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    New England Biolabs bsshii
    Validation of an intact M. genitalium genome by restriction analysis. ( A ) Diagram of the <t>EagI</t> (red), <t>BssHII</t> (blue), and AatII (green) restriction fragments expected for a complete and proper assembly of the synthetic JCVI-1.1 M. genitalium genome. The
    Bsshii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 583 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs bsshii endonuclease
    Production of joint molecules used to test the branch migration activity of proteins. (A) Joint molecules with a 3′ displaced ssDNA tail are produced by RAD51 using gapped DNA and <t>pBS</t> II K (+) dsDNA linearized with <t>XhoI.</t> (B) Joint molecules with
    Bsshii Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bsshii endonuclease/product/New England Biolabs
    Average 99 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    bsshii endonuclease - by Bioz Stars, 2020-07
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    Validation of an intact M. genitalium genome by restriction analysis. ( A ) Diagram of the EagI (red), BssHII (blue), and AatII (green) restriction fragments expected for a complete and proper assembly of the synthetic JCVI-1.1 M. genitalium genome. The

    Journal:

    Article Title: One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

    doi: 10.1073/pnas.0811011106

    Figure Lengend Snippet: Validation of an intact M. genitalium genome by restriction analysis. ( A ) Diagram of the EagI (red), BssHII (blue), and AatII (green) restriction fragments expected for a complete and proper assembly of the synthetic JCVI-1.1 M. genitalium genome. The

    Article Snippet: Plugs were digested according to the Bio-Rad manual with EagI, BssHII, or AatII; restriction enzymes and buffers were supplied by New England Biolabs.

    Techniques:

    DNA mapping of pBluMH. ( A ) Molecular mass markers (lanes 1 and 7). pBluMH digested with Pst I (lane 2), Eag I (lane 3), Bss HII (lane 4), Eag I + Pst I (lane 5), and Bss HII + Pst I (lane 6). ( B ) Southern hybridization of the gel in A . pBluMH digested with Bss HII + Pst I (lane 1), Eag I + Pst I (lane 2), Bss HII (lane 3), Eag I (lane 4), Pst I (lane 5), and DNA molecular mass markers (lane 6).

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Gene cloning, sequence analysis, and expression of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

    doi:

    Figure Lengend Snippet: DNA mapping of pBluMH. ( A ) Molecular mass markers (lanes 1 and 7). pBluMH digested with Pst I (lane 2), Eag I (lane 3), Bss HII (lane 4), Eag I + Pst I (lane 5), and Bss HII + Pst I (lane 6). ( B ) Southern hybridization of the gel in A . pBluMH digested with Bss HII + Pst I (lane 1), Eag I + Pst I (lane 2), Bss HII (lane 3), Eag I (lane 4), Pst I (lane 5), and DNA molecular mass markers (lane 6).

    Article Snippet: According to the pBluescript map, we would expect to see the DNA fragment next to the pBluescript vector at the T3 promoter site in pBluMH to be about 0.1 kb smaller when double-digested with Bss HII + Pst I than when digested with Bss HII alone.

    Techniques: Hybridization

    Location of restriction enzyme Eag I and Bss HII sites in the probe sequence. The Eag I site is located 66 nucleotides and Bss HII site is located 192 nucleotides from the 5′ end. The mark indicates the length representing 75 nucleotides.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Gene cloning, sequence analysis, and expression of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

    doi:

    Figure Lengend Snippet: Location of restriction enzyme Eag I and Bss HII sites in the probe sequence. The Eag I site is located 66 nucleotides and Bss HII site is located 192 nucleotides from the 5′ end. The mark indicates the length representing 75 nucleotides.

    Article Snippet: According to the pBluescript map, we would expect to see the DNA fragment next to the pBluescript vector at the T3 promoter site in pBluMH to be about 0.1 kb smaller when double-digested with Bss HII + Pst I than when digested with Bss HII alone.

    Techniques: Sequencing

    Substrate preferences of Sss I and Dnmt1 by electrochemical and 32 H-SAM assays. (a) For electrochemistry, chips were modified on one half with the hemimethylated BssH II 22-mer (a, left column) and on the other half with the unmethylated BssH II 22-mer (a,

    Journal: Journal of the American Chemical Society

    Article Title: Electrochemical Assay for the Signal-on Detection of Human DNA Methyltransferase Activity

    doi: 10.1021/ja4085918

    Figure Lengend Snippet: Substrate preferences of Sss I and Dnmt1 by electrochemical and 32 H-SAM assays. (a) For electrochemistry, chips were modified on one half with the hemimethylated BssH II 22-mer (a, left column) and on the other half with the unmethylated BssH II 22-mer (a,

    Article Snippet: Sss I methyltransferase, BSA, and the restriction endonucleases BstU I, BssH II, and Rsa I were purchased from New England Biolabs and used as received unless otherwise indicated.

    Techniques: Modification

    Protease treatment restores peak sharpness for samples of high protein content. Chips were modified in all quadrants with the hemimethylated BssH II 22-mer. One half of the chip was treated with 100 nM Dnmt1 with 100 μg/mL BSA and 160 μM

    Journal: Journal of the American Chemical Society

    Article Title: Electrochemical Assay for the Signal-on Detection of Human DNA Methyltransferase Activity

    doi: 10.1021/ja4085918

    Figure Lengend Snippet: Protease treatment restores peak sharpness for samples of high protein content. Chips were modified in all quadrants with the hemimethylated BssH II 22-mer. One half of the chip was treated with 100 nM Dnmt1 with 100 μg/mL BSA and 160 μM

    Article Snippet: Sss I methyltransferase, BSA, and the restriction endonucleases BstU I, BssH II, and Rsa I were purchased from New England Biolabs and used as received unless otherwise indicated.

    Techniques: Modification, Chromatin Immunoprecipitation

    Concentration dependence of Dnmt1 Methyltransferase activity. Chips were modified in all quadrants with the hemimethylated BssH II 22-mer. DNA protection by various concentrations of Dnmt1 was evaluated side by side on the same chip, and CV scans from

    Journal: Journal of the American Chemical Society

    Article Title: Electrochemical Assay for the Signal-on Detection of Human DNA Methyltransferase Activity

    doi: 10.1021/ja4085918

    Figure Lengend Snippet: Concentration dependence of Dnmt1 Methyltransferase activity. Chips were modified in all quadrants with the hemimethylated BssH II 22-mer. DNA protection by various concentrations of Dnmt1 was evaluated side by side on the same chip, and CV scans from

    Article Snippet: Sss I methyltransferase, BSA, and the restriction endonucleases BstU I, BssH II, and Rsa I were purchased from New England Biolabs and used as received unless otherwise indicated.

    Techniques: Concentration Assay, Activity Assay, Modification, Chromatin Immunoprecipitation

    Rearranged BKPyV Dunlop NCCR showed higher EVGR expression than did BKPyVww NCCR in HEK293 cells. (A) Schematic representation of the HPyV genome: noncoding control region (NCCR); early viral gene region (EVGR, in red) encoding large and small T antigens (Tags), alternative spliced Tags; microRNAs (blue arrow); late viral gene region (LVGR) encoding structural proteins (Vp1, Vp2, and Vp3) and the agnoprotein (agno) only in BKPyV and JCPyV. (B) Representation of the bidirectional reporter vector pRG13D12, containing the following: NCCR (in gray) in the early to late orientation cloned via restriction sites MluI and BssHII; the red fluorescence protein dsRed2, used as a marker of EVGR expression; the enhanced green fluorescence protein, EGFP, in the opposite orientation, used as a marker of LVGR expression; SV40 polyadenylation signals [SV40 poly(A)] for the dsRed2 and EGFP expression cassette; E1 ori for bacterial plasmid replication; the ampicillin-resistant gene (Amp) for selecting Escherichia coli transformants. (C) Flow cytometry of HEK293 cells 2 dpt with the pRG13D12 reporter vector alone or containing the NCCR of the archetype BKPyVww, the BKPyV(DUN), or the BKPyV(DUN-R) in the reverse orientation. x axis, EGFP fluorescence; y axis, dsRed2 fluorescence; 10,000 control transfected cells were gated for the live gate, while 5,000 transfected cells were gated for the P3 (Q1, Q2, and Q4) gate. Q1, Q4, and Q2 depict cells expressing red fluorescence, green fluorescence, and both, respectively. Ex, excitation wavelength; Em, emission wavelength. (D) Quantification of cells: red bars, sum of red cells (Q1 + Q2); green bars, sum of green cells (Q2 + Q4); yellow bars, red- and green-fluorescence double-positive cells (Q2); black bars, nonfluorescent cells (Q3, negative). Means with standard deviations (SD) from three independent replicates are shown. (E) Normalized mean fluorescence intensity (MFI). The weighted MFI was calculated for each measurement (see formulas in Materials and Methods); late expression was normalized to BKPyVww NCCR (green MFI was set as 100), while early expression was normalized to BKPyVww NCCR (red MFI was set as 1). Means with SD from three independent replicates are shown.

    Journal: Journal of Virology

    Article Title: Novel Human Polyomavirus Noncoding Control Regions Differ in Bidirectional Gene Expression according to Host Cell, Large T-Antigen Expression, and Clinically Occurring Rearrangements

    doi: 10.1128/JVI.02231-17

    Figure Lengend Snippet: Rearranged BKPyV Dunlop NCCR showed higher EVGR expression than did BKPyVww NCCR in HEK293 cells. (A) Schematic representation of the HPyV genome: noncoding control region (NCCR); early viral gene region (EVGR, in red) encoding large and small T antigens (Tags), alternative spliced Tags; microRNAs (blue arrow); late viral gene region (LVGR) encoding structural proteins (Vp1, Vp2, and Vp3) and the agnoprotein (agno) only in BKPyV and JCPyV. (B) Representation of the bidirectional reporter vector pRG13D12, containing the following: NCCR (in gray) in the early to late orientation cloned via restriction sites MluI and BssHII; the red fluorescence protein dsRed2, used as a marker of EVGR expression; the enhanced green fluorescence protein, EGFP, in the opposite orientation, used as a marker of LVGR expression; SV40 polyadenylation signals [SV40 poly(A)] for the dsRed2 and EGFP expression cassette; E1 ori for bacterial plasmid replication; the ampicillin-resistant gene (Amp) for selecting Escherichia coli transformants. (C) Flow cytometry of HEK293 cells 2 dpt with the pRG13D12 reporter vector alone or containing the NCCR of the archetype BKPyVww, the BKPyV(DUN), or the BKPyV(DUN-R) in the reverse orientation. x axis, EGFP fluorescence; y axis, dsRed2 fluorescence; 10,000 control transfected cells were gated for the live gate, while 5,000 transfected cells were gated for the P3 (Q1, Q2, and Q4) gate. Q1, Q4, and Q2 depict cells expressing red fluorescence, green fluorescence, and both, respectively. Ex, excitation wavelength; Em, emission wavelength. (D) Quantification of cells: red bars, sum of red cells (Q1 + Q2); green bars, sum of green cells (Q2 + Q4); yellow bars, red- and green-fluorescence double-positive cells (Q2); black bars, nonfluorescent cells (Q3, negative). Means with standard deviations (SD) from three independent replicates are shown. (E) Normalized mean fluorescence intensity (MFI). The weighted MFI was calculated for each measurement (see formulas in Materials and Methods); late expression was normalized to BKPyVww NCCR (green MFI was set as 100), while early expression was normalized to BKPyVww NCCR (red MFI was set as 1). Means with SD from three independent replicates are shown.

    Article Snippet: The HPyV NCCRs were chemically synthesized in pUC57 (Eurogentec S.A, Belgium) , excised using the restriction enzymes BssHII and MluI (New England BioLabs, England), and cloned into the corresponding restriction sites of pRG13D12.

    Techniques: Expressing, Plasmid Preparation, Clone Assay, Fluorescence, Marker, Flow Cytometry, Cytometry, Transfection

    Production of joint molecules used to test the branch migration activity of proteins. (A) Joint molecules with a 3′ displaced ssDNA tail are produced by RAD51 using gapped DNA and pBS II K (+) dsDNA linearized with XhoI. (B) Joint molecules with

    Journal: Methods (San Diego, Calif.)

    Article Title: Analyzing the Branch Migration Activities of Eukaryotic Proteins

    doi: 10.1016/j.ymeth.2010.02.010

    Figure Lengend Snippet: Production of joint molecules used to test the branch migration activity of proteins. (A) Joint molecules with a 3′ displaced ssDNA tail are produced by RAD51 using gapped DNA and pBS II K (+) dsDNA linearized with XhoI. (B) Joint molecules with

    Article Snippet: To prepare the linear dsDNA fragment, perform a digest of pBS II K (+) plasmid DNA first with the restriction endonuclease XhoI, and then with AlwNI (New England Biolabs).

    Techniques: Migration, Activity Assay, Produced

    The scheme used to produce gapped DNA. i) pBS II K (+) plasmid DNA is digested with XhoI and AlwNI. ii) The large DNA fragment from this digest is purified by gel electrophoresis in agarose gels, and then iii) annealed to circular ssDNA to generate gapped

    Journal: Methods (San Diego, Calif.)

    Article Title: Analyzing the Branch Migration Activities of Eukaryotic Proteins

    doi: 10.1016/j.ymeth.2010.02.010

    Figure Lengend Snippet: The scheme used to produce gapped DNA. i) pBS II K (+) plasmid DNA is digested with XhoI and AlwNI. ii) The large DNA fragment from this digest is purified by gel electrophoresis in agarose gels, and then iii) annealed to circular ssDNA to generate gapped

    Article Snippet: To prepare the linear dsDNA fragment, perform a digest of pBS II K (+) plasmid DNA first with the restriction endonuclease XhoI, and then with AlwNI (New England Biolabs).

    Techniques: Plasmid Preparation, Purification, Nucleic Acid Electrophoresis

    Illustration of the 0.8% agarose gel used to purify the large (2065 bp) dsDNA fragment of pBS II K (+) following digestion with XhoI and AlwNI. After electrophoresis, lanes A, C, and E are excised from the gel and stained with ethidium bromide (dashed

    Journal: Methods (San Diego, Calif.)

    Article Title: Analyzing the Branch Migration Activities of Eukaryotic Proteins

    doi: 10.1016/j.ymeth.2010.02.010

    Figure Lengend Snippet: Illustration of the 0.8% agarose gel used to purify the large (2065 bp) dsDNA fragment of pBS II K (+) following digestion with XhoI and AlwNI. After electrophoresis, lanes A, C, and E are excised from the gel and stained with ethidium bromide (dashed

    Article Snippet: To prepare the linear dsDNA fragment, perform a digest of pBS II K (+) plasmid DNA first with the restriction endonuclease XhoI, and then with AlwNI (New England Biolabs).

    Techniques: Agarose Gel Electrophoresis, Electrophoresis, Staining