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apurinic DNA + H2O
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double-stranded DNA + H2O
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
FAM-labeled dsDNA + H2O
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Exo III catalyzes the stepwise removal of mononucleotides from the 3'-hydroxyl termini of double-stranded DNA (dsDNA). Development of a fluorescence detection method of Exo III activity, overview. Due to photoinduced electron transfer (PET) between FAM and guanine (G), the fluorescence of the FAMlabeled dsDNA probe is completely quenched. Upon the addition of Exo III, the dsDNA will be digested, and FAM emits very strong fluorescence. Thus, Exo III activity can be facilely measured with a simple fluorescence reader with a detection range from 5 x 10-4 U/ml to 5 U/ml with a detection limit of 3 x 10-4 U/ml. FAM is labeled on the 3' end. Optimization of experimental conditions, overview. HIgh selectivity of the assay for detection of Exo III activity compared to other nucleases
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PUC18 DNA PstI + H2O
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urea-containing DNA + H2O
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double-stranded DNA + H2O
additional information
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DNA + H2O
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the enzyme digests blunt-ended dsDNA successively. ssDNA remains almost completely intact. 3'-recessed dsDNA is digested in the same manner as blunt-ended dsDNA. 3'-protruding ended dsDNA shows resistance to degradation. The enzyme exhibits dsDNA-specific exonuclease activity from the 3' to 5' direction. A nick site in dsDNA and dsDNA with 3'-phosphate termini are also susceptible to digestion. The enzyme can exhibit exonuclease activity from a nick and possesses 3'-phosphomonoesterase activity. The limited length of the product is observed to be 11 nt. the enzyme may require at least 11-nt DNA for binding
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DNA + H2O
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the enzyme digests blunt-ended dsDNA successively. ssDNA remains almost completely intact. 3'-recessed dsDNA is digested in the same manner as blunt-ended dsDNA. 3'-protruding ended dsDNA shows resistance to degradation. The enzyme exhibits dsDNA-specific exonuclease activity from the 3' to 5' direction. A nick site in dsDNA and dsDNA with 3'-phosphate termini are also susceptible to digestion. The enzyme can exhibit exonuclease activity from a nick and possesses 3'-phosphomonoesterase activity. The limited length of the product is observed to be 11 nt. the enzyme may require at least 11-nt DNA for binding
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DNA duplex X1 + H2O
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MtbXthA possesses a 3'-5' exonuclease activity on 3' recessed duplex DNA, substrate is 5'-FAM peptide-labelled 3'-recessed DNA duplex substrate X1. The incubation of substrate X1 with restrictive concentration of purified MtbXthAalone resulted in only 11% cleavage generating shorter-labelled oligomers. The inclusion of beta-clamp in the reaction mixture substantially enhances the exonuclease activity
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DNA duplex X1 + H2O
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MtbXthA possesses a 3'-5' exonuclease activity on 3' recessed duplex DNA, substrate is 5'-FAM peptide-labelled 3'-recessed DNA duplex substrate X1. The incubation of substrate X1 with restrictive concentration of purified MtbXthAalone resulted in only 11% cleavage generating shorter-labelled oligomers. The inclusion of beta-clamp in the reaction mixture substantially enhances the exonuclease activity
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DNA duplex X1 + H2O
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MtbXthA possesses a 3'-5' exonuclease activity on 3' recessed duplex DNA, substrate is 5'-FAM peptide-labelled 3'-recessed DNA duplex substrate X1. The incubation of substrate X1 with restrictive concentration of purified MtbXthAalone resulted in only 11% cleavage generating shorter-labelled oligomers. The inclusion of beta-clamp in the reaction mixture substantially enhances the exonuclease activity
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double-stranded DNA + H2O
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double-stranded DNA + H2O
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double-stranded DNA + H2O
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double-stranded DNA + H2O
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exonuclease III and endonuclease IV remove 3'-blocks from DNA synthesis primers in H2O2-damaged E. coli
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double-stranded DNA + H2O
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the principal biological role is the repair of DNA damage produced by free radicals
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double-stranded DNA + H2O
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major apurinic/apyrimidinic DNA-repair endonuclease
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double-stranded DNA + H2O
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the enzyme is essential for the repair of uracil-containg DNA and apyrimidine sites
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double-stranded DNA + H2O
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the enzyme promotes in vitro binding of the replication initiator protein of plasmid pSC101 to the repeated sequences in the ori region
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double-stranded DNA + H2O
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the enzyme is used to simultaneously quantify various types of DNA modifications, which are induced by agents that generate reactive oxygen species
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double-stranded DNA + H2O
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the enzyme is required for stability of ColE1-related plasmids, pRSF2124 or pMB9, in E. coli. Any combination of exonuclease I, III and V deficiency results in dramatically decreased stability of the plasmids
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double-stranded DNA + H2O
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one of two pathways of repair for hydrogen peroxide-induced DNA damage utilizes exonuclease III and DNA polymerase I
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double-stranded DNA + H2O
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the enzyme is responsible for repair of many types of DNA damage that arise spontaneously under normal growth conditions
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double-stranded DNA + H2O
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bifunctional enzyme EC 2.7.7.7/EC 3.1.11.2. The polymerization and the 3'-5' exonuclease activity of a family B DNA polymerase can be ascribed to physically distinct modules of the enzyme molecule. The enzyme is able to catalyze the excision of mispaired nucleotides at the 3'OH terminus of a primer/template DNA substrate in the presence of Mn2+ ions
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
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the enzyme degrades the phosphodiester bond from the 3 end of double-stranded DNA
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
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the enzyme degrades the phosphodiester bond from the 3 end of double-stranded DNA
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
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the enzyme degrades the phosphodiester bond from the 3 end of double-stranded DNA, vinylphosphonate internucleotide linkages alter the cleavage specificity of enzyme
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
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exonuclease III does not require a specific recognition site, so cleavage occurs irrespective of the sequence present at the blunt terminus. Amplification provided by exonuclease III leads to a 10fold increase in the final fluorescence intensity observed at 37°C upon addition of 0.001 mM target
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double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
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immobilization of fully fluorescently labeled DNA on microarrays enables successive DNA degradation by exonuclease III. Degrades at average reaction rates that do not significantly differ from rates observed with homogeneous catalysis (i.e., in solution)
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N1 duplex DNA + H2O
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5'-FAM peptide-labelled AP DNA duplex substrate
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N1 duplex DNA + H2O
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5'-FAM peptide-labelled AP DNA duplex substrate
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N1 duplex DNA + H2O
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5'-FAM peptide-labelled AP DNA duplex substrate
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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double-stranded DNA + H2O
additional information
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the size of the products after 3'-5' hydrolysis is temperature-dependent. At 25°C the enzyme can hydrolyze a polynucleotide chain up to the last 5'-terminal dinucleotide. A gradation of higher 5'-terminal oligonucleotides of defined chain lengths is produced after limit digestion by the enzyme when the temperature is raised from 25°C to 60°C
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double-stranded DNA + H2O
additional information
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3'-phosphoryl-terminated DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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sonicated T7 DNA
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double-stranded DNA + H2O
additional information
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heat-denatured E. coli DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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heat-denatured E. coli DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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native T7 DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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3'-hydroxyl-terminated DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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dAT copolymer
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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dAT copolymer
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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C-residues are cleaved off rapidly and G-residues slowly, while A and T are released at an intermediate rate
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double-stranded DNA + H2O
additional information
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native T2 DNA, weak activity
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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double stranded DNA
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double-stranded DNA + H2O
additional information
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double stranded DNA
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double-stranded DNA + H2O
additional information
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double stranded DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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PstI + XbaI linearized pUC18 DNA
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double-stranded DNA + H2O
additional information
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native E. coli DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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native E. coli DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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apurinic DNA
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double-stranded DNA + H2O
additional information
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can produce double-strand breaks in heavily alkylated DNA
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double-stranded DNA + H2O
additional information
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recognizes apurinic sites, reduced apurinic sites, urea and O-alkylhydroxylamine residues of PM2 DNA
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double-stranded DNA + H2O
additional information
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attacks double-stranded DNA, degrading it to mononucleotides to an extent of 45-50%
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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some four nucleotide 3'-protrusions are sensitive to digestion
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double-stranded DNA + H2O
additional information
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native Bacillus subtilis DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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native Bacillus subtilis DNA
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
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double-stranded DNA + H2O
additional information
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the enzyme stalls 4-5 bases 3' to DNA bonding site of the two pyrrolobenzodiazepine derivatives - tomamycin and anthramycin
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double-stranded DNA + H2O
additional information
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recognition spectrum: regular, 1'-oxidized and 4'-oxidized apurinic/apyrimidinic sites
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double-stranded DNA + H2O
additional information
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exonuclease III stops one base away from the cyclobutane pyrimidine dimers
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double-stranded DNA + H2O
additional information
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at 5°C in a high salt concentration and a ratio of enzyme to DNA 3'-terminus of one, the enzyme catalyzes the hydrolysis of approximately six nucleotides from each 3'-terminus of the duplex DNA. When the ratio of exonuclease to DNA 3'-terminus is increased to two approximately 12 nucleotides are hydrolyzed from each 3'-terminus
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double-stranded DNA + H2O
additional information
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hydrolyzes the phosphodiester bond 5'- to O-alkylhydroxylamine residue
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double-stranded DNA + H2O
additional information
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up to 40% degradation, residual single stranded chains are resistant
5'-mononucleotides + phosphate + large molecular weight single stranded oligonucleotides
?
double-stranded DNA + H2O
additional information
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heat-denatured E. coli DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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native T7 DNA
5'-mononucleotides
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double-stranded DNA + H2O
additional information
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dAT copolymer
5'-mononucleotides
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additional information
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the enzyme participates in base excision repair and resistance to oxidative killing in Brucella abortus 2308, it is not required for wild-type virulence of this strain in the mouse model
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additional information
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the enzyme possesses strong apurinic/apyrimidinic endonuclease and 3'-diesterase activity, no significant level of 3'-5' exonuclease activity following incision at apurinic/apyrimidinic site
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additional information
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activities exhibited by the enzyme: 1. 3'-5'-exonuclease activity, 2. apurinic/apyrimidinic DNA-repair endonuclease, 3. 3'-repair diesterase, 4. 3'-phosphomonoesterase, 5. ribonuclease
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additional information
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double-strand specific 3'-5'exodeoxyribonuclease
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additional information
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reactions catalyzed by exonuclease III: 1. double-stranded-specific 3'-5' exonuclease activity, 2. removal of a number of 3'-termini from double-stranded DNA, 3. apurinic/apyrimidinic endonuclease, 5. endonucleolytic attack at urea-N-glycoside in double-stranded DNA, 4. Rnase H activity, selectively degrades the RNA strand in RNA-DNA hybrid duplexes
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additional information
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endonucleolytic activity against apurinic DNA and against urea residues, nicking on the 5'-side of the damage
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additional information
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enzyme does not have endonucleolytic activity at depurinated reduced sites or at alkylated sites in DNA
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additional information
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the enzyme can cleave a single or two consecutive ribonucleotides from base-paired or mismatched ribonucleotides
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additional information
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phosphatase activity: release of inorganic phosphate from 3'-phosphoryl terminated deoxyribonucleic acid
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additional information
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no hydrolysis of single-stranded short oligonucleotides, ribosomal ribonucleic acid, or the double-stranded adenylate-uridylate copolymer
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additional information
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the enzyme is a major AP endonuclease activity that is involved in efficient repair of oxidative lesions in bacterial DNA
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additional information
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exonucleae III plays a relevant role against DNA damage induced by oxidative counterpart of UVB radiation
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additional information
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the enzyme is involved in repair of oxidized abasic sites
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additional information
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TRp212 of ExoIII is critical to the apurinic/apyrimidinic endonuclease activity of exonuclease III and binding to DNA containing a apurinic/apyrimidinic site
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additional information
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Exo III catalyzes stepwise removal of mononucleotides from blunt or recessed 3'-hydroxyl termini of duplex DNA, while it is not active on single-stranded DNA or 3'-protruding termini of double-stranded DNA. Different from restriction enzymes, Exo III does not require any specific enzymatic recognition sequence to function
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additional information
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Exo III has a specifical exo-deoxyribonuclease activity for duplex DNAs in the direction from 3' to 5' terminus, however its activity on the duplex DNAs with 3'-overhang and single-strand DNA is limited
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additional information
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Exo III specifically digests double-stranded DNA from 3'-OH blunt or recessed end, while it exhibits less activity on single-stranded DNA or 3'-protruding termini of double-stranded DNA
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additional information
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design of a E-DNA sensor such that, in the presence of target DNA, the electrode self-assembled signaling probe hybridizes with the target DNA to form a duplex in the form of a 3'-blunt end at signaling probe and a 3'-overhang end at target DNA. In this way, Exo III specifically recognizes this structure and selectively digests the signaling probe. As a result, the target DNA dissociates from the duplex and recycles to hybridize with a new signaling probe, leading to the digestion of a large amount of signaling probes gradually, method development and mechanism, overview. The E-DNA sensor has an excellent differentiation ability for single mismatches with fairly good stability
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additional information
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development and evaluation of a more versatile target assisted Exo III-catalyzed amplification fluorescence polarization, TAECA-FP, methodology for the highly sensitive and selective detection of DNA, overview. Achievement of limits of detection of 83 aM target DNA and single-base mismatch differentiation,
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additional information
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development of a homogeneous, colorimetric DNA detection method, that is simple, low-cost, sensitive and selective, and consists of Exo III, a linker DNA, and two DNA-modified gold nanoparticles, overview. The target sequence-independent platform is generally applicable for DNA sensing
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additional information
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development of a label-free assay for the in vitro determination of double-stranded DNA-specific 3'-5' exonuclease, 35dsExo, activity possessing the high sensitivity and high-throughput potential of an established pyrosequencing protocol, overview
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additional information
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optimization of sequence analysis system using the enzyme with linear molecular beacons, i.e. linear oligonucleotide probes with a fluorophore and quencher attached to 3' terminal and penultimate nucleotides, respectively, in Exo III amplification assays to improve hybridization kinetics and reduce background noises, overview
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additional information
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XthA exonuclease converts the blunt ends of double-stranded DNA to 5' protruding ends in the process of in vivo cloning. After the insert and the vector DNA fragments are introduced into the Escherichia coli cell, XthA resects the ends of the DNA fragments from the 3'-to-5' direction, producing 5' overhanging ends. As the ends of insert and vector DNAs have mutually complementary sequences, the 5' overhanging ends of the insert and the vector DNA fragments hybridize to each other as cohesive ends. In addition, the gaps are filled by DNA polymerases and the nicks are repaired by DNA ligases
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additional information
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XthA exonuclease converts the blunt ends of double-stranded DNA to 5' protruding ends in the process of in vivo cloning. After the insert and the vector DNA fragments are introduced into the Escherichia coli cell, XthA resects the ends of the DNA fragments from the 3'-to-5' direction, producing 5' overhanging ends. As the ends of insert and vector DNAs have mutually complementary sequences, the 5' overhanging ends of the insert and the vector DNA fragments hybridize to each other as cohesive ends. In addition, the gaps are filled by DNA polymerases and the nicks are repaired by DNA ligases
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additional information
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XthA, also known as exodeoxyribonuclease III, exhibits 3' to 5' exonuclease activity. The sbcA23 mutant of the Escherichia coli strain JC8679 is used for in vivo cloning, because the expression of RecE exonuclease and RecT recombinase of Rac prophage is activated in this mutant. Multiple fragment cloning by the host strain SN1187. The cat fragment and linearized pUC19 are used for the transformation of indicated strains
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additional information
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XthA, also known as exodeoxyribonuclease III, exhibits 3' to 5' exonuclease activity. The sbcA23 mutant of the Escherichia coli strain JC8679 is used for in vivo cloning, because the expression of RecE exonuclease and RecT recombinase of Rac prophage is activated in this mutant. Multiple fragment cloning by the host strain SN1187. The cat fragment and linearized pUC19 are used for the transformation of indicated strains
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additional information
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phosphatase activity: release of inorganic phosphate from 3'-phosphoryl terminated deoxyribonucleic acid
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additional information
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no hydrolysis of single-stranded short oligonucleotides, ribosomal ribonucleic acid, or the double-stranded adenylate-uridylate copolymer
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additional information
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detection of replicational activity in cells using 5-bromo-2'-deoxyuridine (BrdU), a low concentration of hydrochloric acid, and exonuclease III, method evaluation and optimization, detailed overview. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Already 5 to 10 mM HCl is sufficient for the detection of BrdU labelled DNA if exonuclease III is used. The method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing fluorescent ubiquitin cell cycle indicator (FUCCI). In the case of the short labelling pulses that disable the use of 5-ethynyl-2'-deoxyuridine because of the low specific signal, the described method provides a bright signal enabling reliable recognition of replicating cells. The optimized protocol is also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer
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additional information
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exonuclease III (ExoIII) is a sequence-independent 3'-5' exonuclease, that can catalyze the stepwise removal of mononucleotides from DNA duplexes in the direction from blunt or recessed 3'-termini to 5'-termini, while it is unable to catalyze the removal of bases from single-stranded DNA or DNA duplexes with a protruding 3' end. Establishment of a simple, sensitive, low-cost and label-free method to detect the activity of exonuclease III (Exo III) by using double-strand DNA (dsDNA)-templated copper nanoparticles as fluorescent probe. Design of the label-free fluorescent probe for Exo III activity detection. The sensing system contains two completely complementary nucleic acid strands, which are simply designed based on DNA hybridization. The hybridized dsDNA is introduced to act as both templates for CuNPs formation and substrate of Exo III. Fluorescent Cu nanoparticles (NPs) with maximum emission wavelength of 575 nm are formed by using double-strand DNA (dsDNA) as templates. Upon the addition of Exo III, the dsDNA templates are digested from 3' to 5', and the formation of fluorescent Cu-NPs is inhibited. Thus, the fluorescence intensity of dsDNA-Cu-NPs decreases. This method exhibits a low detection limit of 0.02 U/ml for Exo III. Compared with the previous reports, this method does not need complex DNA sequence design, fluorescence dye label and sophisticated experimental techniques, mechanism and method optimization, detailed overview
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additional information
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MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. Analysis of the 3? phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate. Enzyme substrate specificity analysis of 3'-5' exonuclease activity of MtbXthA using fluorescently labelled ssDNA X3, 3'-overhanging heteroduplex DNA X4, 3'-blunt DNA duplex X5, 3'-recessed heteroduplexDNA X1, and nicked DNA X2, detailed overview. MtbXthA exhibits the strongest exonuclease activity on a 3'-recessed end containing duplex DNA. No significant differences in the excision of the 16 3'-recessed duplex DNA substrates are found under the reaction conditions. These results show that MtbXthA does not differentiate between matched and mismatched base pairs. MtbXthA can effectively remove 3'-blocking termini
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additional information
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nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. Analysis of the 3? phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate. Enzyme substrate specificity analysis of 3'-5' exonuclease activity of MtbXthA using fluorescently labelled ssDNA X3, 3'-overhanging heteroduplex DNA X4, 3'-blunt DNA duplex X5, 3'-recessed heteroduplexDNA X1, and nicked DNA X2, detailed overview. MtbXthA exhibits the strongest exonuclease activity on a 3'-recessed end containing duplex DNA. No significant differences in the excision of the 16 3'-recessed duplex DNA substrates are found under the reaction conditions. These results show that MtbXthA does not differentiate between matched and mismatched base pairs. MtbXthA can effectively remove 3'-blocking termini
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?
additional information
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nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. Analysis of the 3? phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate. Enzyme substrate specificity analysis of 3'-5' exonuclease activity of MtbXthA using fluorescently labelled ssDNA X3, 3'-overhanging heteroduplex DNA X4, 3'-blunt DNA duplex X5, 3'-recessed heteroduplexDNA X1, and nicked DNA X2, detailed overview. MtbXthA exhibits the strongest exonuclease activity on a 3'-recessed end containing duplex DNA. No significant differences in the excision of the 16 3'-recessed duplex DNA substrates are found under the reaction conditions. These results show that MtbXthA does not differentiate between matched and mismatched base pairs. MtbXthA can effectively remove 3'-blocking termini
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?
additional information
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MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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additional information
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nicked DNA and gapped DNA are fair substrates of enzyme MtbXthA, the gap-size does not affect the excision activity, a substrate with a recessed 3'-end is preferred. Analysis of the 3? phosphatase and 3' phosphodiesterase activities of MtbXthA with a DNA substrate. Enzyme substrate specificity analysis of 3'-5' exonuclease activity of MtbXthA using fluorescently labelled ssDNA X3, 3'-overhanging heteroduplex DNA X4, 3'-blunt DNA duplex X5, 3'-recessed heteroduplexDNA X1, and nicked DNA X2, detailed overview. MtbXthA exhibits the strongest exonuclease activity on a 3'-recessed end containing duplex DNA. No significant differences in the excision of the 16 3'-recessed duplex DNA substrates are found under the reaction conditions. These results show that MtbXthA does not differentiate between matched and mismatched base pairs. MtbXthA can effectively remove 3'-blocking termini
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?
additional information
?
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MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
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?
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double-stranded DNA + H2O
?
additional information
?
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double-stranded DNA + H2O
?
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exonuclease III and endonuclease IV remove 3'-blocks from DNA synthesis primers in H2O2-damaged E. coli
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?
double-stranded DNA + H2O
?
-
the principal biological role is the repair of DNA damage produced by free radicals
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?
double-stranded DNA + H2O
?
-
major apurinic/apyrimidinic DNA-repair endonuclease
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?
double-stranded DNA + H2O
?
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the enzyme is essential for the repair of uracil-containg DNA and apyrimidine sites
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-
?
double-stranded DNA + H2O
?
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the enzyme promotes in vitro binding of the replication initiator protein of plasmid pSC101 to the repeated sequences in the ori region
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-
?
double-stranded DNA + H2O
?
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the enzyme is used to simultaneously quantify various types of DNA modifications, which are induced by agents that generate reactive oxygen species
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-
?
double-stranded DNA + H2O
?
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the enzyme is required for stability of ColE1-related plasmids, pRSF2124 or pMB9, in E. coli. Any combination of exonuclease I, III and V deficiency results in dramatically decreased stability of the plasmids
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?
double-stranded DNA + H2O
?
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one of two pathways of repair for hydrogen peroxide-induced DNA damage utilizes exonuclease III and DNA polymerase I
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?
double-stranded DNA + H2O
?
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the enzyme is responsible for repair of many types of DNA damage that arise spontaneously under normal growth conditions
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?
additional information
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the enzyme participates in base excision repair and resistance to oxidative killing in Brucella abortus 2308, it is not required for wild-type virulence of this strain in the mouse model
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?
additional information
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the enzyme is a major AP endonuclease activity that is involved in efficient repair of oxidative lesions in bacterial DNA
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?
additional information
?
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exonucleae III plays a relevant role against DNA damage induced by oxidative counterpart of UVB radiation
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?
additional information
?
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the enzyme is involved in repair of oxidized abasic sites
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?
additional information
?
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Exo III catalyzes stepwise removal of mononucleotides from blunt or recessed 3'-hydroxyl termini of duplex DNA, while it is not active on single-stranded DNA or 3'-protruding termini of double-stranded DNA. Different from restriction enzymes, Exo III does not require any specific enzymatic recognition sequence to function
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?
additional information
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-
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Exo III has a specifical exo-deoxyribonuclease activity for duplex DNAs in the direction from 3' to 5' terminus, however its activity on the duplex DNAs with 3'-overhang and single-strand DNA is limited
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?
additional information
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Exo III specifically digests double-stranded DNA from 3'-OH blunt or recessed end, while it exhibits less activity on single-stranded DNA or 3'-protruding termini of double-stranded DNA
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?
additional information
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XthA exonuclease converts the blunt ends of double-stranded DNA to 5' protruding ends in the process of in vivo cloning. After the insert and the vector DNA fragments are introduced into the Escherichia coli cell, XthA resects the ends of the DNA fragments from the 3'-to-5' direction, producing 5' overhanging ends. As the ends of insert and vector DNAs have mutually complementary sequences, the 5' overhanging ends of the insert and the vector DNA fragments hybridize to each other as cohesive ends. In addition, the gaps are filled by DNA polymerases and the nicks are repaired by DNA ligases
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?
additional information
?
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XthA exonuclease converts the blunt ends of double-stranded DNA to 5' protruding ends in the process of in vivo cloning. After the insert and the vector DNA fragments are introduced into the Escherichia coli cell, XthA resects the ends of the DNA fragments from the 3'-to-5' direction, producing 5' overhanging ends. As the ends of insert and vector DNAs have mutually complementary sequences, the 5' overhanging ends of the insert and the vector DNA fragments hybridize to each other as cohesive ends. In addition, the gaps are filled by DNA polymerases and the nicks are repaired by DNA ligases
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-
?
additional information
?
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MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
-
?
additional information
?
-
-
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
-
?
additional information
?
-
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
-
?
additional information
?
-
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. XthA forms in vivo and in vitro complexes with beta-clamp DNA, the DNA substrate mediates different interaction modes between XthA and the beta-clamp, mechanism and structure, detailed overview
-
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?
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evolution
in general, DNA recombination in Escherichia coli accompanies the conversion of double-stranded DNA to single-stranded DNA by exonuclease. It is reported that Escherichia coli has at least seven exonucleases that prefer double-stranded DNA for their substrates: XthA, RecE, ExoX, RecBCD, SbcCD, Nfo, and TatD. In addition, YgdG is an exonuclease with yet undetermined substrate preference. It seems likely that Escherichia coli K-12 originally acquired iVEC activity, and the iVEC activity was involved in an unknown physiological function in Escherichia coli
malfunction
deletion of the DNA polymerase domain of PolA does not completely abrogate iVEC activity
metabolism
involvement of DNA polymerases in in vivo cloning of Escherichia coli (iVEC) activity, analysis of iVEC activities of various strains, which are deletion mutants of nonessential polymerases in the Keio collection, overview. XthA plays a critical role in the iVEC activity
physiological function
Escherichia coli has an ability to assemble DNA fragments with homologous overlapping sequences of 15 to 40 bp at each end. In vivo cloning of Escherichia coli (iVEC) is independent of both RecA and RecET recombinases but is dependent on XthA, a 3' to 5' exonuclease. XthA resects the 3' ends of linear DNA fragments that are introduced into Escherichia coli cells, resulting in exposure of the single-stranded 5' overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I, molecular iVEC mechanism, overview. XthA helps to repair minor DNA damage, instead of the RecBCD exonuclease. RecBCD produces a 3' overhang and loads RecA onto the single-stranded DNA, causing an SOS response accompanied by cell division arrest. To help avoid such a serious outcome, it is conceivable that XthA functions in a repair pathway of DNA damage
physiological function
exonuclease III (Exo III) is a sequence-independent 3'-5' exonuclease
physiological function
exonuclease III (Exo III) plays crucial roles in maintaining the genome stability
physiological function
key enzyme involved in the repair of abasic sites and DNA strand breaks
physiological function
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
physiological function
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
physiological function
the enzyme is involved in uracil rapair pathway
physiological function
-
the enzyme is involved in uracil rapair pathway
-
physiological function
-
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
-
physiological function
-
key enzyme involved in the repair of abasic sites and DNA strand breaks
-
physiological function
-
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
-
physiological function
-
Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair. The enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5' exonuclease activity is predominant at low ionic environments
-
physiological function
-
MtbXthA is a versatile enzyme withAP endonuclease, 3'-5' exonuclease and 3' phosphodiesterase activities. the sliding DNA beta-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA-binding domain of XthA is found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of beta-clamp located on different domains interact with XthA. The beta-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. Addition of beta-clamp binding peptides disrupts the MtbXthA-clamp complex and inhibits clamp-dependent stimulation of MtbXthA, overview. The beta-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the beta-clamp onto DNA is required for activity stimulation. In the absence of DNA, the PBG located on the second domain of the beta-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. The C-terminal domain of beta-clamp predominantly mediates interactions with XthA in the presence of DNA
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additional information
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
-
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
additional information
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
additional information
-
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
additional information
-
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
-
additional information
-
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
-
additional information
-
enzyme residues E57 and D251 are critical for catalysis, molecular modelling and mutational analysis. Determinants of abasic-site recognition, overview. Homology modeling of MtbXthA using the structure of the Neisseria meningitidis protein (PDB ID 2JC4) as a template
-
additional information
-
the PIP motif mediates critical interactions between AP endonuclease and proliferating cell nuclear antigen (PCNA), both in vitro and in vivo. The PIP motif in PCNA-interacting proteins is a defined consensus sequence (QxxLxxFF), while the consensus sequence corresponding to the beta-clamp interacting motif in prokaryotes is relatively less conserved. Structure comparison of homodimeric mycobacterial beta-clamp and homotrimeric human PCNA, overview
-
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Exonucleases I, III, and V are required for stability of ColE1-related plasmids in Escherichia coli
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Mechanism of action of Escherichia coli exonuclease III
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Multiple pathways for repair of hydrogen peroxide-induced DNA damage in Escherichia coli
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Exonuclease III and endonuclease IV remove 3'-blocks from DNA synthesis primers in H2O2-damaged Escherichia coli
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Exonuclease III recognizes urea residues in oxidized DNA
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Cloning of the exonuclease III gene of Escherichia coli
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Exonuclease III from Escherichia coli
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Exonuclease III promotes in vitro binding of the replication initiator protein of plasmid pSC101 to the repeated sequences in the ori region
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Structure and function of the multifunctional DNA-repair enzyme exonuclease III
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Purification of eucaryotic extrachromosomal circular DNAs using exonuclease III
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Exonuclease III-generated series of homologous competitor DNA fragments for competitive PCR
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29
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Exonuclease III action on microarrays: Observation of DNA degradation by fluorescence correlation spectroscopy
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