nb bsr di  (New England Biolabs)


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    Name:
    BsrDI
    Description:
    BsrDI 1 000 units
    Catalog Number:
    r0574l
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    269
    Size:
    1 000 units
    Category:
    Restriction Enzymes
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    New England Biolabs nb bsr di
    BsrDI
    BsrDI 1 000 units
    https://www.bioz.com/result/nb bsr di/product/New England Biolabs
    Average 96 stars, based on 4536 article reviews
    Price from $9.99 to $1999.99
    nb bsr di - by Bioz Stars, 2020-09
    96/100 stars

    Images

    1) Product Images from "Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq"

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2020.03.027

    Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).
    Figure Legend Snippet: Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Techniques Used: Generated, Genome Wide

    2) Product Images from "High-throughput, cost-effective verification of structural DNA assembly"

    Article Title: High-throughput, cost-effective verification of structural DNA assembly

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkt1088

    In silico evaluation of 236 unique restriction enzyme sequence/cut sites according to frequency metrics cut1 , min100 and max10k . Regimes of low-frequency and high-frequency cutters are highlighted. Best enzymes are found where metrics values are highest. ( a ) max10k values for building blocks cluster ∼1.0 as essentially all have total size (including vector) below 10 kb. In contrast, max10k is discriminating for assemblies (values range from 0.75 to 10) due to larger size distribution. ( b ) Screening against 2236 cloned building blocks using metrics cut1 and min100 . Most suitable enzymes are Afl III and Ava II. ( c ) Screening against 5660 assemblies using metrics cut1 , min100 and max10k . Most suitable enzyme is Bsr DI.
    Figure Legend Snippet: In silico evaluation of 236 unique restriction enzyme sequence/cut sites according to frequency metrics cut1 , min100 and max10k . Regimes of low-frequency and high-frequency cutters are highlighted. Best enzymes are found where metrics values are highest. ( a ) max10k values for building blocks cluster ∼1.0 as essentially all have total size (including vector) below 10 kb. In contrast, max10k is discriminating for assemblies (values range from 0.75 to 10) due to larger size distribution. ( b ) Screening against 2236 cloned building blocks using metrics cut1 and min100 . Most suitable enzymes are Afl III and Ava II. ( c ) Screening against 5660 assemblies using metrics cut1 , min100 and max10k . Most suitable enzyme is Bsr DI.

    Techniques Used: In Silico, Sequencing, Plasmid Preparation, Clone Assay, Antiviral Assay

    3) Product Images from "Human-Specific SNP in Obesity Genes, Adrenergic Receptor Beta2 (ADRB2), Beta3 (ADRB3), and PPAR ?2 (PPARG), during Primate Evolution"

    Article Title: Human-Specific SNP in Obesity Genes, Adrenergic Receptor Beta2 (ADRB2), Beta3 (ADRB3), and PPAR ?2 (PPARG), during Primate Evolution

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0043461

    Nucleotide sequences in ADRB2 of humans and NHPs. Primers 16HF and 16HRc (Rc means the complementary sequence of reverse primer) indicate a primer set used for the PCR to amplify the region for the 16 th amino acid in hominoids. One nucleotide of primer 16HF was changed to create the restriction site of BsrD I. Primers 27MF and 27MRc indicate a primer set used for the PCR to amplify the region for the 27 th amino acid in macaques. The underlines show the restriction site ( GCAATGNN ) with BsrD I for the 16 th amino acid and the restriction site (GCNGC) with Ita I for the 27 th amino acid. The nucleotide sequences for hominoids were determined from G. gorilla (DDBJ Accession No. AB669098), P. pygmaeus (AB669099) and H. agilis (AB669100), and obtained from the Ensembl database for ADRB2 of H. sapiens (ENSG00000169252) and P. troglodytes (ENSPTRG00000017391). All macaques, M. fascicularis , M. fuscata , M. nemestrina , M. radiata (AB669101∼AB669104, respectively) and M. mulatta (ENSMMUG 00000002214), show the same sequence.
    Figure Legend Snippet: Nucleotide sequences in ADRB2 of humans and NHPs. Primers 16HF and 16HRc (Rc means the complementary sequence of reverse primer) indicate a primer set used for the PCR to amplify the region for the 16 th amino acid in hominoids. One nucleotide of primer 16HF was changed to create the restriction site of BsrD I. Primers 27MF and 27MRc indicate a primer set used for the PCR to amplify the region for the 27 th amino acid in macaques. The underlines show the restriction site ( GCAATGNN ) with BsrD I for the 16 th amino acid and the restriction site (GCNGC) with Ita I for the 27 th amino acid. The nucleotide sequences for hominoids were determined from G. gorilla (DDBJ Accession No. AB669098), P. pygmaeus (AB669099) and H. agilis (AB669100), and obtained from the Ensembl database for ADRB2 of H. sapiens (ENSG00000169252) and P. troglodytes (ENSPTRG00000017391). All macaques, M. fascicularis , M. fuscata , M. nemestrina , M. radiata (AB669101∼AB669104, respectively) and M. mulatta (ENSMMUG 00000002214), show the same sequence.

    Techniques Used: Sequencing, Polymerase Chain Reaction

    All hominoids had Gly16 allele in ADRB2 . A) Restriction map of ADRB2 for the 16 th amino acid digested with BsrD I ( GCAATGNN ). This restriction map was predicted from the nucleotide sequences of hominoids ( Fig. 1 ). B) RFLP patterns of PCR products of ADRB2 for the 16 th amino acid digested with BsrD I in hominoids. Lane 1: PCR product of a human; not digested (200 bp). Lane 2: Fragments of human Arg16/Gly16 (130,108 and 56 bp (22 and 14 bp fragments were undetectable)). Lane 3 to lane 6: Fragments from P. troglodytes , G. gorilla , P. pygmaeus , and H. agilis , respectively (108 and 22 bp instead of 130 bp).
    Figure Legend Snippet: All hominoids had Gly16 allele in ADRB2 . A) Restriction map of ADRB2 for the 16 th amino acid digested with BsrD I ( GCAATGNN ). This restriction map was predicted from the nucleotide sequences of hominoids ( Fig. 1 ). B) RFLP patterns of PCR products of ADRB2 for the 16 th amino acid digested with BsrD I in hominoids. Lane 1: PCR product of a human; not digested (200 bp). Lane 2: Fragments of human Arg16/Gly16 (130,108 and 56 bp (22 and 14 bp fragments were undetectable)). Lane 3 to lane 6: Fragments from P. troglodytes , G. gorilla , P. pygmaeus , and H. agilis , respectively (108 and 22 bp instead of 130 bp).

    Techniques Used: Polymerase Chain Reaction

    4) Product Images from "Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq"

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2020.03.027

    Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).
    Figure Legend Snippet: Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Techniques Used: Generated, Genome Wide

    5) Product Images from "Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish"

    Article Title: Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish

    Journal: Genetics

    doi: 10.1534/genetics.116.199133

    Establishment of  foxl2a  and  foxl2b  knockout mutant lines by TALEN. (A and B) The TALEN target sites of zebrafish (A)  foxl2a  and (B)  foxl2b . The coding and untranslated exon regions are depicted as solid and open boxes, respectively. The left and right TALEN binding sites are indicated by underlining. Cleavage sites with  Bst N I and  Bsr D I in the spacer are shown by blue color, and forward and reverse primers (F primer and R primer) are indicated in the corresponding sites. (C and D) Detection of (C)  foxl2a  and (D)  foxl2b  mutants by  Bst N I or  Bsr D I digestion. The amplified fragment sizes (bp) are shown on the right. (E and F) Sequences of different indels of TALEN-induced (E)  foxl2a  and (F)  foxl2b  mutants in F 0  embryos. A total of eight and six indels (number of embryos are indicated in each bracket) at targeted locus are shown for (E)  foxl2a  and (F)  foxl2b , and the numbers at the right-hand side indicate the number of deleted base pairs. (G) Transcription-level confirmation of  foxl2a  and  foxl2b  mutants by RT-PCR. The detected primers are shown on the left, and primer P2 is specific for the deleted sequences. The  actb1  was used as control. F, forward; R, reverse; M, marker.
    Figure Legend Snippet: Establishment of foxl2a and foxl2b knockout mutant lines by TALEN. (A and B) The TALEN target sites of zebrafish (A) foxl2a and (B) foxl2b . The coding and untranslated exon regions are depicted as solid and open boxes, respectively. The left and right TALEN binding sites are indicated by underlining. Cleavage sites with Bst N I and Bsr D I in the spacer are shown by blue color, and forward and reverse primers (F primer and R primer) are indicated in the corresponding sites. (C and D) Detection of (C) foxl2a and (D) foxl2b mutants by Bst N I or Bsr D I digestion. The amplified fragment sizes (bp) are shown on the right. (E and F) Sequences of different indels of TALEN-induced (E) foxl2a and (F) foxl2b mutants in F 0 embryos. A total of eight and six indels (number of embryos are indicated in each bracket) at targeted locus are shown for (E) foxl2a and (F) foxl2b , and the numbers at the right-hand side indicate the number of deleted base pairs. (G) Transcription-level confirmation of foxl2a and foxl2b mutants by RT-PCR. The detected primers are shown on the left, and primer P2 is specific for the deleted sequences. The actb1 was used as control. F, forward; R, reverse; M, marker.

    Techniques Used: Knock-Out, Mutagenesis, Binding Assay, Amplification, Reverse Transcription Polymerase Chain Reaction, Marker

    6) Product Images from "Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq"

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2020.03.027

    Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).
    Figure Legend Snippet: Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Techniques Used: Generated, Genome Wide

    7) Product Images from "Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq"

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

    Journal: Molecular Cell

    doi: 10.1016/j.molcel.2020.03.027

    Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).
    Figure Legend Snippet: Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Techniques Used: Generated, Genome Wide

    8) Product Images from "Identification of Dermatophytes by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Metalloproteinase-1"

    Article Title: Identification of Dermatophytes by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Metalloproteinase-1

    Journal: Annals of Dermatology

    doi: 10.5021/ad.2014.26.3.338

    Restriction fragment length polymorphism patterns obtained upon DNA digestion with BsrD I. M: 100-base pair (bp) marker, 1: Microsporumcanis (IFM45829), 2: M. gypseum (IFM-5292), 3: Trichophyton mentagrophytes var. interdigitale (IFM-48155), 4: T. mentagrophytes var. mentagrophytes (CBS113880), 5: T. rubrum (ATCC28188), 6: T. tonsurans (CBS109036).
    Figure Legend Snippet: Restriction fragment length polymorphism patterns obtained upon DNA digestion with BsrD I. M: 100-base pair (bp) marker, 1: Microsporumcanis (IFM45829), 2: M. gypseum (IFM-5292), 3: Trichophyton mentagrophytes var. interdigitale (IFM-48155), 4: T. mentagrophytes var. mentagrophytes (CBS113880), 5: T. rubrum (ATCC28188), 6: T. tonsurans (CBS109036).

    Techniques Used: Marker

    9) Product Images from "A novel mutation in DAX1 causes delayed-onset adrenal insufficiency and incomplete hypogonadotropic hypogonadism"

    Article Title: A novel mutation in DAX1 causes delayed-onset adrenal insufficiency and incomplete hypogonadotropic hypogonadism

    Journal: Journal of Clinical Investigation

    doi:

    Identification of the DAX1 missense mutation. ( a ) Chromatogram showing the I439S missense mutation in exon 2 of DAX1 . A guanine is present at nucleotide position 1316 in the patient (arrow), whereas a thymine is present at the equivalent position in a genomic sequence from a control subject. ( b ) The thymine-to-guanine nucleotide change creates a novel BsrD I site. PCR products from the patient, his mother, his normal brother, his father, and a normal control were digested with this restriction enzyme (lanes 1–5, respectively). The mutated fragment, characterized by a band 13 bp shorter than the wild-type fragment, is present in the patient and his mother (arrows).
    Figure Legend Snippet: Identification of the DAX1 missense mutation. ( a ) Chromatogram showing the I439S missense mutation in exon 2 of DAX1 . A guanine is present at nucleotide position 1316 in the patient (arrow), whereas a thymine is present at the equivalent position in a genomic sequence from a control subject. ( b ) The thymine-to-guanine nucleotide change creates a novel BsrD I site. PCR products from the patient, his mother, his normal brother, his father, and a normal control were digested with this restriction enzyme (lanes 1–5, respectively). The mutated fragment, characterized by a band 13 bp shorter than the wild-type fragment, is present in the patient and his mother (arrows).

    Techniques Used: Mutagenesis, Sequencing, Polymerase Chain Reaction

    Related Articles

    Nucleic Acid Electrophoresis:

    Article Title: Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish
    Article Snippet: .. After digestion with Bst N I (restriction enzyme cutting site in the spacer of foxl2a ) or Bsr D I (restriction enzyme cutting site in the spacer of foxl2b ) (New England Biolabs, Beverly, MA) respectively at 60° and 65° for 2 hr, the uncleaved DNA fragments were separated by gel electrophoresis and cloned into pMD-18T vector (Promega). .. Sequence alignments were generated to analyze whether or not the gDNA fragments from embryos injected with TALEN mRNAs were mutated.

    Clone Assay:

    Article Title: Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish
    Article Snippet: .. After digestion with Bst N I (restriction enzyme cutting site in the spacer of foxl2a ) or Bsr D I (restriction enzyme cutting site in the spacer of foxl2b ) (New England Biolabs, Beverly, MA) respectively at 60° and 65° for 2 hr, the uncleaved DNA fragments were separated by gel electrophoresis and cloned into pMD-18T vector (Promega). .. Sequence alignments were generated to analyze whether or not the gDNA fragments from embryos injected with TALEN mRNAs were mutated.

    Purification:

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq
    Article Snippet: .. Validation of the GLOE-Seq Method Purified genomic DNA from yeast strain W303 was treated with 1 U/μg DNA of the relevant restriction or nicking enzymes, Bsr DI, Nb.Bsr DI or Not I (New England Biolabs) for 90 min at 65°C (Bsr DI and Nb.Bsr DI) or 37°C (NotI), dephosphorylated with 2 U/μg Antarctic Phosphatase (New England Biolabs) for 30 min at 37°C and purified using AMPure beads (Beckman Coulter). .. The purified DNA was quantified (Qubit, Life Technologies), and 2.5 μg were used for GLOE-Seq library preparation (steps 29-50) and sequencing.

    Electrophoresis:

    Article Title: Identification of Dermatophytes by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Metalloproteinase-1
    Article Snippet: .. After restriction enzyme digestion, BsrD I (NEB, England), the samples were subjected to electrophoresis. ..

    Incubation:

    Article Title: High-throughput, cost-effective verification of structural DNA assembly
    Article Snippet: .. Digest formulations and incubation temperatures for Bsr DI, Afl II and Ava II (NEB) are given in Supplementary Table S2 . ..

    Antiviral Assay:

    Article Title: High-throughput, cost-effective verification of structural DNA assembly
    Article Snippet: .. Digest formulations and incubation temperatures for Bsr DI, Afl II and Ava II (NEB) are given in Supplementary Table S2 . ..

    Variant Assay:

    Article Title: Human-Specific SNP in Obesity Genes, Adrenergic Receptor Beta2 (ADRB2), Beta3 (ADRB3), and PPAR ?2 (PPARG), during Primate Evolution
    Article Snippet: .. ADRB2 fragment with the Arg16Gly variant site with 5 U of BsrD I (New England Bio Labs Co. Ltd.) at 65°C for 1.5 hrs. .. ADRB2 amplicon for the Gln27Glu substitution site (5 µl) was digested with 5 U of Ita I (Roche Applied Science Co. Ltd.) at 37°C for 1 hr.

    Plasmid Preparation:

    Article Title: Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish
    Article Snippet: .. After digestion with Bst N I (restriction enzyme cutting site in the spacer of foxl2a ) or Bsr D I (restriction enzyme cutting site in the spacer of foxl2b ) (New England Biolabs, Beverly, MA) respectively at 60° and 65° for 2 hr, the uncleaved DNA fragments were separated by gel electrophoresis and cloned into pMD-18T vector (Promega). .. Sequence alignments were generated to analyze whether or not the gDNA fragments from embryos injected with TALEN mRNAs were mutated.

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    New England Biolabs nb bsr di
    Validation of GLOE-Seq with Budding Yeast Genomic <t>DNA</t> (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a <t>Bsr</t> DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).
    Nb Bsr Di, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Journal: Molecular Cell

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

    doi: 10.1016/j.molcel.2020.03.027

    Figure Lengend Snippet: Validation of GLOE-Seq with Budding Yeast Genomic DNA (A) GLOE-Seq workflow. Green circle, ligatable 3′-OH terminus; red circle, biotin. (B) 3′ ends of a DSB at a Bsr DI site in genome browser view (FWD, forward or Watson strand; REV, reverse or Crick strand). (C) Histogram plot showing the distribution of read counts for the asymmetric termini generated by Bsr DI. (D) Strand-specific detection of SSBs generated by Nb. Bsr DI treatment. (E) Genome-wide detection of predicted Nb. Bsr DI sites (left). Most undetected sites are absent or poorly covered in a randomly fragmented sample (center). Many of the unexpected breaks reside in the immediate neighborhood of predicted sites (right). (F) Closely spaced SSBs are poorly detected. Nb. Bsr DI signals are plotted against the calculated distance to the (upstream) neighboring site on the same strand (red, mean; pink, SE). (G) Sensitivity of GLOE-Seq. Nb. Bsr DI-treated DNA was diluted with untreated DNA at the indicated ratios. The undiluted sample corresponds to (E).

    Article Snippet: Validation of the GLOE-Seq Method Purified genomic DNA from yeast strain W303 was treated with 1 U/μg DNA of the relevant restriction or nicking enzymes, Bsr DI, Nb.Bsr DI or Not I (New England Biolabs) for 90 min at 65°C (Bsr DI and Nb.Bsr DI) or 37°C (NotI), dephosphorylated with 2 U/μg Antarctic Phosphatase (New England Biolabs) for 30 min at 37°C and purified using AMPure beads (Beckman Coulter).

    Techniques: Generated, Genome Wide

    In silico evaluation of 236 unique restriction enzyme sequence/cut sites according to frequency metrics cut1 , min100 and max10k . Regimes of low-frequency and high-frequency cutters are highlighted. Best enzymes are found where metrics values are highest. ( a ) max10k values for building blocks cluster ∼1.0 as essentially all have total size (including vector) below 10 kb. In contrast, max10k is discriminating for assemblies (values range from 0.75 to 10) due to larger size distribution. ( b ) Screening against 2236 cloned building blocks using metrics cut1 and min100 . Most suitable enzymes are Afl III and Ava II. ( c ) Screening against 5660 assemblies using metrics cut1 , min100 and max10k . Most suitable enzyme is Bsr DI.

    Journal: Nucleic Acids Research

    Article Title: High-throughput, cost-effective verification of structural DNA assembly

    doi: 10.1093/nar/gkt1088

    Figure Lengend Snippet: In silico evaluation of 236 unique restriction enzyme sequence/cut sites according to frequency metrics cut1 , min100 and max10k . Regimes of low-frequency and high-frequency cutters are highlighted. Best enzymes are found where metrics values are highest. ( a ) max10k values for building blocks cluster ∼1.0 as essentially all have total size (including vector) below 10 kb. In contrast, max10k is discriminating for assemblies (values range from 0.75 to 10) due to larger size distribution. ( b ) Screening against 2236 cloned building blocks using metrics cut1 and min100 . Most suitable enzymes are Afl III and Ava II. ( c ) Screening against 5660 assemblies using metrics cut1 , min100 and max10k . Most suitable enzyme is Bsr DI.

    Article Snippet: Digest formulations and incubation temperatures for Bsr DI, Afl II and Ava II (NEB) are given in Supplementary Table S2 .

    Techniques: In Silico, Sequencing, Plasmid Preparation, Clone Assay, Antiviral Assay

    Nucleotide sequences in ADRB2 of humans and NHPs. Primers 16HF and 16HRc (Rc means the complementary sequence of reverse primer) indicate a primer set used for the PCR to amplify the region for the 16 th amino acid in hominoids. One nucleotide of primer 16HF was changed to create the restriction site of BsrD I. Primers 27MF and 27MRc indicate a primer set used for the PCR to amplify the region for the 27 th amino acid in macaques. The underlines show the restriction site ( GCAATGNN ) with BsrD I for the 16 th amino acid and the restriction site (GCNGC) with Ita I for the 27 th amino acid. The nucleotide sequences for hominoids were determined from G. gorilla (DDBJ Accession No. AB669098), P. pygmaeus (AB669099) and H. agilis (AB669100), and obtained from the Ensembl database for ADRB2 of H. sapiens (ENSG00000169252) and P. troglodytes (ENSPTRG00000017391). All macaques, M. fascicularis , M. fuscata , M. nemestrina , M. radiata (AB669101∼AB669104, respectively) and M. mulatta (ENSMMUG 00000002214), show the same sequence.

    Journal: PLoS ONE

    Article Title: Human-Specific SNP in Obesity Genes, Adrenergic Receptor Beta2 (ADRB2), Beta3 (ADRB3), and PPAR ?2 (PPARG), during Primate Evolution

    doi: 10.1371/journal.pone.0043461

    Figure Lengend Snippet: Nucleotide sequences in ADRB2 of humans and NHPs. Primers 16HF and 16HRc (Rc means the complementary sequence of reverse primer) indicate a primer set used for the PCR to amplify the region for the 16 th amino acid in hominoids. One nucleotide of primer 16HF was changed to create the restriction site of BsrD I. Primers 27MF and 27MRc indicate a primer set used for the PCR to amplify the region for the 27 th amino acid in macaques. The underlines show the restriction site ( GCAATGNN ) with BsrD I for the 16 th amino acid and the restriction site (GCNGC) with Ita I for the 27 th amino acid. The nucleotide sequences for hominoids were determined from G. gorilla (DDBJ Accession No. AB669098), P. pygmaeus (AB669099) and H. agilis (AB669100), and obtained from the Ensembl database for ADRB2 of H. sapiens (ENSG00000169252) and P. troglodytes (ENSPTRG00000017391). All macaques, M. fascicularis , M. fuscata , M. nemestrina , M. radiata (AB669101∼AB669104, respectively) and M. mulatta (ENSMMUG 00000002214), show the same sequence.

    Article Snippet: ADRB2 fragment with the Arg16Gly variant site with 5 U of BsrD I (New England Bio Labs Co. Ltd.) at 65°C for 1.5 hrs.

    Techniques: Sequencing, Polymerase Chain Reaction

    All hominoids had Gly16 allele in ADRB2 . A) Restriction map of ADRB2 for the 16 th amino acid digested with BsrD I ( GCAATGNN ). This restriction map was predicted from the nucleotide sequences of hominoids ( Fig. 1 ). B) RFLP patterns of PCR products of ADRB2 for the 16 th amino acid digested with BsrD I in hominoids. Lane 1: PCR product of a human; not digested (200 bp). Lane 2: Fragments of human Arg16/Gly16 (130,108 and 56 bp (22 and 14 bp fragments were undetectable)). Lane 3 to lane 6: Fragments from P. troglodytes , G. gorilla , P. pygmaeus , and H. agilis , respectively (108 and 22 bp instead of 130 bp).

    Journal: PLoS ONE

    Article Title: Human-Specific SNP in Obesity Genes, Adrenergic Receptor Beta2 (ADRB2), Beta3 (ADRB3), and PPAR ?2 (PPARG), during Primate Evolution

    doi: 10.1371/journal.pone.0043461

    Figure Lengend Snippet: All hominoids had Gly16 allele in ADRB2 . A) Restriction map of ADRB2 for the 16 th amino acid digested with BsrD I ( GCAATGNN ). This restriction map was predicted from the nucleotide sequences of hominoids ( Fig. 1 ). B) RFLP patterns of PCR products of ADRB2 for the 16 th amino acid digested with BsrD I in hominoids. Lane 1: PCR product of a human; not digested (200 bp). Lane 2: Fragments of human Arg16/Gly16 (130,108 and 56 bp (22 and 14 bp fragments were undetectable)). Lane 3 to lane 6: Fragments from P. troglodytes , G. gorilla , P. pygmaeus , and H. agilis , respectively (108 and 22 bp instead of 130 bp).

    Article Snippet: ADRB2 fragment with the Arg16Gly variant site with 5 U of BsrD I (New England Bio Labs Co. Ltd.) at 65°C for 1.5 hrs.

    Techniques: Polymerase Chain Reaction