent nucleases activated in the nuclei of rat thymocytes under the action of glucocorticoids].

Spectra of thymocyte's nuclear nucleases of control and glucocorticoid treated (5 mg/kg body weight) adrenalectomized rats have been investigated. Using the method of SDS-electrophoresis of nuclear proteins in 3H-DNA-polyacrylamide gel (PAAG) the authors managed to discover a number of polypeptides of 35, 32, 17.7, 17.0, 16.4 kDa molecular mass possessing a nuclease activity. The enzyme of 35 kDa is only active in the presence of Ca2+ and Mg2+ ions and inhibited by cycloheximide. Nucleases of 32, 17.7, 17.0, 16.4 kDa are active in the presence of Ca2+ ions. The enzymic activity of these nucleases increases 60 min after steroid treatment. Nuclease of 17.7, 17.0, 16.4 kDa are poly(ADP-ribosylated). Glucocorticoid mediated activation don't blocked by poly(ADP-ribosylation). Possible role and mechanism of discovered nucleases are discussed.

Adrenalectomy↗