hpa ii Search Results


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  • 93
    New England Biolabs hpa ii methyltransferase
    The Klf1 exon 2 CGI is unmethylated during development. A ) Schematic of the mouse Klf1 gene across exon 2 and the flanking introns shows salient restriction enzyme sites within the region and a 1.1-kbp cDNA probe used for Southern blot. B ) Genomic DNA samples from whole testis between P5 and P45 (lanes 1–7, left and center panels) and P45 spleen (lane 8). DNAs were purified and double-digested with Eco RI and Bam HI restriction enzymes to liberate the 1.85-kb genomic fragment containing the Klf1 exon 2 CGI. Thereafter, the DNA samples were further digested with <t>Hpa</t> II (left panel) or not digested (center panel) and then Southern blotted using the 1.1-kb probe shown in A . In addition, several samples were methylated using Hpa II <t>-methyltransferase</t> then digested with Hpa II (right panel) and Southern blotted. Because of the total number of samples in this experiment, three Southern blots were generated, and the relevant lanes were used to form composite panels. Data for the P5–P15 lanes (break in Southern blots) were obtained from separate Southern blots. Arrowheads in A , locations of Hpa II restriction sites; FL in B , full-length 1.85-kb Eco RI - Bam HI fragments that are visible in the center and right panels; Spl, spleen.
    Hpa Ii Methyltransferase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher hpa ii digestion
    The Klf1 exon 2 CGI is unmethylated during development. A ) Schematic of the mouse Klf1 gene across exon 2 and the flanking introns shows salient restriction enzyme sites within the region and a 1.1-kbp cDNA probe used for Southern blot. B ) Genomic DNA samples from whole testis between P5 and P45 (lanes 1–7, left and center panels) and P45 spleen (lane 8). DNAs were purified and double-digested with Eco RI and Bam HI restriction enzymes to liberate the 1.85-kb genomic fragment containing the Klf1 exon 2 CGI. Thereafter, the DNA samples were further digested with <t>Hpa</t> II (left panel) or not digested (center panel) and then Southern blotted using the 1.1-kb probe shown in A . In addition, several samples were methylated using Hpa II <t>-methyltransferase</t> then digested with Hpa II (right panel) and Southern blotted. Because of the total number of samples in this experiment, three Southern blots were generated, and the relevant lanes were used to form composite panels. Data for the P5–P15 lanes (break in Southern blots) were obtained from separate Southern blots. Arrowheads in A , locations of Hpa II restriction sites; FL in B , full-length 1.85-kb Eco RI - Bam HI fragments that are visible in the center and right panels; Spl, spleen.
    Hpa Ii Digestion, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher hpa ii
    Production of IFNβ by NIH3T3 cells after nucleofection with methylated or unmethylated phGfΔG plasmid <t>DNA.</t> (A) The phGfΔG plasmid was treated with the methyltransferase M. SssI to methylate the CpG motifs. Prevention of the digestion by <t>Hpa</t> II indicated the methylation state of the plasmid. Untreated plasmid was used as a positive control of Hpa II digestion. (B) Cells were transfected either with unmethylated or methylated plasmid, and the levels of IFNβ production were assayed by ELISA. The data represent the values of two independent experiments.
    Hpa Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 299 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche hpa ii
    Effects of <t>DNA</t> polymerase inhibitors on uracil excision repair by Arabidopsis cell extracts. Duplex DNA containing U opposite G at a <t>Hpa</t> II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either dCTP or all four dNTPs, as indicated, and increasing levels of aphidicolin (left panel: 0, 300, 600 or 1200 μ m ) or 2′,3′-dideoxycytidine 5′-triphosphate (ddCTP, right panel: 0, 20, 200 or 2000 μ m ). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.
    Hpa Ii, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Boehringer Mannheim hpa ii
    Restriction fragment length polymorphism analysis of whole-cell DNAs of C . lipolytica isolates after digestion with <t>Hpa</t> II (A) or Hin fI (B). Lanes: 1 to 10, our clinical isolates; 11, control strain C211; 12, control strain C202; 13, ATCC 9773; M, size marker ( Hin <t>dIII</t> digest of bacteriophage lambda DNA).
    Hpa Ii, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    TaKaRa hpa ii
    MSAP gels electrophoresis of PaWB seedlings with MMS treatment. H 1 and M 1 : bands digested by Eco RI/ <t>Hpa</t> II (H) and Eco RI/ <t>Msp</t> I (M) in PS; H 2 and M 2 : bands digested by H and M in PS-20; H 3 and M 3 : bands digested by H and M in PS-60; H 4 and M 4 : bands digested by H and M in PS-100; H 5 and M 5 : bands digested by H and M in HS; E 25 /HM 52 – E 25 /HM x : primer combination; M: Marker; The arrows only indicated part of the methylation patterns between PS and PS-20 (H 1 , M 1 , H 2 , M 2 ).
    Hpa Ii, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Toyobo hpa ii
    Effects of the DNA methylation-sensitive restriction enzyme on the RAPD bands 143a and 143c ( arrowed ). First, non-, <t>Msp</t> I- and <t>Hpa</t> II-digested DNA samples were amplified by PCR using the decamer primer No. 143. Then, PCR products were digested with ( a ) no restriction enzyme, (b) Msp I or ( c ) Hpa II. Lambda DNA Hin dIII digests in the furthest left lane. Parent A, 2H21-2 (S 1 ), 2H22-1 (S 3 ), 3H94-17 (S 4 ), 4H130-1 (S 5 ), 5H 123-9 (F 1 ), 4H105-7 (S 6 ) ( lanes 1–7 )
    Hpa Ii, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    GE Healthcare hpa ii
    Effects of the DNA methylation-sensitive restriction enzyme on the RAPD bands 143a and 143c ( arrowed ). First, non-, <t>Msp</t> I- and <t>Hpa</t> II-digested DNA samples were amplified by PCR using the decamer primer No. 143. Then, PCR products were digested with ( a ) no restriction enzyme, (b) Msp I or ( c ) Hpa II. Lambda DNA Hin dIII digests in the furthest left lane. Parent A, 2H21-2 (S 1 ), 2H22-1 (S 3 ), 3H94-17 (S 4 ), 4H130-1 (S 5 ), 5H 123-9 (F 1 ), 4H105-7 (S 6 ) ( lanes 1–7 )
    Hpa Ii, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher fastdigest hpa ii
    Effects of the DNA methylation-sensitive restriction enzyme on the RAPD bands 143a and 143c ( arrowed ). First, non-, <t>Msp</t> I- and <t>Hpa</t> II-digested DNA samples were amplified by PCR using the decamer primer No. 143. Then, PCR products were digested with ( a ) no restriction enzyme, (b) Msp I or ( c ) Hpa II. Lambda DNA Hin dIII digests in the furthest left lane. Parent A, 2H21-2 (S 1 ), 2H22-1 (S 3 ), 3H94-17 (S 4 ), 4H130-1 (S 5 ), 5H 123-9 (F 1 ), 4H105-7 (S 6 ) ( lanes 1–7 )
    Fastdigest Hpa Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Roche endonuclease hpa ii
    <t>PCR-RFLP</t> maps of the 232-bp amplicon showing the three types of <t>Hpa</t> II endonuclease restriction fragment patterns. The upper map represents PCR-RFLP 1 with two fragments of 66 and 166 bp. The second map represents PCR-RFLP 2 with three fragments of 18, 66, and 148 bp. The third map represent PCR-RFLP 3 with fragments of 7, 20, 66, and 139 bp. The lower map represents the scaled 232-bp amplicon. The arrows flanking the PCR-RFLP 1 map represent primers which may be AHCF1, -2, or -3 and AHCR1, -2, -3, -4, or -5.
    Endonuclease Hpa Ii, supplied by Roche, used in various techniques. Bioz Stars score: 80/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore hpa ii
    <t>PCR-RFLP</t> maps of the 232-bp amplicon showing the three types of <t>Hpa</t> II endonuclease restriction fragment patterns. The upper map represents PCR-RFLP 1 with two fragments of 66 and 166 bp. The second map represents PCR-RFLP 2 with three fragments of 18, 66, and 148 bp. The third map represent PCR-RFLP 3 with fragments of 7, 20, 66, and 139 bp. The lower map represents the scaled 232-bp amplicon. The arrows flanking the PCR-RFLP 1 map represent primers which may be AHCF1, -2, or -3 and AHCR1, -2, -3, -4, or -5.
    Hpa Ii, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher restriction enzyme hpa ii
    Agarose gel electrophoresis of <t>ITS-PCR</t> products of various Candida species after digestion with <t>Hpa</t> II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker
    Restriction Enzyme Hpa Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    GeneWorks puc19 hpa ii dna
    Agarose gel electrophoresis of <t>ITS-PCR</t> products of various Candida species after digestion with <t>Hpa</t> II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker
    Puc19 Hpa Ii Dna, supplied by GeneWorks, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher hpa ii dna methylase
    Agarose gel electrophoresis of <t>ITS-PCR</t> products of various Candida species after digestion with <t>Hpa</t> II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker
    Hpa Ii Dna Methylase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Sangon Biotech puc19dna msp hpa ii marker
    Agarose gel electrophoresis of <t>ITS-PCR</t> products of various Candida species after digestion with <t>Hpa</t> II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker
    Puc19dna Msp Hpa Ii Marker, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc hpa ii
    Agarose gel electrophoresis of <t>ITS-PCR</t> products of various Candida species after digestion with <t>Hpa</t> II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker
    Hpa Ii, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    hpa ii  (ATUM)
    90
    ATUM hpa ii
    Methylation sensitive restriction enzyme analysis on TYLCSV- or TYLCSV/PSTVd-infected plants. ( A ) TYLCSV <t>DNA</t> accumulation in the plants infected by TYLCSV- or by TYLCSV/PSTVd (T and TP, respectively). ( B ) Position of <t>Hpa</t> II and Msp I sites in the TYLCSV genome; red arrows, primers to amplify the TYLCSV region for bisulfite analysis (see Fig. 4 ). ( C ) Msp I or Hpa II digestion of plant DNA extracts (fragments indicated by red arrows) and of the RCA amplicon (size in bp indicated on the left). U, undigested ss DNA sample with TYLCSV ssDNA (black arrows); TYLCSV size marker (in bp, on the right) are 2773 ( Sst I digestion of a TYLCSV clone), 3328, 1318, 844 ( Sph I/ SnaB I), and 1463, 526, 300 ( Bgl II/ Sal I).
    Hpa Ii, supplied by ATUM, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    TaKaRa eco ri hpa ii
    Changes of DNA methylation pattern in MMS-treated PaWB plantlets. H1 and M1 : band digested by Eco RI/ <t>Hpa</t> II (H) and Eco RI/ <t>Msp</t> I (M) in PaWB plantlets; H2 and M2 : band digested by H and M in plantlets with 15 mg·L −1 MMS treatment; H3 and M3 : band digested by H and M in plantlets with 30 mg·L −1 MMS treatment; H4 and M4 : band digested by H and M in plantlets with 45 mg·L −1 MMS treatment; H5 and M5 : band digested by H and M in HP. E22/HM41–E22/HMx: primer combination; M : marker. The arrows indicated 4 lanes of part of the methylation patterns variations only between PaWB plantlets and the ones with 15 mg·L −1 MMS treatment (H1, M1, H2, M2). D3, A4 and D2 indicated part of the methylation patterns variations. The band of D3, A4 and D2 were (0,1,0,1), (1,0,0,0) and (1,0,1,0), respectively.
    Eco Ri Hpa Ii, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega hpa ii
    Methylation-sensitive amplified polymorphism (MSAP) band patterning determined by <t>Hpa</t> II/ <t>Msp</t> I isoschizomers and correspondence with methylation status of CCGG sites. Black squares indicate methylated cytosines.
    Hpa Ii, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher hpa ii restriction
    Methylation-sensitive amplified polymorphism (MSAP) band patterning determined by <t>Hpa</t> II/ <t>Msp</t> I isoschizomers and correspondence with methylation status of CCGG sites. Black squares indicate methylated cytosines.
    Hpa Ii Restriction, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    GeneWorks puc19 hpa ii
    Methylation-sensitive amplified polymorphism (MSAP) band patterning determined by <t>Hpa</t> II/ <t>Msp</t> I isoschizomers and correspondence with methylation status of CCGG sites. Black squares indicate methylated cytosines.
    Puc19 Hpa Ii, supplied by GeneWorks, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    The Klf1 exon 2 CGI is unmethylated during development. A ) Schematic of the mouse Klf1 gene across exon 2 and the flanking introns shows salient restriction enzyme sites within the region and a 1.1-kbp cDNA probe used for Southern blot. B ) Genomic DNA samples from whole testis between P5 and P45 (lanes 1–7, left and center panels) and P45 spleen (lane 8). DNAs were purified and double-digested with Eco RI and Bam HI restriction enzymes to liberate the 1.85-kb genomic fragment containing the Klf1 exon 2 CGI. Thereafter, the DNA samples were further digested with Hpa II (left panel) or not digested (center panel) and then Southern blotted using the 1.1-kb probe shown in A . In addition, several samples were methylated using Hpa II -methyltransferase then digested with Hpa II (right panel) and Southern blotted. Because of the total number of samples in this experiment, three Southern blots were generated, and the relevant lanes were used to form composite panels. Data for the P5–P15 lanes (break in Southern blots) were obtained from separate Southern blots. Arrowheads in A , locations of Hpa II restriction sites; FL in B , full-length 1.85-kb Eco RI - Bam HI fragments that are visible in the center and right panels; Spl, spleen.

    Journal: Biology of Reproduction

    Article Title: Tissue-Restricted Transcription from a Conserved Intragenic CpG Island in the Klf1 Gene in Mice 1

    doi: 10.1095/biolreprod.112.099879

    Figure Lengend Snippet: The Klf1 exon 2 CGI is unmethylated during development. A ) Schematic of the mouse Klf1 gene across exon 2 and the flanking introns shows salient restriction enzyme sites within the region and a 1.1-kbp cDNA probe used for Southern blot. B ) Genomic DNA samples from whole testis between P5 and P45 (lanes 1–7, left and center panels) and P45 spleen (lane 8). DNAs were purified and double-digested with Eco RI and Bam HI restriction enzymes to liberate the 1.85-kb genomic fragment containing the Klf1 exon 2 CGI. Thereafter, the DNA samples were further digested with Hpa II (left panel) or not digested (center panel) and then Southern blotted using the 1.1-kb probe shown in A . In addition, several samples were methylated using Hpa II -methyltransferase then digested with Hpa II (right panel) and Southern blotted. Because of the total number of samples in this experiment, three Southern blots were generated, and the relevant lanes were used to form composite panels. Data for the P5–P15 lanes (break in Southern blots) were obtained from separate Southern blots. Arrowheads in A , locations of Hpa II restriction sites; FL in B , full-length 1.85-kb Eco RI - Bam HI fragments that are visible in the center and right panels; Spl, spleen.

    Article Snippet: Genomic DNAs purified from testes were restriction digested with Eco RI and Bam HI (New England Biolabs) at 37°C for 4–6 h. DNA samples were then either restriction digested with Hpa II (New England Biolabs) for 4–6 h or methylated in vitro using Hpa II methyltransferase (New England Biolabs) and digested with Hpa II .

    Techniques: Southern Blot, Purification, Methylation, Generated

    A covalent lagging strand protein-DNA adduct forms a stringent block to CMG. ( A ) Schematic of the substrate used in these reactions. The duplex portion of the fork contains the 4-base recognition sequence for the Hpa II methyltransferase. Replacement of the second dCTP in the recognition site with 5-fluorodeoxycytidine (5-FDC) traps a covalent intermediate in the methylation reaction in which M.Hpa II remains bound to the nucleotide base on the lagging strand as shown ( Chen et al., 1991 ). Sequences of the oligos are in Table 1 . ( B ) CMG unwinding reactions using the 5-FDC substrate with (lanes 6–8) or without (lanes 2–4) M.Hpa II modification. Except for the substrate, reactions conditions are the same as those of Figure 3 (no streptavidin). ( C ) The M.Hpa II modified 5-FDC substrate was heated at 65° for 20’ to inactivate M.Hpa II, cooled on ice, and added to a CMG unwinding reaction (lanes 4–6) identical to that in ( B ) except 40 nM CMG was used. Lanes 1–3 show unwinding of the untreated substrate under the same conditions. DOI: http://dx.doi.org/10.7554/eLife.23449.020

    Journal: eLife

    Article Title: Action of CMG with strand-specific DNA blocks supports an internal unwinding mode for the eukaryotic replicative helicase

    doi: 10.7554/eLife.23449

    Figure Lengend Snippet: A covalent lagging strand protein-DNA adduct forms a stringent block to CMG. ( A ) Schematic of the substrate used in these reactions. The duplex portion of the fork contains the 4-base recognition sequence for the Hpa II methyltransferase. Replacement of the second dCTP in the recognition site with 5-fluorodeoxycytidine (5-FDC) traps a covalent intermediate in the methylation reaction in which M.Hpa II remains bound to the nucleotide base on the lagging strand as shown ( Chen et al., 1991 ). Sequences of the oligos are in Table 1 . ( B ) CMG unwinding reactions using the 5-FDC substrate with (lanes 6–8) or without (lanes 2–4) M.Hpa II modification. Except for the substrate, reactions conditions are the same as those of Figure 3 (no streptavidin). ( C ) The M.Hpa II modified 5-FDC substrate was heated at 65° for 20’ to inactivate M.Hpa II, cooled on ice, and added to a CMG unwinding reaction (lanes 4–6) identical to that in ( B ) except 40 nM CMG was used. Lanes 1–3 show unwinding of the untreated substrate under the same conditions. DOI: http://dx.doi.org/10.7554/eLife.23449.020

    Article Snippet: DNA modification enzymes including M.Hpa II methyltransferase were from New England Biolabs.

    Techniques: Blocking Assay, Sequencing, Methylation, Modification

    Production of IFNβ by NIH3T3 cells after nucleofection with methylated or unmethylated phGfΔG plasmid DNA. (A) The phGfΔG plasmid was treated with the methyltransferase M. SssI to methylate the CpG motifs. Prevention of the digestion by Hpa II indicated the methylation state of the plasmid. Untreated plasmid was used as a positive control of Hpa II digestion. (B) Cells were transfected either with unmethylated or methylated plasmid, and the levels of IFNβ production were assayed by ELISA. The data represent the values of two independent experiments.

    Journal: DNA and Cell Biology

    Article Title: Nucleofection of Expression Vectors Induces a Robust Interferon Response and Inhibition of Cell Proliferation

    doi: 10.1089/dna.2012.1950

    Figure Lengend Snippet: Production of IFNβ by NIH3T3 cells after nucleofection with methylated or unmethylated phGfΔG plasmid DNA. (A) The phGfΔG plasmid was treated with the methyltransferase M. SssI to methylate the CpG motifs. Prevention of the digestion by Hpa II indicated the methylation state of the plasmid. Untreated plasmid was used as a positive control of Hpa II digestion. (B) Cells were transfected either with unmethylated or methylated plasmid, and the levels of IFNβ production were assayed by ELISA. The data represent the values of two independent experiments.

    Article Snippet: DNA was subjected to cleavage by restriction enzyme, Hpa II (Thermo Scientific).

    Techniques: Methylation, Plasmid Preparation, Positive Control, Transfection, Enzyme-linked Immunosorbent Assay

    Effects of DNA polymerase inhibitors on uracil excision repair by Arabidopsis cell extracts. Duplex DNA containing U opposite G at a Hpa II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either dCTP or all four dNTPs, as indicated, and increasing levels of aphidicolin (left panel: 0, 300, 600 or 1200 μ m ) or 2′,3′-dideoxycytidine 5′-triphosphate (ddCTP, right panel: 0, 20, 200 or 2000 μ m ). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.

    Journal: The Plant Journal

    Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

    doi: 10.1111/j.1365-313X.2009.03994.x

    Figure Lengend Snippet: Effects of DNA polymerase inhibitors on uracil excision repair by Arabidopsis cell extracts. Duplex DNA containing U opposite G at a Hpa II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either dCTP or all four dNTPs, as indicated, and increasing levels of aphidicolin (left panel: 0, 300, 600 or 1200 μ m ) or 2′,3′-dideoxycytidine 5′-triphosphate (ddCTP, right panel: 0, 20, 200 or 2000 μ m ). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.

    Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

    Techniques: Incubation, Fluorescence

    Partial stimulation of uracil repair by the addition of exogenous proteins. Duplex DNA containing U opposite G at a Hpa II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either deoxycytidine triphosphate (dCTP) or all four deoxyribonucleotide triphosphates (dNTPs), as indicated, and different combinations of T4 DNA ligase (1.5 U), Arabidopsis AtXRCC1 (65 n m ) and human Pol β (2.4 U). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.

    Journal: The Plant Journal

    Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

    doi: 10.1111/j.1365-313X.2009.03994.x

    Figure Lengend Snippet: Partial stimulation of uracil repair by the addition of exogenous proteins. Duplex DNA containing U opposite G at a Hpa II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either deoxycytidine triphosphate (dCTP) or all four deoxyribonucleotide triphosphates (dNTPs), as indicated, and different combinations of T4 DNA ligase (1.5 U), Arabidopsis AtXRCC1 (65 n m ) and human Pol β (2.4 U). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.

    Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

    Techniques: Incubation, Fluorescence

    Repair of base DNA damage by Arabidopsis cell extracts. (a) Schematic diagram of molecules used as DNA substrates. Double-stranded oligonucleotides contained a lesion (X = uracil or AP site) at an Hpa II site on the upper strand. The Alexa Fluor-labeled 5′ end of the lower strand is indicated by a star. The size of the 5′ end-labeled fragment generated after Hpa II digestion of the fully repaired product is indicated on the right. (b) DNA duplexes containing U, a natural AP site, or THF opposite G were incubated with Arabidopsis cell extract at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, as indicated. Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. (c) A DNA duplex containing a U:G mispair was incubated with Arabidopsis cell extracts at 30°C in a reaction mixture containing either dCTP or all four dNTPs. Reactions were stopped at the indicated times and products were analyzed as described above. The percentage of fully repaired DNA product for reactions containing only dCTP (•) or all four dNTPs (○) is shown in the bottom panel. Values are means with standard errors from two independent experiments.

    Journal: The Plant Journal

    Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

    doi: 10.1111/j.1365-313X.2009.03994.x

    Figure Lengend Snippet: Repair of base DNA damage by Arabidopsis cell extracts. (a) Schematic diagram of molecules used as DNA substrates. Double-stranded oligonucleotides contained a lesion (X = uracil or AP site) at an Hpa II site on the upper strand. The Alexa Fluor-labeled 5′ end of the lower strand is indicated by a star. The size of the 5′ end-labeled fragment generated after Hpa II digestion of the fully repaired product is indicated on the right. (b) DNA duplexes containing U, a natural AP site, or THF opposite G were incubated with Arabidopsis cell extract at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, as indicated. Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. (c) A DNA duplex containing a U:G mispair was incubated with Arabidopsis cell extracts at 30°C in a reaction mixture containing either dCTP or all four dNTPs. Reactions were stopped at the indicated times and products were analyzed as described above. The percentage of fully repaired DNA product for reactions containing only dCTP (•) or all four dNTPs (○) is shown in the bottom panel. Values are means with standard errors from two independent experiments.

    Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

    Techniques: Labeling, Generated, Incubation, Fluorescence

    Uracil excision repair involves single-nucleotide insertion and long-patch DNA synthesis. Arabidopsis cell extract was incubated with duplex DNA that contained a U residue in the upper strand, and which was labeled at the 5′ end of the upper strand with fluorescein and at the 5′ end of the lower strand with Alexa Fluor. Reactions were incubated at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, as indicated. Reaction products were separated in a 12% denaturing polyacrylamide gel either before (lanes 2–5) or after (lanes 6–9) Hpa II digestion. Fluorescein- (lanes 2–5) and Alexa Fluor-labeled fragments (lanes 6–9) were detected by fluorescence scanning.

    Journal: The Plant Journal

    Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

    doi: 10.1111/j.1365-313X.2009.03994.x

    Figure Lengend Snippet: Uracil excision repair involves single-nucleotide insertion and long-patch DNA synthesis. Arabidopsis cell extract was incubated with duplex DNA that contained a U residue in the upper strand, and which was labeled at the 5′ end of the upper strand with fluorescein and at the 5′ end of the lower strand with Alexa Fluor. Reactions were incubated at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, as indicated. Reaction products were separated in a 12% denaturing polyacrylamide gel either before (lanes 2–5) or after (lanes 6–9) Hpa II digestion. Fluorescein- (lanes 2–5) and Alexa Fluor-labeled fragments (lanes 6–9) were detected by fluorescence scanning.

    Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

    Techniques: DNA Synthesis, Incubation, Labeling, Fluorescence

    Uracil repair by Arabidopsis cell extracts is dependent on uracil DNA glycosylase (UDG) activity. DNA duplexes containing either U or THF opposite G were incubated with Arabidopsis cell extracts at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, both in the absence or presence of 2 U of uracil-DNA glycosylase inhibitor (Ugi). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown in the bottom panel.

    Journal: The Plant Journal

    Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

    doi: 10.1111/j.1365-313X.2009.03994.x

    Figure Lengend Snippet: Uracil repair by Arabidopsis cell extracts is dependent on uracil DNA glycosylase (UDG) activity. DNA duplexes containing either U or THF opposite G were incubated with Arabidopsis cell extracts at 30°C for 3 h in a reaction mixture containing either dCTP or all four dNTPs, both in the absence or presence of 2 U of uracil-DNA glycosylase inhibitor (Ugi). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown in the bottom panel.

    Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

    Techniques: Activity Assay, Incubation, Fluorescence

    Restriction fragment length polymorphism analysis of whole-cell DNAs of C . lipolytica isolates after digestion with Hpa II (A) or Hin fI (B). Lanes: 1 to 10, our clinical isolates; 11, control strain C211; 12, control strain C202; 13, ATCC 9773; M, size marker ( Hin dIII digest of bacteriophage lambda DNA).

    Journal: Journal of Clinical Microbiology

    Article Title: Catheter-Related Candidemia Caused by Candida lipolytica in a Patient Receiving Allogeneic Bone Marrow Transplantation

    doi: 10.1128/JCM.40.4.1381-1386.2002

    Figure Lengend Snippet: Restriction fragment length polymorphism analysis of whole-cell DNAs of C . lipolytica isolates after digestion with Hpa II (A) or Hin fI (B). Lanes: 1 to 10, our clinical isolates; 11, control strain C211; 12, control strain C202; 13, ATCC 9773; M, size marker ( Hin dIII digest of bacteriophage lambda DNA).

    Article Snippet: The following restriction endonucleases were used: Eco RI, Hin dIII, Hin fI, and Hpa II (Boehringer Mannheim GmbH).

    Techniques: Marker, Lambda DNA Preparation

    MSAP gels electrophoresis of PaWB seedlings with MMS treatment. H 1 and M 1 : bands digested by Eco RI/ Hpa II (H) and Eco RI/ Msp I (M) in PS; H 2 and M 2 : bands digested by H and M in PS-20; H 3 and M 3 : bands digested by H and M in PS-60; H 4 and M 4 : bands digested by H and M in PS-100; H 5 and M 5 : bands digested by H and M in HS; E 25 /HM 52 – E 25 /HM x : primer combination; M: Marker; The arrows only indicated part of the methylation patterns between PS and PS-20 (H 1 , M 1 , H 2 , M 2 ).

    Journal: PLoS ONE

    Article Title: Morphological Changes of Paulownia Seedlings Infected Phytoplasmas Reveal the Genes Associated with Witches' Broom through AFLP and MSAP

    doi: 10.1371/journal.pone.0112533

    Figure Lengend Snippet: MSAP gels electrophoresis of PaWB seedlings with MMS treatment. H 1 and M 1 : bands digested by Eco RI/ Hpa II (H) and Eco RI/ Msp I (M) in PS; H 2 and M 2 : bands digested by H and M in PS-20; H 3 and M 3 : bands digested by H and M in PS-60; H 4 and M 4 : bands digested by H and M in PS-100; H 5 and M 5 : bands digested by H and M in HS; E 25 /HM 52 – E 25 /HM x : primer combination; M: Marker; The arrows only indicated part of the methylation patterns between PS and PS-20 (H 1 , M 1 , H 2 , M 2 ).

    Article Snippet: The MSAP experiment comprised two digestion reactions, the first digestion reaction included 16 U of Eco RI (TaKaRa, Dalian, China) plus 10 U of Msp I (TaKaRa), the second digestion reaction was the same as the first digestion except the Hpa II (TaKaRa) instead of Msp I.

    Techniques: Electrophoresis, Marker, Methylation

    Effects of the DNA methylation-sensitive restriction enzyme on the RAPD bands 143a and 143c ( arrowed ). First, non-, Msp I- and Hpa II-digested DNA samples were amplified by PCR using the decamer primer No. 143. Then, PCR products were digested with ( a ) no restriction enzyme, (b) Msp I or ( c ) Hpa II. Lambda DNA Hin dIII digests in the furthest left lane. Parent A, 2H21-2 (S 1 ), 2H22-1 (S 3 ), 3H94-17 (S 4 ), 4H130-1 (S 5 ), 5H 123-9 (F 1 ), 4H105-7 (S 6 ) ( lanes 1–7 )

    Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

    Article Title: DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis

    doi: 10.1007/s00122-009-1058-6

    Figure Lengend Snippet: Effects of the DNA methylation-sensitive restriction enzyme on the RAPD bands 143a and 143c ( arrowed ). First, non-, Msp I- and Hpa II-digested DNA samples were amplified by PCR using the decamer primer No. 143. Then, PCR products were digested with ( a ) no restriction enzyme, (b) Msp I or ( c ) Hpa II. Lambda DNA Hin dIII digests in the furthest left lane. Parent A, 2H21-2 (S 1 ), 2H22-1 (S 3 ), 3H94-17 (S 4 ), 4H130-1 (S 5 ), 5H 123-9 (F 1 ), 4H105-7 (S 6 ) ( lanes 1–7 )

    Article Snippet: Approximately 8 μg of DNA was digested completely by overnight incubation at 37°C with 25 units of Msp I (Takara Bio Inc., Japan) or 12 units of Hpa II (Toyobo Co., Ltd., Japan).

    Techniques: DNA Methylation Assay, Amplification, Polymerase Chain Reaction, Lambda DNA Preparation

    Dynamic changes of the DNA methylation-sensitive bands 143a, 143b and 143c ( arrowed ) by selfing and hybridization, detected in the RAPD patterns of amplified products from Msp I- and Hpa II-digested DNA using the decamer primer No. 143. Lambda DNA Hin dIII digests in the most left lane

    Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

    Article Title: DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis

    doi: 10.1007/s00122-009-1058-6

    Figure Lengend Snippet: Dynamic changes of the DNA methylation-sensitive bands 143a, 143b and 143c ( arrowed ) by selfing and hybridization, detected in the RAPD patterns of amplified products from Msp I- and Hpa II-digested DNA using the decamer primer No. 143. Lambda DNA Hin dIII digests in the most left lane

    Article Snippet: Approximately 8 μg of DNA was digested completely by overnight incubation at 37°C with 25 units of Msp I (Takara Bio Inc., Japan) or 12 units of Hpa II (Toyobo Co., Ltd., Japan).

    Techniques: DNA Methylation Assay, Hybridization, Amplification, Lambda DNA Preparation

    PCR-RFLP maps of the 232-bp amplicon showing the three types of Hpa II endonuclease restriction fragment patterns. The upper map represents PCR-RFLP 1 with two fragments of 66 and 166 bp. The second map represents PCR-RFLP 2 with three fragments of 18, 66, and 148 bp. The third map represent PCR-RFLP 3 with fragments of 7, 20, 66, and 139 bp. The lower map represents the scaled 232-bp amplicon. The arrows flanking the PCR-RFLP 1 map represent primers which may be AHCF1, -2, or -3 and AHCR1, -2, -3, -4, or -5.

    Journal: Applied and Environmental Microbiology

    Article Title: PCR Detection, Characterization, and Distribution of Virulence Genes in Aeromonas spp.

    doi:

    Figure Lengend Snippet: PCR-RFLP maps of the 232-bp amplicon showing the three types of Hpa II endonuclease restriction fragment patterns. The upper map represents PCR-RFLP 1 with two fragments of 66 and 166 bp. The second map represents PCR-RFLP 2 with three fragments of 18, 66, and 148 bp. The third map represent PCR-RFLP 3 with fragments of 7, 20, 66, and 139 bp. The lower map represents the scaled 232-bp amplicon. The arrows flanking the PCR-RFLP 1 map represent primers which may be AHCF1, -2, or -3 and AHCR1, -2, -3, -4, or -5.

    Article Snippet: The characterization of the 232-bp PCR product from reference strains by restriction enzyme digestion (PCR-RFLP) using endonuclease Hpa II revealed three types of amplicons, as predicted by the Clone Manager software (Fig. and ).

    Techniques: Polymerase Chain Reaction, Amplification

    Agarose gel electrophoresis of ITS-PCR products of various Candida species after digestion with Hpa II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker

    Journal: Caspian Journal of Internal Medicine

    Article Title: Candida infections among neutropenic patients

    doi:

    Figure Lengend Snippet: Agarose gel electrophoresis of ITS-PCR products of various Candida species after digestion with Hpa II. Lanes 1,3,6,8 are C. albicans , and Lanes 2, 4, 5, 7, 9 are C. glabrata , and Lane M: 100 bp DNA size marker

    Article Snippet: Restriction fragment length polymorphism (RFLP): During the second step, PCR products were digested with the restriction enzyme Hpa II (Fermentas, Vilnius, Lithuania).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Marker

    Methylation sensitive restriction enzyme analysis on TYLCSV- or TYLCSV/PSTVd-infected plants. ( A ) TYLCSV DNA accumulation in the plants infected by TYLCSV- or by TYLCSV/PSTVd (T and TP, respectively). ( B ) Position of Hpa II and Msp I sites in the TYLCSV genome; red arrows, primers to amplify the TYLCSV region for bisulfite analysis (see Fig. 4 ). ( C ) Msp I or Hpa II digestion of plant DNA extracts (fragments indicated by red arrows) and of the RCA amplicon (size in bp indicated on the left). U, undigested ss DNA sample with TYLCSV ssDNA (black arrows); TYLCSV size marker (in bp, on the right) are 2773 ( Sst I digestion of a TYLCSV clone), 3328, 1318, 844 ( Sph I/ SnaB I), and 1463, 526, 300 ( Bgl II/ Sal I).

    Journal: Scientific Reports

    Article Title: A nuclear-replicating viroid antagonizes infectivity and accumulation of a geminivirus by upregulating methylation-related genes and inducing hypermethylation of viral DNA

    doi: 10.1038/srep35101

    Figure Lengend Snippet: Methylation sensitive restriction enzyme analysis on TYLCSV- or TYLCSV/PSTVd-infected plants. ( A ) TYLCSV DNA accumulation in the plants infected by TYLCSV- or by TYLCSV/PSTVd (T and TP, respectively). ( B ) Position of Hpa II and Msp I sites in the TYLCSV genome; red arrows, primers to amplify the TYLCSV region for bisulfite analysis (see Fig. 4 ). ( C ) Msp I or Hpa II digestion of plant DNA extracts (fragments indicated by red arrows) and of the RCA amplicon (size in bp indicated on the left). U, undigested ss DNA sample with TYLCSV ssDNA (black arrows); TYLCSV size marker (in bp, on the right) are 2773 ( Sst I digestion of a TYLCSV clone), 3328, 1318, 844 ( Sph I/ SnaB I), and 1463, 526, 300 ( Bgl II/ Sal I).

    Article Snippet: Methylation dependent restriction analysis DNA extracted as above from plants infected by TYLCSV or co-infected by TYLCSV/PSTVd (1.5 or 4.2 μg, respectively), harvested at 6 wpi, was restricted with either Msp I (cutting only when the inner cytosine is methylated, but blocked if the external cytosine is methylated) or Hpa II (cutting only un-methylated DNA) (20 U each, 37 °C for 20 h).

    Techniques: Methylation, Infection, Amplification, Marker

    Changes of DNA methylation pattern in MMS-treated PaWB plantlets. H1 and M1 : band digested by Eco RI/ Hpa II (H) and Eco RI/ Msp I (M) in PaWB plantlets; H2 and M2 : band digested by H and M in plantlets with 15 mg·L −1 MMS treatment; H3 and M3 : band digested by H and M in plantlets with 30 mg·L −1 MMS treatment; H4 and M4 : band digested by H and M in plantlets with 45 mg·L −1 MMS treatment; H5 and M5 : band digested by H and M in HP. E22/HM41–E22/HMx: primer combination; M : marker. The arrows indicated 4 lanes of part of the methylation patterns variations only between PaWB plantlets and the ones with 15 mg·L −1 MMS treatment (H1, M1, H2, M2). D3, A4 and D2 indicated part of the methylation patterns variations. The band of D3, A4 and D2 were (0,1,0,1), (1,0,0,0) and (1,0,1,0), respectively.

    Journal: International Journal of Molecular Sciences

    Article Title: Identification of Genes Related to Paulownia Witches’ Broom by AFLP and MSAP

    doi: 10.3390/ijms150814669

    Figure Lengend Snippet: Changes of DNA methylation pattern in MMS-treated PaWB plantlets. H1 and M1 : band digested by Eco RI/ Hpa II (H) and Eco RI/ Msp I (M) in PaWB plantlets; H2 and M2 : band digested by H and M in plantlets with 15 mg·L −1 MMS treatment; H3 and M3 : band digested by H and M in plantlets with 30 mg·L −1 MMS treatment; H4 and M4 : band digested by H and M in plantlets with 45 mg·L −1 MMS treatment; H5 and M5 : band digested by H and M in HP. E22/HM41–E22/HMx: primer combination; M : marker. The arrows indicated 4 lanes of part of the methylation patterns variations only between PaWB plantlets and the ones with 15 mg·L −1 MMS treatment (H1, M1, H2, M2). D3, A4 and D2 indicated part of the methylation patterns variations. The band of D3, A4 and D2 were (0,1,0,1), (1,0,0,0) and (1,0,1,0), respectively.

    Article Snippet: Two restriction enzyme combinations Eco RI/Msp I (TakaRa, Dalian, China) and Eco RI/Hpa II (TakaRa Dalian, China) were used in the digestion, respectively.

    Techniques: DNA Methylation Assay, Marker, Methylation

    Methylation-sensitive amplified polymorphism (MSAP) band patterning determined by Hpa II/ Msp I isoschizomers and correspondence with methylation status of CCGG sites. Black squares indicate methylated cytosines.

    Journal: Ecology and Evolution

    Article Title: Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

    doi: 10.1002/ece3.758

    Figure Lengend Snippet: Methylation-sensitive amplified polymorphism (MSAP) band patterning determined by Hpa II/ Msp I isoschizomers and correspondence with methylation status of CCGG sites. Black squares indicate methylated cytosines.

    Article Snippet: The digest was split into two equal volumes and 10 U of Hpa II (Promega) and 10 U of Msp I (New England Biolabs) were added to each half, along with 100 ng·μL−1 BSA and the appropriate buffers in a final volume of 20 μL for the second digestion.

    Techniques: Methylation, Amplification