dnapol i  (New England Biolabs)


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    Structured Review

    New England Biolabs dnapol i
    Dnapol I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 87 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnapol i - by Bioz Stars, 2020-04
    87/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: Paragraph title: Cloning of dsRNAs through cDNA library construction and primer walking ... The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min.

    Amplification:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The clones showing an amplicon of at least 200 bp were selected for plasmid purification and sequencing, and the cDNA sequences obtained were analyzed and assembled.

    Ligation:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The ligation mixture was used to transform E. coli DH5α cells using electroporation, and the white colonies that developed on the LB-amp-XGal plates were analyzed by colony-PCR with the vector primers M13F and M13R.

    Chromosome Walking:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: Paragraph title: Cloning of dsRNAs through cDNA library construction and primer walking ... The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min.

    Purification:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The cDNAs were purified on Sephadex G-50 columns (GE Healthcare), mixed with EcoR V-digested pBluescript SK plasmid and 2 U of T4-DNA ligase, incubated at 15°C for 16 h, and dialyzed through a 0.025-μm pore nitrocellulose disk (Millipore).

    Synthesized:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: .. The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The cDNAs were purified on Sephadex G-50 columns (GE Healthcare), mixed with EcoR V-digested pBluescript SK plasmid and 2 U of T4-DNA ligase, incubated at 15°C for 16 h, and dialyzed through a 0.025-μm pore nitrocellulose disk (Millipore).

    cDNA Library Assay:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: Paragraph title: Cloning of dsRNAs through cDNA library construction and primer walking ... The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min.

    Incubation:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: Cloning of dsRNAs through cDNA library construction and primer walking A mixture of gel-purified dsRNAs (200–300 ng) and random hexanucleotide primers (200 ng) was incubated at 95°C for 10 min in the presence of 20% DMSO, chilled in an ice water bath and incubated at 25°C for 10 min. .. The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min.

    Sequencing:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The clones showing an amplicon of at least 200 bp were selected for plasmid purification and sequencing, and the cDNA sequences obtained were analyzed and assembled.

    Electroporation:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The ligation mixture was used to transform E. coli DH5α cells using electroporation, and the white colonies that developed on the LB-amp-XGal plates were analyzed by colony-PCR with the vector primers M13F and M13R.

    Plasmid Preparation:

    Article Title: Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous
    Article Snippet: The second cDNA strand was synthesized using 50 U of DNApol I (New England Biolabs) at 37°C for 120 min, followed by treatments with 2 U of T4-DNA ligase at 22°C for 30 min and 5 U of Klenow fragment at 37°C for 60 min. .. The cDNAs were purified on Sephadex G-50 columns (GE Healthcare), mixed with EcoR V-digested pBluescript SK plasmid and 2 U of T4-DNA ligase, incubated at 15°C for 16 h, and dialyzed through a 0.025-μm pore nitrocellulose disk (Millipore).

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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
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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