Properties of an endonuclease activity in Micrococcus luteus acting on gamma-irradiated DNA and on apurinic DNA

A protein fraction from Micrococcus luteus with endonuclease activity against gamma-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against gamma-irradiated DNA was stimulated five-fold with 5 mM Mg++, whereas that against apurinic sites was less dependent on the Mg++ concentration. 100 mM KCl inhibited the gamma-ray endonuclease, but not the apurinic endonuclease activity. In gamma-irradiated RNA the protein recognized 1.65 endonuclease sensitive sites per radiation induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The affinity of the enzyme for the endonuclease sensitive site was evaluated resulting in a Km-value of 73 nM.     

Purification and amino-terminal amino acid sequence of an apurinic/apyrimidinic endonuclease from calf thymus.

An apurinic/apyrimidinic (AP) endonuclease (E.C.3.1.25.2) has been purified 1100 fold to apparent homogeneity from calf thymus by a series of ion exchange, gel filtration and hydrophobic interaction chromatographies. The purified AP endonuclease is a monomeric protein with an apparent molecular weight on SDS-PAGE of 37,000. On gel filtration the protein behaves as a protein of apparent molecular weight 40,000. DNA cleavage by this AP endonuclease is dependent on the presence of AP sites in the DNA. DNA cleavage requires the divalent cation Mg2+ and has a broad pH optimum of 7.5-9.0. Maximal rates of catalysis occur at NaCl or KCl concentrations of 25-50 mM. The amino acid composition and the amino-terminal amino acid sequence for this AP endonuclease are presented. Comparison of the properties of this AP endonuclease purified from calf thymus with the reported properties of the human AP endonuclease purified from HeLa cells or placenta indicate that the properties of such an AP endonuclease are highly conserved in these two mammalian species.     

Purification and properties of a mouse-cell DNA-repair endonuclease, which recognizes lesions in DNA induced by ultraviolet light, depurination, gamma-rays, and OsO4 treatment

A DNA-repair endonuclease has been purified 117-fold from mouse plasmacytoma cells (line MPC-11) by gel filtration, followed by ion-exchange and affinity chromatography. Its molecular weight was determined by gel filtration to be 28,000 +/- 2000. The enzyme recognizes apurinic and apyrimidinic sites induced by acid and gamma-rays in DNA, as well as another type of lesion(s) which is introduced into DNA by both ultraviolet irradiation and OsO4. Quantitative measurements of the number of nicks the purified DNA-repair endonuclease makes in DNA treated with various amounts of OsO4 and ultraviolet light suggests that the endonuclease may act on 5,6-dihydroxydihydrothymine lesions. The endonuclease activity was sensitive to the ionic strength and was most active in the presence of 100 mM KCl, whereas the presence of divalent cations did not stimulate the activity.     

Purification and properties of DNA endonucleases associated with Friend leukemia virus.

An endonuclease associated with the core of Friend leukemia virus (FLV) has been purified more than 10(3)-fold by ion exchange chromatography and gel filtration. Its molecular weight was determined by gel filtration to be about 40,000. Divalent cations were required for the endonuclease to function and KCl concentrations above 50 mM inhibited the enzyme activity. In the presence of Mg++ the purified enzyme nicked preferentially supercoiled circular DNA duplexes and in most of these molecules only one single-stranded nick was introduced per strand. The regions into which the nick could be introduced appeared to be randomly distributed on the circular molecule. When Mn++ was substituted for Mg++ the number of nicks introduced into DNA by the purified enzyme was greatly increased, and both relaxed circular and linear DNA duplexes were nicked as well as supercoiled circular DNA duplexes. Prior to its purification, however, in the presence of Mn++ the endonuclease activity in the virus extract was able to differentiate between circular and linear DNA duplexes, since both supercoiled and relaxed circular duplexes were nicked much more readily than linear duplexes. Single-stranded DNA functioned poorly as a substrate for the purified enzyme.     

Purification and characterization of an endonuclease from fruiting caps of basidiomycete Coprinus cinereus

An endonuclease was purified from the cap tissues of basidiocarp of Coprinus cinereus collected at early meiotic prophase. It has an optimal activity at pH 7.0 and 37 degrees C. It is a cationic enzyme with a molecular mass of 22 kDa by gel filtration, and contains a 12-kDa and a 14-kDa peptide as revealed by SDS gel electrophoresis and Western blot analysis. An antiserum was produced in rabbits against the purified Coprinus endonuclease. The specificity of this antiserum was demonstrated in a dot-blot analysis and, more critically, in an immunoinhibition of endonuclease activity. The Coprinus endonuclease requires Mg2+ and/or Ca2+ as co-factors. Ca2+ is more efficient than Mg2+ while the effect of combining both co-factors is the highest. The Coprinus endonuclease has a substrate preference for single-strand and supercoiled DNA. It gives only single-strand nicks on supercoiled DNA at low enzyme concentration and limited time of incubation. At high enzyme concentration and/or long incubation time, double-strand fragmentation occurred. As is discussed, this endonuclease is believed to be involved in the early phase of meiotic recombination.     

Purification and characterization of an endonuclease specific for single-stranded DNA from Bacillus subtilis Marburg.

Bacillus subtilis Marburg TI (thy,trpC2) has at least four endonuclease activities as assayed by measuring the conversion of single-stranded circular f1 DNA to the linear form by agarose gel electrophoresis. One of them, which is specific for single-stranded DNA (named endonuclease MII), was purified about 320 times by two chromatographic steps and gel filtration, thereby eliminating exonuclease and phosphomonoesterase activities. This activity requires divalent cations but does not require ATP. The molecular weight estimated by gel filtration was about 57,000 daltons. The cleavage products have 5'-phosphoryl termini. At low concentrations, double-stranded DNA is not split to any detectable extent. At high concentrations, however, double-stranded superhelical DNA is attacked to yield open-circular and linear DNA's. The activity of the enzyme towards single-stranded circular DNA relative to that towards double-stranded linear DNA was calculated to be approximately 5,000:1 by comparing the initial rates of introducing single-strand breaks into the DNA's.     

Yeast tRNA-splicing endonuclease is a heterotrimeric enzyme

tRNA-splicing endonuclease from the yeast Saccharomyces cerevisiae was purified to homogeneity greater than 5000-fold over a crude Triton X-100 extract of yeast total membranes, with 5% overall yield. This nuclear enzyme has the unusual heterotrimeric subunit structure alpha beta gamma (alpha = 31 kDa, beta = 42 kDa, and gamma = 51 kDa), as determined by sodium dodecyl sulfate gel electrophoresis, and has a molecular mass close to the sum of the three subunits, as determined by gel filtration of the native enzyme. From the purification, we estimate that there are approximately 100 molecules of endonuclease/cell.     

Isolation and some properties of the site-specific endonuclease and methylase Bme2161 from Bacillus megaterium 216

The site-specific endonuclease Bme2161 was isolated as a homogeneous preparation by chromatography on phosphocellulose, hydroxyapatite and heparin-agarose. The molecular mass of the enzyme, determined by gel filtration and by electrophoresis under denaturing conditions, was found to be 60 kDa and 30 kDa respectively. These data indicate that the native enzyme consists of two identical subunits. The enzyme recognized the decreases pentanucleotide sequence 5'-GGACC-3' X 3'-CCTGG-5' and cleaves the sequence as indicated by arrows. The increases optimal concentration for endonuclease reaction is 6-7 mM Mg2+. The endonuclease relaxes its specificity in the presence of glycerol or dimethyl sulfoxide at low Mg2+ concentration (1-3 mM). Methylase Bme2161, which protects DNA against endonuclease Bme2161 action by DNA methylation, was isolated from the same bacterial strain.     

DNA-PKcs regulates a single-stranded DNA endonuclease activity of Artemis

Human nuclease Artemis belongs to the metallo-beta-lactamase protein family. It acquires double-stranded DNA endonuclease activity in the presence of DNA-PKcs. This double-stranded DNA endonuclease activity is critical for opening DNA hairpins in V(D)J recombination and is thought to be important for processing overhangs during the nonhomologous DNA end joining (NHEJ) process. Here we show that purified human Artemis exhibits single-stranded DNA endonuclease activity. This activity is proportional to the amount of highly purified Artemis from a gel filtration column. The activity is stimulated by DNA-PKcs and modulated by purified antibodies raised against Artemis. Moreover, the divalent cation-dependence and sequence-dependence of this single-stranded endonuclease activity is the same as the double-stranded DNA endonuclease activity of Artemis:DNA-PKcs. These findings further expand the range of DNA substrates upon which Artemis and Artemis:DNA-PKcs can act. The findings are discussed in the context of NHEJ.     

Isolation, purification and properties of restriction endonuclease EcoRII

The restriction endonuclease Eco RII was isolated and purified to homogeneity. The isolation procedure involved the use of the E. coli strain B834/pSK323, containing the recombinant plasmide pSK323 which provides for the oversynthesis of Eco RII enzymes. Data from gel filtration and Na-DS electrophoresis suggest that the restriction endonuclease Eco RII is a protein made up of two subunits, each with molecular weight of 44 000.     

Partial characterization of an endonuclease activity which appears in nuclease free T4 polynucleotide kinase.

A nuclease activity has been found to appear in preparations of T4 induced polynucleotide kinase which had originally been nuclease free. The nuclease introduced random nicks into T7 DNA suggesting that it was an endonuclease. Destabilization of the kinase molecule by osmotic shock or by the removal of reducing agents, ATP or salts was shown to stimulate the endonuclease appearance. The molecular weight was found to be 32,000 +/- 10% by gel filtration on G100 Sephadex. The nuclease was active over a wide pH range from pH 5.0 to pH 9.2 in a number of buffer systems and required MgCl2 and reducing agent for maximum activity. Sodium azide did not affect the nuclease appearance.     

Purification and characterization of a DNase γ-like endonuclease from Xenopus laevis liver

We recently found that two apoptotic DNase γ-like endonucleases (36 and 38kDa DNases) were present in Xenopus laevis larval and adult liver cell nuclei and that their activities increased in metamorphic climax. Here, we purified the main DNase γ-like endonuclease from Xenopus laevis liver cell nuclei and characterized its physical and enzymatic properties in detail. The molecular mass of Xenopus liver nuclear endonuclease was 38,000 daltons as determined by SDS-polyacrylamide gel electrophoresis. A native molecular mass of 35,000 was estimated by gel filtration. The purified Xenopus liver endonuclease was a neutral one and required both Ca2+ and Mg2+ for DNase activity. Unlike the mammalian DNase γ, the Ca2+/Mg2+ requirement could not be supplied by Mn2+. The inhibition profiles by aurintricarboxylic acid, sodium citrate and divalent metal ions such as Co2+, Ni2+, Cu2+ and Zn2+ were similar to those of mammalian DNase γ. These results suggest that this endonuclease is a Xenopus laevis homolog of the mammalian apoptotic endonuclease DNase γ. This revised version was published online in June 2006 with corrections to the Cover Date.     

Purification and properties of a nuclear DNA endonuclease from HeLa S3 cells.

An endonuclease that can act on calf thymus DNA and circular doublestranded phage PM2 DNA has been isolated from HeLa S3 cell chromatin. Approximately 200-fold purification was achieved by a sequence of subcellular fractionation, differential NaCl solubility and chromatography on CM-Sephadex, DEAE-cellulose and hydroxyapatite, and isoelectric point is pH 5.1 +/- 0.2. Divalent cations are necessary for its activity and the enzyme is heat inactivated at 60 degrees C. The enzyme activity is sensitive to caffeine and sulfhydryl reacting compounds. The molecular weight, determined by gel filtration and SDS gel electrophoresis, is approx. 22 000.     

The restriction endonucleases in Bacillus amyloliquefaciens N strain. Substrate specificities.

Two species of restriction endonuclease were isolated by gel filtration and DEAE-cellulose chromatography from a cell-free extract of Bacillus amyloliquefaciens (B. subtilits) N strain; a lower molecular weight endonuclease (endonuclease R.BamNI) and a higher molecular-weight one (endonuclease R.BamNx). Both of them required only Mg2+ for their activities. Endonuclease R.BamNx introduced a larger number of site-specific scissions in Excherchia coli phage lambda DNA that endonuclease R.BamNI did. Endonuclease R.BamNx cleaved Bacillus phage phi 105C DNA at the specific sites which are classified into two groups: one type of sites is modified by B. amyloliquefaciens H strain in vivo while the other is not affected. It was also active on DNA'S OF E. coli phage T7, lambdadvl, Simian virus 40 (SV40) and colicinogenic factor ColEI and was inactive on DNAs of Bacillus phages phi 29 and M2. Endonuclease R.BamHI isolated from H strain by Wilson and Young. This endonuclease was active on DNAs of phage lambda, lambdadvl and SV40, adn was inactive on DNAs of phages phi 105C, phi 29, M2 and T7, and ColEI DNA.     

限制性核酸内切酶Bsp 63Ⅰ的纯化及性质研究

用Ｂａｃｉｌｌｕｓｓｐｈａｅｒｉｃｕｓ６３菌为材料,经ＤＮＡ－Ｓｅｐｈａｒｏｓｅ和ＣｉｂａｃｒｏｎＢｌｕｅＦ３ＧＡ－Ｓｅｐｈａｒｏｓｅ两步亲和层析,将Ｂｓｐ６３Ⅰ纯化到均一程度。酶比活力达６１４００Ｕ／ｍｇ蛋白。用凝胶过滤法测得该酶分子量为１１３８００。该酶样品在ＳＤＳ－ＰＡＧＥ中呈现为一条蛋白带,并测得其亚基分子量为５６８００。用ＤＮＳ－Ｃｌ法测得该酶Ｎ－末端氨基酸为丙氨酸。上述结果表明该酶分子是由两个相同亚基组成。     

Mn2+-dependent endonuclease activity of chromatin

The endogenous endonuclease activity of chromatin in isolated rat liver nuclei in the presence of Mn2+, Mg2+ and Ca2+ + Mg2+ was studied. The existence of a Mn2+-dependent endonuclease activity not coupled with the Ca2+, Mg2+-dependent endonuclease was demonstrated, which was weaker than the former one in isolated cell nuclei but higher than in the preparation of Ca2+, Mg2+-dependent nuclease obtained by gel filtration through Toyopearl HW 60F. The Mn2+-dependent splitting of chromatin predominantly occurs at linker DNA of distal parts of chromatin loops. A split-off of purified DNA was more universal than in the presence of Ca2+, Mg2+-dependent endonuclease; the hydrolysis rate of native and denaturated DNA appeared to be the same.     

Mg2+-dependent/poly(ADP-ribose)-sensitive endonuclease

A novel endonuclease from adult hen liver nuclei has been purified to a homogeneous state through salt extraction, ammonium sulfate fractionation, gel filtration, acetone fractionation, and successive chromatography of 1) hydroxyapatite and DNA Sepharose and 2) hydroxyapatite and isoelectric focusing. The endonuclease has a pH optimum at 9.0 and requires Mg2+ for activity. The enzyme hydrolyzes more rapidly in the order of polynucleotide: denatured DNA = rRNA greater than poly(dA) = poly(dT) greater than poly(dC) = poly(dG) greater than native DNA. This endonuclease degrades denatured DNA about 20 times more rapidly than does the native DNA. The products contain 5'-phosphoryl and 3'-hydroxyl termini and all four deoxynucleotides are present while dGMP is predominant. The enzyme cleaves the circular duplex PM2 DNA, endonucleotically, via single strand scission. The isoelectric point is 10.2 +/- 0.2 and the molecular weight is 43,000 +/- 2,000, determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration. Pyridoxal 5'-phosphate and 2,3-butanedione inhibit the catalytic activity, respectively. The inhibition of DNA binding activity was also seen with former, but not with the latter. Purified Mg2+-dependent alkaline endonuclease was used to investigate the nature of poly(ADP-ribose) inhibition of the enzyme. In contrast to the Ca2+/Mg2+-dependent endonuclease (Yoshihara, K., Tanigawa, Y., Burzio, L., and Koide, S. S. (1975) Proc. Natl. Acad. Sci. U. S. A. 72, 289-293), ADP-ribosylation of the endonuclease protein was not observed. When 100 ng of the poly(ADP-ribose) having four to five ADP-ribose units per molecule were added to the nuclease assay system (total volume of 0.2 ml) 14% inhibition was observed, and increase in the chain length increased the inhibition. When 100 ng of poly(ADP-ribose) consisting of 20 or more units of the ADP-ribose per mol were added, the inhibition was over 95%. The possible role of the poly(ADP-ribose)-sensitive endonuclease is discussed.     

Characterization of an endonuclease activity associated with Friend-murine leukemia virus

An endonuclease activity shown to be associated with Friend leukemia virus has been characterized using double-stranded phi X174 DNA as substrate. In the presence of Mg2+, the endonuclease activity was able to convert supercoiled circular DNA duplexes to the relaxed form by introducing single-stranded nicks into the DNA. Most of the nicked DNA duplexes contained only one nick per strand, since unit length DNA was the predominant species obtained when the nicked DNA was analyzed by alkaline sucrose gradient centrifugation. The regions into which the nick could be introduced were evenly distributed around the circular DNA molecule. When Mn2+ was substituted for Mg2+ in the reaction mixture, the number of nicks introduced into circular DNA duplexes by the virus associated endonuclease was greatly increased. In contrast to circular duplexes, linear duplexes and single-stranded DNA functioned poorly as substrates for the virus-associated enzyme. The Friend leukemia virus-associated endonuclease activity is with respect to these characteristics very similar to the endonuclease activity associated with the p32 protein of the avian myeloblastosis virus [1]. The molecular weight of the Friend leukemia virus endonuclease was estimated by gel filtration on a Sephacryl S-200 column to be about 45 000.     

Isolation, characterization, and activation of the magnesium dependent endodeoxyribonuclease from Bacillus subtilis.

A major endodeoxyribonulcease was isolated from a mutant of the transformable Bacillus subtilis 168. The magnesium-dependent endonuclease was purified approximately 750-fold to electrophoretic homogeneity. The enzyme had a molecular weight of about 31 000, as determined by gel filtration and polyacrylamide gel electrophoresis. The protein appears to be composed of two subunits. The nuclease was dependent on magnesium or maganese ions for hydrolytic activity. The purified nuclease degraded DNA from several species of Bacillus, as well as Escherichia coli DNA, alkylated, depurinated, and thymine-dimer containing B. subtilis DNA, and hydroxymethyluracil-containing phage DNA. The enzyme also hydrolyzed single-stranded DNA, although native DNA was the preferred substrate. However, the nuclease was unable to degrade ribosomal RNA. The cleavage products of the DNA hydrolysis have 5'-phosphate and 3'-hydroxyl ends. The enzyme could be activated in crude extracts by heat treatment or treatment with guanidine hydrochloride. The nuclease activity was inhibited by phosphate and by high concentrations of NaCl. A possible function for this endonuclease in bacterial transformation is discussed.     

Endonuclease activity in nuclei of Physarum polycephalum. Partial purification and characterization.

An endonuclease, present in the microplasmodia of Physarum polycephalum, has been partially purified from isolated nuclei by DEAE-cellulose and Sephadex G-75 chromatography. 1. The endonuclease produced single-strand scissions in double-stranded DNA which resulted in the generation of 5'-phosphoryl and 3'-hydroxyl termini. No activity was observed with single-stranded DNA as substrate. 2. The pH optimum was approximately 8.5. 3. Divalent cations were essential for enzyme activity. MnCl2 and MgCl2 gave maximal activity. CaCl2, ZnCl2 or CoCl2 did not activate the enzyme. 4. The endonuclease activity was highly sensitive to monovalent cations. 5. Endonuclease activity was found in two forms after gel filtration: an activity in a homogeneous peak with a molecular weight of approx. 20 000, and an activity that had a heterogeneous molecular weight and which was isolated in a complex with DNA. A possible function of the endonuclease in DNA replication is discussed.