hhai  (New England Biolabs)


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    Name:
    HhaI
    Description:
    HhaI 10 000 units
    Catalog Number:
    r0139l
    Price:
    249
    Size:
    10 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs hhai
    HhaI
    HhaI 10 000 units
    https://www.bioz.com/result/hhai/product/New England Biolabs
    Average 99 stars, based on 4521 article reviews
    Price from $9.99 to $1999.99
    hhai - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Fidelity Index Determination of DNA Methyltransferases"

    Article Title: Fidelity Index Determination of DNA Methyltransferases

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0063866

    Radioactive methylation assay using E. coli DNA-comparison between restriction enzyme digested substrate versus undigested substrate. The dilution series and presentation of data are the same as in Figure 3 . A) H 3 -methyl incorporation by M.EcoKDam. At a dilution of 1/2 4 , the substrate is fully methylated and after a dilution of 1/2 2 , the CPMs start to increase indicating star activity. This results in an FI of 4. B) H 3 -methyl incorporation by M.EcoKDam with DNA that has been digested with MboI restriction enzyme to remove all M.EcoKDam cognate sites. After a dilution of 1/2 2 , the CPMs start to increase, indicating methylation at non-cognate sites. C) H 3 -methyl incorporation by M.HhaI. At a dilution of 1/2 8 , the substrate is fully methylated and after a dilution of 1/2 3 , the CPMs start to increase indicating star activity. This results in an FI of 32. D) H 3 -methyl incorporation by M.HhaI with DNA that has been digested with HhaI restriction enzyme to remove all M.HhaI cognate sites. After a dilution of 1/2 3 , the CPMs start to increase, indicating methylation at non-cognate sites.
    Figure Legend Snippet: Radioactive methylation assay using E. coli DNA-comparison between restriction enzyme digested substrate versus undigested substrate. The dilution series and presentation of data are the same as in Figure 3 . A) H 3 -methyl incorporation by M.EcoKDam. At a dilution of 1/2 4 , the substrate is fully methylated and after a dilution of 1/2 2 , the CPMs start to increase indicating star activity. This results in an FI of 4. B) H 3 -methyl incorporation by M.EcoKDam with DNA that has been digested with MboI restriction enzyme to remove all M.EcoKDam cognate sites. After a dilution of 1/2 2 , the CPMs start to increase, indicating methylation at non-cognate sites. C) H 3 -methyl incorporation by M.HhaI. At a dilution of 1/2 8 , the substrate is fully methylated and after a dilution of 1/2 3 , the CPMs start to increase indicating star activity. This results in an FI of 32. D) H 3 -methyl incorporation by M.HhaI with DNA that has been digested with HhaI restriction enzyme to remove all M.HhaI cognate sites. After a dilution of 1/2 3 , the CPMs start to increase, indicating methylation at non-cognate sites.

    Techniques Used: Methylation, Activity Assay

    2) Product Images from "Fidelity Index Determination of DNA Methyltransferases"

    Article Title: Fidelity Index Determination of DNA Methyltransferases

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0063866

    Radioactive methylation assay using E. coli DNA-comparison between restriction enzyme digested substrate versus undigested substrate. The dilution series and presentation of data are the same as in Figure 3 . A) H 3 -methyl incorporation by M.EcoKDam. At a dilution of 1/2 4 , the substrate is fully methylated and after a dilution of 1/2 2 , the CPMs start to increase indicating star activity. This results in an FI of 4. B) H 3 -methyl incorporation by M.EcoKDam with DNA that has been digested with MboI restriction enzyme to remove all M.EcoKDam cognate sites. After a dilution of 1/2 2 , the CPMs start to increase, indicating methylation at non-cognate sites. C) H 3 -methyl incorporation by M.HhaI. At a dilution of 1/2 8 , the substrate is fully methylated and after a dilution of 1/2 3 , the CPMs start to increase indicating star activity. This results in an FI of 32. D) H 3 -methyl incorporation by M.HhaI with DNA that has been digested with HhaI restriction enzyme to remove all M.HhaI cognate sites. After a dilution of 1/2 3 , the CPMs start to increase, indicating methylation at non-cognate sites.
    Figure Legend Snippet: Radioactive methylation assay using E. coli DNA-comparison between restriction enzyme digested substrate versus undigested substrate. The dilution series and presentation of data are the same as in Figure 3 . A) H 3 -methyl incorporation by M.EcoKDam. At a dilution of 1/2 4 , the substrate is fully methylated and after a dilution of 1/2 2 , the CPMs start to increase indicating star activity. This results in an FI of 4. B) H 3 -methyl incorporation by M.EcoKDam with DNA that has been digested with MboI restriction enzyme to remove all M.EcoKDam cognate sites. After a dilution of 1/2 2 , the CPMs start to increase, indicating methylation at non-cognate sites. C) H 3 -methyl incorporation by M.HhaI. At a dilution of 1/2 8 , the substrate is fully methylated and after a dilution of 1/2 3 , the CPMs start to increase indicating star activity. This results in an FI of 32. D) H 3 -methyl incorporation by M.HhaI with DNA that has been digested with HhaI restriction enzyme to remove all M.HhaI cognate sites. After a dilution of 1/2 3 , the CPMs start to increase, indicating methylation at non-cognate sites.

    Techniques Used: Methylation, Activity Assay

    Related Articles

    Clone Assay:

    Article Title: Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota
    Article Snippet: .. Terminal restriction fragments using the restriction enzymes HhaI and MspI were calculated for each of the 16S rRNA-encoding gene clones using a software tool designed to be integrated into the ARB program suite ( ). .. This in silico T-RFLP analysis tool (TRF-CUT) predicts TRFs based on the ARB-aligned sequences.

    GWAS:

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
    Article Snippet: The array contains 659,636 SNPs, including tag-SNPs for imputation, as well as SNPs related to phenotypes from previously reported GWAS and pharmacogenomics studies. .. DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ].

    Amplification:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: Paragraph title: Amplification, methylation of 219bp DNA fragments as the EMSA substrate for Sco5333 ... In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively.

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: .. The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. Restriction fragments were separated on a 2% (wt/vol) agarose gel and visualized by staining with ethidium bromide.

    Article Title: Broad Resistance to ACCase Inhibiting Herbicides in a Ryegrass Population Is Due Only to a Cysteine to Arginine Mutation in the Target Enzyme
    Article Snippet: Paragraph title: Development of a Cleaved Amplified Polymorphic Sequence (CAPS) method for detecting the C2088R ACCase mutation ... Two µl aliquots of neat PCR products were digested with 2 units of Hha I (New England Biolabs, Hertfordshire, UK) in a total volume of 20 µL according to the manufacturer's recommendations and analysed on 2% agarose/1 X TBE buffer gels containing 0.5 µg mL−1 ethidium bromide.

    Whole Genome Amplification:

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
    Article Snippet: Whole-genome-amplification makes DNA fully un-methylated, the (U) samples were used as control samples for the effect of SNPs at enzyme cleavage sites. .. DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ].

    Positive Control:

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: The positive control of B. vinsonii subsp. berkhoffii was systematically prepared last, to prevent possible cross contamination with the tested samples. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Synthesized:

    Article Title: Generation and Molecular Characterization of New Temperature-Sensitive Plasmids Intended for Genetic Engineering of Pasteurellaceae
    Article Snippet: An oligonucleotide primer which is complementary with sequences 3′ from an HsoI site of pBluescript SK was synthesized. .. HsoI or HhaI (New England Biolabs) was added to the end-labeled reaction and was allowed to digest the DNA for 2min.

    Real-time Polymerase Chain Reaction:

    Article Title: Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
    Article Snippet: .. Compare-MS DNA methylation analysis For COMPARE-MS analysis of DNA methylation at newly identified cancer hypermethylated regions in prostate cancer cell lines, tumor-normal paired tissues, and reference samples, DNA samples were digested with R.AluI and R.HhaI (NEB) and methylated fragments were enriched and analyzed by real-time PCR as described previously [ ]. .. COMPARE-MS primers and corresponding annealing temperatures for real time PCR are shown in Additional File .

    Incubation:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively. .. For EMSA, Sco5333 of varied concentrations (0–0.2 μM) was incubated with methylated 219 bp DNA at 37°C for 5 min in 20 μl binding buffer (20 mM Tris–Cl pH 8.0, 100 mM KCl), the reaction mixture was mixed with 4 μl 6 × loading buffer (30 mM EDTA, 36% glycerol, 0.035% xylene cyanol, 0.05% bromophenol blue (TAKARA) and then resolved by 6% native-PAGE (80:1, acrylamide/bis-acrylamide) in 0.5× Tris-borate EDTA (TBE) at 10 mA at room temperature.

    Activity Assay:

    Article Title: 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation
    Article Snippet: Digestion with methylation-sensitive restriction enzymes Genomic DNA (500 ng) was digested with Hpa II (Invitrogen, Carlsbad, CA, USA), Bst UI and Hha I (New England Biolabs, Ipswich, MA, USA) for 6 h at 37°C (Hpa II and Hha I) or 60°C (Bst UI), or was mock-digested without the restriction enzymes. .. Throughout the methylation-based PCR assays, 5me CpG-sensitive restriction endonuclease activity was assessed by genotyping DNA from four healthy males (not shown).

    DNA Sequencing:

    Article Title: Generation and Molecular Characterization of New Temperature-Sensitive Plasmids Intended for Genetic Engineering of Pasteurellaceae
    Article Snippet: Standard dideoxy DNA sequencing reactions were performed, and an additional reaction containing no dideoxy terminator was extended through the HsoI site with the Klenow fragment of DNA polymerase I by using 32 P-end-labeled primer. .. HsoI or HhaI (New England Biolabs) was added to the end-labeled reaction and was allowed to digest the DNA for 2min.

    Polymerase Chain Reaction:

    Article Title: 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation
    Article Snippet: Digestion with methylation-sensitive restriction enzymes Genomic DNA (500 ng) was digested with Hpa II (Invitrogen, Carlsbad, CA, USA), Bst UI and Hha I (New England Biolabs, Ipswich, MA, USA) for 6 h at 37°C (Hpa II and Hha I) or 60°C (Bst UI), or was mock-digested without the restriction enzymes. .. Throughout the methylation-based PCR assays, 5me CpG-sensitive restriction endonuclease activity was assessed by genotyping DNA from four healthy males (not shown).

    Article Title: Plasmodium vivax msp-3α polymorphisms: analysis in the Indian subcontinent
    Article Snippet: RFLP analysis Characterization of the allelic patterns of the 167 PCR single clone isolates obtained was performed using the Alu I and Hha I restriction enzymes based on the methods reported by Bruce et al. [ ]. .. To determine the level of Pvmsp -3α polymorphism, RFLP analysis was carried out using the Hha I and Alu I restriction enzymes (NEB, Inc, Beverly, MA, USA) in a 10-µL reaction volume.

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: Amplification, methylation of 219bp DNA fragments as the EMSA substrate for Sco5333 The 219 bp fragment from NT885–1103 of pUC18 (accession no.: L08752) that contains two Dcm-methylation sites (NT954–958; NT967–971) was PCR amplified using primers 219 bp-F & R and purified, and then treated with 2 μM purified Dcm methyltransferase in buffer (50 mM Tris–HCl pH 7.5, 5 mM β-mercaptoethanol, 10 mM EDTA and 160 μM SAM) in a volume of 30 μl at 37°C for 1 h followed by heat inactivation at 85°C for 10. .. In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively.

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: .. The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. Restriction fragments were separated on a 2% (wt/vol) agarose gel and visualized by staining with ethidium bromide.

    Article Title: Broad Resistance to ACCase Inhibiting Herbicides in a Ryegrass Population Is Due Only to a Cysteine to Arginine Mutation in the Target Enzyme
    Article Snippet: .. Two µl aliquots of neat PCR products were digested with 2 units of Hha I (New England Biolabs, Hertfordshire, UK) in a total volume of 20 µL according to the manufacturer's recommendations and analysed on 2% agarose/1 X TBE buffer gels containing 0.5 µg mL−1 ethidium bromide. .. Upon restriction with Hha I the mutated allele is digested into a 126 bp and 35 bp (invisible on the 2% agarose gel) fragments.

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene. .. Banding patterns were compared to the profiles of B. henselae Houston-1 (ATCC 49882), B. clarridgeiae (ATCC 700095), B. quintana (ATCC VR-358), B. bacilliformis (ATCC 35686), B. elizabethae (ATCC 49927), Bartonella strain cattle-1 (University of California, Davis), B. vinsonii subsp. vinsonii (ATCC VR-152), and B. vinsonii subsp. berkhoffii (ATCC 51672).

    Binding Assay:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively. .. For EMSA, Sco5333 of varied concentrations (0–0.2 μM) was incubated with methylated 219 bp DNA at 37°C for 5 min in 20 μl binding buffer (20 mM Tris–Cl pH 8.0, 100 mM KCl), the reaction mixture was mixed with 4 μl 6 × loading buffer (30 mM EDTA, 36% glycerol, 0.035% xylene cyanol, 0.05% bromophenol blue (TAKARA) and then resolved by 6% native-PAGE (80:1, acrylamide/bis-acrylamide) in 0.5× Tris-borate EDTA (TBE) at 10 mA at room temperature.

    DNA Extraction:

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: Disposable sterile vials and filter tips were used for DNA extraction and PCR reagent preparation. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Methylation:

    Article Title: 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation
    Article Snippet: .. Digestion with methylation-sensitive restriction enzymes Genomic DNA (500 ng) was digested with Hpa II (Invitrogen, Carlsbad, CA, USA), Bst UI and Hha I (New England Biolabs, Ipswich, MA, USA) for 6 h at 37°C (Hpa II and Hha I) or 60°C (Bst UI), or was mock-digested without the restriction enzymes. ..

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
    Article Snippet: .. DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ]. .. A cocktail consisting of 1 μL each of three MSREs was diluted by 5 μL CutSmart Buffer (New England BioLabs) and RNase-free water in a total reaction volume of 50 μL, and 1 μg of DNA was digested at 37°C.

    Article Title: Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
    Article Snippet: .. Compare-MS DNA methylation analysis For COMPARE-MS analysis of DNA methylation at newly identified cancer hypermethylated regions in prostate cancer cell lines, tumor-normal paired tissues, and reference samples, DNA samples were digested with R.AluI and R.HhaI (NEB) and methylated fragments were enriched and analyzed by real-time PCR as described previously [ ]. .. COMPARE-MS primers and corresponding annealing temperatures for real time PCR are shown in Additional File .

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: .. In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively. .. For EMSA, Sco5333 of varied concentrations (0–0.2 μM) was incubated with methylated 219 bp DNA at 37°C for 5 min in 20 μl binding buffer (20 mM Tris–Cl pH 8.0, 100 mM KCl), the reaction mixture was mixed with 4 μl 6 × loading buffer (30 mM EDTA, 36% glycerol, 0.035% xylene cyanol, 0.05% bromophenol blue (TAKARA) and then resolved by 6% native-PAGE (80:1, acrylamide/bis-acrylamide) in 0.5× Tris-borate EDTA (TBE) at 10 mA at room temperature.

    Article Title: Modulation of DNA Binding Protein Affinity Directly Affects Target Site Demethylation
    Article Snippet: .. DNA was methylated with Hha I- or Sss I-methylase overnight under conditions recommended by the manufacturer (New England Biolabs). .. The DNA was phenol-chloroform extracted and ethanol precipitated after in vitro methylation.

    Mutagenesis:

    Article Title: Broad Resistance to ACCase Inhibiting Herbicides in a Ryegrass Population Is Due Only to a Cysteine to Arginine Mutation in the Target Enzyme
    Article Snippet: Paragraph title: Development of a Cleaved Amplified Polymorphic Sequence (CAPS) method for detecting the C2088R ACCase mutation ... Two µl aliquots of neat PCR products were digested with 2 units of Hha I (New England Biolabs, Hertfordshire, UK) in a total volume of 20 µL according to the manufacturer's recommendations and analysed on 2% agarose/1 X TBE buffer gels containing 0.5 µg mL−1 ethidium bromide.

    Isolation:

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
    Article Snippet: DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ]. .. The samples of (D) must be DNA from isolated LPMCs because these samples are for analyzing DNA methylation.

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: The PCR chamber was used only for the preparation of PCR reagents and not for the isolation or subculture of Bartonella spp. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Purification:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: Amplification, methylation of 219bp DNA fragments as the EMSA substrate for Sco5333 The 219 bp fragment from NT885–1103 of pUC18 (accession no.: L08752) that contains two Dcm-methylation sites (NT954–958; NT967–971) was PCR amplified using primers 219 bp-F & R and purified, and then treated with 2 μM purified Dcm methyltransferase in buffer (50 mM Tris–HCl pH 7.5, 5 mM β-mercaptoethanol, 10 mM EDTA and 160 μM SAM) in a volume of 30 μl at 37°C for 1 h followed by heat inactivation at 85°C for 10. .. In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively.

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: The final purified PCR product of the gltA gene was then used for PCR-restriction fragment length polymorphism (PCR-RFLP) and further sequencing analyses. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Sequencing:

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. The restriction enzymes for the differentiation of classical stx 1 and the stx 1c variant were selected with the DNASIS program, version 2.0, from Hitachi Software (San Bruno, Calif.) based on the published sequence of stx 1 from phage 933J (accession no. ) and the sequence of stx 1c from E. coli strain 3115/97 determined in this study.

    Article Title: Generation and Molecular Characterization of New Temperature-Sensitive Plasmids Intended for Genetic Engineering of Pasteurellaceae
    Article Snippet: Paragraph title: Determination of the sequence recognition site for HsoI. ... HsoI or HhaI (New England Biolabs) was added to the end-labeled reaction and was allowed to digest the DNA for 2min.

    Article Title: Broad Resistance to ACCase Inhibiting Herbicides in a Ryegrass Population Is Due Only to a Cysteine to Arginine Mutation in the Target Enzyme
    Article Snippet: Paragraph title: Development of a Cleaved Amplified Polymorphic Sequence (CAPS) method for detecting the C2088R ACCase mutation ... Two µl aliquots of neat PCR products were digested with 2 units of Hha I (New England Biolabs, Hertfordshire, UK) in a total volume of 20 µL according to the manufacturer's recommendations and analysed on 2% agarose/1 X TBE buffer gels containing 0.5 µg mL−1 ethidium bromide.

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: The final purified PCR product of the gltA gene was then used for PCR-restriction fragment length polymorphism (PCR-RFLP) and further sequencing analyses. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Software:

    Article Title: Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota
    Article Snippet: .. Terminal restriction fragments using the restriction enzymes HhaI and MspI were calculated for each of the 16S rRNA-encoding gene clones using a software tool designed to be integrated into the ARB program suite ( ). .. This in silico T-RFLP analysis tool (TRF-CUT) predicts TRFs based on the ARB-aligned sequences.

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. The restriction enzymes for the differentiation of classical stx 1 and the stx 1c variant were selected with the DNASIS program, version 2.0, from Hitachi Software (San Bruno, Calif.) based on the published sequence of stx 1 from phage 933J (accession no. ) and the sequence of stx 1c from E. coli strain 3115/97 determined in this study.

    Agarose Gel Electrophoresis:

    Article Title: Plasmodium vivax msp-3α polymorphisms: analysis in the Indian subcontinent
    Article Snippet: To determine the level of Pvmsp -3α polymorphism, RFLP analysis was carried out using the Hha I and Alu I restriction enzymes (NEB, Inc, Beverly, MA, USA) in a 10-µL reaction volume. .. A 5-µl aliquot of each PCR product was digested individually with the restriction enzymes along with BSA in the buffer supplied with the enzymes at 37 °C for 4 h. The restriction products were then visualized on a 3.0 % agarose gel.

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. Restriction fragments were separated on a 2% (wt/vol) agarose gel and visualized by staining with ethidium bromide.

    Article Title: Broad Resistance to ACCase Inhibiting Herbicides in a Ryegrass Population Is Due Only to a Cysteine to Arginine Mutation in the Target Enzyme
    Article Snippet: Two µl aliquots of neat PCR products were digested with 2 units of Hha I (New England Biolabs, Hertfordshire, UK) in a total volume of 20 µL according to the manufacturer's recommendations and analysed on 2% agarose/1 X TBE buffer gels containing 0.5 µg mL−1 ethidium bromide. .. Upon restriction with Hha I the mutated allele is digested into a 126 bp and 35 bp (invisible on the 2% agarose gel) fragments.

    In Vitro:

    Article Title: Modulation of DNA Binding Protein Affinity Directly Affects Target Site Demethylation
    Article Snippet: Paragraph title: In vitro methylation. ... DNA was methylated with Hha I- or Sss I-methylase overnight under conditions recommended by the manufacturer (New England Biolabs).

    Ethanol Precipitation:

    Article Title: Generation and Molecular Characterization of New Temperature-Sensitive Plasmids Intended for Genetic Engineering of Pasteurellaceae
    Article Snippet: The extension reaction was stopped by phenol-chloroform extraction followed by ethanol precipitation. .. HsoI or HhaI (New England Biolabs) was added to the end-labeled reaction and was allowed to digest the DNA for 2min.

    Gel Permeation Chromatography:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: .. In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively. .. For EMSA, Sco5333 of varied concentrations (0–0.2 μM) was incubated with methylated 219 bp DNA at 37°C for 5 min in 20 μl binding buffer (20 mM Tris–Cl pH 8.0, 100 mM KCl), the reaction mixture was mixed with 4 μl 6 × loading buffer (30 mM EDTA, 36% glycerol, 0.035% xylene cyanol, 0.05% bromophenol blue (TAKARA) and then resolved by 6% native-PAGE (80:1, acrylamide/bis-acrylamide) in 0.5× Tris-borate EDTA (TBE) at 10 mA at room temperature.

    DNA Methylation Assay:

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
    Article Snippet: DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ]. .. The samples of (D) must be DNA from isolated LPMCs because these samples are for analyzing DNA methylation.

    Article Title: Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
    Article Snippet: .. Compare-MS DNA methylation analysis For COMPARE-MS analysis of DNA methylation at newly identified cancer hypermethylated regions in prostate cancer cell lines, tumor-normal paired tissues, and reference samples, DNA samples were digested with R.AluI and R.HhaI (NEB) and methylated fragments were enriched and analyzed by real-time PCR as described previously [ ]. .. COMPARE-MS primers and corresponding annealing temperatures for real time PCR are shown in Additional File .

    Staining:

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. Restriction fragments were separated on a 2% (wt/vol) agarose gel and visualized by staining with ethidium bromide.

    Variant Assay:

    Article Title: Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (stx1c) in Escherichia coli Strains Isolated from Humans
    Article Snippet: The stxB 1 gene was amplified with primers KS7-KS8 (Table ), and 12 μl of each PCR product was digested with restriction endonuclease Fsp I or Hha I (New England BioLabs GmbH, Frankfurt, Germany), as recommended by the manufacturer. .. The restriction enzymes for the differentiation of classical stx 1 and the stx 1c variant were selected with the DNASIS program, version 2.0, from Hitachi Software (San Bruno, Calif.) based on the published sequence of stx 1 from phage 933J (accession no. ) and the sequence of stx 1c from E. coli strain 3115/97 determined in this study.

    Clear Native PAGE:

    Article Title: Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins
    Article Snippet: In addition, the 219 bp DNA fragment was methylated by commercially available methylases M.AluI, M.HhaI, M.HpaII, M.MspI, GpC(M.CviPI) and CpG(M.SssI) (NEB) respectively. .. For EMSA, Sco5333 of varied concentrations (0–0.2 μM) was incubated with methylated 219 bp DNA at 37°C for 5 min in 20 μl binding buffer (20 mM Tris–Cl pH 8.0, 100 mM KCl), the reaction mixture was mixed with 4 μl 6 × loading buffer (30 mM EDTA, 36% glycerol, 0.035% xylene cyanol, 0.05% bromophenol blue (TAKARA) and then resolved by 6% native-PAGE (80:1, acrylamide/bis-acrylamide) in 0.5× Tris-borate EDTA (TBE) at 10 mA at room temperature.

    Hood:

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California
    Article Snippet: To minimize bacterial contamination in the laboratory, all isolations were performed in a safety class II hood cabinet. .. Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

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    New England Biolabs mboi restriction enzyme
    Mboi Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 110 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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