bsphi  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 98
    Name:
    BspHI
    Description:
    BspHI 2 500 units
    Catalog Number:
    R0517L
    Price:
    282
    Category:
    Restriction Enzymes
    Size:
    2 500 units
    Buy from Supplier


    Structured Review

    New England Biolabs bsphi
    BspHI
    BspHI 2 500 units
    https://www.bioz.com/result/bsphi/product/New England Biolabs
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bsphi - by Bioz Stars, 2021-04
    98/100 stars

    Images

    1) Product Images from "Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor"

    Article Title: Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1045

    Schematic illustration (left) and 2.5% agarose gel electrophoresis (right) for endonuclease digestion of the circular dimer, trimer and tetramer with MspI and BspHI. Lane L: DNA ladder with 100–1000 base pairs. Lane 1: tetrahedron monomer as a control; Lane 2: dimer without any enzyme; lane 3: dimer digested with MspI; lane 4: dimer digested with BspHI; lane 5: dimer digested by both of MspI and BspHI; lane 6: trimer without any enzyme; lane 7: trimer digested with MspI; lane 8: trimer digested with BspHI; lane 9: trimer digested by both of MspI and BspHI; lane 10: tetramer without any enzyme; lane 11: tetramer digested with MspI; lane 12: tetramer digested with BspHI; lane 13: tetramer digested by both of MspI and BspHI.
    Figure Legend Snippet: Schematic illustration (left) and 2.5% agarose gel electrophoresis (right) for endonuclease digestion of the circular dimer, trimer and tetramer with MspI and BspHI. Lane L: DNA ladder with 100–1000 base pairs. Lane 1: tetrahedron monomer as a control; Lane 2: dimer without any enzyme; lane 3: dimer digested with MspI; lane 4: dimer digested with BspHI; lane 5: dimer digested by both of MspI and BspHI; lane 6: trimer without any enzyme; lane 7: trimer digested with MspI; lane 8: trimer digested with BspHI; lane 9: trimer digested by both of MspI and BspHI; lane 10: tetramer without any enzyme; lane 11: tetramer digested with MspI; lane 12: tetramer digested with BspHI; lane 13: tetramer digested by both of MspI and BspHI.

    Techniques Used: Agarose Gel Electrophoresis

    2) Product Images from "Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy"

    Article Title: Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

    Journal: Journal for Immunotherapy of Cancer

    doi: 10.1136/jitc-2019-000299

    Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are four restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3′LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5′ overhangs: 5′-CATG-3′, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3′LTR and the 3′LTR/distal transgene junction, indicated by continuous arrows. This is followed by nested PCR, indicated by dotted arrows, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3′ end and a 5′overhang (5′-ATG-3′). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3′ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3′LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a low annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3′LTR primer and the longer cassette strand.
    Figure Legend Snippet: Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are four restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3′LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5′ overhangs: 5′-CATG-3′, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3′LTR and the 3′LTR/distal transgene junction, indicated by continuous arrows. This is followed by nested PCR, indicated by dotted arrows, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3′ end and a 5′overhang (5′-ATG-3′). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3′ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3′LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a low annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3′LTR primer and the longer cassette strand.

    Techniques Used: Polymerase Chain Reaction, Amplification, Genomic Sequencing, Sequencing, Inverse PCR, Nested PCR, Ligation, Blocking Assay

    3) Product Images from "A Simple RFLP-Based Method for HFE Gene Multiplex Amplification and Determination of Hereditary Hemochromatosis-Causing Mutation C282Y and H63D Variant with Highly Sensitive Determination of Contamination"

    Article Title: A Simple RFLP-Based Method for HFE Gene Multiplex Amplification and Determination of Hereditary Hemochromatosis-Causing Mutation C282Y and H63D Variant with Highly Sensitive Determination of Contamination

    Journal: BioMed Research International

    doi: 10.1155/2020/9396318

    Example of a compound heterozygote sample. Electrophoregram of a compound heterozygous sample (C282Y +/+, H63D +/-). (a–d) FAM-labeled PCR products (FGA STR allele), Yakima Yellow-labeled PCR products (SE33 STR alleles), and ATTO 550-labeled PCR products: FZD1 double digestion products of the FZD1 labeled on both primer size are 114 and 147 bp for SexA1 and BspHI digestion, respectively. Uncut FZD1 fragment would be 309 pb (171 or 204 bp in case of digestion failure with SexAI an BspH1, respectively). (c) ATTO 565-labeled HFE fragments digested with SexAI and BSPHI, respectively. Fragments are as labeled on the figure (H63 wild-type allele, C282Y variant, H63D variant, and C282 wild-type allele).
    Figure Legend Snippet: Example of a compound heterozygote sample. Electrophoregram of a compound heterozygous sample (C282Y +/+, H63D +/-). (a–d) FAM-labeled PCR products (FGA STR allele), Yakima Yellow-labeled PCR products (SE33 STR alleles), and ATTO 550-labeled PCR products: FZD1 double digestion products of the FZD1 labeled on both primer size are 114 and 147 bp for SexA1 and BspHI digestion, respectively. Uncut FZD1 fragment would be 309 pb (171 or 204 bp in case of digestion failure with SexAI an BspH1, respectively). (c) ATTO 565-labeled HFE fragments digested with SexAI and BSPHI, respectively. Fragments are as labeled on the figure (H63 wild-type allele, C282Y variant, H63D variant, and C282 wild-type allele).

    Techniques Used: Labeling, Polymerase Chain Reaction, Variant Assay

    4) Product Images from "Herpes Simplex Virus 2 Counteracts Neurite Outgrowth Repulsion during Infection in a Nerve Growth Factor-Dependent Manner"

    Article Title: Herpes Simplex Virus 2 Counteracts Neurite Outgrowth Repulsion during Infection in a Nerve Growth Factor-Dependent Manner

    Journal: Journal of Virology

    doi: 10.1128/JVI.01370-20

    Construction of the self-excisable, TK-positive BAC pHSV2(MS)Lox. (A to H) Schematic representation of the DNA constructs and HSV-2 intermediates during the modification of pHSV2(MS)BAC to pHSV2(MS)Lox, as described in Materials and Methods. cam R , chloramphenicol resistance cassette; ori2, repE, sopA, sopB, and sopC, genes and loci required for BAC replication in E. coli ; cre, eukaryotic Cre recombinase expression cassette, driven by the CMV promoter; loxP , Cre recombinase target sites; aphAI , kanamycin resistance cassette; rpsLneo , kanamycin resistance cassette-streptomycin resistance cassette fusion. (I) Agarose gel showing the results of restriction analysis using AscI and BspHI of BAC DNA from pHSV2(MS)BAC (pBAC) and pHSV2(MS)Lox (pLox) and the corresponding viral DNA isolated from eukaryotic cells transfected with the respective BACs (vBAC and vLox). The size markers on the left are in kilobase pairs. Changes in the restriction pattern resulting from BAC mutagenesis are indicated by asterisks. (J) Southern blot analysis. DNA restriction fragments from the agarose gel in panel I were transferred to a nylon membrane and probed with a 32 P-labeled PCR amplicon of the BAC-encoded chloramphenicol resistance cassette. (K) Determination of the acyclovir sensitivity of HSV2(MS)BAC and HSV2(MS)Lox. The relative number of plaques (considering the number of plaques with the smallest amount of ACV to be 100%) from triplicate titrations is plotted against the indicated concentrations of acyclovir (mean ± standard deviation).
    Figure Legend Snippet: Construction of the self-excisable, TK-positive BAC pHSV2(MS)Lox. (A to H) Schematic representation of the DNA constructs and HSV-2 intermediates during the modification of pHSV2(MS)BAC to pHSV2(MS)Lox, as described in Materials and Methods. cam R , chloramphenicol resistance cassette; ori2, repE, sopA, sopB, and sopC, genes and loci required for BAC replication in E. coli ; cre, eukaryotic Cre recombinase expression cassette, driven by the CMV promoter; loxP , Cre recombinase target sites; aphAI , kanamycin resistance cassette; rpsLneo , kanamycin resistance cassette-streptomycin resistance cassette fusion. (I) Agarose gel showing the results of restriction analysis using AscI and BspHI of BAC DNA from pHSV2(MS)BAC (pBAC) and pHSV2(MS)Lox (pLox) and the corresponding viral DNA isolated from eukaryotic cells transfected with the respective BACs (vBAC and vLox). The size markers on the left are in kilobase pairs. Changes in the restriction pattern resulting from BAC mutagenesis are indicated by asterisks. (J) Southern blot analysis. DNA restriction fragments from the agarose gel in panel I were transferred to a nylon membrane and probed with a 32 P-labeled PCR amplicon of the BAC-encoded chloramphenicol resistance cassette. (K) Determination of the acyclovir sensitivity of HSV2(MS)BAC and HSV2(MS)Lox. The relative number of plaques (considering the number of plaques with the smallest amount of ACV to be 100%) from triplicate titrations is plotted against the indicated concentrations of acyclovir (mean ± standard deviation).

    Techniques Used: BAC Assay, Construct, Modification, Chick Chorioallantoic Membrane Assay, Expressing, Agarose Gel Electrophoresis, Isolation, Transfection, Mutagenesis, Southern Blot, Labeling, Polymerase Chain Reaction, Amplification, Standard Deviation

    5) Product Images from "Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform"

    Article Title: Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform

    Journal: bioRxiv

    doi: 10.1101/833897

    Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are 4 restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3’LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5’ overhangs: 5’-CATG-3’, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3’LTR and the 3’LTR/distal transgene junction. This is followed by nested PCR, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3’ end and a 5’overhang (5’-ATG-3’). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3’ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3’LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a high annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3’LTR primer and the longer cassette strand.
    Figure Legend Snippet: Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are 4 restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3’LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5’ overhangs: 5’-CATG-3’, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3’LTR and the 3’LTR/distal transgene junction. This is followed by nested PCR, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3’ end and a 5’overhang (5’-ATG-3’). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3’ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3’LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a high annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3’LTR primer and the longer cassette strand.

    Techniques Used: Polymerase Chain Reaction, Amplification, Genomic Sequencing, Sequencing, Inverse PCR, Nested PCR, Ligation, Blocking Assay

    6) Product Images from "Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice"

    Article Title: Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice

    Journal: Molecular Therapy. Nucleic Acids

    doi: 10.1016/j.omtn.2017.11.012

    TALEN-Mediated Gene Targeting in Arg1 Δ Mouse iPSCs (A) Schematic diagram showing the site of Arg1 gene modification using TALEN set 7/8. The TALEN 7/8 pair was designed to target intron 6 of Arg1 . Each TALEN arm consists of a DNA-binding domain with repeat variable di-residues (RVDs) corresponding to DNA binding sequence proceeded by a 5′ T nucleotide and a 17-bp spacer region containing a BspHI recognition site (highlighted in yellow) to assay activity. TALE repeat domains are colored to indicate the identity of the RVD. Site-specific double-stranded breaks (DSBs) are generated upon dimerization of fused FokI endonucleases. (B) Electroporation to deliver 7 μg of each TALEN and pMax-GFP into cells to assess transfection efficiency. Images were acquired 24 hr post-electroporation. Scale bars, 95 μm. (C) Surveyor nuclease assay for detection of NHEJ-induced indels resulting from DSBs. The cleavage products were shown as extra bands (between 162 and 186 bp) indicated by the arrows. Mutation frequencies (indels %) were calculated by measuring the band intensities. (D) BspHI digestion results. The cut products were shown as extra bands (169 bp + 183 bp). (E) Sequencing data from PCR amplicons of TALEN-modified genomic DNA showing a few examples of NHEJ-mediated indel mutations at the desired location. The wild-type sequence is shown above with the TALEN-binding sites in red. Deleted bases are indicated by colons, and inserted bases are shown by lowercase letters in blue. The net change in length caused by each indel mutation is to the right of each sequence.
    Figure Legend Snippet: TALEN-Mediated Gene Targeting in Arg1 Δ Mouse iPSCs (A) Schematic diagram showing the site of Arg1 gene modification using TALEN set 7/8. The TALEN 7/8 pair was designed to target intron 6 of Arg1 . Each TALEN arm consists of a DNA-binding domain with repeat variable di-residues (RVDs) corresponding to DNA binding sequence proceeded by a 5′ T nucleotide and a 17-bp spacer region containing a BspHI recognition site (highlighted in yellow) to assay activity. TALE repeat domains are colored to indicate the identity of the RVD. Site-specific double-stranded breaks (DSBs) are generated upon dimerization of fused FokI endonucleases. (B) Electroporation to deliver 7 μg of each TALEN and pMax-GFP into cells to assess transfection efficiency. Images were acquired 24 hr post-electroporation. Scale bars, 95 μm. (C) Surveyor nuclease assay for detection of NHEJ-induced indels resulting from DSBs. The cleavage products were shown as extra bands (between 162 and 186 bp) indicated by the arrows. Mutation frequencies (indels %) were calculated by measuring the band intensities. (D) BspHI digestion results. The cut products were shown as extra bands (169 bp + 183 bp). (E) Sequencing data from PCR amplicons of TALEN-modified genomic DNA showing a few examples of NHEJ-mediated indel mutations at the desired location. The wild-type sequence is shown above with the TALEN-binding sites in red. Deleted bases are indicated by colons, and inserted bases are shown by lowercase letters in blue. The net change in length caused by each indel mutation is to the right of each sequence.

    Techniques Used: Modification, Binding Assay, Sequencing, Activity Assay, Generated, Electroporation, Transfection, Nuclease Assay, Non-Homologous End Joining, Mutagenesis, Polymerase Chain Reaction

    7) Product Images from "Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114"

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl1162

    Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.
    Figure Legend Snippet: Detection of SSBs in the GAL2 UAS region. ( A ) Detection of SSBs by S1 nuclease. Plugs containing genomic DNA from wild-type cells were directly equilibrated in restriction digestion buffer and treated with NcoI and XbaI. Genomic DNA recovered from the melted plugs was then incubated in the presence (lanes designated +) or absence (lanes designated −) of S1 nuclease. Numbers above the panels are culture time (hours) in SPM. The diagram is labeled as for Figure 5 . ( B ) Schematic diagram of SSB detection in rad50S strains using denaturing polyacrylamide gel. Nt.AlwI introduces an SSB into specific sequences of DNA (5′-GGATCNNNN/N-3′). The GAL2 promoter has the sequence only on the + strand. Probes A and B were labeled by multiple round primer extension in the presence of radio-labeled dCTP. ( C ) and ( D ) Detection of SSBs on the −/+ strand by using strand-specific probes. All strains are homozygous for the rad50S allele. After genomic DNA was prepared from the meiotic cells at the indicated times (hours), it was treated with AccI and BspHI. The right two lanes in each panel contain 5% DNA fragments, which were further digested with HhaI or Nt.AlwI. Strains used were YHS363, YHS397, YHS427 and YHS514.

    Techniques Used: Incubation, Labeling, Sequencing

    Related Articles

    Purification:

    Article Title: Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Article Snippet: After cells were spheroplasted with Zymolyase-20T (MP Biomedicals, Inc.) in spheroplast buffer (1% 2-mercaptoethanol, 1 M sorbitol, 0.1 M EDTA [pH 8.0]), they were lysed and digested in lysis buffer (50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0], 0.5% SDS, 200 µg of proteinase K). .. At the GAL2 locus, the purified genomic DNA was treated with AccI, BspHI, HhaI and Nt.AlwI (New England BioLabs) for several hours. .. Nt.AlwI was used as a positive control for SSB detection.

    Polymerase Chain Reaction:

    Article Title: Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice
    Article Snippet: .. The PCR products were also assessed for gene modification by BspHI (NEB, Ipswich, MA) digestion, which gave rise to 183 and 169 bp fragments. .. To confirm TALEN-mediated gene modification, PCR amplicons were subcloned into pCR 2.1-TOPO TA vector (Invitrogen, Carlsbad, CA) and individual colonies were subjected to sequence analysis.

    Modification:

    Article Title: Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice
    Article Snippet: .. The PCR products were also assessed for gene modification by BspHI (NEB, Ipswich, MA) digestion, which gave rise to 183 and 169 bp fragments. .. To confirm TALEN-mediated gene modification, PCR amplicons were subcloned into pCR 2.1-TOPO TA vector (Invitrogen, Carlsbad, CA) and individual colonies were subjected to sequence analysis.

    BAC Assay:

    Article Title: Herpes Simplex Virus 2 Counteracts Neurite Outgrowth Repulsion during Infection in a Nerve Growth Factor-Dependent Manner
    Article Snippet: BAC DNA for analytical purposes was isolated from transformed Escherichia coli GS 1783 cells ( ) overnight culture using a NucleoBond XBAC kit from Macherey-Nagel (Düren, Germany). .. Restriction analysis of BAC DNA.To analyze the restriction fragments of BAC DNA and viral DNA from HSV2(MS)Lox and HSV2(MS)BAC, we used AscI and BspHI (New England Biolabs). ..

    Plasmid Preparation:

    Article Title: Structural Characterization of the Xi Class Glutathione Transferase From the Haloalkaliphilic Archaeon Natrialba magadii
    Article Snippet: Successful amplification was confirmed by agarose gel electrophoresis and the PCR product was first subcloned into pCR2.1-TOPO vector (TOPO TA Cloning Kit, Thermo Fisher Scientific) according to the manufacturer’s protocol and further sequencing to confirm a correct amplification. .. Then, the inserted fragment was digested with BspHI and BamHI (New England BioLabs) from pCR2.1 TOPO vector and inserted into the PciI and BamHI sites of pTA963 expression vector. .. Restriction products were visualized on a 0.8% agarose gel containing ethidium bromide (0.5 μg/mL).

    Expressing:

    Article Title: Structural Characterization of the Xi Class Glutathione Transferase From the Haloalkaliphilic Archaeon Natrialba magadii
    Article Snippet: Successful amplification was confirmed by agarose gel electrophoresis and the PCR product was first subcloned into pCR2.1-TOPO vector (TOPO TA Cloning Kit, Thermo Fisher Scientific) according to the manufacturer’s protocol and further sequencing to confirm a correct amplification. .. Then, the inserted fragment was digested with BspHI and BamHI (New England BioLabs) from pCR2.1 TOPO vector and inserted into the PciI and BamHI sites of pTA963 expression vector. .. Restriction products were visualized on a 0.8% agarose gel containing ethidium bromide (0.5 μg/mL).

    other:

    Article Title: Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor
    Article Snippet: Tris(hydroxymethyl)aminomethane hydrochloride (Tris) was purchased from Bio-Rad (Singapore); MgCl2 were from Quality Reagent Chemical (Singapore); EDTA were from USB biochemical (USA); agarose was purchased from Bio-Rad (Singapore); 100bp DNA ladder was from Thermo Fisher (Singapore); Endonuclease MspI and BspHI were purchased from New England Biolabs (Singapore).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 98
    New England Biolabs bsphi
    Schematic illustration (left) and 2.5% agarose gel electrophoresis (right) for endonuclease digestion of the circular dimer, trimer and tetramer with MspI and <t>BspHI.</t> Lane L: <t>DNA</t> ladder with 100–1000 base pairs. Lane 1: tetrahedron monomer as a control; Lane 2: dimer without any enzyme; lane 3: dimer digested with MspI; lane 4: dimer digested with BspHI; lane 5: dimer digested by both of MspI and BspHI; lane 6: trimer without any enzyme; lane 7: trimer digested with MspI; lane 8: trimer digested with BspHI; lane 9: trimer digested by both of MspI and BspHI; lane 10: tetramer without any enzyme; lane 11: tetramer digested with MspI; lane 12: tetramer digested with BspHI; lane 13: tetramer digested by both of MspI and BspHI.
    Bsphi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bsphi/product/New England Biolabs
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bsphi - by Bioz Stars, 2021-04
    98/100 stars
      Buy from Supplier

    Image Search Results


    Schematic illustration (left) and 2.5% agarose gel electrophoresis (right) for endonuclease digestion of the circular dimer, trimer and tetramer with MspI and BspHI. Lane L: DNA ladder with 100–1000 base pairs. Lane 1: tetrahedron monomer as a control; Lane 2: dimer without any enzyme; lane 3: dimer digested with MspI; lane 4: dimer digested with BspHI; lane 5: dimer digested by both of MspI and BspHI; lane 6: trimer without any enzyme; lane 7: trimer digested with MspI; lane 8: trimer digested with BspHI; lane 9: trimer digested by both of MspI and BspHI; lane 10: tetramer without any enzyme; lane 11: tetramer digested with MspI; lane 12: tetramer digested with BspHI; lane 13: tetramer digested by both of MspI and BspHI.

    Journal: Nucleic Acids Research

    Article Title: Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor

    doi: 10.1093/nar/gkx1045

    Figure Lengend Snippet: Schematic illustration (left) and 2.5% agarose gel electrophoresis (right) for endonuclease digestion of the circular dimer, trimer and tetramer with MspI and BspHI. Lane L: DNA ladder with 100–1000 base pairs. Lane 1: tetrahedron monomer as a control; Lane 2: dimer without any enzyme; lane 3: dimer digested with MspI; lane 4: dimer digested with BspHI; lane 5: dimer digested by both of MspI and BspHI; lane 6: trimer without any enzyme; lane 7: trimer digested with MspI; lane 8: trimer digested with BspHI; lane 9: trimer digested by both of MspI and BspHI; lane 10: tetramer without any enzyme; lane 11: tetramer digested with MspI; lane 12: tetramer digested with BspHI; lane 13: tetramer digested by both of MspI and BspHI.

    Article Snippet: Tris(hydroxymethyl)aminomethane hydrochloride (Tris) was purchased from Bio-Rad (Singapore); MgCl2 were from Quality Reagent Chemical (Singapore); EDTA were from USB biochemical (USA); agarose was purchased from Bio-Rad (Singapore); 100bp DNA ladder was from Thermo Fisher (Singapore); Endonuclease MspI and BspHI were purchased from New England Biolabs (Singapore).

    Techniques: Agarose Gel Electrophoresis

    Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are four restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3′LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5′ overhangs: 5′-CATG-3′, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3′LTR and the 3′LTR/distal transgene junction, indicated by continuous arrows. This is followed by nested PCR, indicated by dotted arrows, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3′ end and a 5′overhang (5′-ATG-3′). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3′ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3′LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a low annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3′LTR primer and the longer cassette strand.

    Journal: Journal for Immunotherapy of Cancer

    Article Title: Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

    doi: 10.1136/jitc-2019-000299

    Figure Lengend Snippet: Schematic for PCR amplification of flanking genomic sequences. (A) Genomic DNA is digested with two 6-cutter restriction enzymes, NcoI and BspHI , which together are anticipated to cut at approximately 2 kb intervals. There are four restriction sites within the transgene sequence, the most distal of which is 1185 bp from the 3′LTR / genomic junction. NcoI and BspHI generate identical 4-nucleotide 5′ overhangs: 5′-CATG-3′, which can be circularized for inverse PCR or ligated to linker cassettes. (B) Inverse PCR begins with circularization with T4 DNA ligase, followed by PCR amplification of the unknown flanking genomic sequences using primers targeting the 3′LTR and the 3′LTR/distal transgene junction, indicated by continuous arrows. This is followed by nested PCR, indicated by dotted arrows, which incorporates tailing sequences for subsequent barcoding. The combined lengths of the dotted lines in the inner circle indicate the minimum theoretical length prior to the addition of tailing sequences and barcodes. (C) The ligation cassette comprises two partially complementary strands: a 27-nucleotide strand and a 14-nucleotide strand, the latter with a mismatched A at the 3′ end and a 5′overhang (5′-ATG-3′). Before cassette ligation, the genomic DNA fragments are filled with a single ddCTP to prevent elongation or ligation at the recessed 3′ end. Cassette ligation results in a nick on this strand, indicated by ‘X’. During the first cycle of PCR, fragments containing flanking genomic DNA are amplified by a primer spanning the transgene/3′LTR. The longer cassette strand does not prime because its complementary shorter strand has not ligated; whereas the shorter cassette strand does not prime because only 10 nucleotides are complementary to the longer cassette strand, resulting in a low annealing temperature. This cassette design limits the amplification of non-flanking genomic DNA and reduces PCR blocking by the shorter cassette strand. Subsequent cycles are primed by both the transgene/3′LTR primer and the longer cassette strand.

    Article Snippet: Genomic DNA was digested with two 6-cutter restriction enzymes which generate compatible cohesive ends (underlined): NcoI , which cuts at C/ CATG G and BspHI , which cuts at T/ CATG A (both from New England BioLabs, Ipswich, MA).

    Techniques: Polymerase Chain Reaction, Amplification, Genomic Sequencing, Sequencing, Inverse PCR, Nested PCR, Ligation, Blocking Assay

    Example of a compound heterozygote sample. Electrophoregram of a compound heterozygous sample (C282Y +/+, H63D +/-). (a–d) FAM-labeled PCR products (FGA STR allele), Yakima Yellow-labeled PCR products (SE33 STR alleles), and ATTO 550-labeled PCR products: FZD1 double digestion products of the FZD1 labeled on both primer size are 114 and 147 bp for SexA1 and BspHI digestion, respectively. Uncut FZD1 fragment would be 309 pb (171 or 204 bp in case of digestion failure with SexAI an BspH1, respectively). (c) ATTO 565-labeled HFE fragments digested with SexAI and BSPHI, respectively. Fragments are as labeled on the figure (H63 wild-type allele, C282Y variant, H63D variant, and C282 wild-type allele).

    Journal: BioMed Research International

    Article Title: A Simple RFLP-Based Method for HFE Gene Multiplex Amplification and Determination of Hereditary Hemochromatosis-Causing Mutation C282Y and H63D Variant with Highly Sensitive Determination of Contamination

    doi: 10.1155/2020/9396318

    Figure Lengend Snippet: Example of a compound heterozygote sample. Electrophoregram of a compound heterozygous sample (C282Y +/+, H63D +/-). (a–d) FAM-labeled PCR products (FGA STR allele), Yakima Yellow-labeled PCR products (SE33 STR alleles), and ATTO 550-labeled PCR products: FZD1 double digestion products of the FZD1 labeled on both primer size are 114 and 147 bp for SexA1 and BspHI digestion, respectively. Uncut FZD1 fragment would be 309 pb (171 or 204 bp in case of digestion failure with SexAI an BspH1, respectively). (c) ATTO 565-labeled HFE fragments digested with SexAI and BSPHI, respectively. Fragments are as labeled on the figure (H63 wild-type allele, C282Y variant, H63D variant, and C282 wild-type allele).

    Article Snippet: SexAI and BspHI were from New England Biolabs (Evry, France).

    Techniques: Labeling, Polymerase Chain Reaction, Variant Assay

    Construction of the self-excisable, TK-positive BAC pHSV2(MS)Lox. (A to H) Schematic representation of the DNA constructs and HSV-2 intermediates during the modification of pHSV2(MS)BAC to pHSV2(MS)Lox, as described in Materials and Methods. cam R , chloramphenicol resistance cassette; ori2, repE, sopA, sopB, and sopC, genes and loci required for BAC replication in E. coli ; cre, eukaryotic Cre recombinase expression cassette, driven by the CMV promoter; loxP , Cre recombinase target sites; aphAI , kanamycin resistance cassette; rpsLneo , kanamycin resistance cassette-streptomycin resistance cassette fusion. (I) Agarose gel showing the results of restriction analysis using AscI and BspHI of BAC DNA from pHSV2(MS)BAC (pBAC) and pHSV2(MS)Lox (pLox) and the corresponding viral DNA isolated from eukaryotic cells transfected with the respective BACs (vBAC and vLox). The size markers on the left are in kilobase pairs. Changes in the restriction pattern resulting from BAC mutagenesis are indicated by asterisks. (J) Southern blot analysis. DNA restriction fragments from the agarose gel in panel I were transferred to a nylon membrane and probed with a 32 P-labeled PCR amplicon of the BAC-encoded chloramphenicol resistance cassette. (K) Determination of the acyclovir sensitivity of HSV2(MS)BAC and HSV2(MS)Lox. The relative number of plaques (considering the number of plaques with the smallest amount of ACV to be 100%) from triplicate titrations is plotted against the indicated concentrations of acyclovir (mean ± standard deviation).

    Journal: Journal of Virology

    Article Title: Herpes Simplex Virus 2 Counteracts Neurite Outgrowth Repulsion during Infection in a Nerve Growth Factor-Dependent Manner

    doi: 10.1128/JVI.01370-20

    Figure Lengend Snippet: Construction of the self-excisable, TK-positive BAC pHSV2(MS)Lox. (A to H) Schematic representation of the DNA constructs and HSV-2 intermediates during the modification of pHSV2(MS)BAC to pHSV2(MS)Lox, as described in Materials and Methods. cam R , chloramphenicol resistance cassette; ori2, repE, sopA, sopB, and sopC, genes and loci required for BAC replication in E. coli ; cre, eukaryotic Cre recombinase expression cassette, driven by the CMV promoter; loxP , Cre recombinase target sites; aphAI , kanamycin resistance cassette; rpsLneo , kanamycin resistance cassette-streptomycin resistance cassette fusion. (I) Agarose gel showing the results of restriction analysis using AscI and BspHI of BAC DNA from pHSV2(MS)BAC (pBAC) and pHSV2(MS)Lox (pLox) and the corresponding viral DNA isolated from eukaryotic cells transfected with the respective BACs (vBAC and vLox). The size markers on the left are in kilobase pairs. Changes in the restriction pattern resulting from BAC mutagenesis are indicated by asterisks. (J) Southern blot analysis. DNA restriction fragments from the agarose gel in panel I were transferred to a nylon membrane and probed with a 32 P-labeled PCR amplicon of the BAC-encoded chloramphenicol resistance cassette. (K) Determination of the acyclovir sensitivity of HSV2(MS)BAC and HSV2(MS)Lox. The relative number of plaques (considering the number of plaques with the smallest amount of ACV to be 100%) from triplicate titrations is plotted against the indicated concentrations of acyclovir (mean ± standard deviation).

    Article Snippet: Restriction analysis of BAC DNA.To analyze the restriction fragments of BAC DNA and viral DNA from HSV2(MS)Lox and HSV2(MS)BAC, we used AscI and BspHI (New England Biolabs).

    Techniques: BAC Assay, Construct, Modification, Chick Chorioallantoic Membrane Assay, Expressing, Agarose Gel Electrophoresis, Isolation, Transfection, Mutagenesis, Southern Blot, Labeling, Polymerase Chain Reaction, Amplification, Standard Deviation