apali restriction enzyme  (New England Biolabs)


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    Name:
    ApaLI
    Description:
    ApaLI 12 500 units
    Catalog Number:
    r0507l
    Price:
    269
    Size:
    12 500 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs apali restriction enzyme
    ApaLI
    ApaLI 12 500 units
    https://www.bioz.com/result/apali restriction enzyme/product/New England Biolabs
    Average 90 stars, based on 43 article reviews
    Price from $9.99 to $1999.99
    apali restriction enzyme - by Bioz Stars, 2020-04
    90/100 stars

    Images

    1) Product Images from "Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *"

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M109.058586

    Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Figure Legend Snippet: Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Techniques Used:

    Related Articles

    Clone Assay:

    Article Title: Hypotonicity Stimulates Potassium Flux through the WNK-SPAK/OSR1 Kinase Cascade and the Ncc69 Sodium-Potassium-2-Chloride Cotransporter in the Drosophila Renal Tubule *
    Article Snippet: Paragraph title: wnk Cloning ... The resultant product, as well as pENTR containing segment one, was then digested with ApaLI (New England Biolabs, Ipswich, MA) and ligated together to yield the final full-length wnk cDNA in pENTR.

    Article Title: High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Ig\u03ba/Ig\u03bb Loci Bearing the Rat CH Region
    Article Snippet: The resulting plasmid contains CEN4 cloned in between S. cerevisiae URA3 and a hygromycin-resistance expression cassette ( HygR ). .. From this plasmid, an ApaLI-BamHI fragment containing URA3 followed by CEN4 or a PmlI–SphI fragment containing CEN4 followed by HygR was cut out and ligated to ApaLI and BamHI or HpaI and SphI doubly digested pBACBelo11 (New England BioLabs) to yield pBelo-CEN-URA and pBelo-CEN-HYG.

    Amplification:

    Article Title: Hypotonicity Stimulates Potassium Flux through the WNK-SPAK/OSR1 Kinase Cascade and the Ncc69 Sodium-Potassium-2-Chloride Cotransporter in the Drosophila Renal Tubule *
    Article Snippet: The third segment was amplified with primers W13711D and W15754U. .. The resultant product, as well as pENTR containing segment one, was then digested with ApaLI (New England Biolabs, Ipswich, MA) and ligated together to yield the final full-length wnk cDNA in pENTR.

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer. .. The 393-bp AAVS1 -specific probe was obtained by PCR amplification of human chromosomal DNA using 0.012 U/µl Phusion High-Fidelity DNA polymerase (Finnzymes), 200 µM deoxynucleoside triphosphates (dNTPs; Fermentas), 1× GC buffer (Finnzymes) plus 0.2 µM of primers #633 (5′-GGTCCCCAGCATGTCTTCCTA-3′) and #634 (5′-CTCCCGAACCTCAGATCTCC-3′).

    Construct:

    Article Title: High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Ig\u03ba/Ig\u03bb Loci Bearing the Rat CH Region
    Article Snippet: To convert a linear YAC into a cYAC or to assemble DNA fragments with overlapping ends into a single cYAC in S. cerevisiae , which can also be maintained as a BAC in E. coli , two self-replicating S. cerevisiae / E. coli shuttle vectors, pBelo-CEN-URA and pBelo-CEN-HYG, were constructed. .. From this plasmid, an ApaLI-BamHI fragment containing URA3 followed by CEN4 or a PmlI–SphI fragment containing CEN4 followed by HygR was cut out and ligated to ApaLI and BamHI or HpaI and SphI doubly digested pBACBelo11 (New England BioLabs) to yield pBelo-CEN-URA and pBelo-CEN-HYG.

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene. .. Additional plasmids with early N4 promoters P1 (pKMK63), P2 (pKMK64), or P3 (pKMK65); four mutant P2 promoters (–10G to T, pKMK66; –11G to T, pKMK67; –12A to T, pKMK68; and +1C to T, pKMK69); and a control lacking the promoter (pKMK62) were constructed.

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein
    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer. .. H-NS was added in increasing concentrations to DNA constructs and incubated for 6 min at 37 °C before the addition of restriction enzymes.

    Incubation:

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein
    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer. .. H-NS was added in increasing concentrations to DNA constructs and incubated for 6 min at 37 °C before the addition of restriction enzymes.

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *
    Article Snippet: .. SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min. .. Samples were diluted with T4 DNA ligase buffer (New England Biolabs) to achieve ∼3 ng of DNA/μl, and then 200 units of T4 DNA ligase (New England Biolabs) were added and incubated for 4 h at 16 °C.

    Activity Assay:

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: .. Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene. .. The resulting plasmid, pIK1, was used to determine in vivo activity of N4 mini-vRNAP variants.

    Expressing:

    Article Title: High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Ig\u03ba/Ig\u03bb Loci Bearing the Rat CH Region
    Article Snippet: The resulting plasmid contains CEN4 cloned in between S. cerevisiae URA3 and a hygromycin-resistance expression cassette ( HygR ). .. From this plasmid, an ApaLI-BamHI fragment containing URA3 followed by CEN4 or a PmlI–SphI fragment containing CEN4 followed by HygR was cut out and ligated to ApaLI and BamHI or HpaI and SphI doubly digested pBACBelo11 (New England BioLabs) to yield pBelo-CEN-URA and pBelo-CEN-HYG.

    Transformation Assay:

    Article Title: Profiling the Extended Cleavage Specificity of the House Dust Mite Protease Allergens Der p 1, Der p 3 and Der p 6 for the Prediction of New Cell Surface Protein Substrates
    Article Snippet: These oligonucleotides were annealed to a short complementary primer 5′-CAACAAGTTTCTGCGGCCGC -3′, treated with the large Klenow fragment to generate double-stranded DNA, double-digested with restriction endonucleases ApaLI and NotI (Italic) (NEB, Ipswich, SFK, UK). .. The final constructions were used for transformation of electrocompetent E. coli TG1 cells and tetracycline-resistant colonies were then selected.

    High Performance Liquid Chromatography:

    Article Title: The HsRAD51B-HsRAD51C stabilizes the HsRAD51 nucleoprotein filament
    Article Snippet: For surface plasmon resonance (SPR) analysis, a 5’-biotinylated oligo dT50 was used as ssDNA and for dsDNA 5’-biotinylated 50-mer 5’-TCG AGA GGG TAA ACC ACA-ATT ATT GAT ATA AAA TAG TTT TGG GTA GGC GA was annealed with its complement and purified by HPLC on a Gen-Pak FAX column (Waters). .. RFIII DNA was obtained by linearizing RFI ϕX174 with ApaLI restriction enzyme (NEB).

    Southern Blot:

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: The purified DNA was subjected to Southern blot analysis. .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: Paragraph title: Detection of gene targeting events by Southern blot analysis ... After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer.

    Ligation:

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: MNase nucleosome mapping and restriction enzyme accessibility assays Micrococcal nuclease (MNase) digestion and ligation-mediated PCR (LM-PCR) were performed as described ( ). .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Shikonin, dually functions as a proteasome inhibitor and a necroptosis inducer in multiple myeloma cells
    Article Snippet: Paragraph title: Reverse transcription-polymerase chain reaction (RT-PCR) ... ER stress was assessed by detecting activated XBP-1 , which was analyzed by digestion of PCR products with ApaLI (New England Biolabs Inc., MA, USA), as previously described ( ).

    Sequencing:

    Article Title: Hypotonicity Stimulates Potassium Flux through the WNK-SPAK/OSR1 Kinase Cascade and the Ncc69 Sodium-Potassium-2-Chloride Cotransporter in the Drosophila Renal Tubule *
    Article Snippet: The resultant product, as well as pENTR containing segment one, was then digested with ApaLI (New England Biolabs, Ipswich, MA) and ligated together to yield the final full-length wnk cDNA in pENTR. .. The cDNA was sequenced in its entirety, and the sequence has been deposited in GenBankTM .

    Recombinant:

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: E. coli strain BL21 ( F – ompT hsd SB r B– m B– ) was used for the purification of recombinant proteins. .. Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene.

    In Vivo:

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: .. Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene. .. The resulting plasmid, pIK1, was used to determine in vivo activity of N4 mini-vRNAP variants.

    Mutagenesis:

    Article Title: Different allelic frequency of progressive rod-cone degeneration in two populations of Labrador Retrievers in Japan
    Article Snippet: .. The PCR product was digested with 5 units of ApaLI (New England Biolab, MA, U.S.A.) at 37°C for 90 min to yield 151 and 81-bp fragments in the wild genotype (GG), but not in the mutant genotype (AA). .. After digestion, the PCR products were electrophoresed on a 2% agarose gel and visualized by UltraPowerTM DNA Dye solution (Gelex International, Tokyo, Japan).

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: Bacterial Strains and Plasmids — E. coli strain DH5α ( supE44 Δ lacU169 (φ80 lacZ Δ M15 ) hsdR17 recA1 endA1 gyrA96 thi-1 relA1 ) was used to determine the in vivo activity of wild-type and mutant mini-vRNAP enzymes. .. Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene.

    Isolation:

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min. .. The purified genomic DNA was re-digested with 100 U of ApaI completely (for first digestion with XhoI, PstI and SmaI) or 100 U of PstI (for first digestion with SpeI and ApaLI).

    Size-exclusion Chromatography:

    Article Title: Different allelic frequency of progressive rod-cone degeneration in two populations of Labrador Retrievers in Japan
    Article Snippet: Thermal cycling conditions were initial denaturation at 95°C for 1 min, followed by 35 cycles of denaturation at 94°C for 30 sec, annealing at 61°C for 20 sec, and extension at 72°C for 20 sec. .. The PCR product was digested with 5 units of ApaLI (New England Biolab, MA, U.S.A.) at 37°C for 90 min to yield 151 and 81-bp fragments in the wild genotype (GG), but not in the mutant genotype (AA).

    Purification:

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: The purified DNA was subjected to Southern blot analysis. .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: E. coli strain BL21 ( F – ompT hsd SB r B– m B– ) was used for the purification of recombinant proteins. .. Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene.

    Article Title: The HsRAD51B-HsRAD51C stabilizes the HsRAD51 nucleoprotein filament
    Article Snippet: For surface plasmon resonance (SPR) analysis, a 5’-biotinylated oligo dT50 was used as ssDNA and for dsDNA 5’-biotinylated 50-mer 5’-TCG AGA GGG TAA ACC ACA-ATT ATT GAT ATA AAA TAG TTT TGG GTA GGC GA was annealed with its complement and purified by HPLC on a Gen-Pak FAX column (Waters). .. RFIII DNA was obtained by linearizing RFI ϕX174 with ApaLI restriction enzyme (NEB).

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: Detection of gene targeting events by Southern blot analysis Chromosomal DNA was purified according to a published method ( ). .. After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer.

    Article Title: Role of the conserved lysine within the Walker A motif of human DMC1
    Article Snippet: The ϕX174 replicative form I was digest with ApaLI (New England Biolabs) to linearize the DNA. .. The supercoiled pBluescript DNA was purified using a commercially available kit (Qiagen).

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *
    Article Snippet: SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min. .. This was followed by the addition of 10 μg of RNase/ml, and the DNA was purified by phenol/chloroform extraction.

    Polymerase Chain Reaction:

    Article Title: Different allelic frequency of progressive rod-cone degeneration in two populations of Labrador Retrievers in Japan
    Article Snippet: .. The PCR product was digested with 5 units of ApaLI (New England Biolab, MA, U.S.A.) at 37°C for 90 min to yield 151 and 81-bp fragments in the wild genotype (GG), but not in the mutant genotype (AA). .. After digestion, the PCR products were electrophoresed on a 2% agarose gel and visualized by UltraPowerTM DNA Dye solution (Gelex International, Tokyo, Japan).

    Article Title: Hypotonicity Stimulates Potassium Flux through the WNK-SPAK/OSR1 Kinase Cascade and the Ncc69 Sodium-Potassium-2-Chloride Cotransporter in the Drosophila Renal Tubule *
    Article Snippet: PCR was performed with primers W5024D and W6483U, revealing an alternatively spliced exon within the 5′-UTR as well as redefining the splicing events in the 5′-UTR and suggesting a “new” start codon. .. The resultant product, as well as pENTR containing segment one, was then digested with ApaLI (New England Biolabs, Ipswich, MA) and ligated together to yield the final full-length wnk cDNA in pENTR.

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: MNase nucleosome mapping and restriction enzyme accessibility assays Micrococcal nuclease (MNase) digestion and ligation-mediated PCR (LM-PCR) were performed as described ( ). .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Article Title: Shikonin, dually functions as a proteasome inhibitor and a necroptosis inducer in multiple myeloma cells
    Article Snippet: .. ER stress was assessed by detecting activated XBP-1 , which was analyzed by digestion of PCR products with ApaLI (New England Biolabs Inc., MA, USA), as previously described ( ). .. Because the ApaLI site in XBP-1 mRNA is spliced out upon activation, activated XBP-1 shows one large band after ApaLI digestion, while inactivated XBP-1 shows two ApaLI-digested bands.

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer. .. The 393-bp AAVS1 -specific probe was obtained by PCR amplification of human chromosomal DNA using 0.012 U/µl Phusion High-Fidelity DNA polymerase (Finnzymes), 200 µM deoxynucleoside triphosphates (dNTPs; Fermentas), 1× GC buffer (Finnzymes) plus 0.2 µM of primers #633 (5′-GGTCCCCAGCATGTCTTCCTA-3′) and #634 (5′-CTCCCGAACCTCAGATCTCC-3′).

    Gel Extraction:

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer. .. The resulting DNA fragment was purified after agarose gel electrophoresis with the aid of the QIAEX II gel extraction kit (Qiagen).

    Concentration Assay:

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein
    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer. .. The reactions were stopped by the addition of 50 mm EDTA and 0.2% SDS (final concentration).

    SPR Assay:

    Article Title: The HsRAD51B-HsRAD51C stabilizes the HsRAD51 nucleoprotein filament
    Article Snippet: For surface plasmon resonance (SPR) analysis, a 5’-biotinylated oligo dT50 was used as ssDNA and for dsDNA 5’-biotinylated 50-mer 5’-TCG AGA GGG TAA ACC ACA-ATT ATT GAT ATA AAA TAG TTT TGG GTA GGC GA was annealed with its complement and purified by HPLC on a Gen-Pak FAX column (Waters). .. RFIII DNA was obtained by linearizing RFI ϕX174 with ApaLI restriction enzyme (NEB).

    Plasmid Preparation:

    Article Title: High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Ig\u03ba/Ig\u03bb Loci Bearing the Rat CH Region
    Article Snippet: .. From this plasmid, an ApaLI-BamHI fragment containing URA3 followed by CEN4 or a PmlI–SphI fragment containing CEN4 followed by HygR was cut out and ligated to ApaLI and BamHI or HpaI and SphI doubly digested pBACBelo11 (New England BioLabs) to yield pBelo-CEN-URA and pBelo-CEN-HYG. .. To construct BAC6-VH 3-11, initially two fragments, a 115-kb NotI-PmeI and a 110-kb RsrII-SgrAI, were cut out from the BAC clone 3054M17 CITB.

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene. .. The resulting plasmid, pIK1, was used to determine in vivo activity of N4 mini-vRNAP variants.

    Article Title: Profiling the Extended Cleavage Specificity of the House Dust Mite Protease Allergens Der p 1, Der p 3 and Der p 6 for the Prediction of New Cell Surface Protein Substrates
    Article Snippet: 4.2 Construction of Phage Substrate Libraries Three phage substrate libraries were created using the fd-Tet-DOG 1 vector based on previously described protocols [ , , ]. .. These oligonucleotides were annealed to a short complementary primer 5′-CAACAAGTTTCTGCGGCCGC -3′, treated with the large Klenow fragment to generate double-stranded DNA, double-digested with restriction endonucleases ApaLI and NotI (Italic) (NEB, Ipswich, SFK, UK).

    Software:

    Article Title: Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein
    Article Snippet: Probing with restriction enzymes The cleavage reactions of the H-NS nucleoprotein complexes were carried out for 5 min with BamHI-EcoRI and BamHI-HindIII and for 10 min with ApaLI at 37 °C in the same standard New England BioLabs CutSmart buffer. .. The samples containing reaction products were loaded on agarose gels, and the intensities of individual DNA bands were analyzed using Gel analysis option on ImageJ software.

    Agarose Gel Electrophoresis:

    Article Title: Different allelic frequency of progressive rod-cone degeneration in two populations of Labrador Retrievers in Japan
    Article Snippet: The PCR product was digested with 5 units of ApaLI (New England Biolab, MA, U.S.A.) at 37°C for 90 min to yield 151 and 81-bp fragments in the wild genotype (GG), but not in the mutant genotype (AA). .. After digestion, the PCR products were electrophoresed on a 2% agarose gel and visualized by UltraPowerTM DNA Dye solution (Gelex International, Tokyo, Japan).

    Article Title: Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
    Article Snippet: .. After overnight digestion with ApaLI (New England Biolabs), 10 µg DNA samples were resolved in a 0.8% agarose gel in 1× Tris–acetate–EDTA buffer. .. Next, the DNA was transferred by capillary action to an Amersham Hybond-XL membrane (GE Healthcare) using a standard Southern blot technique.

    Activation Assay:

    Article Title: Shikonin, dually functions as a proteasome inhibitor and a necroptosis inducer in multiple myeloma cells
    Article Snippet: ER stress was assessed by detecting activated XBP-1 , which was analyzed by digestion of PCR products with ApaLI (New England Biolabs Inc., MA, USA), as previously described ( ). .. Because the ApaLI site in XBP-1 mRNA is spliced out upon activation, activated XBP-1 shows one large band after ApaLI digestion, while inactivated XBP-1 shows two ApaLI-digested bands.

    BAC Assay:

    Article Title: High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Ig\u03ba/Ig\u03bb Loci Bearing the Rat CH Region
    Article Snippet: To convert a linear YAC into a cYAC or to assemble DNA fragments with overlapping ends into a single cYAC in S. cerevisiae , which can also be maintained as a BAC in E. coli , two self-replicating S. cerevisiae / E. coli shuttle vectors, pBelo-CEN-URA and pBelo-CEN-HYG, were constructed. .. From this plasmid, an ApaLI-BamHI fragment containing URA3 followed by CEN4 or a PmlI–SphI fragment containing CEN4 followed by HygR was cut out and ligated to ApaLI and BamHI or HpaI and SphI doubly digested pBACBelo11 (New England BioLabs) to yield pBelo-CEN-URA and pBelo-CEN-HYG.

    Lysis:

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *
    Article Snippet: Cross-linked cells were washed with ice-cold phosphate-buffered saline and lysed for 1 h with ice-cold lysis buffer containing 10 m m Tris (pH 8.0), 10 m m NaCl, 0.2% Nonidet P-40, and 1 m m dithiothreitol. .. SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min.

    Variant Assay:

    Article Title: Identification of Bacteriophage N4 Virion RNA Polymerase-Nucleic Acid Interactions in Transcription Complexes *
    Article Snippet: Reporter Plasmids to Determine in Vivo Activity of Mini-vRNAP —A fragment flanked by ApaLI- and BamHI restriction sites that includes vRNAP promoter P2 (–19 to +2) followed by the lacZ ′ gene from M13mp18 was inserted into ApaLI and BamHI-digested pACYC177 (New England Biolabs), disrupting the β-lactamase gene. .. In Vivo Activity of Mini-vRNAP Variants and Mutant Promoters — E. coli strain DH5α cells carrying pIK1 and a plasmid encoding a mini-vRNAP variant (see below) were grown in Lennox Broth base medium containing 100 μg/ml ampicillin and 50 μl/ml kanamycin (Sigma) until they reached a density of ∼109 cells/ml.

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  • 90
    New England Biolabs apali restriction enzyme
    Confirmation of chromatin looping by 3C assay with <t>BglII</t> and/or <t>ApaLI</t> restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII
    Apali Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Journal: The Journal of Biological Chemistry

    Article Title: Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells *

    doi: 10.1074/jbc.M109.058586

    Figure Lengend Snippet: Confirmation of chromatin looping by 3C assay with BglII and/or ApaLI restriction enzyme. A , schematic showing potential interaction between the fragments containing HS-2 region and the internal enhancer ( square ) and transcription factor(s) ( TF ). B , BglII

    Article Snippet: SDS was then sequestered from the samples by the addition of 1.8% Triton X-100 (Fisher), and the samples were incubated at 37 °C for 1 h. The samples were digested with BglII and/or ApaLI restriction enzyme (New England Biolabs) at 37 °C for 16 h. Restriction enzymes were inactivated by the addition of 1.6% SDS and further incubation at 65 °C for 20 min.

    Techniques: