sfani  (New England Biolabs)


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    Structured Review

    New England Biolabs sfani
    PAGE analysis for determining the effects of DNA lesions on transcription. ( a ) Sample processing for restriction digestion using <t>NcoI</t> and <t>SfaNI</t> and postlabeling assay (p* indicates a 32 P-labeled phosphate group). The recognition sequences for restriction
    Sfani, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sfani/product/New England Biolabs
    Average 93 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    sfani - by Bioz Stars, 2022-12
    93/100 stars

    Images

    1) Product Images from "Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo"

    Article Title: Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo

    Journal: Nature protocols

    doi: 10.1038/nprot.2015.094

    PAGE analysis for determining the effects of DNA lesions on transcription. ( a ) Sample processing for restriction digestion using NcoI and SfaNI and postlabeling assay (p* indicates a 32 P-labeled phosphate group). The recognition sequences for restriction
    Figure Legend Snippet: PAGE analysis for determining the effects of DNA lesions on transcription. ( a ) Sample processing for restriction digestion using NcoI and SfaNI and postlabeling assay (p* indicates a 32 P-labeled phosphate group). The recognition sequences for restriction

    Techniques Used: Polyacrylamide Gel Electrophoresis, Postlabeling Assay, Labeling

    2) Product Images from "Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo"

    Article Title: Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo

    Journal: Nature protocols

    doi: 10.1038/nprot.2015.094

    PAGE analysis for determining the effects of DNA lesions on transcription. ( a ) Sample processing for restriction digestion using NcoI and SfaNI and postlabeling assay (p* indicates a 32 P-labeled phosphate group). The recognition sequences for restriction
    Figure Legend Snippet: PAGE analysis for determining the effects of DNA lesions on transcription. ( a ) Sample processing for restriction digestion using NcoI and SfaNI and postlabeling assay (p* indicates a 32 P-labeled phosphate group). The recognition sequences for restriction

    Techniques Used: Polyacrylamide Gel Electrophoresis, Postlabeling Assay, Labeling

    3) Product Images from "Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas platyrhynchos)"

    Article Title: Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas platyrhynchos)

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0125883

    Polymorphism analyses of EDNRB2 gene in non-spot and spot ducks. (A) SfaNI-PCR-RFLP analysis for the c.995G > A site. M1, molecular marker (low ladder); lane 1, GG genotype; lanes 2 to 4, GA genotype; lane 5, AA genotype. (B) NlaIII-PCR- RFLP analysis for the c.940 G > A site. M2, molecular marker (marker I); lane 1, AA genotype; lane 2, GA genotype; lanes 3 to 5, GG genotype.
    Figure Legend Snippet: Polymorphism analyses of EDNRB2 gene in non-spot and spot ducks. (A) SfaNI-PCR-RFLP analysis for the c.995G > A site. M1, molecular marker (low ladder); lane 1, GG genotype; lanes 2 to 4, GA genotype; lane 5, AA genotype. (B) NlaIII-PCR- RFLP analysis for the c.940 G > A site. M2, molecular marker (marker I); lane 1, AA genotype; lane 2, GA genotype; lanes 3 to 5, GG genotype.

    Techniques Used: Polymerase Chain Reaction, Marker

    4) Product Images from "Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II"

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gku1183

    Experimental outline. ( a ) Chemical structures of N 3-EtdT, O 2 -EtdT and O 4 -EtdT. ( b ) Schematic diagrams showing the procedures for the construction of the plasmids harboring a site-specifically incorporated N 3-EtdT, O 2 -EtdT or O 4 -EtdT. ( c ) Strategy for assessing the impact of the EtdT lesions on DNA transcription. ‘X’ indicates N 3-EtdT, O 2 -EtdT or O 4 -EtdT, which was located on the transcribed strand of TurboGFP gene downstream of the CMV and T7 promoters. The +1 transcription start sites are indicated by arrowheads. Lesion-bearing or lesion-free control plasmids were mixed with the competitor vector as DNA templates for in vitro or in vivo transcription assay. Although truncated RNA may be produced when transcription arrests at or near a lesion site, only run-off RNA is shown and used for RT-PCR. Among the RT-PCR products, only the wild-type sequence arising from the lesion-containing vector is shown. The arrows indicate the cleavage sites of Nt.BstNBI, NcoI and SfaNI. The last two enzymes are used to digest the RT-PCR products for subsequent PAGE and LC-MS/MS analyses.
    Figure Legend Snippet: Experimental outline. ( a ) Chemical structures of N 3-EtdT, O 2 -EtdT and O 4 -EtdT. ( b ) Schematic diagrams showing the procedures for the construction of the plasmids harboring a site-specifically incorporated N 3-EtdT, O 2 -EtdT or O 4 -EtdT. ( c ) Strategy for assessing the impact of the EtdT lesions on DNA transcription. ‘X’ indicates N 3-EtdT, O 2 -EtdT or O 4 -EtdT, which was located on the transcribed strand of TurboGFP gene downstream of the CMV and T7 promoters. The +1 transcription start sites are indicated by arrowheads. Lesion-bearing or lesion-free control plasmids were mixed with the competitor vector as DNA templates for in vitro or in vivo transcription assay. Although truncated RNA may be produced when transcription arrests at or near a lesion site, only run-off RNA is shown and used for RT-PCR. Among the RT-PCR products, only the wild-type sequence arising from the lesion-containing vector is shown. The arrows indicate the cleavage sites of Nt.BstNBI, NcoI and SfaNI. The last two enzymes are used to digest the RT-PCR products for subsequent PAGE and LC-MS/MS analyses.

    Techniques Used: Plasmid Preparation, In Vitro, In Vivo, Produced, Reverse Transcription Polymerase Chain Reaction, Sequencing, Polyacrylamide Gel Electrophoresis, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    5) Product Images from "Effects of Tet-mediated Oxidation Products of 5-Methylcytosine on DNA Transcription in vitro and in Mammalian Cells"

    Article Title: Effects of Tet-mediated Oxidation Products of 5-Methylcytosine on DNA Transcription in vitro and in Mammalian Cells

    Journal: Scientific Reports

    doi: 10.1038/srep07052

    Experimental outline. (a) Schematic diagrams showing the procedures for the construction of the plasmids harboring a site-specifically incorporated 5-HmC, 5-FoC, or 5-CaC. (b) CTAB assay for assessing the impact of the oxidized 5-mC derivatives on DNA transcription. “X” indicates 5-HmC, 5-FoC or 5-CaC, which was located on the transcribed strand of TurboGFP gene downstream of the CMV and T7 promoters. The +1 transcription start sites are indicated by arrowheads. Oxidized 5-mC derivative-bearing or unmodified control plasmids were mixed individually with the competitor genome as DNA templates for in vitro or in vivo transcription. Although truncated RNA may be produced when transcription arrests at or near a lesion site, only run-off RNA is shown and used for RT-PCR. Among the RT-PCR products, only the wild-type sequence arising from the cytosine derivative-containing vector is shown. The arrows indicate the cleavage sites of Nt.BstNBI, NcoI and SfaNI. The last two enzymes were used to digest the RT-PCR products for subsequent PAGE and LC-MS/MS analyses.
    Figure Legend Snippet: Experimental outline. (a) Schematic diagrams showing the procedures for the construction of the plasmids harboring a site-specifically incorporated 5-HmC, 5-FoC, or 5-CaC. (b) CTAB assay for assessing the impact of the oxidized 5-mC derivatives on DNA transcription. “X” indicates 5-HmC, 5-FoC or 5-CaC, which was located on the transcribed strand of TurboGFP gene downstream of the CMV and T7 promoters. The +1 transcription start sites are indicated by arrowheads. Oxidized 5-mC derivative-bearing or unmodified control plasmids were mixed individually with the competitor genome as DNA templates for in vitro or in vivo transcription. Although truncated RNA may be produced when transcription arrests at or near a lesion site, only run-off RNA is shown and used for RT-PCR. Among the RT-PCR products, only the wild-type sequence arising from the cytosine derivative-containing vector is shown. The arrows indicate the cleavage sites of Nt.BstNBI, NcoI and SfaNI. The last two enzymes were used to digest the RT-PCR products for subsequent PAGE and LC-MS/MS analyses.

    Techniques Used: In Vitro, In Vivo, Produced, Reverse Transcription Polymerase Chain Reaction, Sequencing, Plasmid Preparation, Polyacrylamide Gel Electrophoresis, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    6) Product Images from "The expression profile of microRNAs in mouse embryos"

    Article Title: The expression profile of microRNAs in mouse embryos

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl096

    Construction of a small RNA-derived cDNA library. Small RNAs were dephosphorylated, followed by ligation with a phosphorylated RNA–DNA chimeric 3′-adaptor (3′ end of the adaptor was biotinylated to prevent self-ligation.) RNA fraction with the attached adapter was purified using PAGE gel, phosphorylated and followed by a second round of T4 RNA ligation with a DNA–RNA chimeric 5′-adaptor containing a GAUC site. The ligated product was converted to cDNA by reverse transcriptase. The cDNA was amplified by PCR with primers having a SfaNI site. PCR products were purified, digested by SfaNI and cloned into the BamHI–BbsI site of Tag vector pMBS I, which contains distinct 32mer oligonucleotide tags along with the cloning site.
    Figure Legend Snippet: Construction of a small RNA-derived cDNA library. Small RNAs were dephosphorylated, followed by ligation with a phosphorylated RNA–DNA chimeric 3′-adaptor (3′ end of the adaptor was biotinylated to prevent self-ligation.) RNA fraction with the attached adapter was purified using PAGE gel, phosphorylated and followed by a second round of T4 RNA ligation with a DNA–RNA chimeric 5′-adaptor containing a GAUC site. The ligated product was converted to cDNA by reverse transcriptase. The cDNA was amplified by PCR with primers having a SfaNI site. PCR products were purified, digested by SfaNI and cloned into the BamHI–BbsI site of Tag vector pMBS I, which contains distinct 32mer oligonucleotide tags along with the cloning site.

    Techniques Used: Derivative Assay, cDNA Library Assay, Ligation, Purification, Polyacrylamide Gel Electrophoresis, Amplification, Polymerase Chain Reaction, Clone Assay, Plasmid Preparation

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    New England Biolabs sfani
    Sfani, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sfani/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    sfani - by Bioz Stars, 2022-12
    93/100 stars
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