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  • 99
    New England Biolabs flanking enzymes ncoi
    Detecting CRISPR interference in bacterial colonies. A. Design of target sequence inserted into pACYC-GFP. The perfect target is shown, similar oligonucleotides bearing G1C, A4G, AAA PAM or AGA PAM (non-target strand sequences) mutations were used for mutant target sequences. Positions of seed mutations are indicated. The target-strand protospacer is highlighted in yellow, the seed in blue, and the PAM in red. <t>NcoI</t> and <t>NotI</t> overhangs are labeled. B. Typhoon scanned plates for perfect target, empty pACYC-GFP lacking a CRISPR target, and the four mutant target plasmids. C. Box plot of quantified intensities for colonies on each plate. The mean intensity for each colony was normalized against the average mean intensity for colonies from the empty pACYC-GFP plate ([mean intensity induced colony]/[average mean intensity for all empty pACYC-GFP colonies]). Boxes depict variation from 25 th to 75 th percentile with the line within the box representing the median value and the X marking the mean. Error bars depict the local minimum and maximum, outliers are shown as circles.
    Flanking Enzymes Ncoi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher fastdigest ncoi
    Detecting CRISPR interference in bacterial colonies. A. Design of target sequence inserted into pACYC-GFP. The perfect target is shown, similar oligonucleotides bearing G1C, A4G, AAA PAM or AGA PAM (non-target strand sequences) mutations were used for mutant target sequences. Positions of seed mutations are indicated. The target-strand protospacer is highlighted in yellow, the seed in blue, and the PAM in red. <t>NcoI</t> and <t>NotI</t> overhangs are labeled. B. Typhoon scanned plates for perfect target, empty pACYC-GFP lacking a CRISPR target, and the four mutant target plasmids. C. Box plot of quantified intensities for colonies on each plate. The mean intensity for each colony was normalized against the average mean intensity for colonies from the empty pACYC-GFP plate ([mean intensity induced colony]/[average mean intensity for all empty pACYC-GFP colonies]). Boxes depict variation from 25 th to 75 th percentile with the line within the box representing the median value and the X marking the mean. Error bars depict the local minimum and maximum, outliers are shown as circles.
    Fastdigest Ncoi, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 74 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega ncoi
    Detection of wild-type, <t>Asp299Gly,</t> and Thr399Ile alleles in the human TLR4 gene. Genomic DNA of individuals recruited into the current study was amplified according to the method of Lorenz et al. (reference 4 ). PCR products were digested with the enzymes <t>NcoI</t> (299 allele) or HinfI (399 allele). Lanes 1 and 14, 100 base pair marker. Lanes 2–7, RFLP of the 299 section of TLR4 gene from three wild-type donors and three heterozygotes. Lanes 8–13, RFLP of the 399 section of TLR4 gene from three wild-type donors and three heterozygotes. Top band represents presence of wild-type allele, bottom band indicates presence of mutant allele. Genotypes were confirmed by sequencing.
    Ncoi, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 1246 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Millipore ncoi
    Domain architecture of <t>Rdh54</t> and rdh54 truncation mutants. A , schematic overview depicting the conserved regions of Rdh54, a 924-amino acid DNA translocase with a Rad51-binding domain of ∼100 amino acid ( aa ). The boxed regions represent the seven helicase-like Swi2/Snf2 motifs in Rdh54. The N-terminal truncations of Rdh54 used in this study are represented below. B , domain architecture of the Rad54-Rdh54 hybrid construct. The arrow represents an <t>NcoI</t> site used to fuse the Rad54 N-terminal domain with the C terminus of Rdh54.
    Ncoi, supplied by Millipore, used in various techniques. Bioz Stars score: 96/100, based on 3275 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Kaneka Corp ncoi ncoi insert
    Domain architecture of <t>Rdh54</t> and rdh54 truncation mutants. A , schematic overview depicting the conserved regions of Rdh54, a 924-amino acid DNA translocase with a Rad51-binding domain of ∼100 amino acid ( aa ). The boxed regions represent the seven helicase-like Swi2/Snf2 motifs in Rdh54. The N-terminal truncations of Rdh54 used in this study are represented below. B , domain architecture of the Rad54-Rdh54 hybrid construct. The arrow represents an <t>NcoI</t> site used to fuse the Rad54 N-terminal domain with the C terminus of Rdh54.
    Ncoi Ncoi Insert, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs ncoi hf
    In vivo recombination of plasmids by mutants of Cre a) Plasmid architecture of the three expected recombination products. Recombination sites are shown as triangles. For simplicity, the map is in linear form, where the <t>NcoI</t> sites at the ends represent a single NcoI site on the circular plasmids. The numbers under each segment indicate distance in bp (map not drawn to scale). The numbers adjacent to each map are the sizes of the expected digestion products, with the asterisks indicating the product size that is unique to the particular configuration. b) Digest analysis of loxP x loxP (left five lanes) and ψlox h7q21 x ψCore h7q21 (right five lanes) recombination. (c d) Inversion and recombination frequency of (c) loxP x loxP and (d) ψCore h7q21 x ψlox h7q21 recombination obtained by quantifying band intensities. Error bars correspond to 95% C.I. (n= 2 independent experiment). NI: NcoI site; SI: <t>ScaI</t> site.
    Ncoi Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 226 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ncoi  (Toyobo)
    92
    Toyobo ncoi
    In vivo recombination of plasmids by mutants of Cre a) Plasmid architecture of the three expected recombination products. Recombination sites are shown as triangles. For simplicity, the map is in linear form, where the <t>NcoI</t> sites at the ends represent a single NcoI site on the circular plasmids. The numbers under each segment indicate distance in bp (map not drawn to scale). The numbers adjacent to each map are the sizes of the expected digestion products, with the asterisks indicating the product size that is unique to the particular configuration. b) Digest analysis of loxP x loxP (left five lanes) and ψlox h7q21 x ψCore h7q21 (right five lanes) recombination. (c d) Inversion and recombination frequency of (c) loxP x loxP and (d) ψCore h7q21 x ψlox h7q21 recombination obtained by quantifying band intensities. Error bars correspond to 95% C.I. (n= 2 independent experiment). NI: NcoI site; SI: <t>ScaI</t> site.
    Ncoi, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ncoi  (Roche)
    93
    Roche ncoi
    In vivo recombination of plasmids by mutants of Cre a) Plasmid architecture of the three expected recombination products. Recombination sites are shown as triangles. For simplicity, the map is in linear form, where the <t>NcoI</t> sites at the ends represent a single NcoI site on the circular plasmids. The numbers under each segment indicate distance in bp (map not drawn to scale). The numbers adjacent to each map are the sizes of the expected digestion products, with the asterisks indicating the product size that is unique to the particular configuration. b) Digest analysis of loxP x loxP (left five lanes) and ψlox h7q21 x ψCore h7q21 (right five lanes) recombination. (c d) Inversion and recombination frequency of (c) loxP x loxP and (d) ψCore h7q21 x ψlox h7q21 recombination obtained by quantifying band intensities. Error bars correspond to 95% C.I. (n= 2 independent experiment). NI: NcoI site; SI: <t>ScaI</t> site.
    Ncoi, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 288 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Detecting CRISPR interference in bacterial colonies. A. Design of target sequence inserted into pACYC-GFP. The perfect target is shown, similar oligonucleotides bearing G1C, A4G, AAA PAM or AGA PAM (non-target strand sequences) mutations were used for mutant target sequences. Positions of seed mutations are indicated. The target-strand protospacer is highlighted in yellow, the seed in blue, and the PAM in red. NcoI and NotI overhangs are labeled. B. Typhoon scanned plates for perfect target, empty pACYC-GFP lacking a CRISPR target, and the four mutant target plasmids. C. Box plot of quantified intensities for colonies on each plate. The mean intensity for each colony was normalized against the average mean intensity for colonies from the empty pACYC-GFP plate ([mean intensity induced colony]/[average mean intensity for all empty pACYC-GFP colonies]). Boxes depict variation from 25 th to 75 th percentile with the line within the box representing the median value and the X marking the mean. Error bars depict the local minimum and maximum, outliers are shown as circles.

    Journal: Methods in enzymology

    Article Title: Fluorescence-based methods for measuring target interference by CRISPR-Cas systems

    doi: 10.1016/bs.mie.2018.10.027

    Figure Lengend Snippet: Detecting CRISPR interference in bacterial colonies. A. Design of target sequence inserted into pACYC-GFP. The perfect target is shown, similar oligonucleotides bearing G1C, A4G, AAA PAM or AGA PAM (non-target strand sequences) mutations were used for mutant target sequences. Positions of seed mutations are indicated. The target-strand protospacer is highlighted in yellow, the seed in blue, and the PAM in red. NcoI and NotI overhangs are labeled. B. Typhoon scanned plates for perfect target, empty pACYC-GFP lacking a CRISPR target, and the four mutant target plasmids. C. Box plot of quantified intensities for colonies on each plate. The mean intensity for each colony was normalized against the average mean intensity for colonies from the empty pACYC-GFP plate ([mean intensity induced colony]/[average mean intensity for all empty pACYC-GFP colonies]). Boxes depict variation from 25 th to 75 th percentile with the line within the box representing the median value and the X marking the mean. Error bars depict the local minimum and maximum, outliers are shown as circles.

    Article Snippet: T4 polynucleotide kinase (PNK), NotI, NcoI, T4 DNA ligase and accompanying buffers purchased from New England Biolabs 100 mM ATP 100 µM CRISPR target oligonucleotides (designed as in ) and pACYC-GFP Gel purification kit (e.g. Qiagen QIAquick Gel Extraction kit or Promega Wizard SV Gel and PCR Clean-Up System) One Shot TOP10 Competent Cells (Thermo-Fisher) or similar cloning E. coli strain Miniprep kit (Qiagen or Promega)

    Techniques: CRISPR, Sequencing, Mutagenesis, Labeling

    Detection of wild-type, Asp299Gly, and Thr399Ile alleles in the human TLR4 gene. Genomic DNA of individuals recruited into the current study was amplified according to the method of Lorenz et al. (reference 4 ). PCR products were digested with the enzymes NcoI (299 allele) or HinfI (399 allele). Lanes 1 and 14, 100 base pair marker. Lanes 2–7, RFLP of the 299 section of TLR4 gene from three wild-type donors and three heterozygotes. Lanes 8–13, RFLP of the 399 section of TLR4 gene from three wild-type donors and three heterozygotes. Top band represents presence of wild-type allele, bottom band indicates presence of mutant allele. Genotypes were confirmed by sequencing.

    Journal: The Journal of Experimental Medicine

    Article Title: Monocytes Heterozygous for the Asp299Gly and Thr399Ile Mutations in the Toll-like Receptor 4 Gene Show No Deficit in Lipopolysaccharide Signalling

    doi: 10.1084/jem.20022078

    Figure Lengend Snippet: Detection of wild-type, Asp299Gly, and Thr399Ile alleles in the human TLR4 gene. Genomic DNA of individuals recruited into the current study was amplified according to the method of Lorenz et al. (reference 4 ). PCR products were digested with the enzymes NcoI (299 allele) or HinfI (399 allele). Lanes 1 and 14, 100 base pair marker. Lanes 2–7, RFLP of the 299 section of TLR4 gene from three wild-type donors and three heterozygotes. Lanes 8–13, RFLP of the 399 section of TLR4 gene from three wild-type donors and three heterozygotes. Top band represents presence of wild-type allele, bottom band indicates presence of mutant allele. Genotypes were confirmed by sequencing.

    Article Snippet: Thermal cycling was: 95°C for 4 min, then 30 cycles of 95°C for 30 s, 55°C for 30 s, and 72°C for 30 s. Asp299Gly or Thr399Ile PCR products (20 μl) were digested with NcoI (Promega) or HinfI (Promega), respectively, and visualized on a 3% high resolution agar gel (Nusieve 3.1; Flowgen).

    Techniques: Amplification, Polymerase Chain Reaction, Marker, Mutagenesis, Sequencing

    TNFB Nco1 polymorphism. The polymerase chain reaction (PCR) was used to amplify a 368-bp fragment of the of the TNFβ genomic sequence and the PCR product was digested directly with 1 U of NcoI restriction enzyme. Lane 1 shows a homozygous for the cleaved product produced bands at 133 and 235 bp (with incomplete digestion of the 368-bp band) representing the allele TNFB1, while the uncleaved 368-bp product in lane 3 represents the allele TNFB2. Lane 2 shows a heterozygote pattern.

    Journal: Clinical and Experimental Immunology

    Article Title: Two polymorphisms of the tumour necrosis factor gene do not influence survival in pancreatic cancer

    doi: 10.1046/j.1365-2249.1999.01005.x

    Figure Lengend Snippet: TNFB Nco1 polymorphism. The polymerase chain reaction (PCR) was used to amplify a 368-bp fragment of the of the TNFβ genomic sequence and the PCR product was digested directly with 1 U of NcoI restriction enzyme. Lane 1 shows a homozygous for the cleaved product produced bands at 133 and 235 bp (with incomplete digestion of the 368-bp band) representing the allele TNFB1, while the uncleaved 368-bp product in lane 3 represents the allele TNFB2. Lane 2 shows a heterozygote pattern.

    Article Snippet: The PCR product was digested directly with 1 U of NcoI restriction enzyme (Promega, Madison, WI) at 37°C for 4 h. Restriction enzyme products were analysed on 1% NuSieve agarose (FMC Bioproducts, Rockland, ME) or 6% polyacrylamide gels (BioRad, Hemel Hempstead, UK).

    Techniques: Polymerase Chain Reaction, Sequencing, Produced

    Domain architecture of Rdh54 and rdh54 truncation mutants. A , schematic overview depicting the conserved regions of Rdh54, a 924-amino acid DNA translocase with a Rad51-binding domain of ∼100 amino acid ( aa ). The boxed regions represent the seven helicase-like Swi2/Snf2 motifs in Rdh54. The N-terminal truncations of Rdh54 used in this study are represented below. B , domain architecture of the Rad54-Rdh54 hybrid construct. The arrow represents an NcoI site used to fuse the Rad54 N-terminal domain with the C terminus of Rdh54.

    Journal: The Journal of Biological Chemistry

    Article Title: Characterization of the Interaction between the Saccharomyces cerevisiae Rad51 Recombinase and the DNA Translocase Rdh54

    doi: 10.1074/jbc.M113.480475

    Figure Lengend Snippet: Domain architecture of Rdh54 and rdh54 truncation mutants. A , schematic overview depicting the conserved regions of Rdh54, a 924-amino acid DNA translocase with a Rad51-binding domain of ∼100 amino acid ( aa ). The boxed regions represent the seven helicase-like Swi2/Snf2 motifs in Rdh54. The N-terminal truncations of Rdh54 used in this study are represented below. B , domain architecture of the Rad54-Rdh54 hybrid construct. The arrow represents an NcoI site used to fuse the Rad54 N-terminal domain with the C terminus of Rdh54.

    Article Snippet: DNA plasmids for bacterial expression and protein purification were generated by PCR amplification and cloning of wild-type RDH54 , rdh54 truncation alleles, and RAD54-RDH54 hybrid sequence into the NcoI and XhoI sites of the pET32a vector (Novagen) to add thioredoxin and His6 tags to the N terminus of each protein.

    Techniques: Binding Assay, Construct

    In vivo recombination of plasmids by mutants of Cre a) Plasmid architecture of the three expected recombination products. Recombination sites are shown as triangles. For simplicity, the map is in linear form, where the NcoI sites at the ends represent a single NcoI site on the circular plasmids. The numbers under each segment indicate distance in bp (map not drawn to scale). The numbers adjacent to each map are the sizes of the expected digestion products, with the asterisks indicating the product size that is unique to the particular configuration. b) Digest analysis of loxP x loxP (left five lanes) and ψlox h7q21 x ψCore h7q21 (right five lanes) recombination. (c d) Inversion and recombination frequency of (c) loxP x loxP and (d) ψCore h7q21 x ψlox h7q21 recombination obtained by quantifying band intensities. Error bars correspond to 95% C.I. (n= 2 independent experiment). NI: NcoI site; SI: ScaI site.

    Journal: Nature communications

    Article Title: Mutants of Cre recombinase with improved accuracy

    doi: 10.1038/ncomms3509

    Figure Lengend Snippet: In vivo recombination of plasmids by mutants of Cre a) Plasmid architecture of the three expected recombination products. Recombination sites are shown as triangles. For simplicity, the map is in linear form, where the NcoI sites at the ends represent a single NcoI site on the circular plasmids. The numbers under each segment indicate distance in bp (map not drawn to scale). The numbers adjacent to each map are the sizes of the expected digestion products, with the asterisks indicating the product size that is unique to the particular configuration. b) Digest analysis of loxP x loxP (left five lanes) and ψlox h7q21 x ψCore h7q21 (right five lanes) recombination. (c d) Inversion and recombination frequency of (c) loxP x loxP and (d) ψCore h7q21 x ψlox h7q21 recombination obtained by quantifying band intensities. Error bars correspond to 95% C.I. (n= 2 independent experiment). NI: NcoI site; SI: ScaI site.

    Article Snippet: The purified plasmids were digested for 20 min at 37 °C in 60 μL reactions containing all of the collected DNA and 20 U of both ScaI-HF and NcoI-HF (both from New England Biolabs) in NEBuffer 4 (1 mM DTT, 50 mM potassium acetate, 20 mM tris-acetate, 10 mM magnesium acetate, pH 7.9).

    Techniques: In Vivo, Plasmid Preparation