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hpaii endonuclease  (New England Biolabs)


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    New England Biolabs hpaii endonuclease
    Hpaii Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 2384 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/hpaii/HpaII/10__3390_slash_agronomy16090936-104-8-11
    Average 97 stars, based on 2384 article reviews
    hpaii endonuclease - by Bioz Stars, 2026-09
    97/100 stars

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    Related Articles

    Methylation:

    Article Title: MethylAmp: One-step isothermal amplification with preservation of DNA methylation patterns
    Article Snippet: .. To evaluate methylation efficiency, parallel digestion reactions were prepared by combining 5 μL of each purified sample with 5 μL of digestion buffer containing either no enzyme (undigested control) or 3 U of HpaII (New England Biolabs, Cat. No. R0171) in rCutSmartTM buffer. ..

    Purification:

    Article Title: MethylAmp: One-step isothermal amplification with preservation of DNA methylation patterns
    Article Snippet: .. To evaluate methylation efficiency, parallel digestion reactions were prepared by combining 5 μL of each purified sample with 5 μL of digestion buffer containing either no enzyme (undigested control) or 3 U of HpaII (New England Biolabs, Cat. No. R0171) in rCutSmartTM buffer. ..

    Control:

    Article Title: MethylAmp: One-step isothermal amplification with preservation of DNA methylation patterns
    Article Snippet: .. To evaluate methylation efficiency, parallel digestion reactions were prepared by combining 5 μL of each purified sample with 5 μL of digestion buffer containing either no enzyme (undigested control) or 3 U of HpaII (New England Biolabs, Cat. No. R0171) in rCutSmartTM buffer. ..

    Mutagenesis:

    Article Title: Pluripotent stem-cell-based screening uncovers sildenafil as a mitochondrial disease therapy.
    Article Snippet: 27 Genomic DNA was isolated using the Nucleo-Spin Tissue kit (Macherey-Nagel). .. We used re- striction enzyme StuI (NEB, R0187, 10,000 units/ml) for the m.9185T>C mutation (wild-type: 24+90 pb, mutation: 114 pb), HpaII (NEB, R0171, 10,000 units/ml) for m.8993T>C and m.8993T>G (wild type: 25+155 bp; mutant: 180 bp), XbaI (NEB, R0145, 10,000 units/ml) for m.9176 T>G (wild type: 24+155 bp, mutant: 179 bp). .. The percentage of cleaved versus uncleaved fragments was determined by capillary electrophoresis and laser detection of the FAM-labelled RFLP-fragments using the 3,500 Series Genetic Analyzer (Applied Biosystems, RRID:SCR_021901) and normalized to a standard curve of known degrees of heteroplasmy.

    Polymerase Chain Reaction:

    Article Title: High-throughput analyses of Phocaeicola vulgatus reveal fitness determinants for gut colonization and during colitis
    Article Snippet: .. This PCR product was then digested with HpaII (NEB), which cuts asymmetrically within the invertible region so that the on fragment would produce 431 bp and 149 bp digestion products while the promoter off orientation would produce 313 bp and 267 bp cleavage products. ..



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    New England Biolabs hpaii endonuclease
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
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    hpaii restriction enzyme  (New England Biolabs)
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    New England Biolabs hpaii restriction enzyme
    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
    Hpaii Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    hpaii restriction endonuclease  (New England Biolabs)
    97
    New England Biolabs hpaii restriction endonuclease
    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on <t>HpaII-</t> digestion. (d) Ct plotted as function of log <t>2</t> <t>[DNA]);</t> used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.
    Hpaii Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/hpaii/HpaII/us12601006-241-25-28
    Average 97 stars, based on 1 article reviews
    hpaii restriction endonuclease - by Bioz Stars, 2026-09
    97/100 stars
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    Image Search Results


    (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on HpaII- digestion. (d) Ct plotted as function of log 2 [DNA]); used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.

    Journal: bioRxiv

    Article Title: SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy

    doi: 10.64898/2026.04.26.720516

    Figure Lengend Snippet: (a) Details of L1 ES-qPCR. (i) L1 5’UTR ES-qPCR oligonucleotides, (ii) L1 reference oligonucleotides. (iii) Sequence of L1 ES-qPCR reactions. (1) Restriction digestion; (2) Annealing of L1-specific foligos; (3) extension of 3’-ends created by restriction digestion – if the 3’-ends are annealed to a foligo; (4) copying of (green) foligo-tagged templates or (red) reference templates by PCR; (5) detection of products by quenched probes. (b) Sensitivity of (solid symbols) original versus (open symbols) updated L1 ES-qPCR reagents. (c) Dependence of L1 ES-qPCR FAM signals on HpaII- digestion. (d) Ct plotted as function of log 2 [DNA]); used for (e) PCR efficiency calculations (top) and relative L1 demethylation calculations (bottom). (f) Examples of targeted amplicon recoveries from (i) Hpa II-digested genomic gDNA or (ii) Hpa II-digested first strand cDNA. (g) Averaged heat map of gene coverage by the pilot SCIMETAR-seq. Low recovery in the first 2 rows was due to evaporation during primary PCR. (h) Rationale for filtering of L1 ES-qPCR outliers: All single cells contain the same number of L1 refernce DNA templates, but will vary in L1 methylation, Therefore, reference (HEX) Ct that fall outside 2xMAD were excluded as failed outliers (white dots). Note that not all HEX Ct outliers are also FAM (demethylation) Ct outliers. (i) Detail of complete target amplicons: (green) Hpa II sites, (red) target mutations sites, (purple N) I5 or i7 index, (X…X) well barcodes, ( underlined ) exonic sequence.

    Article Snippet: Reaction mixtures contained 20 mM Tris-HCl (pH ∼8.3; Merck, 648310-M), 50 mM KCl (Merck, 60142-100mL-F), 7 mM MgCl2 (Merck, M1028-10X1mL), 200 μM dNTP mix (Thermo Fisher Scientific, R0181), 0.5 U of Hot Start Taq DNA polymerase (New England Biolabs, M0495L), and 2 U of HpaII (New England Biolabs, R0171L).

    Techniques: Sequencing, Amplification, Evaporation, Methylation