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  • 99
    New England Biolabs restriction sites ecori
    Repair of MB + VL-induced 8-oxoG from the Ad-encoded lacZ gene in human and rodent cells measured by loss of <t>Fpg-sensitive</t> sites. ( A ) Southern blot analysis of the repair of MB + VL-induced 8-oxoG in the Ad lacZ gene. Shown here is a representative blot. Lanes 1 and 2 contain untreated Ad DNA, while lanes 3 and 4 contain Ad DNA exposed to 480 s VL in phosphate buffer with 20 mg/ml MB. Lanes 1–4 have not undergone any repair incubation. The presence of ssDNA breaks in the 3-kb <t>EcoRI</t> lacZ fragment produce smaller ssDNA fragments that migrate further than the full-length fragment. These smaller fragments appear as a smear or tail below the defined 3-kb band. Smearing below the 3-kb band in samples that have not been treated with Fpg (lanes 1 and 3) represent ssDNA breaks from other sources. It can be seen that a small amount of Fpg-sensitive 8-oxoG lesions are present prior to treatment with MB + VL (compare lanes 1 and 2). Following MB + VL exposure, a large number of Fpg-sensitive sites are generated (compare lanes 2 and 4). During repair incubation, BER removes 8-oxoG resulting in the loss of T4pdg-sensitive sites and recovery of the full-length 3-kb lacZ fragment. As long as 8-oxoG lesions persist in the lacZ DNA, Fpg will induce ssDNA breaks resulting in fewer full-length fragments and less signal compared to the control. ( B ) Quantification of the percent removal of Fpg-sensitive sites from the Ad-encoded lacZ gene in GM637F and CHO-AA8 cells. Each point on the graphs represents the arithmetic mean ± SE of the percent removal of MB + VL-induced Fpg-sensitive sites from three independent experiments. A significant increase in the percent removal of MB + VL-induced Fpg-sensitive sites was observed in GM637F at 24 h (indicated by an asterisk) and a significant difference in the percent removal of Fpg-sensitive sites was observed between GM637F and CHO-AA8 at 24 h (indicated by a cross/plus sign).
    Restriction Sites Ecori, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher ecori ecori
    Southern blot analysis of T 4 progenies of line IO6-97. Stable integration of RGA2 intron was detected in transgenic rice plants, no hybridization signal was observed in the respective non-transgenic control. Each lane consists of 10 µg genomic <t>DNA,</t> digested with <t>EcoR</t> I or Hind III. The position and sizes of markers are indicated (NT = Non-transgenic control, E = EcoR I and H = Hind III).
    Ecori Ecori, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori ecori/product/Thermo Fisher
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    99
    Millipore ecori
    Determination of the origin of the 10.9-kb fragment from the index patient. A: Southern blot using PstI digestion only showing bands of 0.99, 1.03, and 1.08 kb (the largest band approximately 1.1 kb in size). An abnormal control (AC, lane 6 ) shows a full mutation (Coriell GM07537A), with an additional 2.1-kb band (336 CGG repeats). No CGG expansion was noted in the family study ( lanes 2 to 4 ) or in a normal control (NC, lane 5 ). MW, the Lambda/HindIII MW marker (Chemicon International). B: Southern analysis of the family digested with <t>EcoRI,</t> with (+) and without (−) <t>NruI.</t> MW, molecular marker as in A ; NFC, normal female control; M, mother; IP, index patient; F, father; NMC, normal male control; AC, abnormal control as in A . Note that father and the index patient both showed the 10.9-kb fragment ( lanes 6 , 7 , and 9 ). C: PCR products with (+) and without (−) EcoRI digestion. MR, 100-bp Molecular Ruler (Bio-Rad); NC, normal control; M, mother; IP, index patient; F, father.
    Ecori, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 3869 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher ecori
    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with <t>BamHI</t> and <t>EcoRI</t> (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).
    Ecori, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 12201 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher fastdigest ecori
    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with <t>BamHI</t> and <t>EcoRI</t> (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).
    Fastdigest Ecori, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 259 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher ecori buffer
    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with <t>BamHI</t> and <t>EcoRI</t> (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).
    Ecori Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Repair of MB + VL-induced 8-oxoG from the Ad-encoded lacZ gene in human and rodent cells measured by loss of Fpg-sensitive sites. ( A ) Southern blot analysis of the repair of MB + VL-induced 8-oxoG in the Ad lacZ gene. Shown here is a representative blot. Lanes 1 and 2 contain untreated Ad DNA, while lanes 3 and 4 contain Ad DNA exposed to 480 s VL in phosphate buffer with 20 mg/ml MB. Lanes 1–4 have not undergone any repair incubation. The presence of ssDNA breaks in the 3-kb EcoRI lacZ fragment produce smaller ssDNA fragments that migrate further than the full-length fragment. These smaller fragments appear as a smear or tail below the defined 3-kb band. Smearing below the 3-kb band in samples that have not been treated with Fpg (lanes 1 and 3) represent ssDNA breaks from other sources. It can be seen that a small amount of Fpg-sensitive 8-oxoG lesions are present prior to treatment with MB + VL (compare lanes 1 and 2). Following MB + VL exposure, a large number of Fpg-sensitive sites are generated (compare lanes 2 and 4). During repair incubation, BER removes 8-oxoG resulting in the loss of T4pdg-sensitive sites and recovery of the full-length 3-kb lacZ fragment. As long as 8-oxoG lesions persist in the lacZ DNA, Fpg will induce ssDNA breaks resulting in fewer full-length fragments and less signal compared to the control. ( B ) Quantification of the percent removal of Fpg-sensitive sites from the Ad-encoded lacZ gene in GM637F and CHO-AA8 cells. Each point on the graphs represents the arithmetic mean ± SE of the percent removal of MB + VL-induced Fpg-sensitive sites from three independent experiments. A significant increase in the percent removal of MB + VL-induced Fpg-sensitive sites was observed in GM637F at 24 h (indicated by an asterisk) and a significant difference in the percent removal of Fpg-sensitive sites was observed between GM637F and CHO-AA8 at 24 h (indicated by a cross/plus sign).

    Journal: Mutagenesis

    Article Title: Host cell reactivation of gene expression for an adenovirus-encoded reporter gene reflects the repair of UVC-induced cyclobutane pyrimidine dimers and methylene blue plus visible light-induced 8-oxoguanine

    doi: 10.1093/mutage/get027

    Figure Lengend Snippet: Repair of MB + VL-induced 8-oxoG from the Ad-encoded lacZ gene in human and rodent cells measured by loss of Fpg-sensitive sites. ( A ) Southern blot analysis of the repair of MB + VL-induced 8-oxoG in the Ad lacZ gene. Shown here is a representative blot. Lanes 1 and 2 contain untreated Ad DNA, while lanes 3 and 4 contain Ad DNA exposed to 480 s VL in phosphate buffer with 20 mg/ml MB. Lanes 1–4 have not undergone any repair incubation. The presence of ssDNA breaks in the 3-kb EcoRI lacZ fragment produce smaller ssDNA fragments that migrate further than the full-length fragment. These smaller fragments appear as a smear or tail below the defined 3-kb band. Smearing below the 3-kb band in samples that have not been treated with Fpg (lanes 1 and 3) represent ssDNA breaks from other sources. It can be seen that a small amount of Fpg-sensitive 8-oxoG lesions are present prior to treatment with MB + VL (compare lanes 1 and 2). Following MB + VL exposure, a large number of Fpg-sensitive sites are generated (compare lanes 2 and 4). During repair incubation, BER removes 8-oxoG resulting in the loss of T4pdg-sensitive sites and recovery of the full-length 3-kb lacZ fragment. As long as 8-oxoG lesions persist in the lacZ DNA, Fpg will induce ssDNA breaks resulting in fewer full-length fragments and less signal compared to the control. ( B ) Quantification of the percent removal of Fpg-sensitive sites from the Ad-encoded lacZ gene in GM637F and CHO-AA8 cells. Each point on the graphs represents the arithmetic mean ± SE of the percent removal of MB + VL-induced Fpg-sensitive sites from three independent experiments. A significant increase in the percent removal of MB + VL-induced Fpg-sensitive sites was observed in GM637F at 24 h (indicated by an asterisk) and a significant difference in the percent removal of Fpg-sensitive sites was observed between GM637F and CHO-AA8 at 24 h (indicated by a cross/plus sign).

    Article Snippet: Prior to treatment of Ad DNA with either T4 pyrimidine-DNA glycosylase [T4pdg; New England Biolabs (NEB) M0308S] or formamidopyrimidine (Fapy)-DNA glycosylase (Fpg; NEB M02040), all samples were digested overnight by 40 units of EcoRI (NEB R0101) in a total reaction volume of 50 µl in 1× NEB buffer 1.

    Techniques: Southern Blot, Incubation, Generated

    Replication capacity of the HBV genome linearized by ApaI and SphI restriction enzymes. The EcoRI dimer of clone 4B was digested with ApaI or SphI, with or without further treatment with T4 DNA ligase before transfection into Huh7 cells. The uncut dimer

    Journal: Journal of Clinical Microbiology

    Article Title: Improved Method for Rapid and Efficient Determination of Genome Replication and Protein Expression of Clinical Hepatitis B Virus Isolates ▿

    doi: 10.1128/JCM.02340-10

    Figure Lengend Snippet: Replication capacity of the HBV genome linearized by ApaI and SphI restriction enzymes. The EcoRI dimer of clone 4B was digested with ApaI or SphI, with or without further treatment with T4 DNA ligase before transfection into Huh7 cells. The uncut dimer

    Article Snippet: A single copy of the full-length HBV genome was released by the EcoRI digestion of the EcoRI monomer, ApaI or SphI digestion of the EcoRI dimer, and digestion of the monomeric PCR clones or clone pools at 50°C with BspQI (New England BioLabs).

    Techniques: Transfection

    Southern blot analysis of T 4 progenies of line IO6-97. Stable integration of RGA2 intron was detected in transgenic rice plants, no hybridization signal was observed in the respective non-transgenic control. Each lane consists of 10 µg genomic DNA, digested with EcoR I or Hind III. The position and sizes of markers are indicated (NT = Non-transgenic control, E = EcoR I and H = Hind III).

    Journal: PLoS ONE

    Article Title: Development of Low Phytate Rice by RNAi Mediated Seed-Specific Silencing of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Gene (IPK1)

    doi: 10.1371/journal.pone.0068161

    Figure Lengend Snippet: Southern blot analysis of T 4 progenies of line IO6-97. Stable integration of RGA2 intron was detected in transgenic rice plants, no hybridization signal was observed in the respective non-transgenic control. Each lane consists of 10 µg genomic DNA, digested with EcoR I or Hind III. The position and sizes of markers are indicated (NT = Non-transgenic control, E = EcoR I and H = Hind III).

    Article Snippet: Genomic DNA (10 µg) was digested separately with EcoR I and Hind III (Fermentas), separated on a 1% agarose gel, and transferred to a nylon membrane (Hybond N+, Amersham, GE Healthcare).

    Techniques: Southern Blot, Transgenic Assay, Hybridization

    Determination of the origin of the 10.9-kb fragment from the index patient. A: Southern blot using PstI digestion only showing bands of 0.99, 1.03, and 1.08 kb (the largest band approximately 1.1 kb in size). An abnormal control (AC, lane 6 ) shows a full mutation (Coriell GM07537A), with an additional 2.1-kb band (336 CGG repeats). No CGG expansion was noted in the family study ( lanes 2 to 4 ) or in a normal control (NC, lane 5 ). MW, the Lambda/HindIII MW marker (Chemicon International). B: Southern analysis of the family digested with EcoRI, with (+) and without (−) NruI. MW, molecular marker as in A ; NFC, normal female control; M, mother; IP, index patient; F, father; NMC, normal male control; AC, abnormal control as in A . Note that father and the index patient both showed the 10.9-kb fragment ( lanes 6 , 7 , and 9 ). C: PCR products with (+) and without (−) EcoRI digestion. MR, 100-bp Molecular Ruler (Bio-Rad); NC, normal control; M, mother; IP, index patient; F, father.

    Journal: The Journal of Molecular Diagnostics : JMD

    Article Title: A Pseudo-Full Mutation Identified in Fragile X Assay Reveals a Novel Base Change Abolishing an EcoRI Restriction Site

    doi: 10.2353/jmoldx.2008.080059

    Figure Lengend Snippet: Determination of the origin of the 10.9-kb fragment from the index patient. A: Southern blot using PstI digestion only showing bands of 0.99, 1.03, and 1.08 kb (the largest band approximately 1.1 kb in size). An abnormal control (AC, lane 6 ) shows a full mutation (Coriell GM07537A), with an additional 2.1-kb band (336 CGG repeats). No CGG expansion was noted in the family study ( lanes 2 to 4 ) or in a normal control (NC, lane 5 ). MW, the Lambda/HindIII MW marker (Chemicon International). B: Southern analysis of the family digested with EcoRI, with (+) and without (−) NruI. MW, molecular marker as in A ; NFC, normal female control; M, mother; IP, index patient; F, father; NMC, normal male control; AC, abnormal control as in A . Note that father and the index patient both showed the 10.9-kb fragment ( lanes 6 , 7 , and 9 ). C: PCR products with (+) and without (−) EcoRI digestion. MR, 100-bp Molecular Ruler (Bio-Rad); NC, normal control; M, mother; IP, index patient; F, father.

    Article Snippet: For the standard Southern analysis, 6 μg of genomic DNA was double-digested with NruI (a methylation-sensitive enzyme, cutting only unmethylated, active X chromosome) and EcoRI (100 U of each enzyme at 37°C for 6 hours), electrophoresed on a 0.7% agarose gel, transferred to a nylon membrane, and hybridized with digoxiginin-labeled probe pFXa1NHE (Chemicon International, Temecula, CA).

    Techniques: Southern Blot, Mutagenesis, Marker, Polymerase Chain Reaction

    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with BamHI and EcoRI (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).

    Journal: Genome Research

    Article Title: Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences

    doi: 10.1101/gr.094953.109

    Figure Lengend Snippet: Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with BamHI and EcoRI (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).

    Article Snippet: The pellets containing ∼5 × 108 nuclei were then resuspended in BamHI buffer and digested with 2000 U each of EcoRI and BamHI (Invitrogen) for 90 min at 37°C with gentle agitation, allowing digested DNA to leach out of the nuclei.

    Techniques: