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    Name:
    Nt CviPII
    Description:
    Nt CviPII 40 units
    Catalog Number:
    r0626s
    Price:
    129
    Size:
    40 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs nt cvipii
    Nt CviPII
    Nt CviPII 40 units
    https://www.bioz.com/result/nt cvipii/product/New England Biolabs
    Average 98 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    nt cvipii - by Bioz Stars, 2020-07
    98/100 stars

    Images

    1) Product Images from "NicE-seq: high resolution open chromatin profiling"

    Article Title: NicE-seq: high resolution open chromatin profiling

    Journal: Genome Biology

    doi: 10.1186/s13059-017-1247-6

    Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody
    Figure Legend Snippet: Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Techniques Used: Labeling, Agarose Gel Electrophoresis, Molecular Weight, Staining, Dot Blot

    2) Product Images from "Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues"

    Article Title: Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues

    Journal: bioRxiv

    doi: 10.1101/2020.04.27.064592

    Addition of 5mdCTP in UniNicE-seq work flow. (A) Schematic diagram showing Nt.CviPII is blocked by 5-methylcytosine in recognition (CCD) sequence. During nick translation 5mdCTP can be incorporated at one or both cytosine position. Nucleotide mixtures containing biotinylated dCTP and 5mdCTP would allow both labels at CCD sites. Lower panel shows blocking of nicking by the presence of 5mC at CCD sites. After the nicking reaction the denatured oligonucleotides were resolved in a urea-acrylamide denaturing gel by electrophoresis. C is control input oligos, − or + indicate absence or presence of Nt.CviPII in the reaction. mC and btC represents 5-methylcytosine and biotinylated-cytosine respectively. Nicked oligonucleotide migrates faster on the denaturing urea gel. (B) Schematic diagram of UniNicE-seq method for accessible chromatin library preparation. (C) Substitution of dATP by Texas Red conjugated dATP will allow accessible chromatin visualization in the nucleus. (D) IGV screen shot of the normalized read density of UniNicE-seq using 2.5U (top track), 25U (middle track) and 50U (bottom track) of Nt.CviPII in HCT116 (E) Venn diagram showing overlap of peaks in various amounts of Nt.CviPII in the universal NicE-seq (UniNicE-seq) reaction in HCT116 cells.
    Figure Legend Snippet: Addition of 5mdCTP in UniNicE-seq work flow. (A) Schematic diagram showing Nt.CviPII is blocked by 5-methylcytosine in recognition (CCD) sequence. During nick translation 5mdCTP can be incorporated at one or both cytosine position. Nucleotide mixtures containing biotinylated dCTP and 5mdCTP would allow both labels at CCD sites. Lower panel shows blocking of nicking by the presence of 5mC at CCD sites. After the nicking reaction the denatured oligonucleotides were resolved in a urea-acrylamide denaturing gel by electrophoresis. C is control input oligos, − or + indicate absence or presence of Nt.CviPII in the reaction. mC and btC represents 5-methylcytosine and biotinylated-cytosine respectively. Nicked oligonucleotide migrates faster on the denaturing urea gel. (B) Schematic diagram of UniNicE-seq method for accessible chromatin library preparation. (C) Substitution of dATP by Texas Red conjugated dATP will allow accessible chromatin visualization in the nucleus. (D) IGV screen shot of the normalized read density of UniNicE-seq using 2.5U (top track), 25U (middle track) and 50U (bottom track) of Nt.CviPII in HCT116 (E) Venn diagram showing overlap of peaks in various amounts of Nt.CviPII in the universal NicE-seq (UniNicE-seq) reaction in HCT116 cells.

    Techniques Used: Sequencing, Nick Translation, Blocking Assay, Nucleic Acid Electrophoresis

    Related Articles

    DNA Extraction:

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. 800 ul of 2.5 U of Nt.CviPII, 50 U of DNA Polymerase I and 30 μM of dNTP mix were added to the cells for 2 h at 37°C with constant rotation. dNTP mix contained all four dNTPs plus 6 μM of Fluorescein-12-dATP and 6 μM of biotinylated-dCTP for fluorescent labeling subsequent DNA isolation and sequencing analysis. .. 50 mM of EDTA were used to block the labeling reaction for 30 min at 37°C.

    Labeling:

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. 800 ul of 2.5 U of Nt.CviPII, 50 U of DNA Polymerase I and 30 μM of dNTP mix were added to the cells for 2 h at 37°C with constant rotation. dNTP mix contained all four dNTPs plus 6 μM of Fluorescein-12-dATP and 6 μM of biotinylated-dCTP for fluorescent labeling subsequent DNA isolation and sequencing analysis. .. 50 mM of EDTA were used to block the labeling reaction for 30 min at 37°C.

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. Fluorescent open chromatin DNA labeling was performed by incubating the nuclei in presence of 2.5 U of Nt.CviPII (NEB R0626S), 50 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of Fluorescein-12-dATP (Perkin Elmer, NEL465001EA) or 6 μM of Texas Red-5-dATP (Perkin Elmer, NEL471001EA) in 800 μl of 1 × NEBuffer 2 and carried out at 37°C for 2 h. 80 μl of 0.5 M EDTA and 2 μg of RNase A was added to the labeling reaction and incubated at 37°C for 30 min to stop the labeling reaction and digest cellular RNA. ..

    Article Title: NicE-seq: high resolution open chromatin profiling
    Article Snippet: .. Open chromatin DNA was labeled with biotin by incubating the nuclei in the presence of 2.5 U of Nt.CviPII (NEB R0626S), 10 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of biotin-14-dATP (Invitrogen, 19524-016) and 6 μM of biotin-16-dCTP (ChemCyte, CC-6003-1) in 200 μL of 1× NEB buffer 2. .. The labeling reaction was carried out at 37 °C in a thermo-mixer at 800 RPM for 2 h. We added 20 μL of 0.5 M EDTA and 2 μg of RNase A to the labeling reaction and incubated it at 37 °C for 0.5 h to stop the reaction and digest RNA.

    Incubation:

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. Fluorescent open chromatin DNA labeling was performed by incubating the nuclei in presence of 2.5 U of Nt.CviPII (NEB R0626S), 50 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of Fluorescein-12-dATP (Perkin Elmer, NEL465001EA) or 6 μM of Texas Red-5-dATP (Perkin Elmer, NEL471001EA) in 800 μl of 1 × NEBuffer 2 and carried out at 37°C for 2 h. 80 μl of 0.5 M EDTA and 2 μg of RNase A was added to the labeling reaction and incubated at 37°C for 30 min to stop the labeling reaction and digest cellular RNA. ..

    Article Title: Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues
    Article Snippet: .. Proteinase K was inactivated by incubating the reaction tube at 95 °C for 2 min. We next added 2.5 units of Nt.CviPII to the reaction mix and incubated for 16 hrs at 37 °C. .. CviPII enzyme in the reaction was heat inactivated at 65 °C for 15 min.

    other:

    Article Title: Northern lights assay: a versatile method for comprehensive detection of DNA damage
    Article Snippet: Induction of nicking in DNA in solution Nicks were formed in 1 μg DNA using either a range of 0.1–1 U Nt.BstNB I (NEB, cat no. R0607S) or 0.008–10 U Nt.CviPII (NEB, cat no. R0626S) in buffer NEB 3 at 55°C for 1 h in total volume of 50 μl.

    Article Title: Electrochemical detection of aqueous Ag+ based on Ag+-assisted ligation reaction
    Article Snippet: Materials and chemicals Nt.CviPII, a kind of nicking endonuclease, and T4 DNA ligase, were purchased from New England Biolabs Ltd. (Beijing, China).

    Article Title: Northern lights assay: a versatile method for comprehensive detection of DNA damage
    Article Snippet: Nicks were formed in 1 μg DNA using either a range of 0.1–1 U Nt.BstNB I (NEB, cat no. R0607S) or 0.008–10 U Nt.CviPII (NEB, cat no. R0626S) in buffer NEB 3 at 55°C for 1 h in total volume of 50 μl.

    Article Title: Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues
    Article Snippet: CviPII enzyme in the reaction was heat inactivated at 65 °C for 15 min.

    DNA Labeling:

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. Fluorescent open chromatin DNA labeling was performed by incubating the nuclei in presence of 2.5 U of Nt.CviPII (NEB R0626S), 50 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of Fluorescein-12-dATP (Perkin Elmer, NEL465001EA) or 6 μM of Texas Red-5-dATP (Perkin Elmer, NEL471001EA) in 800 μl of 1 × NEBuffer 2 and carried out at 37°C for 2 h. 80 μl of 0.5 M EDTA and 2 μg of RNase A was added to the labeling reaction and incubated at 37°C for 30 min to stop the labeling reaction and digest cellular RNA. ..

    Sequencing:

    Article Title: Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
    Article Snippet: .. 800 ul of 2.5 U of Nt.CviPII, 50 U of DNA Polymerase I and 30 μM of dNTP mix were added to the cells for 2 h at 37°C with constant rotation. dNTP mix contained all four dNTPs plus 6 μM of Fluorescein-12-dATP and 6 μM of biotinylated-dCTP for fluorescent labeling subsequent DNA isolation and sequencing analysis. .. 50 mM of EDTA were used to block the labeling reaction for 30 min at 37°C.

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  • 98
    New England Biolabs nt cvipii
    Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of <t>Nt.CviPII.</t> A 1% agarose gel showing differential nicking of HCT116 genomic <t>DNA</t> based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody
    Nt Cvipii, 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/nt cvipii/product/New England Biolabs
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nt cvipii - by Bioz Stars, 2020-07
    98/100 stars
      Buy from Supplier

    Image Search Results


    Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Journal: Genome Biology

    Article Title: NicE-seq: high resolution open chromatin profiling

    doi: 10.1186/s13059-017-1247-6

    Figure Lengend Snippet: Nicking enzyme-mediated labeling of open chromatin. a Nicking of crosslinked chromatin using varying amounts of Nt.CviPII. A 1% agarose gel showing differential nicking of HCT116 genomic DNA based on amount of nicking enzyme (10 U, 5 U, 2.5 U, 1 U, 0.3 U, 0 U). M is a DNA molecular weight ladder. b Open chromatin labeling in fixed HeLa cells using dNTPs supplemented with TexasRed-dATP. Top panel : labeling reaction performed in the presence of Nt.CviPII and DNA polymerase I. Middle panel : labeling reaction performed in the presence of DNA polymerase I only. Bottom panel : labeling reaction performed in the absence of Nt.CviPII and DNA polymerase I. TexasRed-dATP was included in all reactions. DNA staining was performed using DAPI ( blue ) and TexasRed stain ( red ) represents labeled OCSs. Magenta stain ( Merge ) represents the colocalization. c Labeling efficiency of OCSs in all three assayed conditions. The y-axis represents the ratio of the intensity of the red pixels to the intensity of the blue pixels ( OCS labeling efficiency ). d Dot blot showing labeling of open chromatin by Nt.CviPII nicking enzyme in both native and formaldehyde-fixed HCT116 cells. The level of labeling was revealed using HRP-conjugated goat anti-biotin antibody

    Article Snippet: Open chromatin DNA was labeled with biotin by incubating the nuclei in the presence of 2.5 U of Nt.CviPII (NEB R0626S), 10 U of DNA polymerase I (M0209S) and 30 μM of each dNTP including 6 μM of biotin-14-dATP (Invitrogen, 19524-016) and 6 μM of biotin-16-dCTP (ChemCyte, CC-6003-1) in 200 μL of 1× NEB buffer 2.

    Techniques: Labeling, Agarose Gel Electrophoresis, Molecular Weight, Staining, Dot Blot

    Addition of 5mdCTP in UniNicE-seq work flow. (A) Schematic diagram showing Nt.CviPII is blocked by 5-methylcytosine in recognition (CCD) sequence. During nick translation 5mdCTP can be incorporated at one or both cytosine position. Nucleotide mixtures containing biotinylated dCTP and 5mdCTP would allow both labels at CCD sites. Lower panel shows blocking of nicking by the presence of 5mC at CCD sites. After the nicking reaction the denatured oligonucleotides were resolved in a urea-acrylamide denaturing gel by electrophoresis. C is control input oligos, − or + indicate absence or presence of Nt.CviPII in the reaction. mC and btC represents 5-methylcytosine and biotinylated-cytosine respectively. Nicked oligonucleotide migrates faster on the denaturing urea gel. (B) Schematic diagram of UniNicE-seq method for accessible chromatin library preparation. (C) Substitution of dATP by Texas Red conjugated dATP will allow accessible chromatin visualization in the nucleus. (D) IGV screen shot of the normalized read density of UniNicE-seq using 2.5U (top track), 25U (middle track) and 50U (bottom track) of Nt.CviPII in HCT116 (E) Venn diagram showing overlap of peaks in various amounts of Nt.CviPII in the universal NicE-seq (UniNicE-seq) reaction in HCT116 cells.

    Journal: bioRxiv

    Article Title: Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues

    doi: 10.1101/2020.04.27.064592

    Figure Lengend Snippet: Addition of 5mdCTP in UniNicE-seq work flow. (A) Schematic diagram showing Nt.CviPII is blocked by 5-methylcytosine in recognition (CCD) sequence. During nick translation 5mdCTP can be incorporated at one or both cytosine position. Nucleotide mixtures containing biotinylated dCTP and 5mdCTP would allow both labels at CCD sites. Lower panel shows blocking of nicking by the presence of 5mC at CCD sites. After the nicking reaction the denatured oligonucleotides were resolved in a urea-acrylamide denaturing gel by electrophoresis. C is control input oligos, − or + indicate absence or presence of Nt.CviPII in the reaction. mC and btC represents 5-methylcytosine and biotinylated-cytosine respectively. Nicked oligonucleotide migrates faster on the denaturing urea gel. (B) Schematic diagram of UniNicE-seq method for accessible chromatin library preparation. (C) Substitution of dATP by Texas Red conjugated dATP will allow accessible chromatin visualization in the nucleus. (D) IGV screen shot of the normalized read density of UniNicE-seq using 2.5U (top track), 25U (middle track) and 50U (bottom track) of Nt.CviPII in HCT116 (E) Venn diagram showing overlap of peaks in various amounts of Nt.CviPII in the universal NicE-seq (UniNicE-seq) reaction in HCT116 cells.

    Article Snippet: CviPII enzyme in the reaction was heat inactivated at 65 °C for 15 min.

    Techniques: Sequencing, Nick Translation, Blocking Assay, Nucleic Acid Electrophoresis