nrui  (New England Biolabs)


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    Structured Review

    New England Biolabs nrui
    Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes <t>ApaI,</t> AscI, MluI, <t>NruI,</t> PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost
    Nrui, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nrui/product/New England Biolabs
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nrui - by Bioz Stars, 2022-07
    86/100 stars

    Images

    1) Product Images from "Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach"

    Article Title: Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach

    Journal:

    doi: 10.1128/AEM.71.3.1311-1317.2005

    Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost
    Figure Legend Snippet: Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost

    Techniques Used:

    2) Product Images from "Comparative analysis of the end-joining activity of several DNA ligases"

    Article Title: Comparative analysis of the end-joining activity of several DNA ligases

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0190062

    Wild type DNA ligase λ DNA digest ligation assay. Agarose gel electrophoresis of λ DNA cut by EcoRV (A/T Blunt, 1 ), NruI (G/C Blunt, 2 ), BstNI (5′ SBO, 3 ), Hpy188I (3′SBO, 4 ), NdeI (2 BO, 5 ) and BamHI (4 BO, 6 ), generating DNA fragments with ligatable ends. 0.5 ng of the cut DNA was ligated in the presence of T4 ligase reaction buffer (50 mM Tris-HCl pH 7.5 @ 25°C, 1 mM ATP and 10 mM MgCl 2 ) or NEBNext ® Quick Ligation reaction buffer (66 mM Tris pH 7.6 @ 25°C, 10 mM MgCl2, 1 mM DTT, 1 mM ATP, 6% polyethylene glycol (PEG 6000)) and 7 μM of the indicated DNA ligase for 1 hour at 25°C. Ligation assays performed with T4 DNA ligase (A), T3 DNA ligase (B), PBCV1 DNA ligase (C) and, hLig3 (D), respectively. E) Gel of restriction enzyme digested λ DNA samples as well as a schematic depiction of each substrate. The DNA fragments were visualized using ethidium bromide stain.
    Figure Legend Snippet: Wild type DNA ligase λ DNA digest ligation assay. Agarose gel electrophoresis of λ DNA cut by EcoRV (A/T Blunt, 1 ), NruI (G/C Blunt, 2 ), BstNI (5′ SBO, 3 ), Hpy188I (3′SBO, 4 ), NdeI (2 BO, 5 ) and BamHI (4 BO, 6 ), generating DNA fragments with ligatable ends. 0.5 ng of the cut DNA was ligated in the presence of T4 ligase reaction buffer (50 mM Tris-HCl pH 7.5 @ 25°C, 1 mM ATP and 10 mM MgCl 2 ) or NEBNext ® Quick Ligation reaction buffer (66 mM Tris pH 7.6 @ 25°C, 10 mM MgCl2, 1 mM DTT, 1 mM ATP, 6% polyethylene glycol (PEG 6000)) and 7 μM of the indicated DNA ligase for 1 hour at 25°C. Ligation assays performed with T4 DNA ligase (A), T3 DNA ligase (B), PBCV1 DNA ligase (C) and, hLig3 (D), respectively. E) Gel of restriction enzyme digested λ DNA samples as well as a schematic depiction of each substrate. The DNA fragments were visualized using ethidium bromide stain.

    Techniques Used: Ligation, Agarose Gel Electrophoresis, Staining

    Effect of DBDs on blunt/cohesive end λ DNA Re-ligation. Agarose gel electrophoresis of λ DNA cut by EcoRV (A/T Blunt, 1), NruI (G/C Blunt, 2), BstNI (5′ SBO, 3), Hpy188I (3′SBO, 4), NdeI (2 BO, 5) and BamHI (4 BO, 6), generating DNA fragments with ligatable ends. 0.5 ng of the cut DNA was ligated in T4 ligase reaction buffer (50 mM Tris-HCl pH 7.5 @ 25°C, 1 mM ATP and 10 mM MgCl 2 ) or NEBNext ® Quick Ligation reaction buffer (66 mM Tris pH 7.6 @ 25°C, 10 mM MgCl 2 , 1 mM DTT, 1 mM ATP, 6% Polyethylene glycol (PEG 6000)) and 7 μM of the indicated DNA ligase for 1 hour at 25°C. Ligation assays performed with PBCV1-Nterm-Sso7d (A), PBCV1-Cterm-Sso7d terminus (B), PBCV1-Nterm-ZnF (C), PBCV1-Nterm-T4NTD (D). (E) Gel of restriction enzyme digested λ DNA samples as well as a schematic depiction of each substrate. The DNA fragments were visualized using ethidium bromide stain.
    Figure Legend Snippet: Effect of DBDs on blunt/cohesive end λ DNA Re-ligation. Agarose gel electrophoresis of λ DNA cut by EcoRV (A/T Blunt, 1), NruI (G/C Blunt, 2), BstNI (5′ SBO, 3), Hpy188I (3′SBO, 4), NdeI (2 BO, 5) and BamHI (4 BO, 6), generating DNA fragments with ligatable ends. 0.5 ng of the cut DNA was ligated in T4 ligase reaction buffer (50 mM Tris-HCl pH 7.5 @ 25°C, 1 mM ATP and 10 mM MgCl 2 ) or NEBNext ® Quick Ligation reaction buffer (66 mM Tris pH 7.6 @ 25°C, 10 mM MgCl 2 , 1 mM DTT, 1 mM ATP, 6% Polyethylene glycol (PEG 6000)) and 7 μM of the indicated DNA ligase for 1 hour at 25°C. Ligation assays performed with PBCV1-Nterm-Sso7d (A), PBCV1-Cterm-Sso7d terminus (B), PBCV1-Nterm-ZnF (C), PBCV1-Nterm-T4NTD (D). (E) Gel of restriction enzyme digested λ DNA samples as well as a schematic depiction of each substrate. The DNA fragments were visualized using ethidium bromide stain.

    Techniques Used: Ligation, Agarose Gel Electrophoresis, Staining

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    New England Biolabs nru i
    Domain structure of Fer and targeting strategy of fer locus. (A) Fer consists of three CC motifs, a central SH2 domain, and a kinase domain. The catalytic subdomains are shown, with subdomain IX encoded by exon 19 contained within genomic clone 3B. The targeting vector contains a 6-kbp long arm of homology, followed by the PGK-neo cassette, a 0.9-kbp short arm of homology, and a PGK-tk cassette. The D743R mutation was generated within exon 19, which also introduces an <t>Nru</t> I (N) site. A schematic of the targeted allele following homologous recombination is shown, with positions of <t>PCR</t> primers and Southern blot probe indicated. Positions of Xba I (X), Xho I (Xh), Nhe I (Nh), Eco RI (E), and Sac I (S) sites are shown. Sites in parentheses were destroyed. (B) Southern blot analysis of Sac I-digested genomic DNA from animals that were wild type (+/+), heterozygous (+/−), or homozygous (−/−) for fer D743R . Hybridization with a probe located 3′ to the sequence used for the short arm of homology reveals bands of 4.0 kbp for the wild-type allele and 5.8 kbp for the fer D743R allele. (C) Genotyping PCR analysis of genomic DNA from +/+, +/−, or −/− animals. The resulting 871-bp fragment is resistant to Nru I digestion in wild-type samples, yields additional 605- and 266-bp bands in heterozygous samples, and yields only 605- and 266-bp fragments in homozygous samples.
    Nru I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Price from $9.99 to $1999.99
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    86
    New England Biolabs nrui
    Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes <t>ApaI,</t> AscI, MluI, <t>NruI,</t> PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost
    Nrui, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nrui/product/New England Biolabs
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nrui - by Bioz Stars, 2022-07
    86/100 stars
      Buy from Supplier

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    Domain structure of Fer and targeting strategy of fer locus. (A) Fer consists of three CC motifs, a central SH2 domain, and a kinase domain. The catalytic subdomains are shown, with subdomain IX encoded by exon 19 contained within genomic clone 3B. The targeting vector contains a 6-kbp long arm of homology, followed by the PGK-neo cassette, a 0.9-kbp short arm of homology, and a PGK-tk cassette. The D743R mutation was generated within exon 19, which also introduces an Nru I (N) site. A schematic of the targeted allele following homologous recombination is shown, with positions of PCR primers and Southern blot probe indicated. Positions of Xba I (X), Xho I (Xh), Nhe I (Nh), Eco RI (E), and Sac I (S) sites are shown. Sites in parentheses were destroyed. (B) Southern blot analysis of Sac I-digested genomic DNA from animals that were wild type (+/+), heterozygous (+/−), or homozygous (−/−) for fer D743R . Hybridization with a probe located 3′ to the sequence used for the short arm of homology reveals bands of 4.0 kbp for the wild-type allele and 5.8 kbp for the fer D743R allele. (C) Genotyping PCR analysis of genomic DNA from +/+, +/−, or −/− animals. The resulting 871-bp fragment is resistant to Nru I digestion in wild-type samples, yields additional 605- and 266-bp bands in heterozygous samples, and yields only 605- and 266-bp fragments in homozygous samples.

    Journal: Molecular and Cellular Biology

    Article Title: Mice Devoid of Fer Protein-Tyrosine Kinase Activity Are Viable and Fertile but Display Reduced Cortactin Phosphorylation

    doi: 10.1128/MCB.21.2.603-613.2001

    Figure Lengend Snippet: Domain structure of Fer and targeting strategy of fer locus. (A) Fer consists of three CC motifs, a central SH2 domain, and a kinase domain. The catalytic subdomains are shown, with subdomain IX encoded by exon 19 contained within genomic clone 3B. The targeting vector contains a 6-kbp long arm of homology, followed by the PGK-neo cassette, a 0.9-kbp short arm of homology, and a PGK-tk cassette. The D743R mutation was generated within exon 19, which also introduces an Nru I (N) site. A schematic of the targeted allele following homologous recombination is shown, with positions of PCR primers and Southern blot probe indicated. Positions of Xba I (X), Xho I (Xh), Nhe I (Nh), Eco RI (E), and Sac I (S) sites are shown. Sites in parentheses were destroyed. (B) Southern blot analysis of Sac I-digested genomic DNA from animals that were wild type (+/+), heterozygous (+/−), or homozygous (−/−) for fer D743R . Hybridization with a probe located 3′ to the sequence used for the short arm of homology reveals bands of 4.0 kbp for the wild-type allele and 5.8 kbp for the fer D743R allele. (C) Genotyping PCR analysis of genomic DNA from +/+, +/−, or −/− animals. The resulting 871-bp fragment is resistant to Nru I digestion in wild-type samples, yields additional 605- and 266-bp bands in heterozygous samples, and yields only 605- and 266-bp fragments in homozygous samples.

    Article Snippet: The PCR-generated 871-bp fragment was subsequently digested with Nru I (NEB), yielding bands of 605 and 266 bp in the presence of the D743R mutation.

    Techniques: Plasmid Preparation, Mutagenesis, Generated, Homologous Recombination, Polymerase Chain Reaction, Southern Blot, Hybridization, Sequencing

    (A) Genomic map of the tyrP region. Sequencing data revealed a 1,649-bp polymorphism containing a duplication of the tyrP and ycc ). Lines indicate the cutting sites of Nru I resulting in 3,974- and 5,623-bp fragments, respectively. The bar indicates the region amplified by the duplication-PCR. (B) Southern blot analysis after Nru I digestion. The MUL-250 wild-type strain shows two bands of 3,974 and 5,623 bp, respectively, indicating the presence of both a single tyrP copy population and a double tyrP copy population. Clones obtained by the focus assay showed either a double copy (clone 38) or a single copy (clone 41). HeLa DNA was used as a negative control (line 4). (C) Agarose gel analysis of duplication-PCR products (93 bp). Screening of 60 C. pneumoniae strain MUL-250 clones revealed a single clone (clone 38) containing a duplicated tyrP gene as indicated by a positive PCR product. A negative duplication-PCR for clone 41 indicates the presence of a single tyrP copy only. The MUL-250 wild-type strain was used as a positive control, and H 2 O was used as a negative control (lane 4).

    Journal: Infection and Immunity

    Article Title: Isolation of Chlamydia pneumoniae Clonal Variants by a Focus-Forming Assay

    doi: 10.1128/IAI.70.10.5827-5834.2002

    Figure Lengend Snippet: (A) Genomic map of the tyrP region. Sequencing data revealed a 1,649-bp polymorphism containing a duplication of the tyrP and ycc ). Lines indicate the cutting sites of Nru I resulting in 3,974- and 5,623-bp fragments, respectively. The bar indicates the region amplified by the duplication-PCR. (B) Southern blot analysis after Nru I digestion. The MUL-250 wild-type strain shows two bands of 3,974 and 5,623 bp, respectively, indicating the presence of both a single tyrP copy population and a double tyrP copy population. Clones obtained by the focus assay showed either a double copy (clone 38) or a single copy (clone 41). HeLa DNA was used as a negative control (line 4). (C) Agarose gel analysis of duplication-PCR products (93 bp). Screening of 60 C. pneumoniae strain MUL-250 clones revealed a single clone (clone 38) containing a duplicated tyrP gene as indicated by a positive PCR product. A negative duplication-PCR for clone 41 indicates the presence of a single tyrP copy only. The MUL-250 wild-type strain was used as a positive control, and H 2 O was used as a negative control (lane 4).

    Article Snippet: Two hundred nanograms of DNA prepared from each clone and uninfected HeLa cells were digested with Nru I (New England BioLabs, Beverly, Mass.), separated on a 1% agarose gel, and transferred to Hybond-N+ membrane (Amersham Pharmacia Biotech, Little Chalfont, Buckinghamshire, Great Britain) by capillary blotting using the neutral transfer protocol as described by the manufacturer.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Southern Blot, Clone Assay, Negative Control, Agarose Gel Electrophoresis, Positive Control

    Loss or mutation of AT1 in the resistant lines . a Genomic 454 reads of STIB900-P and STIB900-M mapped to STIB900 visualized for the AT1 locus on chromosome 5 using BamView [ 59 ] (smaller scale for STIB900-M). There is a deletion of AT1 in STIB900-M and a coding point mutation in STIB900-P ( red ). b AT1 PCR products (1636 bp) were amplified from genomic DNA of STIB900 and STIB900-P, and digested with the endonuclease Nru I. G1288C mutant alleles are cut to fragments of 1339 and 257 bp. STIB900-P appears to be heterozygous for the mutation

    Journal: Cellular and Molecular Life Sciences

    Article Title: Comparative genomics of drug resistance in Trypanosoma brucei rhodesiense

    doi: 10.1007/s00018-016-2173-6

    Figure Lengend Snippet: Loss or mutation of AT1 in the resistant lines . a Genomic 454 reads of STIB900-P and STIB900-M mapped to STIB900 visualized for the AT1 locus on chromosome 5 using BamView [ 59 ] (smaller scale for STIB900-M). There is a deletion of AT1 in STIB900-M and a coding point mutation in STIB900-P ( red ). b AT1 PCR products (1636 bp) were amplified from genomic DNA of STIB900 and STIB900-P, and digested with the endonuclease Nru I. G1288C mutant alleles are cut to fragments of 1339 and 257 bp. STIB900-P appears to be heterozygous for the mutation

    Article Snippet: The PCR product was purified on silica-membrane columns (Nucleospin gel and PCR clean up, Macherey–Nagel) and digested with Nru I (New England Biolabs), run on a 1.5 % agarose gel and visualized with ethidium bromide.

    Techniques: Mutagenesis, Polymerase Chain Reaction, Amplification

    Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost

    Journal:

    Article Title: Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach

    doi: 10.1128/AEM.71.3.1311-1317.2005

    Figure Lengend Snippet: Digestion patterns of type A (ATCC 3502) and type B (FT 243) proteolytic C. botulinum strains using the rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, and RsrII. The pulse time ramp was 1 to 22 s, and the running time was 20 h. The outermost

    Article Snippet: Nine rare-cutting restriction enzymes, ApaI, AscI, MluI, NruI, PmeI, RsrII, SacII, SmaI, and XhoI (New England Biolabs), were chosen for testing the cleavage of DNA of proteolytic C. botulinum .

    Techniques: