bseri  (New England Biolabs)


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    BseRI
    Description:
    BseRI 1 000 units
    Catalog Number:
    r0581l
    Price:
    302
    Category:
    Restriction Enzymes
    Size:
    1 000 units
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    New England Biolabs bseri
    BseRI
    BseRI 1 000 units
    https://www.bioz.com/result/bseri/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bseri - by Bioz Stars, 2021-03
    93/100 stars

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    1) Product Images from "TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers"

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

    Journal: bioRxiv

    doi: 10.1101/2020.09.30.321323

    Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.
    Figure Legend Snippet: Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Techniques Used: Clone Assay, Plasmid Preparation, Sequencing, Amplification, Construct, Labeling

    Related Articles

    Plasmid Preparation:

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Article Snippet: Further below, we describe our sequencing strategy for associating random barcodes with guides. .. Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment. .. The ORI minimal promoter and flanking region was PCR amplified from the hSTARR-seq plasmid (Addgene #99296) with a custom primer that included homology for Gibson cloning and KAPA HiFi HotStart ReadyMix (Kapa KK2602) and then was agarose gel size-selected.

    Article Title: Rapid modification of the pET-28 expression vector for ligation independent cloning using homologous recombination in Saccharomyces cerevisiae
    Article Snippet: Amplification of the desired gene is followed by agarose gel purification, and eluted into 50 μl of water. .. Two micrograms of the pGAY-28 vector are restricted with BseRI (NEB), agarose gel purified, and eluted into 50 μl of water. .. The A260 for both the insert and vector are recorded.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Article Snippet: Several individual colonies were isolated, grown, maxi-prepped (Zymo D4202), and verified with Sanger sequencing. .. We digested the resulting plasmid with BseRI (NEB R0581L) and agarose gel-size selected the linearized fragment. .. The custom DNA fragment with the gRNA library, a Cas9 scaffold, spacer cloning site with two BseRI cut sites, and custom designed barcode was amplified with library-specific primers and the KAPA HiFi HotStart ReadyMix (Kapa KK2602) and then was agarose gel size-selected.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Agarose Gel Electrophoresis:

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Article Snippet: Further below, we describe our sequencing strategy for associating random barcodes with guides. .. Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment. .. The ORI minimal promoter and flanking region was PCR amplified from the hSTARR-seq plasmid (Addgene #99296) with a custom primer that included homology for Gibson cloning and KAPA HiFi HotStart ReadyMix (Kapa KK2602) and then was agarose gel size-selected.

    Article Title: Rapid modification of the pET-28 expression vector for ligation independent cloning using homologous recombination in Saccharomyces cerevisiae
    Article Snippet: Amplification of the desired gene is followed by agarose gel purification, and eluted into 50 μl of water. .. Two micrograms of the pGAY-28 vector are restricted with BseRI (NEB), agarose gel purified, and eluted into 50 μl of water. .. The A260 for both the insert and vector are recorded.

    Polymerase Chain Reaction:

    Article Title: Identification and characterization of two CD4 alleles in Microminipigs
    Article Snippet: CD4 genotyping by PCR-restriction fragment length polymorphism (PCR-RFLP) method The PCR-RFLP technique in association with the restriction enzyme Bse RI was used to identify and differentiate between the two CD4 alleles. .. PCR amplification was performed on genomic DNA to amplify CD4 exon 3, and the PCR products were digested with an enzyme, Bse RI (New England Biolabs Inc., Ipswich, MA). .. The allele-specific bands were analyzed by 2 % agarose gel electrophoresis.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Article Title: Topoisomerase II? Binding Protein 1 c.*229C > T (rs115160714) Gene Polymorphism and Endometrial Cancer Risk
    Article Snippet: The PCR condition for rs115160714 and rs112843513 comprised an initiation denaturation step at 94 °C for 4 min, followed by 30 cycles of 96 °C for 1 min, 59 °C for 1 min, 72 °C for 1 min and final extension step at 72 °C for 10 min. .. Subsequently, RFLP analysis was performed on 20 microliters each of the respective PCR products by subjecting them to the following restriction enzymes: at a 5U concentration: BseR I (at 37 °C for 3 h) for rs115160714 and Ras I (at 37 °C for 16 h) for rs112843513 (both from New England Biolabs, UK). .. In the case of rs115160714 the lengths of fragments obtained by digestion of each 211-bp fragment by BseR I were 84 bp and 127 bp for wild type, and 211 bp for mutant type.

    Amplification:

    Article Title: Identification and characterization of two CD4 alleles in Microminipigs
    Article Snippet: CD4 genotyping by PCR-restriction fragment length polymorphism (PCR-RFLP) method The PCR-RFLP technique in association with the restriction enzyme Bse RI was used to identify and differentiate between the two CD4 alleles. .. PCR amplification was performed on genomic DNA to amplify CD4 exon 3, and the PCR products were digested with an enzyme, Bse RI (New England Biolabs Inc., Ipswich, MA). .. The allele-specific bands were analyzed by 2 % agarose gel electrophoresis.

    Purification:

    Article Title: Rapid modification of the pET-28 expression vector for ligation independent cloning using homologous recombination in Saccharomyces cerevisiae
    Article Snippet: Amplification of the desired gene is followed by agarose gel purification, and eluted into 50 μl of water. .. Two micrograms of the pGAY-28 vector are restricted with BseRI (NEB), agarose gel purified, and eluted into 50 μl of water. .. The A260 for both the insert and vector are recorded.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Concentration Assay:

    Article Title: Topoisomerase II? Binding Protein 1 c.*229C > T (rs115160714) Gene Polymorphism and Endometrial Cancer Risk
    Article Snippet: The PCR condition for rs115160714 and rs112843513 comprised an initiation denaturation step at 94 °C for 4 min, followed by 30 cycles of 96 °C for 1 min, 59 °C for 1 min, 72 °C for 1 min and final extension step at 72 °C for 10 min. .. Subsequently, RFLP analysis was performed on 20 microliters each of the respective PCR products by subjecting them to the following restriction enzymes: at a 5U concentration: BseR I (at 37 °C for 3 h) for rs115160714 and Ras I (at 37 °C for 16 h) for rs112843513 (both from New England Biolabs, UK). .. In the case of rs115160714 the lengths of fragments obtained by digestion of each 211-bp fragment by BseR I were 84 bp and 127 bp for wild type, and 211 bp for mutant type.

    De-Phosphorylation Assay:

    Article Title: A versatile expression vector for the growth and amplification of unmodified phage display polypeptides.
    Article Snippet: Proteins and polypeptides represent nature's most complex and versatile polymer. .. Proteins and polypeptides represent nature's most complex and versatile polymer. .. Proteins and polypeptides represent nature's most complex and versatile polymer.

    Ligation:

    Article Title: A versatile expression vector for the growth and amplification of unmodified phage display polypeptides.
    Article Snippet: Proteins and polypeptides represent nature's most complex and versatile polymer. .. Proteins and polypeptides represent nature's most complex and versatile polymer. .. Proteins and polypeptides represent nature's most complex and versatile polymer.

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  • 90
    New England Biolabs bse ri
    Electrophoretic pattern of PCR-RFLP of genomic DNA. The lanes are AA: <t>CD4.AA;</t> AB: CD4.AB ; BB: CD4.BB; and the 100 bp ladder. The 366 bp-fragment was amplified from genomic DNA using primer pair for exon 3 (See Table 1 ). The PCR product was digested with <t>Bse</t> RI. PCR fragments with genotype of CD4.AA , CD4.AB , and CD4.BB showed single fragment (366 bp), three fragments (366, 260, and 106 bp), and two fragments (260 and 106 bp), respectively
    Bse Ri, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bse ri/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bse ri - by Bioz Stars, 2021-03
    90/100 stars
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    Electrophoretic pattern of PCR-RFLP of genomic DNA. The lanes are AA: CD4.AA; AB: CD4.AB ; BB: CD4.BB; and the 100 bp ladder. The 366 bp-fragment was amplified from genomic DNA using primer pair for exon 3 (See Table 1 ). The PCR product was digested with Bse RI. PCR fragments with genotype of CD4.AA , CD4.AB , and CD4.BB showed single fragment (366 bp), three fragments (366, 260, and 106 bp), and two fragments (260 and 106 bp), respectively

    Journal: BMC Veterinary Research

    Article Title: Identification and characterization of two CD4 alleles in Microminipigs

    doi: 10.1186/s12917-016-0856-8

    Figure Lengend Snippet: Electrophoretic pattern of PCR-RFLP of genomic DNA. The lanes are AA: CD4.AA; AB: CD4.AB ; BB: CD4.BB; and the 100 bp ladder. The 366 bp-fragment was amplified from genomic DNA using primer pair for exon 3 (See Table 1 ). The PCR product was digested with Bse RI. PCR fragments with genotype of CD4.AA , CD4.AB , and CD4.BB showed single fragment (366 bp), three fragments (366, 260, and 106 bp), and two fragments (260 and 106 bp), respectively

    Article Snippet: PCR amplification was performed on genomic DNA to amplify CD4 exon 3, and the PCR products were digested with an enzyme, Bse RI (New England Biolabs Inc., Ipswich, MA).

    Techniques: Polymerase Chain Reaction, Amplification

    Electrophoretic pattern of RT-PCR products after enzyme digestion with Bse RI. The lanes are AA: CD4.AA ; AB: CD4.AB ; BB: CD4.BB; and the 100 bp ladder . The 400 bp ( a ) and 595 bp ( b ) of the CD4 sequence were amplified from cDNA using primer sets shown in Table 2 and the amplified products were digested with Bse RI. a After digestion with Bse RI, CD4.AA , CD4.AB , and CD4.BB showed a 400 bp-fragment (400 bp), three fragments of 400, 303 and 97 bp, and two fragments of 303 and 97 bp, respectively. b After digestion with Bse RI, CD4.AA , CD4.AB , and CD4.BB showed a 595 bp-fragment, three fragments of 595, 300 and 295 bp, and two fragments of 300 and 295 bp, respectively

    Journal: BMC Veterinary Research

    Article Title: Identification and characterization of two CD4 alleles in Microminipigs

    doi: 10.1186/s12917-016-0856-8

    Figure Lengend Snippet: Electrophoretic pattern of RT-PCR products after enzyme digestion with Bse RI. The lanes are AA: CD4.AA ; AB: CD4.AB ; BB: CD4.BB; and the 100 bp ladder . The 400 bp ( a ) and 595 bp ( b ) of the CD4 sequence were amplified from cDNA using primer sets shown in Table 2 and the amplified products were digested with Bse RI. a After digestion with Bse RI, CD4.AA , CD4.AB , and CD4.BB showed a 400 bp-fragment (400 bp), three fragments of 400, 303 and 97 bp, and two fragments of 303 and 97 bp, respectively. b After digestion with Bse RI, CD4.AA , CD4.AB , and CD4.BB showed a 595 bp-fragment, three fragments of 595, 300 and 295 bp, and two fragments of 300 and 295 bp, respectively

    Article Snippet: PCR amplification was performed on genomic DNA to amplify CD4 exon 3, and the PCR products were digested with an enzyme, Bse RI (New England Biolabs Inc., Ipswich, MA).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Sequencing, Amplification

    Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Journal: bioRxiv

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

    doi: 10.1101/2020.09.30.321323

    Figure Lengend Snippet: Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Article Snippet: Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment.

    Techniques: Clone Assay, Plasmid Preparation, Sequencing, Amplification, Construct, Labeling