escherichia coli dna polymerase i  (New England Biolabs)


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    Name:
    DNA Polymerase I E coli
    Description:
    DNA Polymerase I E coli 2 500 units
    Catalog Number:
    m0209l
    Price:
    277
    Size:
    2 500 units
    Category:
    DNA Polymerases
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    New England Biolabs escherichia coli dna polymerase i
    DNA Polymerase I E coli
    DNA Polymerase I E coli 2 500 units
    https://www.bioz.com/result/escherichia coli dna polymerase i/product/New England Biolabs
    Average 99 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    escherichia coli dna polymerase i - by Bioz Stars, 2020-05
    99/100 stars

    Images

    1) Product Images from "DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide"

    Article Title: DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms150713111

    DSBs ( a ) and SSBs ( b – d ) generated in presence of Top2 ( a ); ETO ( b ); Top1 ( c ); and DNA-damaging agents that modify the DNA termini ( d ). Red arrow represents successful nick translation. Stop sign represents unsuccessful nick translation. Nick translation by DNA polymerase I necessitates a 3'-OH, which is not reconstituted in case of Top1 cleavage or when the DNA termini is damaged (shown by asterisk). In these cases the principal enzymes involved in processing and repair of the ends are listed below the black arrow. TDP1, tyrosyl-DNA phosphodiesterase 1, PNKP, polynucleotide kinase 3'-phosphatase, APE1, AP endonuclease I [ 17 ]
    Figure Legend Snippet: DSBs ( a ) and SSBs ( b – d ) generated in presence of Top2 ( a ); ETO ( b ); Top1 ( c ); and DNA-damaging agents that modify the DNA termini ( d ). Red arrow represents successful nick translation. Stop sign represents unsuccessful nick translation. Nick translation by DNA polymerase I necessitates a 3'-OH, which is not reconstituted in case of Top1 cleavage or when the DNA termini is damaged (shown by asterisk). In these cases the principal enzymes involved in processing and repair of the ends are listed below the black arrow. TDP1, tyrosyl-DNA phosphodiesterase 1, PNKP, polynucleotide kinase 3'-phosphatase, APE1, AP endonuclease I [ 17 ]

    Techniques Used: Generated, Nick Translation

    2) Product Images from "DNA Polymerase I Is Essential for Growth of Methylobacterium dichloromethanicum DM4 with Dichloromethane"

    Article Title: DNA Polymerase I Is Essential for Growth of Methylobacterium dichloromethanicum DM4 with Dichloromethane

    Journal: Journal of Bacteriology

    doi:

    DNA polymerase I activity of wild-type M. dichloromethanicum DM4 and of the polA mutant. Shown is an autoradiogram of cell extract protein (100 μg) of wild-type strain DM4 (lane 1), mutant DM4-1445 (lane 2), and complemented mutant DM4-1445(pME8112) (lane 3), separated by SDS-PAGE in a gel containing nicked DNA, after incubation with dideoxynucleotides and α- 32 P-labeled dCTP (see Materials and Methods). Lane M, prestained marker from the scanned gel; lanes 4 and 5, E. coli DNA polymerase I and Klenow fragment, respectively (0.02 U [∼0.1 ng] each).
    Figure Legend Snippet: DNA polymerase I activity of wild-type M. dichloromethanicum DM4 and of the polA mutant. Shown is an autoradiogram of cell extract protein (100 μg) of wild-type strain DM4 (lane 1), mutant DM4-1445 (lane 2), and complemented mutant DM4-1445(pME8112) (lane 3), separated by SDS-PAGE in a gel containing nicked DNA, after incubation with dideoxynucleotides and α- 32 P-labeled dCTP (see Materials and Methods). Lane M, prestained marker from the scanned gel; lanes 4 and 5, E. coli DNA polymerase I and Klenow fragment, respectively (0.02 U [∼0.1 ng] each).

    Techniques Used: Activity Assay, Mutagenesis, SDS Page, Incubation, Labeling, Marker

    Related Articles

    Clone Assay:

    Article Title: Unique Substrate Spectrum and PCR Application of Nanoarchaeum equitans Family B DNA Polymerase ▿
    Article Snippet: .. Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans . ..

    Amplification:

    Article Title: Enhanced Protocol for Determining the 3? Terminus of Hepatitis C Virus
    Article Snippet: .. Fifth, the first round of PCR amplification was tried with different DNA polymerases, including rTth XL, DyNAzyme EXT, Vent (New England Biolabs), DeepVent (New England Biolabs) and Phusion High-Fidelity (New England Biolabs). ..

    Incubation:

    Article Title: DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide
    Article Snippet: .. 500 μg of DNA was incubated for 40 s at 16 °C with a mixture of 200 μM of dATP, dGTP, dCTP and 20 μM of digoxigenin-11-dUTP (Roche), 117 μM of ddATP, ddGTP, ddCTP (Roche) and 1000 units of Escherichia coli DNA Polymerase I (New England Biolabs, Ipswich, MA, USA). .. As a control for labeling, 500 μg of DNA was incubated with the same reagents except digoxigenin-11-dUTP was substituted by 20 μM of dTTP.

    other:

    Article Title: Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69
    Article Snippet: The T4 genomic region that specifies DNA polymerase and the DNA polymerase accessory proteins (T4 gene 46-43 cluster [Fig. ]) is known to include three types of genetic elements: structural genes for essential replication proteins (gp46, gp45, gp44/62, and gp43), structural genes for seemingly nonessential regulatory proteins (RpbA and RegA), and untranslated intercistronic nucleotide sequences that harbor signals for transcriptional and posttranscriptional regulation of the structural genes ( ).

    Article Title: Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69
    Article Snippet: For example, in the T4 system, differential overproduction of DNA polymerase by translational-operator-constitutive mutations ( , ) or polymerase accessory proteins by regA mutations ( ) is consistent with normal levels of DNA replication and phage production.

    Expressing:

    Article Title: Unique Substrate Spectrum and PCR Application of Nanoarchaeum equitans Family B DNA Polymerase ▿
    Article Snippet: .. Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans . ..

    Polymerase Chain Reaction:

    Article Title: Enhanced Protocol for Determining the 3? Terminus of Hepatitis C Virus
    Article Snippet: .. Fifth, the first round of PCR amplification was tried with different DNA polymerases, including rTth XL, DyNAzyme EXT, Vent (New England Biolabs), DeepVent (New England Biolabs) and Phusion High-Fidelity (New England Biolabs). ..

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    New England Biolabs dna polymerase
    End protection by <t>DNA</t> ligase IV–XRCC4 protein can occur in the absence of DNA end joining. Protein extracts (40 µg) prepared from control lymphoblastoid cell lines, AHH1 and Nalm-6, the LIG4 syndrome cell line LB2304 and the LIG4 -null cell line N114P2 were incubated with a <t>non-ligatable</t> 5′- 32 P-end-labeled substrate (20 ng). Recombinant DNA ligase IV–XRCC4 (180 ng) was added where shown. Product formation was analyzed by agarose gel electrophoresis followed by autoradiography.
    Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 389 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna polymerase/product/New England Biolabs
    Average 99 stars, based on 389 article reviews
    Price from $9.99 to $1999.99
    dna polymerase - by Bioz Stars, 2020-05
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    End protection by DNA ligase IV–XRCC4 protein can occur in the absence of DNA end joining. Protein extracts (40 µg) prepared from control lymphoblastoid cell lines, AHH1 and Nalm-6, the LIG4 syndrome cell line LB2304 and the LIG4 -null cell line N114P2 were incubated with a non-ligatable 5′- 32 P-end-labeled substrate (20 ng). Recombinant DNA ligase IV–XRCC4 (180 ng) was added where shown. Product formation was analyzed by agarose gel electrophoresis followed by autoradiography.

    Journal: Nucleic Acids Research

    Article Title: Impact of DNA ligase IV on the fidelity of end joining in human cells

    doi:

    Figure Lengend Snippet: End protection by DNA ligase IV–XRCC4 protein can occur in the absence of DNA end joining. Protein extracts (40 µg) prepared from control lymphoblastoid cell lines, AHH1 and Nalm-6, the LIG4 syndrome cell line LB2304 and the LIG4 -null cell line N114P2 were incubated with a non-ligatable 5′- 32 P-end-labeled substrate (20 ng). Recombinant DNA ligase IV–XRCC4 (180 ng) was added where shown. Product formation was analyzed by agarose gel electrophoresis followed by autoradiography.

    Article Snippet: To generate a non-ligatable substrate, a single nucleotide (dTTP) was incorporated using DNA polymerase I large Klenow fragment (New England Biolabs).

    Techniques: Incubation, Labeling, Recombinant, Agarose Gel Electrophoresis, Autoradiography

    Overview of the nonhomologous random recombination (NRR) method. (A) Starting DNA sequences are randomly digested with DNase I, blunt-ended with T4 DNA polymerase, and recombined with T4 DNA ligase under conditions that strongly favor intermolecular ligation over intramolecular circularization. (B) A defined stoichiometry of hairpin DNA added to the ligation reaction controls the average length of the recombined products. The completed ligation reaction is digested with a restriction endonuclease to provide a library of double-stranded recombined DNA flanked by defined primer-binding sequences.

    Journal: Nature biotechnology

    Article Title: Nucleic acid evolution and minimization by nonhomologous random recombination

    doi: 10.1038/nbt736

    Figure Lengend Snippet: Overview of the nonhomologous random recombination (NRR) method. (A) Starting DNA sequences are randomly digested with DNase I, blunt-ended with T4 DNA polymerase, and recombined with T4 DNA ligase under conditions that strongly favor intermolecular ligation over intramolecular circularization. (B) A defined stoichiometry of hairpin DNA added to the ligation reaction controls the average length of the recombined products. The completed ligation reaction is digested with a restriction endonuclease to provide a library of double-stranded recombined DNA flanked by defined primer-binding sequences.

    Article Snippet: Restriction endonucleases, T4 DNA ligase, Vent DNA polymerase, T4 polynucleotide kinase, and T4 DNA polymerase were obtained from New England Biolabs (Beverly, MA).

    Techniques: Ligation, Binding Assay

    Amino acid sequence alignment, corresponding to residues 1 to 147 of Neq DNA polymerase of archaeal family B DNA polymerases. Multiple alignments were produced using the AlignX software (Invitrogen): Tko, Thermococcus kodakarensis KOD1 (GenBank accession number TK0001); Tfu, Thermococcus fumicolans (CAA93738); Tgo, Thermococcus gorgonarius (P56689); Tli, Thermococcus litoralis (AAA72101); Pfu, Pyrococcus furiosus (PF0212); Pwo, Pyrococcus woesei (P61876); Neq, Nanoarchaeum equitans (NEQ068). Shaded amino acid residues indicate identical and conserved residues in those DNA polymerases. The amino acid residues indicated by asterisks comprise the uracil-binding pocket of Tgo ). To assist in recognizing obvious differences of amino acids concerning the uracil-binding pocket, nonidentical residues of Neq DNA polymerase are rounded with rectangle borders.

    Journal: Applied and Environmental Microbiology

    Article Title: Unique Substrate Spectrum and PCR Application of Nanoarchaeum equitans Family B DNA Polymerase ▿

    doi: 10.1128/AEM.00624-08

    Figure Lengend Snippet: Amino acid sequence alignment, corresponding to residues 1 to 147 of Neq DNA polymerase of archaeal family B DNA polymerases. Multiple alignments were produced using the AlignX software (Invitrogen): Tko, Thermococcus kodakarensis KOD1 (GenBank accession number TK0001); Tfu, Thermococcus fumicolans (CAA93738); Tgo, Thermococcus gorgonarius (P56689); Tli, Thermococcus litoralis (AAA72101); Pfu, Pyrococcus furiosus (PF0212); Pwo, Pyrococcus woesei (P61876); Neq, Nanoarchaeum equitans (NEQ068). Shaded amino acid residues indicate identical and conserved residues in those DNA polymerases. The amino acid residues indicated by asterisks comprise the uracil-binding pocket of Tgo ). To assist in recognizing obvious differences of amino acids concerning the uracil-binding pocket, nonidentical residues of Neq DNA polymerase are rounded with rectangle borders.

    Article Snippet: Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans .

    Techniques: Sequencing, Produced, Software, Binding Assay

    Diagrammatic representation of λZAPII genomic library screening for RB69 DNA fragments (A) and partial restriction maps of the gene 46-43 regions of T4 and RB69 (B). Endonucleases Dra I and Ssp ). The solid horizontal bars designated PBS3K1, SP101, and SPR45-5 (A) represent 32 P-labeled riboprobes that were used to identify recombinant plasmids carrying the DNA fragments PBY16, PBS3, and LY6, respectively (see Materials and Methods). The SP101 probe corresponds to an internal Ssp I fragment of RB69 gene 43 , PBS3K1 corresponds to a Kpn I deletion of PBS3, and SPR45-5 corresponds to a 3′-terminal gene 45 segment that was generated from purified RB69 phage DNA by PCR amplification. ▿ in panel A denotes a terminal deletion for the respective gene. Restriction site abbreviations in panel B: H, Hin dIII; Sa, Sal I; Sc, Sac I; P, Pst I.

    Journal: Journal of Bacteriology

    Article Title: Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69

    doi:

    Figure Lengend Snippet: Diagrammatic representation of λZAPII genomic library screening for RB69 DNA fragments (A) and partial restriction maps of the gene 46-43 regions of T4 and RB69 (B). Endonucleases Dra I and Ssp ). The solid horizontal bars designated PBS3K1, SP101, and SPR45-5 (A) represent 32 P-labeled riboprobes that were used to identify recombinant plasmids carrying the DNA fragments PBY16, PBS3, and LY6, respectively (see Materials and Methods). The SP101 probe corresponds to an internal Ssp I fragment of RB69 gene 43 , PBS3K1 corresponds to a Kpn I deletion of PBS3, and SPR45-5 corresponds to a 3′-terminal gene 45 segment that was generated from purified RB69 phage DNA by PCR amplification. ▿ in panel A denotes a terminal deletion for the respective gene. Restriction site abbreviations in panel B: H, Hin dIII; Sa, Sal I; Sc, Sac I; P, Pst I.

    Article Snippet: The T4 genomic region that specifies DNA polymerase and the DNA polymerase accessory proteins (T4 gene 46-43 cluster [Fig. ]) is known to include three types of genetic elements: structural genes for essential replication proteins (gp46, gp45, gp44/62, and gp43), structural genes for seemingly nonessential regulatory proteins (RpbA and RegA), and untranslated intercistronic nucleotide sequences that harbor signals for transcriptional and posttranscriptional regulation of the structural genes ( ).

    Techniques: Library Screening, Labeling, Recombinant, Generated, Purification, Polymerase Chain Reaction, Amplification

    Complementation between phage-encoded and plasmid-encoded T4 and RB69 DNA polymerase accessory proteins. The abilities of polymerase accessory proteins to be functionally exchanged between T4 and RB69 were examined by burst size measurements (Materials and Methods) and qualitative spot tests. (A) Results of plasmid-phage complementation tests involving gene 45 and genes 44 and 62 together; (B and C) results of similar tests involving genes 44 and 62 separately. In the “Spot test” blocks, each pair of spots represents growth responses (cell lysis) from 5 μl of two phage concentrations, ∼10 4 and ∼10 7 /ml, respectively. Numbers shown in parentheses in the “Relative burst size” blocks are the actual bursts corresponding to the 1.0 reference values for the pairs of infections compared. Note that although the T4 and RB69 counterparts of gp45 and the gp44/62 complex can exchange effectively, with some preferences by the gene functions to support replication of the phage from which they originated (values in panel A), the gp44(RB69)/gp62(T4) combination is largely inactive for phage replication (C). Also note that plasmid-expressed wild-type (wt) RB69 gene 44 is inhibitory to replication of wild-type T4 (T4 wt phage on pRB69g44-bearing host [B]).

    Journal: Journal of Bacteriology

    Article Title: Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69

    doi:

    Figure Lengend Snippet: Complementation between phage-encoded and plasmid-encoded T4 and RB69 DNA polymerase accessory proteins. The abilities of polymerase accessory proteins to be functionally exchanged between T4 and RB69 were examined by burst size measurements (Materials and Methods) and qualitative spot tests. (A) Results of plasmid-phage complementation tests involving gene 45 and genes 44 and 62 together; (B and C) results of similar tests involving genes 44 and 62 separately. In the “Spot test” blocks, each pair of spots represents growth responses (cell lysis) from 5 μl of two phage concentrations, ∼10 4 and ∼10 7 /ml, respectively. Numbers shown in parentheses in the “Relative burst size” blocks are the actual bursts corresponding to the 1.0 reference values for the pairs of infections compared. Note that although the T4 and RB69 counterparts of gp45 and the gp44/62 complex can exchange effectively, with some preferences by the gene functions to support replication of the phage from which they originated (values in panel A), the gp44(RB69)/gp62(T4) combination is largely inactive for phage replication (C). Also note that plasmid-expressed wild-type (wt) RB69 gene 44 is inhibitory to replication of wild-type T4 (T4 wt phage on pRB69g44-bearing host [B]).

    Article Snippet: The T4 genomic region that specifies DNA polymerase and the DNA polymerase accessory proteins (T4 gene 46-43 cluster [Fig. ]) is known to include three types of genetic elements: structural genes for essential replication proteins (gp46, gp45, gp44/62, and gp43), structural genes for seemingly nonessential regulatory proteins (RpbA and RegA), and untranslated intercistronic nucleotide sequences that harbor signals for transcriptional and posttranscriptional regulation of the structural genes ( ).

    Techniques: Plasmid Preparation, Lysis

    Nucleotide sequences of the T4 and RB69 gene 44-62 junctures (A) and expression of cloned gene 62 from RB69 and T4 (B). (A) Open reading frames for genes 44 and 62 , which are separated by one base pair at the g 44-62 ). No such structure can be predicted for RB69. (B) Results of plasmid-mediated expression of comparable genomic segments encompassing the gene 45-62 intervals from T4 mutant 44amN82 and RB69 mutant 44am51 . The desired DNA segments were PCR amplified from the respective phage mutants as well as wild-type strains and cloned in λpLN vector, and their plasmid-mediated expression was subsequently analyzed in E. coli CAJ70 as described in Materials and Methods. The short arrows mark the positions of gp45, gp44, and gp62 bands on the SDS-PAGE autoradiogram (10% gel) from the experiment; dots mark the positions of gp44 amber fragments. Note that expression of gene 62 (from either T4 or RB69) is lower when DNA from gene 44 amber mutants is used than with DNA carrying the wild-type gene 44 alleles.

    Journal: Journal of Bacteriology

    Article Title: Divergence of a DNA Replication Gene Cluster in the T4-Related Bacteriophage RB69

    doi:

    Figure Lengend Snippet: Nucleotide sequences of the T4 and RB69 gene 44-62 junctures (A) and expression of cloned gene 62 from RB69 and T4 (B). (A) Open reading frames for genes 44 and 62 , which are separated by one base pair at the g 44-62 ). No such structure can be predicted for RB69. (B) Results of plasmid-mediated expression of comparable genomic segments encompassing the gene 45-62 intervals from T4 mutant 44amN82 and RB69 mutant 44am51 . The desired DNA segments were PCR amplified from the respective phage mutants as well as wild-type strains and cloned in λpLN vector, and their plasmid-mediated expression was subsequently analyzed in E. coli CAJ70 as described in Materials and Methods. The short arrows mark the positions of gp45, gp44, and gp62 bands on the SDS-PAGE autoradiogram (10% gel) from the experiment; dots mark the positions of gp44 amber fragments. Note that expression of gene 62 (from either T4 or RB69) is lower when DNA from gene 44 amber mutants is used than with DNA carrying the wild-type gene 44 alleles.

    Article Snippet: The T4 genomic region that specifies DNA polymerase and the DNA polymerase accessory proteins (T4 gene 46-43 cluster [Fig. ]) is known to include three types of genetic elements: structural genes for essential replication proteins (gp46, gp45, gp44/62, and gp43), structural genes for seemingly nonessential regulatory proteins (RpbA and RegA), and untranslated intercistronic nucleotide sequences that harbor signals for transcriptional and posttranscriptional regulation of the structural genes ( ).

    Techniques: Expressing, Clone Assay, Plasmid Preparation, Mutagenesis, Polymerase Chain Reaction, Amplification, SDS Page