sfa ni  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    Name:
    SfaNI
    Description:
    SfaNI 1 500 units
    Catalog Number:
    r0172l
    Price:
    493
    Size:
    1 500 units
    Category:
    Restriction Enzymes
    Buy from Supplier


    Structured Review

    New England Biolabs sfa ni
    SfaNI
    SfaNI 1 500 units
    https://www.bioz.com/result/sfa ni/product/New England Biolabs
    Average 94 stars, based on 238 article reviews
    Price from $9.99 to $1999.99
    sfa ni - by Bioz Stars, 2020-09
    94/100 stars

    Images

    1) Product Images from "Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast"

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast

    Journal: Molecular and Cellular Biology

    doi:

    Mapping scheme for repeat tract changes. The repeat tract (thickened bars), interruption (vertical tics), PCR primers (arrowhead lines), and 5′-end label (asterisks) are shown. To map changes, the sizes of the undigested PCR products were compared first, and then the products were digested with Sfa NI to observe whether the labeled digestion product is the same as or smaller or larger than that of the parental size fragment. In the examples, the contraction occurred proximal to the interruption and the expansion distal to the interruption with respect to the label.
    Figure Legend Snippet: Mapping scheme for repeat tract changes. The repeat tract (thickened bars), interruption (vertical tics), PCR primers (arrowhead lines), and 5′-end label (asterisks) are shown. To map changes, the sizes of the undigested PCR products were compared first, and then the products were digested with Sfa NI to observe whether the labeled digestion product is the same as or smaller or larger than that of the parental size fragment. In the examples, the contraction occurred proximal to the interruption and the expansion distal to the interruption with respect to the label.

    Techniques Used: Polymerase Chain Reaction, 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 "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

    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 "CAG?CTG repeat instability in cultured human astrocytes"

    Article Title: CAG?CTG repeat instability in cultured human astrocytes

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl614

    Influence of interruptions on CTG repeat contractions in SVG-A cells. ( A ) Corrected contraction frequencies ( Table 1 , entries 9L and 9M) are plotted for starting tracts of (CTG) 6 (ATG) 2 (CTG) 25 (filled bar) and for (CTG) 33 (unfilled bar). Error bars indicate ±1 SEM. ( B ) Mutation spectra for (CTG) 6 (ATG) 2 (CTG) 25 (filled bars) versus (CTG) 33 (unfilled bars). The number of observed events is plotted on the ordinate versus the size of the contraction (as determined by PCR) on the abscissa. ( C ) Representative gel showing results of the SfaNI-resistance assay. PCR products were analyzed on 6% denaturing polyacrylamide gels prior to (odd number lanes) or following (even number lanes) treatment with SfaNI, as described in Materials and Methods. Lanes 1–4 show results with PCR products from control 33-repeat plasmids that are interrupted (lanes 1 and 2) or perfect (lanes 3 and 4). The asterisk indicates the starting position of the 33-repeat uncut and SfaNI-resistant perfect repeat tracts. Lanes 5–10 show results with PCR products from contractions of the (CTG) 6 (ATG) 2 (CTG) 25 allele in SVG-A cells. The letters a–c indicate the position of the uncut samples in lanes 5, 7 and 9, respectively. The letters below the gel image indicate the assignment of SfaNI sensitivity (S) or resistance (R). To become resistant, both ATG interruptions must be lost.
    Figure Legend Snippet: Influence of interruptions on CTG repeat contractions in SVG-A cells. ( A ) Corrected contraction frequencies ( Table 1 , entries 9L and 9M) are plotted for starting tracts of (CTG) 6 (ATG) 2 (CTG) 25 (filled bar) and for (CTG) 33 (unfilled bar). Error bars indicate ±1 SEM. ( B ) Mutation spectra for (CTG) 6 (ATG) 2 (CTG) 25 (filled bars) versus (CTG) 33 (unfilled bars). The number of observed events is plotted on the ordinate versus the size of the contraction (as determined by PCR) on the abscissa. ( C ) Representative gel showing results of the SfaNI-resistance assay. PCR products were analyzed on 6% denaturing polyacrylamide gels prior to (odd number lanes) or following (even number lanes) treatment with SfaNI, as described in Materials and Methods. Lanes 1–4 show results with PCR products from control 33-repeat plasmids that are interrupted (lanes 1 and 2) or perfect (lanes 3 and 4). The asterisk indicates the starting position of the 33-repeat uncut and SfaNI-resistant perfect repeat tracts. Lanes 5–10 show results with PCR products from contractions of the (CTG) 6 (ATG) 2 (CTG) 25 allele in SVG-A cells. The letters a–c indicate the position of the uncut samples in lanes 5, 7 and 9, respectively. The letters below the gel image indicate the assignment of SfaNI sensitivity (S) or resistance (R). To become resistant, both ATG interruptions must be lost.

    Techniques Used: CTG Assay, Mutagenesis, Polymerase Chain Reaction

    6) 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

    7) Product Images from "Stabilizing Effects of Interruptions on Trinucleotide Repeat Expansions in Saccharomyces cerevisiae"

    Article Title: Stabilizing Effects of Interruptions on Trinucleotide Repeat Expansions in Saccharomyces cerevisiae

    Journal: Molecular and Cellular Biology

    doi:

    Example of Sfa NI digests to identify interruptions and to determine polarity of expansions. (A) Schematic diagram of the PCR products of the unexpanded TNRs tested. The thin line represents the TNR, the open boxes represent the nonrepetitive flanking sequence, filled boxes show the location of the PCR primers, and the filled circles represent the location of the interruptions within the TNR tract. The expected fragments after digestion of these PCR products with Sfa NI are shown (labeled A to F). The cut site for Sfa NI is displaced by five nucleotides from the recognition sequence, and restriction fragments A to F are adjusted in size accordingly. Due to the four-nucleotide overhang generated by Sfa NI and the fact that the PCR fragments are uniformly labeled in the presence of [α- 32 P]dCTP, cleaved samples should show two bands differing in size by four bases. The expected sizes (in nucleotides) are: fragment A, 90 and 94; fragment B, 101 and 97; fragment C, 123 and 127; fragment D, 68 and 64; fragment E, 105 and 109; and fragment F, 86 and 82. (B) Autoradiograph of representative digests of each of the TNRs tested. Markers were determined from a M13 sequence ladder, and the arrow indicates the size of the uncleaved starting tract. The table above the autoradiograph identifies which lanes have the starting or expanded products and which of these products were subjected to Sfa NI digestion. The designation “P” for lanes 1 and 2 indicates a perfect repeat. Labeled fragments A to F refer to the expected fragments listed in panel A. The asterisks in lanes 6 and 10 designate the expanded alleles of fragments B and C, respectively. Fragment G is the result of a duplicated interruption. The brackets indicate the products of both strands of the digestion products, separated by four nucleotides as explained above. Shadow bands are due to polymerase “chatter” which is commonly seen during PCR of TNRs.
    Figure Legend Snippet: Example of Sfa NI digests to identify interruptions and to determine polarity of expansions. (A) Schematic diagram of the PCR products of the unexpanded TNRs tested. The thin line represents the TNR, the open boxes represent the nonrepetitive flanking sequence, filled boxes show the location of the PCR primers, and the filled circles represent the location of the interruptions within the TNR tract. The expected fragments after digestion of these PCR products with Sfa NI are shown (labeled A to F). The cut site for Sfa NI is displaced by five nucleotides from the recognition sequence, and restriction fragments A to F are adjusted in size accordingly. Due to the four-nucleotide overhang generated by Sfa NI and the fact that the PCR fragments are uniformly labeled in the presence of [α- 32 P]dCTP, cleaved samples should show two bands differing in size by four bases. The expected sizes (in nucleotides) are: fragment A, 90 and 94; fragment B, 101 and 97; fragment C, 123 and 127; fragment D, 68 and 64; fragment E, 105 and 109; and fragment F, 86 and 82. (B) Autoradiograph of representative digests of each of the TNRs tested. Markers were determined from a M13 sequence ladder, and the arrow indicates the size of the uncleaved starting tract. The table above the autoradiograph identifies which lanes have the starting or expanded products and which of these products were subjected to Sfa NI digestion. The designation “P” for lanes 1 and 2 indicates a perfect repeat. Labeled fragments A to F refer to the expected fragments listed in panel A. The asterisks in lanes 6 and 10 designate the expanded alleles of fragments B and C, respectively. Fragment G is the result of a duplicated interruption. The brackets indicate the products of both strands of the digestion products, separated by four nucleotides as explained above. Shadow bands are due to polymerase “chatter” which is commonly seen during PCR of TNRs.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Labeling, Generated, Autoradiography

    8) Product Images from "Association of genetic polymorphisms in interferon-γ, interleukin-6 and transforming growth factor-β1 gene with oral lichen planus susceptibility"

    Article Title: Association of genetic polymorphisms in interferon-γ, interleukin-6 and transforming growth factor-β1 gene with oral lichen planus susceptibility

    Journal: BMC Oral Health

    doi: 10.1186/s12903-016-0277-x

    Amplified DNA digested with SfaNI showing genotypes of IL-6(174G/C). Lane M: 100 bp DNA marker, Lane 1, 2, 3,5,6,7 and 8 for genotype GC (3 bands of 198, 140 and 58 bp), Lane 4 for genotype CC (uncut DNA of 198 bp), Lane 10 for genotype GG (2 bands of 140 and 58 bp)
    Figure Legend Snippet: Amplified DNA digested with SfaNI showing genotypes of IL-6(174G/C). Lane M: 100 bp DNA marker, Lane 1, 2, 3,5,6,7 and 8 for genotype GC (3 bands of 198, 140 and 58 bp), Lane 4 for genotype CC (uncut DNA of 198 bp), Lane 10 for genotype GG (2 bands of 140 and 58 bp)

    Techniques Used: Amplification, Marker

    9) 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

    10) Product Images from "CAG?CTG repeat instability in cultured human astrocytes"

    Article Title: CAG?CTG repeat instability in cultured human astrocytes

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl614

    Influence of interruptions on CTG repeat contractions in SVG-A cells. ( A ) Corrected contraction frequencies ( Table 1 , entries 9L and 9M) are plotted for starting tracts of (CTG) 6 (ATG) 2 (CTG) 25 (filled bar) and for (CTG) 33 (unfilled bar). Error bars indicate ±1 SEM. ( B ) Mutation spectra for (CTG) 6 (ATG) 2 (CTG) 25 (filled bars) versus (CTG) 33 (unfilled bars). The number of observed events is plotted on the ordinate versus the size of the contraction (as determined by PCR) on the abscissa. ( C ) Representative gel showing results of the SfaNI-resistance assay. PCR products were analyzed on 6% denaturing polyacrylamide gels prior to (odd number lanes) or following (even number lanes) treatment with SfaNI, as described in Materials and Methods. Lanes 1–4 show results with PCR products from control 33-repeat plasmids that are interrupted (lanes 1 and 2) or perfect (lanes 3 and 4). The asterisk indicates the starting position of the 33-repeat uncut and SfaNI-resistant perfect repeat tracts. Lanes 5–10 show results with PCR products from contractions of the (CTG) 6 (ATG) 2 (CTG) 25 allele in SVG-A cells. The letters a–c indicate the position of the uncut samples in lanes 5, 7 and 9, respectively. The letters below the gel image indicate the assignment of SfaNI sensitivity (S) or resistance (R). To become resistant, both ATG interruptions must be lost.
    Figure Legend Snippet: Influence of interruptions on CTG repeat contractions in SVG-A cells. ( A ) Corrected contraction frequencies ( Table 1 , entries 9L and 9M) are plotted for starting tracts of (CTG) 6 (ATG) 2 (CTG) 25 (filled bar) and for (CTG) 33 (unfilled bar). Error bars indicate ±1 SEM. ( B ) Mutation spectra for (CTG) 6 (ATG) 2 (CTG) 25 (filled bars) versus (CTG) 33 (unfilled bars). The number of observed events is plotted on the ordinate versus the size of the contraction (as determined by PCR) on the abscissa. ( C ) Representative gel showing results of the SfaNI-resistance assay. PCR products were analyzed on 6% denaturing polyacrylamide gels prior to (odd number lanes) or following (even number lanes) treatment with SfaNI, as described in Materials and Methods. Lanes 1–4 show results with PCR products from control 33-repeat plasmids that are interrupted (lanes 1 and 2) or perfect (lanes 3 and 4). The asterisk indicates the starting position of the 33-repeat uncut and SfaNI-resistant perfect repeat tracts. Lanes 5–10 show results with PCR products from contractions of the (CTG) 6 (ATG) 2 (CTG) 25 allele in SVG-A cells. The letters a–c indicate the position of the uncut samples in lanes 5, 7 and 9, respectively. The letters below the gel image indicate the assignment of SfaNI sensitivity (S) or resistance (R). To become resistant, both ATG interruptions must be lost.

    Techniques Used: CTG Assay, Mutagenesis, Polymerase Chain Reaction

    11) 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

    Related Articles

    High Performance Liquid Chromatography:

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II
    Article Snippet: .. Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water. .. The resultant ODN mixture was subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis following previously described conditions ( , ).

    Transfection:

    Article Title: Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo
    Article Snippet: .. SfaNI (New England BioLabs, cat. no. R0172S) NcoI (New England BioLabs, cat. no. R0193S) NotI (New England BioLabs, cat. no. R0189S) T7 RNA polymerase, supplied with 5× transcription buffer (Promega, cat. no. P2075) 100 mM DTT (Promega, cat. no. P1171) 100 mM rATP (Promega, cat. no. E6011) 100 mM rUTP (Promega, cat. no. E6021) 100 mM rGTP (Promega, cat. no. E6031) 100 mM rCTP (Promega, cat. no. E6041) RNase inhibitor (New England BioLabs, cat. no. M0307S) HeLaScribe nuclear extract in vitro transcription system, supplied with HeLa nuclear extract, 1× transcription buffer and HeLa extract stop solution (Promega, cat. no. E3110) pGEM-T vector (Promega, cat. no. A3600) Lipofectamine 2000 transfection reagent (Invitrogen, cat. no. 11668-019) DMEM (Life Technologies, cat. no. 11995-073) FBS (Life Technologies, cat. no. 16000-044) Penicillin-streptomycin solution (American Type Culture Collection, cat. no. 30-2300) 0.25% (wt/vol) trypsin-EDTA (Life Technologies, cat. no. 25200-056) 10× PBS solution (VWR, cat. no. 97064-158) E.Z.N.A. .. Total RNA kit I (Omega Bio-Tek, cat. no. 101319-240) Ambion DNA-free kit (Life Technologies, cat. no. AM1906) M-MLV reverse transcriptase, supplied with 5× reaction buffer and HeLa extract stop solution (Promega, cat. no. E3110) MluCI (New England BioLabs, cat. no. R0538S) Cac8I (New England BioLabs, cat. no. R0579L) 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP; Oakwood Chemical, cat. no. 003409) Methanol (Fisher Scientific, cat. no. A452-SK4) Sodium chloride (EMD, cat. no. 7710) Sodium hydroxide (Fisher Scientific, cat. no. S318-10) Agarose (Sigma-Aldrich, cat. no. A9539) Sodium acetate (Sigma-Aldrich, cat. no. S2889) Tris base (Fisher Scientific, cat. no. BP152-5) EDTA (Teknova, cat. no. E5599) Hydrochloric acid (Fisher Scientific, cat. no. A144-500) !

    Sequencing:

    Article Title: CAG?CTG repeat instability in cultured human astrocytes
    Article Snippet: .. The presence of either one or two ATG interruptions in a CTG repeat sequence introduces a recognition site for the restriction enzyme SfaNI (New England Biolabs). .. After passage through SVG-A cells and transformation into yeast, PCR products from contracted interrupted and perfect TNR alleles were isolated by the QIAQuick PCR Purification Kit (QIAGEN Inc.) and digested with SfaNI.

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast
    Article Snippet: .. One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels. .. In some cases, e.g., when changes of a single repeat unit occurred or when the size of the digestion product was discordant with the magnitude of the size change, the analysis was repeated with an end label on the second PCR primer.

    In Vitro:

    Article Title: Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo
    Article Snippet: .. SfaNI (New England BioLabs, cat. no. R0172S) NcoI (New England BioLabs, cat. no. R0193S) NotI (New England BioLabs, cat. no. R0189S) T7 RNA polymerase, supplied with 5× transcription buffer (Promega, cat. no. P2075) 100 mM DTT (Promega, cat. no. P1171) 100 mM rATP (Promega, cat. no. E6011) 100 mM rUTP (Promega, cat. no. E6021) 100 mM rGTP (Promega, cat. no. E6031) 100 mM rCTP (Promega, cat. no. E6041) RNase inhibitor (New England BioLabs, cat. no. M0307S) HeLaScribe nuclear extract in vitro transcription system, supplied with HeLa nuclear extract, 1× transcription buffer and HeLa extract stop solution (Promega, cat. no. E3110) pGEM-T vector (Promega, cat. no. A3600) Lipofectamine 2000 transfection reagent (Invitrogen, cat. no. 11668-019) DMEM (Life Technologies, cat. no. 11995-073) FBS (Life Technologies, cat. no. 16000-044) Penicillin-streptomycin solution (American Type Culture Collection, cat. no. 30-2300) 0.25% (wt/vol) trypsin-EDTA (Life Technologies, cat. no. 25200-056) 10× PBS solution (VWR, cat. no. 97064-158) E.Z.N.A. .. Total RNA kit I (Omega Bio-Tek, cat. no. 101319-240) Ambion DNA-free kit (Life Technologies, cat. no. AM1906) M-MLV reverse transcriptase, supplied with 5× reaction buffer and HeLa extract stop solution (Promega, cat. no. E3110) MluCI (New England BioLabs, cat. no. R0538S) Cac8I (New England BioLabs, cat. no. R0579L) 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP; Oakwood Chemical, cat. no. 003409) Methanol (Fisher Scientific, cat. no. A452-SK4) Sodium chloride (EMD, cat. no. 7710) Sodium hydroxide (Fisher Scientific, cat. no. S318-10) Agarose (Sigma-Aldrich, cat. no. A9539) Sodium acetate (Sigma-Aldrich, cat. no. S2889) Tris base (Fisher Scientific, cat. no. BP152-5) EDTA (Teknova, cat. no. E5599) Hydrochloric acid (Fisher Scientific, cat. no. A144-500) !

    Chromatography:

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II
    Article Snippet: .. Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water. .. The resultant ODN mixture was subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis following previously described conditions ( , ).

    CTG Assay:

    Article Title: CAG?CTG repeat instability in cultured human astrocytes
    Article Snippet: .. The presence of either one or two ATG interruptions in a CTG repeat sequence introduces a recognition site for the restriction enzyme SfaNI (New England Biolabs). .. After passage through SVG-A cells and transformation into yeast, PCR products from contracted interrupted and perfect TNR alleles were isolated by the QIAQuick PCR Purification Kit (QIAGEN Inc.) and digested with SfaNI.

    Labeling:

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast
    Article Snippet: .. One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels. .. In some cases, e.g., when changes of a single repeat unit occurred or when the size of the digestion product was discordant with the magnitude of the size change, the analysis was repeated with an end label on the second PCR primer.

    Purification:

    Article Title: Stabilizing Effects of Interruptions on Trinucleotide Repeat Expansions in Saccharomyces cerevisiae
    Article Snippet: .. Purified PCR products were subjected to restriction analysis with Sfa NI (New England Biolabs). ..

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast
    Article Snippet: .. One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels. .. In some cases, e.g., when changes of a single repeat unit occurred or when the size of the digestion product was discordant with the magnitude of the size change, the analysis was repeated with an end label on the second PCR primer.

    Electrophoresis:

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast
    Article Snippet: .. One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels. .. In some cases, e.g., when changes of a single repeat unit occurred or when the size of the digestion product was discordant with the magnitude of the size change, the analysis was repeated with an end label on the second PCR primer.

    Polymerase Chain Reaction:

    Article Title: Stabilizing Effects of Interruptions on Trinucleotide Repeat Expansions in Saccharomyces cerevisiae
    Article Snippet: .. Purified PCR products were subjected to restriction analysis with Sfa NI (New England Biolabs). ..

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast
    Article Snippet: .. One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels. .. In some cases, e.g., when changes of a single repeat unit occurred or when the size of the digestion product was discordant with the magnitude of the size change, the analysis was repeated with an end label on the second PCR primer.

    Article Title: Association of genetic polymorphisms in interferon-γ, interleukin-6 and transforming growth factor-β1 gene with oral lichen planus susceptibility
    Article Snippet: .. The PCR product (198 bp) DNA was digested with SfaNI restriction enzyme (New England BioLabs, Beverly, MA) at 37 ° C for 3 h. Resulting into two fragment of 140 and 58 bp indicating GG genotype, while three fragment of 198, 140 and 58 bp indicating GC genotype. ..

    Incubation:

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II
    Article Snippet: .. Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water. .. The resultant ODN mixture was subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis following previously described conditions ( , ).

    Mass Spectrometry:

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II
    Article Snippet: .. Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water. .. The resultant ODN mixture was subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis following previously described conditions ( , ).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II
    Article Snippet: .. Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water. .. The resultant ODN mixture was subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis following previously described conditions ( , ).

    Article Title: Effects of Tet-mediated Oxidation Products of 5-Methylcytosine on DNA Transcription in vitro and in Mammalian Cells
    Article Snippet: .. LC-MS/MS analysis To identify the transcription products using LC-MS/MS, RT-PCR products were treated with 50 U NcoI, 50 U SfaNI and 20 U shrimp alkaline phosphatase in 250 μL NEB buffer 4 at 37°C for 4 h, followed by heating at 80°C for 20 min. .. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with HPLC and dissolved in water.

    Plasmid Preparation:

    Article Title: Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo
    Article Snippet: .. SfaNI (New England BioLabs, cat. no. R0172S) NcoI (New England BioLabs, cat. no. R0193S) NotI (New England BioLabs, cat. no. R0189S) T7 RNA polymerase, supplied with 5× transcription buffer (Promega, cat. no. P2075) 100 mM DTT (Promega, cat. no. P1171) 100 mM rATP (Promega, cat. no. E6011) 100 mM rUTP (Promega, cat. no. E6021) 100 mM rGTP (Promega, cat. no. E6031) 100 mM rCTP (Promega, cat. no. E6041) RNase inhibitor (New England BioLabs, cat. no. M0307S) HeLaScribe nuclear extract in vitro transcription system, supplied with HeLa nuclear extract, 1× transcription buffer and HeLa extract stop solution (Promega, cat. no. E3110) pGEM-T vector (Promega, cat. no. A3600) Lipofectamine 2000 transfection reagent (Invitrogen, cat. no. 11668-019) DMEM (Life Technologies, cat. no. 11995-073) FBS (Life Technologies, cat. no. 16000-044) Penicillin-streptomycin solution (American Type Culture Collection, cat. no. 30-2300) 0.25% (wt/vol) trypsin-EDTA (Life Technologies, cat. no. 25200-056) 10× PBS solution (VWR, cat. no. 97064-158) E.Z.N.A. .. Total RNA kit I (Omega Bio-Tek, cat. no. 101319-240) Ambion DNA-free kit (Life Technologies, cat. no. AM1906) M-MLV reverse transcriptase, supplied with 5× reaction buffer and HeLa extract stop solution (Promega, cat. no. E3110) MluCI (New England BioLabs, cat. no. R0538S) Cac8I (New England BioLabs, cat. no. R0579L) 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP; Oakwood Chemical, cat. no. 003409) Methanol (Fisher Scientific, cat. no. A452-SK4) Sodium chloride (EMD, cat. no. 7710) Sodium hydroxide (Fisher Scientific, cat. no. S318-10) Agarose (Sigma-Aldrich, cat. no. A9539) Sodium acetate (Sigma-Aldrich, cat. no. S2889) Tris base (Fisher Scientific, cat. no. BP152-5) EDTA (Teknova, cat. no. E5599) Hydrochloric acid (Fisher Scientific, cat. no. A144-500) !

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    New England Biolabs sfa ni
    Mapping scheme for repeat tract changes. The repeat tract (thickened bars), interruption (vertical tics), <t>PCR</t> primers (arrowhead lines), and 5′-end label (asterisks) are shown. To map changes, the sizes of the undigested PCR products were compared first, and then the products were digested with <t>Sfa</t> NI to observe whether the labeled digestion product is the same as or smaller or larger than that of the parental size fragment. In the examples, the contraction occurred proximal to the interruption and the expansion distal to the interruption with respect to the label.
    Sfa Ni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 159 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sfa ni/product/New England Biolabs
    Average 94 stars, based on 159 article reviews
    Price from $9.99 to $1999.99
    sfa ni - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    Image Search Results


    Mapping scheme for repeat tract changes. The repeat tract (thickened bars), interruption (vertical tics), PCR primers (arrowhead lines), and 5′-end label (asterisks) are shown. To map changes, the sizes of the undigested PCR products were compared first, and then the products were digested with Sfa NI to observe whether the labeled digestion product is the same as or smaller or larger than that of the parental size fragment. In the examples, the contraction occurred proximal to the interruption and the expansion distal to the interruption with respect to the label.

    Journal: Molecular and Cellular Biology

    Article Title: Mapping the Polarity of Changes That Occur in Interrupted CAG Repeat Tracts in Yeast

    doi:

    Figure Lengend Snippet: Mapping scheme for repeat tract changes. The repeat tract (thickened bars), interruption (vertical tics), PCR primers (arrowhead lines), and 5′-end label (asterisks) are shown. To map changes, the sizes of the undigested PCR products were compared first, and then the products were digested with Sfa NI to observe whether the labeled digestion product is the same as or smaller or larger than that of the parental size fragment. In the examples, the contraction occurred proximal to the interruption and the expansion distal to the interruption with respect to the label.

    Article Snippet: One of the two primers was 5′-end labeled with 32 P. The PCR products were purified with Prep-a-gene (BioRad), digested with Sfa NI (New England BioLabs), and displayed by electrophoresis on sequencing gels.

    Techniques: Polymerase Chain Reaction, Labeling

    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

    Journal: Nature protocols

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

    doi: 10.1038/nprot.2015.094

    Figure Lengend 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

    Article Snippet: SfaNI (New England BioLabs, cat. no. R0172S) NcoI (New England BioLabs, cat. no. R0193S) NotI (New England BioLabs, cat. no. R0189S) T7 RNA polymerase, supplied with 5× transcription buffer (Promega, cat. no. P2075) 100 mM DTT (Promega, cat. no. P1171) 100 mM rATP (Promega, cat. no. E6011) 100 mM rUTP (Promega, cat. no. E6021) 100 mM rGTP (Promega, cat. no. E6031) 100 mM rCTP (Promega, cat. no. E6041) RNase inhibitor (New England BioLabs, cat. no. M0307S) HeLaScribe nuclear extract in vitro transcription system, supplied with HeLa nuclear extract, 1× transcription buffer and HeLa extract stop solution (Promega, cat. no. E3110) pGEM-T vector (Promega, cat. no. A3600) Lipofectamine 2000 transfection reagent (Invitrogen, cat. no. 11668-019) DMEM (Life Technologies, cat. no. 11995-073) FBS (Life Technologies, cat. no. 16000-044) Penicillin-streptomycin solution (American Type Culture Collection, cat. no. 30-2300) 0.25% (wt/vol) trypsin-EDTA (Life Technologies, cat. no. 25200-056) 10× PBS solution (VWR, cat. no. 97064-158) E.Z.N.A.

    Techniques: Polyacrylamide Gel Electrophoresis, Postlabeling Assay, Labeling

    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.

    Journal: Nucleic Acids Research

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

    doi: 10.1093/nar/gku1183

    Figure Lengend 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.

    Article Snippet: Liquid chromatography-tandem mass spectrometry analysis The RT-PCR products were treated with 20 U SfaNI and 20 U shrimp alkaline phosphatase in 120 μl NEB buffer 3 at 37°C for 2 h, and then at 70°C for 20 min. To the mixture, 50 U NcoI was added, and the mixture was incubated at 37°C for 2 h. The resulting solution was extracted with phenol/chloroform/isoamyl alcohol (25:24:1, v/v) and the aqueous portion was dried with Speed-vac, desalted with high performance liquid chromatography and dissolved in water.

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