restriction endonuclease nspi  (New England Biolabs)


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    Structured Review

    New England Biolabs restriction endonuclease nspi
    Restriction Endonuclease Nspi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction endonuclease nspi/product/New England Biolabs
    Average 90 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    restriction endonuclease nspi - by Bioz Stars, 2020-04
    90/100 stars

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    Related Articles

    Centrifugation:

    Article Title: Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription
    Article Snippet: Nuclei were isolated by centrifugation for 5 min at 400 g , resuspended with 500 μl of CutSmart Buffer 1.2× (New England BioLabs) supplemented with 0.3% SDS. .. DNA was then digested overnight at 37°C with 400U of NspI (New England BioLabs, ON, Canada).

    Amplification:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: PCR-RFLP Analysis Amplification of the PRNP gene sequence (NCBI Accession: AL133396) by the polymerase chain reaction (PCR) involved forward primer (5'-TGA TAC CAT TGC TAT GCA CTC ATT C-3') and reverse primer (5'-GAC ACC ACC ACT AAA AGG GCT GCA G-3') at 5 pmoles each per reaction (Eurofins MWG Operon, Germany), that are specific for a 956 bp sequence. .. Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK).

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs). .. A generic primer that recognizes the adaptor sequence was used to amplify adaptor-ligated DNA fragments (TITANIUM DNA Amplification Kit by Clontech).

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol. .. The pooled, purified digestion-ligation product was used as the template for a single selective PCR reaction using a selective primer (100 μM), an amplification primer (100 μM) and Phusion High-Fidelity PCR Master Mix with HF Buffer [New England Biolabs (Beverly, MA, USA), No. M0531L].

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA). .. This was used as a template in PCR amplification using Titanium Taq (Clontech, Mountainview, CA) and a single primer complementary to the adaptor sequence.

    Article Title: Lack of Prion Infectivity in Fixed Heart Tissue from Patients with Creutzfeldt-Jakob Disease or Amyloid Heart Disease
    Article Snippet: .. Extracted DNA was amplified by PCR, and the product was digested with the restriction endonuclease NspI (New England BioLabs) as described earlier ( ). ..

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: .. Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA). .. Forty-five microliters of the Agencourt AMPure-purified (Beckman Coulter, Brea, CA) DNA was fragmented and labeled (Affymetrix).

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: .. Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers. .. PCR products were fragmented, labeled and loaded on the SNP 6.0 arrays.

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C. .. After dilution with water, samples were subjected to PCR using primers specific to the adaptor sequence with the following amplification parameters: 95°C for 3 min (initial denaturation), 95°C for 20 s, 59°C for 15 s, 72°C for 15 s for a total of 35 cycles, followed by 72°C for 7 min (final extension).

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: The 25-μl amplification reaction contained ∼75 ng genomic DNA, 10 pmol each primer, 1× Bioline buffer (Bioline), 0.875 U Biolase DNA polymerase (Bioline), 200 μ M each dNTP, and 15% glycerol. .. Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min.

    Filtration:

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA). .. PCR products were purified from excess primers and salts by column filtration and the eluted products were fragmented using DNase I.

    Real-time Polymerase Chain Reaction:

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. Precipitated DNA was eluted in 95% formamide, 10 mM EDTA for 5 min at 65°C, purified using the Qiagen PCR purification Kit (Qiagen) and analyzed by real-time PCR. (See for an overview of the SLOT assay).

    Microarray:

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: This microarray allows genotyping of approximately 1.8 million single nucleotide polymorphisms (SNPs) and CNAs permitting thus to detect abnormalities with a median intermarker distance of around 1 kb. .. Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA).

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: Paragraph title: Chromosomal microarray mapping (CMM) ... In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C.

    Incubation:

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. To test the specificity of the SLOT assay, the pRYG plasmid, which contains a TOP2 cleavage and recognition site was incubated with recombinant TOP2A (TopoGen, Inc, Port Orange, FL) for 30 min at 37°C in the absence or presence of Etoposide (Sigma).

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol. .. The T4 DNA ligase was inactivated by incubation at 80°C for 20 min. All digestion-ligation products were pooled and 1 ml of pooled product was purified using the QiaQuick PCR purification kit [QIAGEN (Valencia, CA, USA), No. 28106].

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: The collection tubes containing saliva were incubated at 50° C and DNA extracted using the manufacture’s protocol with slight modifications as described previously [ ]. .. Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers.

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: .. Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min. .. Resulting fragments were resolved on 2% agarose gels and were visualized under UV light after ethidium bromide staining.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Lack of Prion Infectivity in Fixed Heart Tissue from Patients with Creutzfeldt-Jakob Disease or Amyloid Heart Disease
    Article Snippet: DNA was extracted from FFPE tissue using the Puregene DNA purification kit (Qiagen) according to the manufacturer's instructions. .. Extracted DNA was amplified by PCR, and the product was digested with the restriction endonuclease NspI (New England BioLabs) as described earlier ( ).

    Genome Wide:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: Briefly, 500 ng of highly purified genomic DNA from each patient was processed in each step by a provided Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6. and other prescribed kits. .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: Genotyping and copy number variant (CNV) detection were performed in all of the patients using the Genome-Wide Human SNP Array 6.0 kit (Affymetrix, Santa Clara, CA). .. Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA).

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: DNAs from six affected individuals and three unaffected spouses were genotyped at the Hussman Institute for Human Genomics Center for Genome Technology using the Affymetrix Genome-Wide Human SNP Array 6.0 (Santa Clara, CA). .. Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers.

    Chloramphenicol Acetyltransferase Assay:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: PCR-RFLP Analysis Amplification of the PRNP gene sequence (NCBI Accession: AL133396) by the polymerase chain reaction (PCR) involved forward primer (5'-TGA TAC CAT TGC TAT GCA CTC ATT C-3') and reverse primer (5'-GAC ACC ACC ACT AAA AGG GCT GCA G-3') at 5 pmoles each per reaction (Eurofins MWG Operon, Germany), that are specific for a 956 bp sequence. .. Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK).

    Hybridization:

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers. .. Hybridization was performed in a GeneChip Hybridization Oven (Affymetrix, Santa Clara, CA).

    Ligation:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs). .. A generic primer that recognizes the adaptor sequence was used to amplify adaptor-ligated DNA fragments (TITANIUM DNA Amplification Kit by Clontech).

    Article Title: Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription
    Article Snippet: DNA was then digested overnight at 37°C with 400U of NspI (New England BioLabs, ON, Canada). .. Ligation step was performed with 400U of T4 DNA Ligase (New England BioLabs, ON, Canada) at 16°C overnight.

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol. .. Unique, barcoded oligos (100 μM) and a universal single-strand oligo (100 μM) were added to each sample for ligation with T4 DNA ligase [New England Biolabs (Beverly, MA, USA), No. R0602L].

    Mapping Assay:

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Genotyping of DNA samples was performed with the Affymetrix GeneChipR Human SNP Mapping 6.0 array according to the GeneChip Mapping Assay Manual (Affymetrix, Santa Clara, CA). .. Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA).

    Generated:

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: A 474-bp amplification fragment containing the WASP alternate promoter and untranslated first exon was generated with the primer pair WAS-F and WAS-R. .. Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min.

    Polymerase Chain Reaction:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: Paragraph title: PCR-RFLP Analysis ... Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK).

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. Precipitated DNA was eluted in 95% formamide, 10 mM EDTA for 5 min at 65°C, purified using the Qiagen PCR purification Kit (Qiagen) and analyzed by real-time PCR. (See for an overview of the SLOT assay).

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol. .. The T4 DNA ligase was inactivated by incubation at 80°C for 20 min. All digestion-ligation products were pooled and 1 ml of pooled product was purified using the QiaQuick PCR purification kit [QIAGEN (Valencia, CA, USA), No. 28106].

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA). .. This was used as a template in PCR amplification using Titanium Taq (Clontech, Mountainview, CA) and a single primer complementary to the adaptor sequence.

    Article Title: Lack of Prion Infectivity in Fixed Heart Tissue from Patients with Creutzfeldt-Jakob Disease or Amyloid Heart Disease
    Article Snippet: .. Extracted DNA was amplified by PCR, and the product was digested with the restriction endonuclease NspI (New England BioLabs) as described earlier ( ). ..

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: .. Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA). .. Forty-five microliters of the Agencourt AMPure-purified (Beckman Coulter, Brea, CA) DNA was fragmented and labeled (Affymetrix).

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers. .. PCR products were fragmented, labeled and loaded on the SNP 6.0 arrays.

    Article Title: Copy Number Variation at the APOL1 Locus
    Article Snippet: .. 10 μL of each PCR product was digested with HindIII or NspI (cleaving G0 at S342G and G1 at I384M, respectively) according to manufacturer’s directions (New England Biolabs) for 3–4 hrs at 37C. ..

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C. .. After dilution with water, samples were subjected to PCR using primers specific to the adaptor sequence with the following amplification parameters: 95°C for 3 min (initial denaturation), 95°C for 20 s, 59°C for 15 s, 72°C for 15 s for a total of 35 cycles, followed by 72°C for 7 min (final extension).

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: The thermal profile was 1 cycle at 94°C for 3 min; 31 cycles at 94°C for 30 s, 66°C for 55 s, and 72°C for 1 min; and a final extension cycle at 72°C for 5 min. PCR gel-extraction purifications were performed with QIAquick gel extraction–purification columns, according to the manufacturer's specifications (Qiagen), and were eluted into 40 μl of 10 mM Tris Cl, pH 8.5. .. Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min.

    Recombinant:

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. To test the specificity of the SLOT assay, the pRYG plasmid, which contains a TOP2 cleavage and recognition site was incubated with recombinant TOP2A (TopoGen, Inc, Port Orange, FL) for 30 min at 37°C in the absence or presence of Etoposide (Sigma).

    DNA Extraction:

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: Saliva was collected in Oragene DISCOVER (OGR-500) tubes from DNA Genotek (Ottawa, Canada) and stored at room temperature until DNA extraction could be performed. .. Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers.

    Magnetic Beads:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs). .. PCR products were then purified (Magnetic Beads by Agencourt) fragmented and labeled with a fluorochrome.

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: .. Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. Precipitated DNA was eluted in 95% formamide, 10 mM EDTA for 5 min at 65°C, purified using the Qiagen PCR purification Kit (Qiagen) and analyzed by real-time PCR. (See for an overview of the SLOT assay).

    Isolation:

    Article Title: Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription
    Article Snippet: Nuclei were isolated by centrifugation for 5 min at 400 g , resuspended with 500 μl of CutSmart Buffer 1.2× (New England BioLabs) supplemented with 0.3% SDS. .. DNA was then digested overnight at 37°C with 400U of NspI (New England BioLabs, ON, Canada).

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: High resolution mapping of the deletion breakpoints was performed using the Affymetrix 500K SNP platform, as described previously ( ) using total genomic isolated DNA isolated from fresh whole blood. .. In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C.

    Electrophoretic Mobility Shift Assay:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK). .. The presence of a 24 bp deletion in the octapeptide repeat region could be observed from the codon 129 genotyping agarose gel data due to an additional band shift for the restriction enzyme digest products.

    Purification:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: Briefly, 500 ng of highly purified genomic DNA from each patient was processed in each step by a provided Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6. and other prescribed kits. .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. Precipitated DNA was eluted in 95% formamide, 10 mM EDTA for 5 min at 65°C, purified using the Qiagen PCR purification Kit (Qiagen) and analyzed by real-time PCR. (See for an overview of the SLOT assay).

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol. .. The T4 DNA ligase was inactivated by incubation at 80°C for 20 min. All digestion-ligation products were pooled and 1 ml of pooled product was purified using the QiaQuick PCR purification kit [QIAGEN (Valencia, CA, USA), No. 28106].

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA). .. PCR products were purified from excess primers and salts by column filtration and the eluted products were fragmented using DNase I.

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C. .. PCR products were purified and fragmented using 0.24 units of DNase I at 37°C for 30 min.

    Sequencing:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: PCR-RFLP Analysis Amplification of the PRNP gene sequence (NCBI Accession: AL133396) by the polymerase chain reaction (PCR) involved forward primer (5'-TGA TAC CAT TGC TAT GCA CTC ATT C-3') and reverse primer (5'-GAC ACC ACC ACT AAA AGG GCT GCA G-3') at 5 pmoles each per reaction (Eurofins MWG Operon, Germany), that are specific for a 956 bp sequence. .. Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK).

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs). .. A generic primer that recognizes the adaptor sequence was used to amplify adaptor-ligated DNA fragments (TITANIUM DNA Amplification Kit by Clontech).

    Article Title: Enhancing Diagnosis, Prognosis, and Therapeutic Outcome Prediction of Gliomas Using Genomics
    Article Snippet: Briefly, 250 ng of DNA was digested using either Sty I or Nsp I (New England Biolabs, Ipswich, MA). .. This was used as a template in PCR amplification using Titanium Taq (Clontech, Mountainview, CA) and a single primer complementary to the adaptor sequence.

    Article Title: Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice
    Article Snippet: In short, 250 ng of genomic DNA is digested with 10 units of NspI or StyI (New England Biolabs, Beverly, MA, USA) for 2 h at 37°C. .. After dilution with water, samples were subjected to PCR using primers specific to the adaptor sequence with the following amplification parameters: 95°C for 3 min (initial denaturation), 95°C for 20 s, 59°C for 15 s, 72°C for 15 s for a total of 35 cycles, followed by 72°C for 7 min (final extension).

    Labeling:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs). .. PCR products were then purified (Magnetic Beads by Agencourt) fragmented and labeled with a fluorochrome.

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Tyrosine residues covalently linked to DNA were labeled using EDC and Amine-PEG3-Biotin (Thermo Scientific). .. Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl).

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA). .. Forty-five microliters of the Agencourt AMPure-purified (Beckman Coulter, Brea, CA) DNA was fragmented and labeled (Affymetrix).

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers. .. PCR products were fragmented, labeled and loaded on the SNP 6.0 arrays.

    Staining:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK). .. This allowed for discrimination of the three genotypes: MM, MV, and VV by agarose gel electrophoresis and ethidium bromide staining, Figure .

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA). .. The labeled DNAwas hybridized to the single nucleotide polymorphism (SNP) arrays for 16 hours, then washed, stained (Fluidics Station 450, Affymetrix), and scanned (Scanner, Affymetrix).

    Article Title: North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene
    Article Snippet: Briefly, DNA was digested with NspI and StyI restriction enzymes (New England Biolabs, Ipswich, MA), ligated to adapters and amplified using adapter-specific primers. .. Arrays were washed and stained with streptavidin phycoerythrin and scanned on a GeneChip Scanner 3000 7G (Affymetrix).

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min. .. Resulting fragments were resolved on 2% agarose gels and were visualized under UV light after ethidium bromide staining.

    Activated Clotting Time Assay:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: PCR-RFLP Analysis Amplification of the PRNP gene sequence (NCBI Accession: AL133396) by the polymerase chain reaction (PCR) involved forward primer (5'-TGA TAC CAT TGC TAT GCA CTC ATT C-3') and reverse primer (5'-GAC ACC ACC ACT AAA AGG GCT GCA G-3') at 5 pmoles each per reaction (Eurofins MWG Operon, Germany), that are specific for a 956 bp sequence. .. Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK).

    Plasmid Preparation:

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl). .. To test the specificity of the SLOT assay, the pRYG plasmid, which contains a TOP2 cleavage and recognition site was incubated with recombinant TOP2A (TopoGen, Inc, Port Orange, FL) for 30 min at 37°C in the absence or presence of Etoposide (Sigma).

    Software:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: CA, U.S.A.) Concentration and quality samples were quantified by Nanodrop ND-1000 spectrophotometer running software version 3.0.1 (NanoDrop Technologies, Inc., Rockland DE). .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Agarose Gel Electrophoresis:

    Article Title: PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism
    Article Snippet: Confirmation of the codon 129 genotype was performed by restriction enzyme digestion at 37°C with NspI (New England Biolabs, UK). .. This allowed for discrimination of the three genotypes: MM, MV, and VV by agarose gel electrophoresis and ethidium bromide staining, Figure .

    Spectrophotometry:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: CA, U.S.A.) Concentration and quality samples were quantified by Nanodrop ND-1000 spectrophotometer running software version 3.0.1 (NanoDrop Technologies, Inc., Rockland DE). .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Concentration Assay:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: CA, U.S.A.) Concentration and quality samples were quantified by Nanodrop ND-1000 spectrophotometer running software version 3.0.1 (NanoDrop Technologies, Inc., Rockland DE). .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Article Title: Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription
    Article Snippet: Cell pellets were resuspended in 10 ml of PBS 1×/SVF 10% and cross-linked by adding paraformaldehyde solution to a final concentration 1%, directly to the media for 15 min at room temperature (Sigma-Aldrich). .. DNA was then digested overnight at 37°C with 400U of NspI (New England BioLabs, ON, Canada).

    DNA Purification:

    Article Title: Lack of Prion Infectivity in Fixed Heart Tissue from Patients with Creutzfeldt-Jakob Disease or Amyloid Heart Disease
    Article Snippet: DNA was extracted from FFPE tissue using the Puregene DNA purification kit (Qiagen) according to the manufacturer's instructions. .. Extracted DNA was amplified by PCR, and the product was digested with the restriction endonuclease NspI (New England BioLabs) as described earlier ( ).

    Lysis:

    Article Title: Enhancer-mediated enrichment of interacting JMJD3–DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription
    Article Snippet: Next, cells were centrifuged 5 min at 400 g at 4°C, resuspended in 5 ml of lysis buffer (10 mM Tris–HCl pH7.5; 10mM NaCl; 0.2% NP40; PIC 1×) and incubated for 10 min on ice. .. DNA was then digested overnight at 37°C with 400U of NspI (New England BioLabs, ON, Canada).

    Article Title: Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements
    Article Snippet: SLOT assay Cells were lysed in SLOT lysis buffer (2% SDS, 10 mM EDTA in 10 mM Tris-HCl pH 8) and DNA was extracted after proteinase K digestion using the Qiagen Blood and Tissue Kit (Qiagen). .. Biotin-labeled DNA was precipitated using Strepavidin coated magnetic beads (NEB), digested with NspI (NEB), and unbound fragments were removed by washing with wash Buffer (10 mM Tris HCl, 1mM EDTA, 2 M NaCl).

    Marker:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: DNA was then treated as far manufacturer's instructions (Affymetrix, Santa Clara, CA, USA) and finally hybridized to the Genome-Wide SNP array 6.0 (Affymetrix, Santa Clara, CA, USA).This array contains 906,600 Single Nucleotide Polymorphism (SNP) probes and more than 945,826 copy number variant (CNV) probes, providing marker spacing in the range of as low as 700 bases. .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Gel Extraction:

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3
    Article Snippet: The thermal profile was 1 cycle at 94°C for 3 min; 31 cycles at 94°C for 30 s, 66°C for 55 s, and 72°C for 1 min; and a final extension cycle at 72°C for 5 min. PCR gel-extraction purifications were performed with QIAquick gel extraction–purification columns, according to the manufacturer's specifications (Qiagen), and were eluted into 40 μl of 10 mM Tris Cl, pH 8.5. .. Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min.

    Variant Assay:

    Article Title: SNPs Array Karyotyping Reveals a Novel Recurrent 20p13 Amplification in Primary Myelofibrosis
    Article Snippet: DNA was then treated as far manufacturer's instructions (Affymetrix, Santa Clara, CA, USA) and finally hybridized to the Genome-Wide SNP array 6.0 (Affymetrix, Santa Clara, CA, USA).This array contains 906,600 Single Nucleotide Polymorphism (SNP) probes and more than 945,826 copy number variant (CNV) probes, providing marker spacing in the range of as low as 700 bases. .. First DNA was cut by restriction enzymes NspI and StyI (Nsp I Enzyme, Sty I Enzyme by New England Biolabs) followed by adaptor ligation (T4 DNA Ligase by New England Biolabs).

    Article Title: Exome Sequencing Identifies a Novel FOXP3 Mutation in a 2-Generation Family With Inflammatory Bowel Disease
    Article Snippet: Paragraph title: Array-Based Genotyping and Copy Number Variant Detection ... Two aliquots of 250 ng DNA were digested with Sty I and Nsp I (New England Biolabs, Ipswich, MA), ligated with respective oligonucleotide adaptors (Affymetrix), and amplified by polymerase chain reaction (PCR) (Clontech Laboratories, Mountain View, CA).

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    New England Biolabs restriction endonuclease nspi
    Restriction Endonuclease Nspi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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