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nmp lesion site  (New England Biolabs)


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    New England Biolabs nmp lesion site
    ( A ) <t>NMP-seq</t> methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG <t>and</t> <t>APE1</t> to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.
    Nmp Lesion Site, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 91 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/nmp+lesion+site/Human+Alkyladenine+Glycosylase/pmc08970589-213-1-8
    Average 94 stars, based on 91 article reviews
    nmp lesion site - by Bioz Stars, 2026-09
    94/100 stars

    Images

    1) Product Images from "High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors"

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

    Journal: eLife

    doi: 10.7554/eLife.73943

    ( A ) NMP-seq methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG and APE1 to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.
    Figure Legend Snippet: ( A ) NMP-seq methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG and APE1 to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.

    Techniques Used: Sonication, Blocking Assay, Ligation, Purification, Amplification, Sequencing

    Related Articles

    Sonication:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.

    Blocking Assay:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.

    Ligation:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.

    Purification:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.

    Amplification:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.

    Sequencing:

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95°C and cooled on ice, followed by ligation to the second adaptor.

    Article Title: High-resolution mapping of DNA alkylation damage and base excision repair at yeast transcription factor binding sites
    Article Snippet: ligation product was purified and incubated with terminal transferase and dideoxy-ATP (ddATP) to block all free 3’ ends ( ). .. The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end. .. DNA was denatured at 95 °C and cooled on ice, followed by ligation to the second adaptor.



    Similar Products

    nmp lesion site  (New England Biolabs)
    94
    New England Biolabs nmp lesion site
    ( A ) <t>NMP-seq</t> methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG <t>and</t> <t>APE1</t> to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.
    Nmp Lesion Site, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/nmp+lesion+site/Human+Alkyladenine+Glycosylase/pmc08970589-213-1-8
    Average 94 stars, based on 1 article reviews
    nmp lesion site - by Bioz Stars, 2026-09
    94/100 stars
    		  Buy from Supplier

    Image Search Results


    ( A ) NMP-seq methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG and APE1 to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.

    Journal: eLife

    Article Title: High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

    doi: 10.7554/eLife.73943

    Figure Lengend Snippet: ( A ) NMP-seq methodology. Genomic DNA was first sonicated to short fragments (~400 bp) and ligated to the 1st adaptor (green). After blocking all free 3’-OH groups with terminal transferase and dideoxy-ATP (dd), DNA fragments were digested with AAG and APE1 to generate a new nick with a ligatable 3’-OH group at the NMP damage site. After denaturing to obtain single-stranded DNA, the new 3’ end is ligated to a splint adaptor (2nd adaptor; purple) and the ligation occurs exactly at the damage site. The biotin on the 2nd adaptor allows purification of ligation product with the Streptavidin beads. The purified product is used as the template for PCR amplification, using primers complementary to the 1st and 2nd adaptors. The resulting library is sequenced on an Iron Torrent sequencer using a sequencing primer complementary to the 2nd adaptor. ( B ) NMP-seq read counts in MMS-treated mag1 cells (0.4% MMS for 10 min). (G) and (A) reads are associated with 7meG and 3meA lesions in the genome. ( C ) Schematic for damage mapping in naked yeast genomic DNA. It differs from mapping cellular NMP lesions by inducing damage in purified DNA, instead of cellular DNA bound by proteins. ( D ) NMP-seq read counts for naked genomic DNA treated with 0.4 or 0.2% of MMS for 10 min.

    Article Snippet: The NMP lesion site was cleaved by hAAG (NEB, M0313S) and APE1 (NEB, M0282S) to generate a new ligatable 3’ end.

    Techniques: Sonication, Blocking Assay, Ligation, Purification, Amplification, Sequencing