msei  (New England Biolabs)


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    Name:
    MseI
    Description:
    MseI 2 500 units
    Catalog Number:
    R0525L
    Price:
    282
    Category:
    Restriction Enzymes
    Size:
    2 500 units
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    Structured Review

    New England Biolabs msei
    MseI
    MseI 2 500 units
    https://www.bioz.com/result/msei/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    msei - by Bioz Stars, 2021-06
    99/100 stars

    Images

    1) Product Images from "Detection of Cryptosporidium and Identification to the Species Level by Nested PCR and Restriction Fragment Length Polymorphism"

    Article Title: Detection of Cryptosporidium and Identification to the Species Level by Nested PCR and Restriction Fragment Length Polymorphism

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.43.3.1017-1023.2005

    Comparative restriction patterns of C. hominis (A), C. parvum (B), C. felis (C), and C. meleagridis (D) obtained with the following enzymes: TaqI (lanes 1), AseI (lanes 2), MseI (lanes 3), BstUI (lanes 4), and SspI (lanes 5). Lanes 6, undigested C. hominis
    Figure Legend Snippet: Comparative restriction patterns of C. hominis (A), C. parvum (B), C. felis (C), and C. meleagridis (D) obtained with the following enzymes: TaqI (lanes 1), AseI (lanes 2), MseI (lanes 3), BstUI (lanes 4), and SspI (lanes 5). Lanes 6, undigested C. hominis

    Techniques Used:

    2) Product Images from "A Mouse Model of Early-Onset Renal Failure Due to a Xanthine Dehydrogenase Nonsense Mutation"

    Article Title: A Mouse Model of Early-Onset Renal Failure Due to a Xanthine Dehydrogenase Nonsense Mutation

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0045217

    Mapping and identification of the gene mutation causing RENF. (A) The RENF locus was mapped to a 5.8Mbp interval flanked by the SNPs rs3657117 and rs33373680 on chromosome 17, which contained 40 genes. (B) DNA sequence analysis of the Xdh gene revealed a homozygous G > T transversion in exon 2, changing codon 26 from GAA to TAA, resulting in a nonsense mutation. (C) The Glu26Stop mutation also generated a MseI restriction endonuclease recognition site, thus cleavage of a 209 bp PCR product by MseI yielded 115bp and 94bp fragments in mutant alleles but did not cut wild-type alleles. (D) MseI digest was used to genotype unaffected and affected RENF mice. All affected RENF mice were homozygous for the Glu26Stop mutation. (E) Immunohistochemistry showed loss of hepatic XDH expression in RENF mice compared to unaffected littermates. Scale bars = 200 µm.
    Figure Legend Snippet: Mapping and identification of the gene mutation causing RENF. (A) The RENF locus was mapped to a 5.8Mbp interval flanked by the SNPs rs3657117 and rs33373680 on chromosome 17, which contained 40 genes. (B) DNA sequence analysis of the Xdh gene revealed a homozygous G > T transversion in exon 2, changing codon 26 from GAA to TAA, resulting in a nonsense mutation. (C) The Glu26Stop mutation also generated a MseI restriction endonuclease recognition site, thus cleavage of a 209 bp PCR product by MseI yielded 115bp and 94bp fragments in mutant alleles but did not cut wild-type alleles. (D) MseI digest was used to genotype unaffected and affected RENF mice. All affected RENF mice were homozygous for the Glu26Stop mutation. (E) Immunohistochemistry showed loss of hepatic XDH expression in RENF mice compared to unaffected littermates. Scale bars = 200 µm.

    Techniques Used: Mutagenesis, Sequencing, Generated, Polymerase Chain Reaction, Mouse Assay, Immunohistochemistry, Expressing

    3) Product Images from "Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth"

    Article Title: Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkz1043

    Two conserved cysteines of NSUN5 are required for RNA methyltransferase activity and normal proliferation. ( A ) Principle of the COBRA assay to measure m 5 C3782. Digestion with MseI generates two products (56 bp and 45 bp) in the presence of m 5 C3782 and three products (56, 29 and 16 bp) in the absence of m 5 C3782. A band at 101 bp represents the undigested PCR product. ( B ) COBRA assay of HeLa, NSUN5 KO, HeLa GFP-mNSUN5 and NSUN5 KO GFP-mNSUN5 demonstrates that mouse Nsun5 fully restores methylation of C3782 upon loss of human NSUN5. A representative 20% TBE gel of MseI-digested PCR products is shown. Numbers indicate size of fragments in basepairs. Arrow indicates methylation-specific band, whereas asterisk (*) indicates band upon non-methylation. ( C ) Quantitation of COBRA assay in (B), n = 3 independent experiments. Error bars represent standard deviation. *** P
    Figure Legend Snippet: Two conserved cysteines of NSUN5 are required for RNA methyltransferase activity and normal proliferation. ( A ) Principle of the COBRA assay to measure m 5 C3782. Digestion with MseI generates two products (56 bp and 45 bp) in the presence of m 5 C3782 and three products (56, 29 and 16 bp) in the absence of m 5 C3782. A band at 101 bp represents the undigested PCR product. ( B ) COBRA assay of HeLa, NSUN5 KO, HeLa GFP-mNSUN5 and NSUN5 KO GFP-mNSUN5 demonstrates that mouse Nsun5 fully restores methylation of C3782 upon loss of human NSUN5. A representative 20% TBE gel of MseI-digested PCR products is shown. Numbers indicate size of fragments in basepairs. Arrow indicates methylation-specific band, whereas asterisk (*) indicates band upon non-methylation. ( C ) Quantitation of COBRA assay in (B), n = 3 independent experiments. Error bars represent standard deviation. *** P

    Techniques Used: Activity Assay, Combined Bisulfite Restriction Analysis Assay, Polymerase Chain Reaction, Methylation, Quantitation Assay, Standard Deviation

    Partial loss of NSUN5 in Williams-Beuren-Syndrome is sufficient to reduce m 5 C3782. ( A ) Relative expression levels of NSUN5 mRNA of two healthy donors as well as two WBS patients were determined by RT-qPCR. ( B ) Protein expression levels of NSUN5 were measured in fibroblasts of a healthy donor and two WBS patients. ( C ) DIC and IF images of fibroblasts of a healthy donor and the two WBS patients. NSUN5 is stained in green and nuclei are counterstained with DAPI. Scale bar represents 10 μm. ( D ) COBRA assay of fibroblasts of two healthy donors and two WBS patients indicates that methylation of C3782 is decreased in WBS. A representative 20% TBE gel of MseI-digested PCR products is shown. Numbers indicate size of fragments in basepairs. Arrow indicates methylation-specific band, whereas asterisk (*) indicates band upon non-methylation. ( E ) Quantitation of COBRA assay in (D).
    Figure Legend Snippet: Partial loss of NSUN5 in Williams-Beuren-Syndrome is sufficient to reduce m 5 C3782. ( A ) Relative expression levels of NSUN5 mRNA of two healthy donors as well as two WBS patients were determined by RT-qPCR. ( B ) Protein expression levels of NSUN5 were measured in fibroblasts of a healthy donor and two WBS patients. ( C ) DIC and IF images of fibroblasts of a healthy donor and the two WBS patients. NSUN5 is stained in green and nuclei are counterstained with DAPI. Scale bar represents 10 μm. ( D ) COBRA assay of fibroblasts of two healthy donors and two WBS patients indicates that methylation of C3782 is decreased in WBS. A representative 20% TBE gel of MseI-digested PCR products is shown. Numbers indicate size of fragments in basepairs. Arrow indicates methylation-specific band, whereas asterisk (*) indicates band upon non-methylation. ( E ) Quantitation of COBRA assay in (D).

    Techniques Used: Expressing, Quantitative RT-PCR, Staining, Combined Bisulfite Restriction Analysis Assay, Methylation, Polymerase Chain Reaction, Quantitation Assay

    4) Product Images from "A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples"

    Article Title: A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0016118

    Enhanced amplification of viral fragments using one restriction enzyme in VIDISCA. Visualization of VIDISCA fragments digested with HinP1-I+MseI or MseI alone. VIDISCA fragments are visualized on a 1% agarose gel, which were generated after a single first round PCR of 40 cycles. The dots indicate viral fragments which were only visible with MseI digestion.
    Figure Legend Snippet: Enhanced amplification of viral fragments using one restriction enzyme in VIDISCA. Visualization of VIDISCA fragments digested with HinP1-I+MseI or MseI alone. VIDISCA fragments are visualized on a 1% agarose gel, which were generated after a single first round PCR of 40 cycles. The dots indicate viral fragments which were only visible with MseI digestion.

    Techniques Used: Amplification, Agarose Gel Electrophoresis, Generated, Polymerase Chain Reaction

    5) Product Images from "Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq)"

    Article Title: Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq)

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0134855

    Analysis of the cDNA, digested cDNA, and RARseq libraries using Fragment Analyzer. (A) Double stranded cDNA, (B) MseI digested cDNA, (C) Styl digested cDNA, (D) MseI-Styl double digested cDNA, (E) MseI RARseq library, (F) MseI-Styl RARseq library, (G) Pool of MseI RARseq libraries, (H) Pool of MseI RARseq libraries after 1X SPRI cleaning.
    Figure Legend Snippet: Analysis of the cDNA, digested cDNA, and RARseq libraries using Fragment Analyzer. (A) Double stranded cDNA, (B) MseI digested cDNA, (C) Styl digested cDNA, (D) MseI-Styl double digested cDNA, (E) MseI RARseq library, (F) MseI-Styl RARseq library, (G) Pool of MseI RARseq libraries, (H) Pool of MseI RARseq libraries after 1X SPRI cleaning.

    Techniques Used:

    Heterozygozity and homoygozity in RARseq data. Illustration of the observed and expected hetero- and homozygosity calculated from MseI and MseI-Styl RARseq data using both de novo and reference approaches.
    Figure Legend Snippet: Heterozygozity and homoygozity in RARseq data. Illustration of the observed and expected hetero- and homozygosity calculated from MseI and MseI-Styl RARseq data using both de novo and reference approaches.

    Techniques Used:

    The correlation between haplotype and gene diversity inferred from RARseq data. Both haplotype and gene diversities were calculated from the de novo analysis (top plots) and the reference-based analysis (bottom plots) of MseI and MesI-Styl RARtags.
    Figure Legend Snippet: The correlation between haplotype and gene diversity inferred from RARseq data. Both haplotype and gene diversities were calculated from the de novo analysis (top plots) and the reference-based analysis (bottom plots) of MseI and MesI-Styl RARtags.

    Techniques Used:

    6) Product Images from "Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis"

    Article Title: Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.70.5.2786-2790.2004

    Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for
    Figure Legend Snippet: Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for

    Techniques Used: Generated

    7) Product Images from "A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples"

    Article Title: A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0016118

    Enhanced amplification of viral fragments using one restriction enzyme in VIDISCA. Visualization of VIDISCA fragments digested with HinP1-I+MseI or MseI alone. VIDISCA fragments are visualized on a 1% agarose gel, which were generated after a single first round PCR of 40 cycles. The dots indicate viral fragments which were only visible with MseI digestion.
    Figure Legend Snippet: Enhanced amplification of viral fragments using one restriction enzyme in VIDISCA. Visualization of VIDISCA fragments digested with HinP1-I+MseI or MseI alone. VIDISCA fragments are visualized on a 1% agarose gel, which were generated after a single first round PCR of 40 cycles. The dots indicate viral fragments which were only visible with MseI digestion.

    Techniques Used: Amplification, Agarose Gel Electrophoresis, Generated, Polymerase Chain Reaction

    8) Product Images from "Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping"

    Article Title: Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gku564

    4C-sequencing analysis of chromosome interactions of the H19 ICR bait sequence in neonatal mouse forebrain. ( a ) 3C libraries were generated from neonatal forebrain utilizing EcoRI, then re-digested with MseI and self-ligated to form circular 3C recombined molecules. The samples were then amplified with primers directed from the H19 ICR ‘bait sequence’ across the interacting fragments and sequenced. Venn diagrams show the number of common sequences between 4C-seq biological replicates. Interactions of the H19 ICR in trans are represented on the left and interactions in cis are represented on the right. ( b ) Analysis of genomic distribution of H19 ICR interacting fragments on each chromosome reveals that the majority of reproducible interactions occur within chromosome 7 while trans interactions are distributed across the genome. ( c ) Representative 4C interaction profile across chromosome 7 (top) and the H19/Igf2 imprinted domain (bottom). Local interactions are observe with the Igf2 DMR1, MAR3, CCD and downstream enhancers. The 4C-seq data was aligned to an EcoRI digested genome and the H19 ICR bait sequence is highlighted in yellow.
    Figure Legend Snippet: 4C-sequencing analysis of chromosome interactions of the H19 ICR bait sequence in neonatal mouse forebrain. ( a ) 3C libraries were generated from neonatal forebrain utilizing EcoRI, then re-digested with MseI and self-ligated to form circular 3C recombined molecules. The samples were then amplified with primers directed from the H19 ICR ‘bait sequence’ across the interacting fragments and sequenced. Venn diagrams show the number of common sequences between 4C-seq biological replicates. Interactions of the H19 ICR in trans are represented on the left and interactions in cis are represented on the right. ( b ) Analysis of genomic distribution of H19 ICR interacting fragments on each chromosome reveals that the majority of reproducible interactions occur within chromosome 7 while trans interactions are distributed across the genome. ( c ) Representative 4C interaction profile across chromosome 7 (top) and the H19/Igf2 imprinted domain (bottom). Local interactions are observe with the Igf2 DMR1, MAR3, CCD and downstream enhancers. The 4C-seq data was aligned to an EcoRI digested genome and the H19 ICR bait sequence is highlighted in yellow.

    Techniques Used: Sequencing, Generated, Amplification

    9) Product Images from "Rapid and sensitive detection of CpG-methylation using methyl-binding (MB)-PCR"

    Article Title: Rapid and sensitive detection of CpG-methylation using methyl-binding (MB)-PCR

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl437

    MB-PCR detects methylation of CpG island promoters. ( A ) Schematic presentation of the detected MseI-fragments (indicated as gray boxes) of ESR1 , CDKN2B (p15 INK4b ), ICSBP , ETV3 and DDX20 . The position of CpG-dinucleotides, MseI-restriction sites, transcription start site, first exon and relative position of primers are marked. ( B ) P -reaction for ICSBP using a serial dilution of MseI-digested genomic DNA. ( C ) Representative MB-PCR results of normal (unmethylated) and in vitro methylated genomic DNA for the indicated promoters and CpG-free regions. The P -reaction directly amplifies the genomic DNA, whereas the M -reaction only amplifies CpG-methylated DNA fragments.
    Figure Legend Snippet: MB-PCR detects methylation of CpG island promoters. ( A ) Schematic presentation of the detected MseI-fragments (indicated as gray boxes) of ESR1 , CDKN2B (p15 INK4b ), ICSBP , ETV3 and DDX20 . The position of CpG-dinucleotides, MseI-restriction sites, transcription start site, first exon and relative position of primers are marked. ( B ) P -reaction for ICSBP using a serial dilution of MseI-digested genomic DNA. ( C ) Representative MB-PCR results of normal (unmethylated) and in vitro methylated genomic DNA for the indicated promoters and CpG-free regions. The P -reaction directly amplifies the genomic DNA, whereas the M -reaction only amplifies CpG-methylated DNA fragments.

    Techniques Used: Polymerase Chain Reaction, Methylation, Serial Dilution, In Vitro

    Outline of MB-PCR. The major steps of the MB-PCR procedure are illustrated. MB-PCR comprises two separate reactions, the control-PCR ( P -reaction) which amplifies a candidate locus directly from a genomic template, and the MB-PCR which amplifies the candidate locus from the template DNA that was bound previously by the methyl-CpG-binding polypeptide in the reaction vessel ( M -reaction). In the first step, the inner walls of both reaction vessels are coated with a methyl-binding polypeptide and subsequently saturated using blocking reagents (step 2). The template DNA (genomic DNA restricted with MseI or similar enzymes) is then added to one tube ( M -reaction) and allowed to bind (step 3). In the last step, the PCR mixture is added directly into both tubes and 50% of template DNA used previously for the M -reaction is added to the P -reaction. After gene-specific PCR, products may be analyzed, e.g. by agarose gel electrophoresis.
    Figure Legend Snippet: Outline of MB-PCR. The major steps of the MB-PCR procedure are illustrated. MB-PCR comprises two separate reactions, the control-PCR ( P -reaction) which amplifies a candidate locus directly from a genomic template, and the MB-PCR which amplifies the candidate locus from the template DNA that was bound previously by the methyl-CpG-binding polypeptide in the reaction vessel ( M -reaction). In the first step, the inner walls of both reaction vessels are coated with a methyl-binding polypeptide and subsequently saturated using blocking reagents (step 2). The template DNA (genomic DNA restricted with MseI or similar enzymes) is then added to one tube ( M -reaction) and allowed to bind (step 3). In the last step, the PCR mixture is added directly into both tubes and 50% of template DNA used previously for the M -reaction is added to the P -reaction. After gene-specific PCR, products may be analyzed, e.g. by agarose gel electrophoresis.

    Techniques Used: Polymerase Chain Reaction, Binding Assay, Blocking Assay, Agarose Gel Electrophoresis

    10) Product Images from "Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma"

    Article Title: Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkm094

    CGI methylation and mRNA expression of ZIC2 in pediatric medulloblastoma. ( a ) Schematic presentation of the predicted ZIC2 CpG island in the 5' UTR of the gene (chr13: 99428130-99428406) delineated according to the criteria by Gardiner-Garden and Frommer ( 52 ). MseI-sites flanking the ends of the CGI clone are shown together with their position in relation to the transcription start site. Pyrosequencing was performed for the indicated region. ( b ) Comparison between pyrosequencing results (grey bars) and aPRIMES results (black bars). For comparison, aPRIMES ratios were linearized and are given in relation to the linear ratio of tumor M3 that displayed the highest ratio among all aPRIMES samples, and was therefore set to 100%. For the pyrosequencing data, a median over all 12 investigated individual CpG sites was calculated. The right panel illustrates non-normalized spot-data after performance of aRPIMES. Triplicate spots for both ZIC2 clones, namely CGI-027A11 and CGI-028A11 are indicated Fem. (male) pool = DNA derived from the peripheral blood mononuclear cells (PBMCs) of 10 healthy donors below age 35. Cb pool = pool of cerebellum DNA from five unaffected donors, age 25–33 years. M1–M20: pediatric medulloblastoma samples. For medulloblastoma M8 no chip data are available. ( c ) mRNA abundance of ZIC2 was assessed by quantitative real-time PCR and normalized to the expression of ZIC2 in a cerebellum mRNA pool of 24 unaffected individuals. Medians and MADs of two independent experiments are shown. ZIC2 was downregulated to different degrees in all tested medulloblastomas, most profoundly in tumor M3 that displayed the highest methylation of the CGI.
    Figure Legend Snippet: CGI methylation and mRNA expression of ZIC2 in pediatric medulloblastoma. ( a ) Schematic presentation of the predicted ZIC2 CpG island in the 5' UTR of the gene (chr13: 99428130-99428406) delineated according to the criteria by Gardiner-Garden and Frommer ( 52 ). MseI-sites flanking the ends of the CGI clone are shown together with their position in relation to the transcription start site. Pyrosequencing was performed for the indicated region. ( b ) Comparison between pyrosequencing results (grey bars) and aPRIMES results (black bars). For comparison, aPRIMES ratios were linearized and are given in relation to the linear ratio of tumor M3 that displayed the highest ratio among all aPRIMES samples, and was therefore set to 100%. For the pyrosequencing data, a median over all 12 investigated individual CpG sites was calculated. The right panel illustrates non-normalized spot-data after performance of aRPIMES. Triplicate spots for both ZIC2 clones, namely CGI-027A11 and CGI-028A11 are indicated Fem. (male) pool = DNA derived from the peripheral blood mononuclear cells (PBMCs) of 10 healthy donors below age 35. Cb pool = pool of cerebellum DNA from five unaffected donors, age 25–33 years. M1–M20: pediatric medulloblastoma samples. For medulloblastoma M8 no chip data are available. ( c ) mRNA abundance of ZIC2 was assessed by quantitative real-time PCR and normalized to the expression of ZIC2 in a cerebellum mRNA pool of 24 unaffected individuals. Medians and MADs of two independent experiments are shown. ZIC2 was downregulated to different degrees in all tested medulloblastomas, most profoundly in tumor M3 that displayed the highest methylation of the CGI.

    Techniques Used: Methylation, Expressing, Clone Assay, Derivative Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Related Articles

    Sequencing:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿
    Article Snippet: The enzyme MseI recognizes and cuts the sequence TTAA present at nucleotide positions 792 to 795 in the HA of the positive control virus A/Duck/Singapore-Q/F119-3/1997. .. The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion. .. The products of enzyme digestion were visualized by ethidium bromide staining following electrophoresis on a 3% molecular screening agarose gel (Roche Diagnostics).

    Quantitative RT-PCR:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿
    Article Snippet: The enzyme MseI recognizes and cuts the sequence TTAA present at nucleotide positions 792 to 795 in the HA of the positive control virus A/Duck/Singapore-Q/F119-3/1997. .. The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion. .. The products of enzyme digestion were visualized by ethidium bromide staining following electrophoresis on a 3% molecular screening agarose gel (Roche Diagnostics).

    Polymerase Chain Reaction:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿
    Article Snippet: The enzyme MseI recognizes and cuts the sequence TTAA present at nucleotide positions 792 to 795 in the HA of the positive control virus A/Duck/Singapore-Q/F119-3/1997. .. The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion. .. The products of enzyme digestion were visualized by ethidium bromide staining following electrophoresis on a 3% molecular screening agarose gel (Roche Diagnostics).

    Article Title: A Mouse Model of Early-Onset Renal Failure Due to a Xanthine Dehydrogenase Nonsense Mutation
    Article Snippet: Individual exons and intron-exon boundaries of the Xdh gene were amplified from genomic DNA by PCR using gene-specific primers and Taq PCR Mastermix (Qiagen), and the PCR products sequenced using BigDye terminator reagents and ABI 3100 sequencer (Life Technologies, Carlsbad, USA) . .. For genotyping, DNA was amplified by PCR using primers specific for exon 2 of Xdh , and PCR products were subject to restriction endonuclease digest using MseI (New England Biolabs). .. Digested products were analysed by agarose gel electrophoresis and images captured using a ChemiDoc XRS+ and Image Lab software (BioRad).

    Article Title: Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth
    Article Snippet: Purified plasmids of the indicated number of clones were analysed by Sanger sequencing (Eurofins Genomics). .. Combined bisulfite restriction analysis (COBRA) COBRA was performed as previously described ( ) with minor modifications: The PCR product after bisulfite conversion and reverse transcription was digested with MseI (New England Biolabs), resulting in either two products of 45 and 56 bp (methylated) or three bands at 16, 29 and 56 bp (non-methylated). .. Digested DNA samples were separated on a 20% TBE gel (Life Technologies) followed by incubation for 20 min with SYBR Safe (Life Technologies).

    Article Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS
    Article Snippet: Sequencing results were analyzed using ChromasPro software (ChromasPro 2.1, Technelysium Pty Ltd, Tewantin QLD, Australia). .. The identified mutation and its segregation was confirmed by agarose gel electrophoresis of Mse I (New England Biolabs, Ipswich, MA, USA) digested PCR fragments. ..

    Amplification:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿
    Article Snippet: The enzyme MseI recognizes and cuts the sequence TTAA present at nucleotide positions 792 to 795 in the HA of the positive control virus A/Duck/Singapore-Q/F119-3/1997. .. The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion. .. The products of enzyme digestion were visualized by ethidium bromide staining following electrophoresis on a 3% molecular screening agarose gel (Roche Diagnostics).

    Article Title: A Mouse Model of Early-Onset Renal Failure Due to a Xanthine Dehydrogenase Nonsense Mutation
    Article Snippet: Individual exons and intron-exon boundaries of the Xdh gene were amplified from genomic DNA by PCR using gene-specific primers and Taq PCR Mastermix (Qiagen), and the PCR products sequenced using BigDye terminator reagents and ABI 3100 sequencer (Life Technologies, Carlsbad, USA) . .. For genotyping, DNA was amplified by PCR using primers specific for exon 2 of Xdh , and PCR products were subject to restriction endonuclease digest using MseI (New England Biolabs). .. Digested products were analysed by agarose gel electrophoresis and images captured using a ChemiDoc XRS+ and Image Lab software (BioRad).

    Ligation:

    Article Title: A method for measuring the distribution of the shortest telomeres in cells and tissues
    Article Snippet: The inactivated mixture including two units of Cvi AII in 10 μl 1× CutSmart buffer was incubated at 25 °C for 2 h to generate genomic DNA fragments with 5′ AT overhangs. .. After Cvi AII digestion, two units of Bfa I, Nde I, and Mse I (New England Biolabs) in 10 μl 1× CutSmart buffer was added to the Cvi AII digested mixture to further digest genomic DNA as well as to generate DNA fragments with a 5′ TA overhang by incubating at 37 °C for 2 h. One unit of Shrimp Alkaline Phosphatase (rSAP; New England Biolabs) in 10 μl 1× CutSmart buffer was subsequently added to the digested mixture to remove 5′ phosphate from each DNA fragment to improve the specificity of ligation between overhang adapters and genomic DNA fragments (37 °C for 30–60 min) and subsequently heat inactivated at 80 °C for 20 min. After heat inactivation, the mixture was allowed to gradually cool down to 25 °C. .. For adaptor ligation, 10 μl of the inactivated mixture was combined with 1000 units of T4 DNA ligase to a final volume of 20 μl in 1× CutSmart buffer with 1 mM ATP, 1 μM of AT adapter, and 1 μM of TA adapter.

    Combined Bisulfite Restriction Analysis Assay:

    Article Title: Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth
    Article Snippet: Purified plasmids of the indicated number of clones were analysed by Sanger sequencing (Eurofins Genomics). .. Combined bisulfite restriction analysis (COBRA) COBRA was performed as previously described ( ) with minor modifications: The PCR product after bisulfite conversion and reverse transcription was digested with MseI (New England Biolabs), resulting in either two products of 45 and 56 bp (methylated) or three bands at 16, 29 and 56 bp (non-methylated). .. Digested DNA samples were separated on a 20% TBE gel (Life Technologies) followed by incubation for 20 min with SYBR Safe (Life Technologies).

    Methylation:

    Article Title: Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth
    Article Snippet: Purified plasmids of the indicated number of clones were analysed by Sanger sequencing (Eurofins Genomics). .. Combined bisulfite restriction analysis (COBRA) COBRA was performed as previously described ( ) with minor modifications: The PCR product after bisulfite conversion and reverse transcription was digested with MseI (New England Biolabs), resulting in either two products of 45 and 56 bp (methylated) or three bands at 16, 29 and 56 bp (non-methylated). .. Digested DNA samples were separated on a 20% TBE gel (Life Technologies) followed by incubation for 20 min with SYBR Safe (Life Technologies).

    Mutagenesis:

    Article Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS
    Article Snippet: Sequencing results were analyzed using ChromasPro software (ChromasPro 2.1, Technelysium Pty Ltd, Tewantin QLD, Australia). .. The identified mutation and its segregation was confirmed by agarose gel electrophoresis of Mse I (New England Biolabs, Ipswich, MA, USA) digested PCR fragments. ..

    Agarose Gel Electrophoresis:

    Article Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS
    Article Snippet: Sequencing results were analyzed using ChromasPro software (ChromasPro 2.1, Technelysium Pty Ltd, Tewantin QLD, Australia). .. The identified mutation and its segregation was confirmed by agarose gel electrophoresis of Mse I (New England Biolabs, Ipswich, MA, USA) digested PCR fragments. ..

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    New England Biolabs mse i
    Overall strategy for cloning methylated CpG islands. In step 1, genomic <t>DNA</t> was digested with <t>Mse</t> I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.
    Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Journal: Genome Research

    Article Title: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

    doi: 10.1101/gr.224102

    Figure Lengend Snippet: Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Article Snippet: Genomic DNA was digested with Mse I alone or Mse I together with a methylcytosine-sensitive (Hpa II, LTI, or Sma I, NEB) or methyl-insensitive (Msp I or Xma I, NEB) restriction endonuclease according to the manufacturer’s conditions.

    Techniques: Clone Assay, Methylation, Transformation Assay

    ( a ) Representative chromatogram of the heterozygous mutation (463 T > G) in ZRS. ( b ) Wild type. ( c ) Restriction analysis using Mse I restriction enzyme in all the sampled family members (normal and affected); the 268-bp mutant allele is indicated

    Journal: European Journal of Human Genetics

    Article Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS

    doi: 10.1038/ejhg.2009.225

    Figure Lengend Snippet: ( a ) Representative chromatogram of the heterozygous mutation (463 T > G) in ZRS. ( b ) Wild type. ( c ) Restriction analysis using Mse I restriction enzyme in all the sampled family members (normal and affected); the 268-bp mutant allele is indicated

    Article Snippet: The identified mutation and its segregation was confirmed by agarose gel electrophoresis of Mse I (New England Biolabs, Ipswich, MA, USA) digested PCR fragments.

    Techniques: Mutagenesis

    Comparative restriction patterns of C. hominis (A), C. parvum (B), C. felis (C), and C. meleagridis (D) obtained with the following enzymes: TaqI (lanes 1), AseI (lanes 2), MseI (lanes 3), BstUI (lanes 4), and SspI (lanes 5). Lanes 6, undigested C. hominis

    Journal: Journal of Clinical Microbiology

    Article Title: Detection of Cryptosporidium and Identification to the Species Level by Nested PCR and Restriction Fragment Length Polymorphism

    doi: 10.1128/JCM.43.3.1017-1023.2005

    Figure Lengend Snippet: Comparative restriction patterns of C. hominis (A), C. parvum (B), C. felis (C), and C. meleagridis (D) obtained with the following enzymes: TaqI (lanes 1), AseI (lanes 2), MseI (lanes 3), BstUI (lanes 4), and SspI (lanes 5). Lanes 6, undigested C. hominis

    Article Snippet: The enzymes used were TaqI (Roche-Bohringer, Mannheim, Germany), AseI, MseI, BstUI, and SspI (New England Biolabs, Beverly, Mass.)

    Techniques:

    Restriction enzyme analysis of influenza A H5 HA real-time RT-PCR amplicons. (a) MseI and Taq α I digestion of H5 WT (clade 1 and 2) and positive control (clade 3) HA amplicons. In the lane descriptions below, numbers in brackets after strain names

    Journal:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿

    doi: 10.1128/JCM.02007-06

    Figure Lengend Snippet: Restriction enzyme analysis of influenza A H5 HA real-time RT-PCR amplicons. (a) MseI and Taq α I digestion of H5 WT (clade 1 and 2) and positive control (clade 3) HA amplicons. In the lane descriptions below, numbers in brackets after strain names

    Article Snippet: The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion.

    Techniques: Quantitative RT-PCR, Positive Control