hha i New England Biolabs Search Results


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  • 99
    New England Biolabs hha i
    Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic DNA or DNA digested with <t>Hpa</t> II, <t>Hha</t> I or Bst UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).
    Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 863 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs hpa ii
    Effects of <t>DNA</t> methylation on the translational positioning of nucleosomes on the human HPRT promoter in vitro. Nucleosomes were assembled in vitro onto methylated and unmethylated DNA templates containing the human HPRT promoter. <t>Hpa</t> II methylase, Hha I methylase, and Sss I methylase, DNA methyltransferases used to methylate each template; uncut, reconstituted chromatin that was digested with MNase but not Bam HI; Bam HI, reconstituted chromatin that was digested with MNase, purified, and then digested with Bam HI. All samples were probed with Bam HINuc1Probe, an 18-mer oligonucleotide immediately upstream of the Bam HI site in the first intron of the HPRT gene. Triangles indicate increasing MNase digestion times used to cleave the reconstituted chromatin. Numbers to the left, approximate sizes of the bands.
    Hpa Ii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1077 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs rsa i
    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, <t>Alu</t> I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Rsa I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1005 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs alu i
    PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by <t>Alu</t> I (a) or Hha I (b) and analysed by electrophoresis on a 6 % Visigel matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588
    Alu I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 823 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs msp i
    Effect of PCR cycle number on the extent of pseudo-T-RF formation observed with amplicons of clone PeM75 after <t>Msp</t> I digestion. The peak area of the pseudo-T-RF is compared to the peak area of the primary T-RF and given as a percentage. Error bars (which represent standard deviation) are based on three replicates.
    Msp I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1274 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs bst ui
    Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic <t>DNA</t> or DNA digested with Hpa II, Hha I or <t>Bst</t> UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).
    Bst Ui, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 366 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs t4 dna ligase
    Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic <t>DNA</t> or DNA digested with Hpa II, Hha I or <t>Bst</t> UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).
    T4 Dna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 49148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    New England Biolabs hhai methyltransferase
    Protection of DNA against HsoI and <t>HhaI</t> cleavage by HhaI <t>methyltransferase.</t> Plasmid DNAs in lanes 1 to 3 were protected by in vitro methylation with HhaI methyltransferase. Plasmid DNAs in lanes 4 to 6 were not methylated. The plasmids in lanes 1 and
    Hhai Methyltransferase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs aci i
    PCR-RFLP of a gltA gene fragment using the restriction endonuclease <t>Aci</t> I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).
    Aci I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 243 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs hinf i
    Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus grape isolates. Restriction digestion patterns (designated as A , B and C ) of ribosomal 5.8S-ITS DNA amplicons from various Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases <t>Hha</t> I and <t>Hinf</t> I . 50 bp ( l ) and 100 bp (L) DNA ladders are also shown.
    Hinf I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 464 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mse i
    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, <t>Alu</t> I, Hha I and <t>Mse</t> I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1428 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick pcr purification kit
    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, <t>Alu</t> I, Hha I and <t>Mse</t> I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Qiaquick Pcr Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 137129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs hha i restriction endonuclease
    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, <t>Alu</t> I, Hha I and <t>Mse</t> I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Hha I Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa hha i
    PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and <t>Hha</t> I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the <t>M2</t> protein, respectively; M, 50-bp molecular size marker.
    Hha I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 192 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nla iii
    PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and <t>Hha</t> I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the <t>M2</t> protein, respectively; M, 50-bp molecular size marker.
    Nla Iii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 875 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick gel extraction kit
    PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and <t>Hha</t> I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the <t>M2</t> protein, respectively; M, 50-bp molecular size marker.
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Promega taq i
    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, <t>Taq</t> I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Taq I, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs cutsmart buffer
    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, <t>Taq</t> I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Cutsmart Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2628 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dde i
    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, <t>Taq</t> I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Dde I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 274 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    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: 94/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mcrbc
    Comparison of HM-PCR and HM-WGA-PCR results for eleven CGIs . Genomic DNA from peripheral blood leukocytes was digested with Mock (lane 1), <t>Hpa</t> II or Hha I (lane 2), Msp I (lane 3), or <t>McrBC</t> (lane 4). The digested genomic DNA were used for PCR amplification either directly (left; HM-PCR) or after whole-genome-amplification (right; HM-WGA-PCR) using primer pairs for the eight CGIs on chromosome 21 (A~D) and three CGIs on chromosome 11 (E). Here, when Hha I-digested genomic DNA was used in lane 2, 1 ul of distilled water was used in lane 3 in place of Msp I-digested genomic DNA. PCR products were electrophoresed, stained with ethidium bromide, and visualized by UV illumination. Results of bisulfite sequencing are shown for the eight CGIs on chromosome 21 (A~D). Open and closed circles indicate unmethylated and methylated CpG dinucleotides, respectively. Each row of circles represents each sequenced clone of bisufite PCR products.
    Mcrbc, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 585 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Stratagene visigel separation matrix
    PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by Alu I (a) or Hha I (b) and analysed by electrophoresis on a 6 % <t>Visigel</t> matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588
    Visigel Separation Matrix, supplied by Stratagene, used in various techniques. Bioz Stars score: 88/100, based on 66 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic DNA or DNA digested with Hpa II, Hha I or Bst UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).

    Journal: PLoS ONE

    Article Title: 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation

    doi: 10.1371/journal.pone.0103714

    Figure Lengend Snippet: Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic DNA or DNA digested with Hpa II, Hha I or Bst UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).

    Article Snippet: Digestion with methylation-sensitive restriction enzymes Genomic DNA (500 ng) was digested with Hpa II (Invitrogen, Carlsbad, CA, USA), Bst UI and Hha I (New England Biolabs, Ipswich, MA, USA) for 6 h at 37°C (Hpa II and Hha I) or 60°C (Bst UI), or was mock-digested without the restriction enzymes.

    Techniques: Methylation, Generated, Polymerase Chain Reaction, Fluorescence

    Decreased AP-2α expression reduces proliferation; and AP-2α is required for target remethylation following demethylation. a) AP-2α western blot analysis of SCC22B cells with AP-2α overexpression. b) Cell cycle analysis via flow cytometry comparing WT, AP-2α-overexpressing, and AP-2α-downregulated SCC22B cells. * P-value = 0.0003. c) Methylation sensitive HhaI digests were performed on DNAs from SCC22B cells with and without AP-2α downregulation, revealing no distinguishable difference in global DNA methylation. “M” = methylated; “U” = unmethylated. d) 1 µM 5-aza-2′deoxycytidine was applied to the cells for 96 hours, changing the media daily. After 96 hours, the 5-aza-2′deoxycytidine was removed and the cells were continued in culture for 10 days, collecting cells at 0, 7, and 10 days post-treatment. Combined bisulfite restriction analysis on bisulfite-treated DNA obtained from these cells at 0, 7, and 10 days. Increased methylation at 10 days is seen in the AP-2α-expressing cells (i.e. the digested band indicated by the arrow).

    Journal: PLoS ONE

    Article Title: AP-2? Induces Epigenetic Silencing of Tumor Suppressive Genes and Microsatellite Instability in Head and Neck Squamous Cell Carcinoma

    doi: 10.1371/journal.pone.0006931

    Figure Lengend Snippet: Decreased AP-2α expression reduces proliferation; and AP-2α is required for target remethylation following demethylation. a) AP-2α western blot analysis of SCC22B cells with AP-2α overexpression. b) Cell cycle analysis via flow cytometry comparing WT, AP-2α-overexpressing, and AP-2α-downregulated SCC22B cells. * P-value = 0.0003. c) Methylation sensitive HhaI digests were performed on DNAs from SCC22B cells with and without AP-2α downregulation, revealing no distinguishable difference in global DNA methylation. “M” = methylated; “U” = unmethylated. d) 1 µM 5-aza-2′deoxycytidine was applied to the cells for 96 hours, changing the media daily. After 96 hours, the 5-aza-2′deoxycytidine was removed and the cells were continued in culture for 10 days, collecting cells at 0, 7, and 10 days post-treatment. Combined bisulfite restriction analysis on bisulfite-treated DNA obtained from these cells at 0, 7, and 10 days. Increased methylation at 10 days is seen in the AP-2α-expressing cells (i.e. the digested band indicated by the arrow).

    Article Snippet: 1ug of DNA was incubated with 1 unit HhaI (New England Biolabs) at 37 degrees Celsius for 3 hours.

    Techniques: Expressing, Western Blot, Over Expression, Cell Cycle Assay, Flow Cytometry, Cytometry, Methylation, DNA Methylation Assay

    Effects of DNA methylation on the translational positioning of nucleosomes on the human HPRT promoter in vitro. Nucleosomes were assembled in vitro onto methylated and unmethylated DNA templates containing the human HPRT promoter. Hpa II methylase, Hha I methylase, and Sss I methylase, DNA methyltransferases used to methylate each template; uncut, reconstituted chromatin that was digested with MNase but not Bam HI; Bam HI, reconstituted chromatin that was digested with MNase, purified, and then digested with Bam HI. All samples were probed with Bam HINuc1Probe, an 18-mer oligonucleotide immediately upstream of the Bam HI site in the first intron of the HPRT gene. Triangles indicate increasing MNase digestion times used to cleave the reconstituted chromatin. Numbers to the left, approximate sizes of the bands.

    Journal: Molecular and Cellular Biology

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Figure Lengend Snippet: Effects of DNA methylation on the translational positioning of nucleosomes on the human HPRT promoter in vitro. Nucleosomes were assembled in vitro onto methylated and unmethylated DNA templates containing the human HPRT promoter. Hpa II methylase, Hha I methylase, and Sss I methylase, DNA methyltransferases used to methylate each template; uncut, reconstituted chromatin that was digested with MNase but not Bam HI; Bam HI, reconstituted chromatin that was digested with MNase, purified, and then digested with Bam HI. All samples were probed with Bam HINuc1Probe, an 18-mer oligonucleotide immediately upstream of the Bam HI site in the first intron of the HPRT gene. Triangles indicate increasing MNase digestion times used to cleave the reconstituted chromatin. Numbers to the left, approximate sizes of the bands.

    Article Snippet: DNA methylation at CpG dinucleotides in vitro was performed using Hpa II, Hha I, and Sss I methylases (New England Biolabs) essentially as described by the supplier.

    Techniques: DNA Methylation Assay, In Vitro, Methylation, Purification

    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    doi: 10.1007/s13337-011-0023-6

    Figure Lengend Snippet: Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Article Snippet: A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer.

    Techniques: Polymerase Chain Reaction, Amplification

    Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    doi: 10.1007/s13337-011-0023-6

    Figure Lengend Snippet: Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Article Snippet: A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer.

    Techniques: Nested PCR, Amplification

    PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by Alu I (a) or Hha I (b) and analysed by electrophoresis on a 6 % Visigel matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588

    Journal: Journal of Medical Microbiology

    Article Title: Helicobactermarmotae and novel Helicobacter and Campylobacter species isolated from the livers and intestines of prairie dogs

    doi: 10.1099/jmm.0.032144-0

    Figure Lengend Snippet: PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by Alu I (a) or Hha I (b) and analysed by electrophoresis on a 6 % Visigel matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588

    Article Snippet: The PCR-amplified 1.2 kb fragment of the 16S rRNA gene (20 µl) was digested with 10 U Alu I and Hha I (New England BioLabs) in appropriate buffer, as recommended by the manufacturer, at 37 °C for 3 h ( ).

    Techniques: Polymerase Chain Reaction, Produced, Electrophoresis

    Effect of PCR cycle number on the extent of pseudo-T-RF formation observed with amplicons of clone PeM75 after Msp I digestion. The peak area of the pseudo-T-RF is compared to the peak area of the primary T-RF and given as a percentage. Error bars (which represent standard deviation) are based on three replicates.

    Journal: Applied and Environmental Microbiology

    Article Title: Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

    doi: 10.1128/AEM.69.5.2555-2562.2003

    Figure Lengend Snippet: Effect of PCR cycle number on the extent of pseudo-T-RF formation observed with amplicons of clone PeM75 after Msp I digestion. The peak area of the pseudo-T-RF is compared to the peak area of the primary T-RF and given as a percentage. Error bars (which represent standard deviation) are based on three replicates.

    Article Snippet: DNA (75 ng for amplicons from the gut DNA extract, 50 ng for clonal amplicons), 2.5 U of restriction enzymes ( Msp I, Taq I, and Alu I [Promega, Mannheim, Germany]; Msp I, Hpa II, Hha I, Hae III, and Bst UI [New England Biolabs, Frankfurt am Main, Germany]; and BsiS I [Minotech Biotechnology, Heraklion, Crete, Greece]), 1 μl of 10× incubation buffer, and 1 μg of bovine serum albumin (if recommended) were combined in a total volume of 10 μl and digested for 3 h at 37°C ( Msp I, Alu I, Hpa II, Hha I, and Hae III), 55°C ( Bsi SI), 60°C ( Bst UI), 65°C ( Taq I), or 70°C ( Bsi SI).

    Techniques: Polymerase Chain Reaction, Standard Deviation

    Effect of the position of the terminal restriction site on the extent of pseudo-T-RF formation, based on in vitro T-RF formation of 56 bacterial clones with Msp I as the restriction endonuclease. The peak area of the pseudo-T-RF is compared to the peak area of the primary T-RF and given as a percentage. Clones were obtained from a 16S rRNA gene clone library derived from the midgut of cetoniid beetle larvae (Egert et al., unpublished).

    Journal: Applied and Environmental Microbiology

    Article Title: Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

    doi: 10.1128/AEM.69.5.2555-2562.2003

    Figure Lengend Snippet: Effect of the position of the terminal restriction site on the extent of pseudo-T-RF formation, based on in vitro T-RF formation of 56 bacterial clones with Msp I as the restriction endonuclease. The peak area of the pseudo-T-RF is compared to the peak area of the primary T-RF and given as a percentage. Clones were obtained from a 16S rRNA gene clone library derived from the midgut of cetoniid beetle larvae (Egert et al., unpublished).

    Article Snippet: DNA (75 ng for amplicons from the gut DNA extract, 50 ng for clonal amplicons), 2.5 U of restriction enzymes ( Msp I, Taq I, and Alu I [Promega, Mannheim, Germany]; Msp I, Hpa II, Hha I, Hae III, and Bst UI [New England Biolabs, Frankfurt am Main, Germany]; and BsiS I [Minotech Biotechnology, Heraklion, Crete, Greece]), 1 μl of 10× incubation buffer, and 1 μg of bovine serum albumin (if recommended) were combined in a total volume of 10 μl and digested for 3 h at 37°C ( Msp I, Alu I, Hpa II, Hha I, and Hae III), 55°C ( Bsi SI), 60°C ( Bst UI), 65°C ( Taq I), or 70°C ( Bsi SI).

    Techniques: In Vitro, Clone Assay, Derivative Assay

    (A to C) T-RFLP analysis of clone PeH59 (affiliated with the CFB phylum) amplicons after restriction digestion with different enzymes, resulting in the expected T-RFs only ( Msp I [A]) or in the formation of pseudo-T-RFs ( Alu I [B] and Hha I [C]). (D) 16S rRNA gene secondary structure of clone PeH59 as predicted by the mfold software including the sequence stretches around detected pseudo-T-RFs. RS, restriction sites. Bold numbers indicate restriction sites with corresponding T-RFs in the electropherogram. RFU, relative fluorescence units.

    Journal: Applied and Environmental Microbiology

    Article Title: Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

    doi: 10.1128/AEM.69.5.2555-2562.2003

    Figure Lengend Snippet: (A to C) T-RFLP analysis of clone PeH59 (affiliated with the CFB phylum) amplicons after restriction digestion with different enzymes, resulting in the expected T-RFs only ( Msp I [A]) or in the formation of pseudo-T-RFs ( Alu I [B] and Hha I [C]). (D) 16S rRNA gene secondary structure of clone PeH59 as predicted by the mfold software including the sequence stretches around detected pseudo-T-RFs. RS, restriction sites. Bold numbers indicate restriction sites with corresponding T-RFs in the electropherogram. RFU, relative fluorescence units.

    Article Snippet: DNA (75 ng for amplicons from the gut DNA extract, 50 ng for clonal amplicons), 2.5 U of restriction enzymes ( Msp I, Taq I, and Alu I [Promega, Mannheim, Germany]; Msp I, Hpa II, Hha I, Hae III, and Bst UI [New England Biolabs, Frankfurt am Main, Germany]; and BsiS I [Minotech Biotechnology, Heraklion, Crete, Greece]), 1 μl of 10× incubation buffer, and 1 μg of bovine serum albumin (if recommended) were combined in a total volume of 10 μl and digested for 3 h at 37°C ( Msp I, Alu I, Hpa II, Hha I, and Hae III), 55°C ( Bsi SI), 60°C ( Bst UI), 65°C ( Taq I), or 70°C ( Bsi SI).

    Techniques: Software, Sequencing, Fluorescence

    Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic DNA or DNA digested with Hpa II, Hha I or Bst UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).

    Journal: PLoS ONE

    Article Title: 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation

    doi: 10.1371/journal.pone.0103714

    Figure Lengend Snippet: Methylation statuses at CpG sites near the RP2 onshore tandem GAAA repeat. Random ( A ) and non-random ( B ) X-inactivation patterns generated for different CpG-containing 5 me CpG-sensitive restriction endonuclease sites obtained using the 5 me CpG-based PCR RP2 / AR biplex assay across the restriction sites. Electropherograms of alleles observed in either undigested genomic DNA or DNA digested with Hpa II, Hha I or Bst UI from females genotyped via quantitative fluorescent PCR are shown. The boxed numbers correspond to the areas under the allele peaks and the intensity of each peak is in relative fluorescence units (RFU).

    Article Snippet: Digestion with methylation-sensitive restriction enzymes Genomic DNA (500 ng) was digested with Hpa II (Invitrogen, Carlsbad, CA, USA), Bst UI and Hha I (New England Biolabs, Ipswich, MA, USA) for 6 h at 37°C (Hpa II and Hha I) or 60°C (Bst UI), or was mock-digested without the restriction enzymes.

    Techniques: Methylation, Generated, Polymerase Chain Reaction, Fluorescence

    The pattern of Mycobacterium leprae by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis. Lane 3, lane 4, and lane 5: The nested PCR product of M. leprae sample showed the bands of 130 bp, 130 bp, and 120 bp after Hha I , Mbo I , and BstU I digestion, versus 75 + 65 bp, 130 bp, and 120 bp (lane 6, lane 7, and lane 8) from bacillus Calmette–Guérin; lane 1 and lane 9: Φ174 bp ladder DNA marker (Biolabs, New England); lane 2: The nest-PCR product.

    Journal: Chinese Medical Journal

    Article Title: Rapid Identification of Mycobacterium Leprae by Polymerase Chain Reaction-restriction Fragment Length Polymorphism Analysis of the Heat Shock Protein 65 Gene from Skin Specimens

    doi: 10.4103/0366-6999.168076

    Figure Lengend Snippet: The pattern of Mycobacterium leprae by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis. Lane 3, lane 4, and lane 5: The nested PCR product of M. leprae sample showed the bands of 130 bp, 130 bp, and 120 bp after Hha I , Mbo I , and BstU I digestion, versus 75 + 65 bp, 130 bp, and 120 bp (lane 6, lane 7, and lane 8) from bacillus Calmette–Guérin; lane 1 and lane 9: Φ174 bp ladder DNA marker (Biolabs, New England); lane 2: The nest-PCR product.

    Article Snippet: Restriction analysis The nested PCR products were digested by Hha I, Mbo I (Promega, Madison, USA), and BstU I (Biolabs, New England).

    Techniques: Polymerase Chain Reaction, Nested PCR, Marker

    Protection of DNA against HsoI and HhaI cleavage by HhaI methyltransferase. Plasmid DNAs in lanes 1 to 3 were protected by in vitro methylation with HhaI methyltransferase. Plasmid DNAs in lanes 4 to 6 were not methylated. The plasmids in lanes 1 and

    Journal: Applied and Environmental Microbiology

    Article Title: Generation and Molecular Characterization of New Temperature-Sensitive Plasmids Intended for Genetic Engineering of Pasteurellaceae

    doi: 10.1128/AEM.71.11.7187-7195.2005

    Figure Lengend Snippet: Protection of DNA against HsoI and HhaI cleavage by HhaI methyltransferase. Plasmid DNAs in lanes 1 to 3 were protected by in vitro methylation with HhaI methyltransferase. Plasmid DNAs in lanes 4 to 6 were not methylated. The plasmids in lanes 1 and

    Article Snippet: Introduction of plasmid DNA into H. somnus was increased by approximately 4 orders of magnitude by in vitro methylation with HhaI methyltransferase, although the efficiency of transformation dropped as the size of the plasmid increased.

    Techniques: Plasmid Preparation, In Vitro, Methylation

    PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Journal: PLoS ONE

    Article Title: Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats

    doi: 10.1371/journal.pone.0148299

    Figure Lengend Snippet: PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Article Snippet: The amplified product of the gltA gene was digested with Taq I (Promega, Madison, WI), Hha I (New England Biolabs, Beverly, M.A.), Mse I (New England Biolabs) and Aci I (New England Biolabs); the amplified product of the 16S rRNA gene was digested with Dde I (New England Biolabs); the amplified product of the ribC gene was digested with Taq I; and the amplified product of the 16S-23S ITS region was digested with Taq I and Hae III.

    Techniques: Polymerase Chain Reaction

    Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus grape isolates. Restriction digestion patterns (designated as A , B and C ) of ribosomal 5.8S-ITS DNA amplicons from various Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I and Hinf I . 50 bp ( l ) and 100 bp (L) DNA ladders are also shown.

    Journal: PLoS ONE

    Article Title: Biodiversity and ITS-RFLP Characterisation of Aspergillus Section Nigri Isolates in Grapes from Four Traditional Grape-Producing Areas in Greece

    doi: 10.1371/journal.pone.0093923

    Figure Lengend Snippet: Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus grape isolates. Restriction digestion patterns (designated as A , B and C ) of ribosomal 5.8S-ITS DNA amplicons from various Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I and Hinf I . 50 bp ( l ) and 100 bp (L) DNA ladders are also shown.

    Article Snippet: The PCR reactions were performed in a MJ Research PTC-200 thermal cycler (Bio-Rad Laboratories, USA), starting with an initial denaturation step at 95°C for 5 min, followed by 37 cycles consisting of 30 sec at 95°C, 30 sec at 52°C and 40 sec at 72°C, and a final extension step at 72°C for 10 min. PCR products were digested with the Hha I, Hinf I and Rsa I (New England Biolabs, UK) restriction endonucleases.

    Techniques:

    Restriction digestion patterns of sequenced ribosomal 5.8S-ITS region amplicons. Restriction digestion patterns (designated as A , B , C and D ) of five sequenced ribosomal 5.8S-ITS DNA amplicons from five different Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I , Hinf I and Rsa I . Each isolate is a representative of the five different Aspergillus species characterized in this study. L : DNA ladder.

    Journal: PLoS ONE

    Article Title: Biodiversity and ITS-RFLP Characterisation of Aspergillus Section Nigri Isolates in Grapes from Four Traditional Grape-Producing Areas in Greece

    doi: 10.1371/journal.pone.0093923

    Figure Lengend Snippet: Restriction digestion patterns of sequenced ribosomal 5.8S-ITS region amplicons. Restriction digestion patterns (designated as A , B , C and D ) of five sequenced ribosomal 5.8S-ITS DNA amplicons from five different Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I , Hinf I and Rsa I . Each isolate is a representative of the five different Aspergillus species characterized in this study. L : DNA ladder.

    Article Snippet: The PCR reactions were performed in a MJ Research PTC-200 thermal cycler (Bio-Rad Laboratories, USA), starting with an initial denaturation step at 95°C for 5 min, followed by 37 cycles consisting of 30 sec at 95°C, 30 sec at 52°C and 40 sec at 72°C, and a final extension step at 72°C for 10 min. PCR products were digested with the Hha I, Hinf I and Rsa I (New England Biolabs, UK) restriction endonucleases.

    Techniques:

    Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus reference strains. Restriction digestion patterns (designated as A and B ) of ribosomal 5.8S-ITS DNA amplicons from Aspergillus reference strains, after digestion with the restriction endonucleases Hinf I , Hha I and Rsa I . Ac : Aspergillus carbonarius , An : Aspergillus niger , At : Aspergillus tubingensis , Aw : Aspergillus westerdijkiae , Ao : Aspergillus ochraceus , L : Low molecular weight DNA ladder (molecular sizes are 766, 500, 350, 300, 250, 200, 150, 100, 75, 50 and 25 bp respectively).

    Journal: PLoS ONE

    Article Title: Biodiversity and ITS-RFLP Characterisation of Aspergillus Section Nigri Isolates in Grapes from Four Traditional Grape-Producing Areas in Greece

    doi: 10.1371/journal.pone.0093923

    Figure Lengend Snippet: Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus reference strains. Restriction digestion patterns (designated as A and B ) of ribosomal 5.8S-ITS DNA amplicons from Aspergillus reference strains, after digestion with the restriction endonucleases Hinf I , Hha I and Rsa I . Ac : Aspergillus carbonarius , An : Aspergillus niger , At : Aspergillus tubingensis , Aw : Aspergillus westerdijkiae , Ao : Aspergillus ochraceus , L : Low molecular weight DNA ladder (molecular sizes are 766, 500, 350, 300, 250, 200, 150, 100, 75, 50 and 25 bp respectively).

    Article Snippet: The PCR reactions were performed in a MJ Research PTC-200 thermal cycler (Bio-Rad Laboratories, USA), starting with an initial denaturation step at 95°C for 5 min, followed by 37 cycles consisting of 30 sec at 95°C, 30 sec at 52°C and 40 sec at 72°C, and a final extension step at 72°C for 10 min. PCR products were digested with the Hha I, Hinf I and Rsa I (New England Biolabs, UK) restriction endonucleases.

    Techniques: Molecular Weight

    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    doi: 10.1007/s13337-011-0023-6

    Figure Lengend Snippet: Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Article Snippet: A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer.

    Techniques: Polymerase Chain Reaction, Amplification

    Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    doi: 10.1007/s13337-011-0023-6

    Figure Lengend Snippet: Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Article Snippet: A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer.

    Techniques: Nested PCR, Amplification

    PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and Hha I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the M2 protein, respectively; M, 50-bp molecular size marker.

    Journal: Journal of Clinical Microbiology

    Article Title: Detection of Amantadine-Resistant Influenza A Virus Strains in Nursing Homes by PCR-Restriction Fragment Length Polymorphism Analysis with Nasopharyngeal Swabs

    doi: 10.1128/JCM.40.1.84-88.2002

    Figure Lengend Snippet: PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and Hha I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the M2 protein, respectively; M, 50-bp molecular size marker.

    Article Snippet: Those amplified by M2-For4 and M2-30Rev, or M2-For5 and M2-31, were digested with 5 U of Hha I (Takara Biomedicals, Ohtsu, Japan) or Sca I (New England Biolabs, Beverly, Mass.), for 2 h at 37°C, respectively, with the same mixture ratio of buffer to distilled water.

    Techniques: Polymerase Chain Reaction, Amplification, Marker

    Mosaicism in maternal allele-specific methylation. ( A ) Maternal allele-specific methylation of CGI #59. Direct sequencing was performed using the PCR products from mock-treated ( bottom left ), HhaI- ( bottom center ), and McrBC-digested ( bottom right ) DNA isolated from PBLs. The arrowhead indicatesthe A/C SNP site. Note that the maternally inherited A allele wasdetected from both Hha I-treated (or methylated) DNA and McrBC-treated (or unmethylated) DNA. ( B ) Bisulfite genomic sequencing of CGI #59. Each row of circles corresponds to each clone of bisulfite PCR products. Open and closed circles stand for unmethylated and methylated C residues, respectively. The A/C SNP site is also indicated. Note that the clonesfor the maternally inherited A allele are composed of two populations, one completely methylated and the other completely escaping methylation.

    Journal: Genome Research

    Article Title: A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q

    doi: 10.1101/gr.1351604

    Figure Lengend Snippet: Mosaicism in maternal allele-specific methylation. ( A ) Maternal allele-specific methylation of CGI #59. Direct sequencing was performed using the PCR products from mock-treated ( bottom left ), HhaI- ( bottom center ), and McrBC-digested ( bottom right ) DNA isolated from PBLs. The arrowhead indicatesthe A/C SNP site. Note that the maternally inherited A allele wasdetected from both Hha I-treated (or methylated) DNA and McrBC-treated (or unmethylated) DNA. ( B ) Bisulfite genomic sequencing of CGI #59. Each row of circles corresponds to each clone of bisulfite PCR products. Open and closed circles stand for unmethylated and methylated C residues, respectively. The A/C SNP site is also indicated. Note that the clonesfor the maternally inherited A allele are composed of two populations, one completely methylated and the other completely escaping methylation.

    Article Snippet: Human genomic DNA (0.5 μg) was digested with 30 units of HpaII, HhaI, MspI (TaKaRa), or McrBC (New England Biolabs) overnight at 37°C in 50 μL of the buffers recommended by the suppliers.

    Techniques: Methylation, Sequencing, Polymerase Chain Reaction, Isolation, Genomic Sequencing

    Allele-specific, parental-origin-independent methylation of CGI #130. Direct sequencing was performed using the PCR products from mock-treated ( bottom left ), HhaI- ( bottom center ), and McrBC-digested ( bottom right ) DNA. In the pedigree shown in A , the paternally inherited C allele ismethylated. On the other hand, the maternally inherited C allele ismethylated in the pedigree shown in B .

    Journal: Genome Research

    Article Title: A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q

    doi: 10.1101/gr.1351604

    Figure Lengend Snippet: Allele-specific, parental-origin-independent methylation of CGI #130. Direct sequencing was performed using the PCR products from mock-treated ( bottom left ), HhaI- ( bottom center ), and McrBC-digested ( bottom right ) DNA. In the pedigree shown in A , the paternally inherited C allele ismethylated. On the other hand, the maternally inherited C allele ismethylated in the pedigree shown in B .

    Article Snippet: Human genomic DNA (0.5 μg) was digested with 30 units of HpaII, HhaI, MspI (TaKaRa), or McrBC (New England Biolabs) overnight at 37°C in 50 μL of the buffers recommended by the suppliers.

    Techniques: Methylation, Sequencing, Polymerase Chain Reaction

    Maternal allele-specific methylation pinpointed to tandem repeats. ( A ) Maternal allele-specific methylation of CGI #112. A map of CGI #112 (500 bp) isshown on the top with the positionsof A/T and C/T SNPs(i.e., SNP1 and SNP2). The arrowsin the map indicate the tandem repeats. The CGI wasPCR-amplified from untreated ( bottom left ), HhaI-digested ( bottom center ), and McrBC-digested ( bottom right ) genomic DNA isolated from PBLs of a C/T heterozygote at SNP2. The amplified productswere subjected to direct sequencing. The vertical arrowhead in each electropherogram denotes the SNP2 (C/T) sites. ( B ) Bisulfite genomic sequencing of CGI #112. Each row of circles corresponds to each clone of bisulfite PCR products. Open and closed circles stand for unmethylated and methylated C residues, respectively. The SNP1 (A/T) site is indicated by the arrowhead.

    Journal: Genome Research

    Article Title: A Comprehensive Analysis of Allelic Methylation Status of CpG Islands on Human Chromosome 21q

    doi: 10.1101/gr.1351604

    Figure Lengend Snippet: Maternal allele-specific methylation pinpointed to tandem repeats. ( A ) Maternal allele-specific methylation of CGI #112. A map of CGI #112 (500 bp) isshown on the top with the positionsof A/T and C/T SNPs(i.e., SNP1 and SNP2). The arrowsin the map indicate the tandem repeats. The CGI wasPCR-amplified from untreated ( bottom left ), HhaI-digested ( bottom center ), and McrBC-digested ( bottom right ) genomic DNA isolated from PBLs of a C/T heterozygote at SNP2. The amplified productswere subjected to direct sequencing. The vertical arrowhead in each electropherogram denotes the SNP2 (C/T) sites. ( B ) Bisulfite genomic sequencing of CGI #112. Each row of circles corresponds to each clone of bisulfite PCR products. Open and closed circles stand for unmethylated and methylated C residues, respectively. The SNP1 (A/T) site is indicated by the arrowhead.

    Article Snippet: Human genomic DNA (0.5 μg) was digested with 30 units of HpaII, HhaI, MspI (TaKaRa), or McrBC (New England Biolabs) overnight at 37°C in 50 μL of the buffers recommended by the suppliers.

    Techniques: Methylation, Amplification, Isolation, Sequencing, Genomic Sequencing, Polymerase Chain Reaction

    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Article Snippet: The amplified product of the gltA gene obtained with the set of primers suggested by Regnery et al. ( ) was digested with Taq I (Promega, Madison, Wis.) and Hha I (new England BioLabs, Beverly, Mass.) restriction endonucleases.

    Techniques: Polymerase Chain Reaction

    PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Article Snippet: The amplified product of the gltA gene obtained with the set of primers suggested by Regnery et al. ( ) was digested with Taq I (Promega, Madison, Wis.) and Hha I (new England BioLabs, Beverly, Mass.) restriction endonucleases.

    Techniques: Polymerase Chain Reaction

    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

    Comparison of HM-PCR and HM-WGA-PCR results for eleven CGIs . Genomic DNA from peripheral blood leukocytes was digested with Mock (lane 1), Hpa II or Hha I (lane 2), Msp I (lane 3), or McrBC (lane 4). The digested genomic DNA were used for PCR amplification either directly (left; HM-PCR) or after whole-genome-amplification (right; HM-WGA-PCR) using primer pairs for the eight CGIs on chromosome 21 (A~D) and three CGIs on chromosome 11 (E). Here, when Hha I-digested genomic DNA was used in lane 2, 1 ul of distilled water was used in lane 3 in place of Msp I-digested genomic DNA. PCR products were electrophoresed, stained with ethidium bromide, and visualized by UV illumination. Results of bisulfite sequencing are shown for the eight CGIs on chromosome 21 (A~D). Open and closed circles indicate unmethylated and methylated CpG dinucleotides, respectively. Each row of circles represents each sequenced clone of bisufite PCR products.

    Journal: BMC Research Notes

    Article Title: Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification

    doi: 10.1186/1756-0500-4-179

    Figure Lengend Snippet: Comparison of HM-PCR and HM-WGA-PCR results for eleven CGIs . Genomic DNA from peripheral blood leukocytes was digested with Mock (lane 1), Hpa II or Hha I (lane 2), Msp I (lane 3), or McrBC (lane 4). The digested genomic DNA were used for PCR amplification either directly (left; HM-PCR) or after whole-genome-amplification (right; HM-WGA-PCR) using primer pairs for the eight CGIs on chromosome 21 (A~D) and three CGIs on chromosome 11 (E). Here, when Hha I-digested genomic DNA was used in lane 2, 1 ul of distilled water was used in lane 3 in place of Msp I-digested genomic DNA. PCR products were electrophoresed, stained with ethidium bromide, and visualized by UV illumination. Results of bisulfite sequencing are shown for the eight CGIs on chromosome 21 (A~D). Open and closed circles indicate unmethylated and methylated CpG dinucleotides, respectively. Each row of circles represents each sequenced clone of bisufite PCR products.

    Article Snippet: HM-WGA-PCR Genomic DNA (500 ng) was digested with 50 U of Hpa II, Hha I, Msp I (TaKaRa), or McrBC (New England Biolabs) overnight at 37°C in 50 μl of the recommended buffers.

    Techniques: Polymerase Chain Reaction, Whole Genome Amplification, Amplification, Staining, Methylation Sequencing, Methylation

    Principles of the Hpa II- McrBC whole-genome-amplification PCR (HM-WGA-PCR) method . The two parallel lines in the

    Journal: BMC Research Notes

    Article Title: Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification

    doi: 10.1186/1756-0500-4-179

    Figure Lengend Snippet: Principles of the Hpa II- McrBC whole-genome-amplification PCR (HM-WGA-PCR) method . The two parallel lines in the "Digestion" panel indicate genomic amplicons from both alleles. The circled "m" indicates a methylated CpG dinucleotide. Hpa II digests unmethylated CCGG, but not methylated C m CGG. In contrast, McrBC digests methylated R m C 40-80 R m C sequences, but not unmethylated RC 40-80 RC. Genomic DNA is digested with Hpa II and McrBC independently. Subsequently, an aliquot of each restriction-enzyme-digested DNA (50 ng) is subjected to whole-genome-amplification (WGA) to yield 5 μg of whole-genome-amplified DNA. Using an aliquot of the amplified DNA (50 ng), the target DNA region is PCR-amplified by the primer pair (dotted arrows). The PCR products from the Hpa II/ Hha I-digested and McrBC -digested DNA are electrophoresed, stained with ethidium bromide, and visualized by UV illumination. If an amplicon is fully methylated (i.e., complete methylation), it is digested by McrBC , but not by Hpa II. Thus, it is amplified from the Hpa II-digested and whole-genome-amplified DNA, but not from the McrBC -digested and whole-genome-amplified DNA. By contrast, if an amplicon totally escapes methylation (i.e., null methylation), it is digested by Hpa II, but not by McrBC . Thus, it is amplified from McrBC -digested and whole-genome-amplified DNA, but not from Hpa II-digested and whole-genome-amplified DNA. If an amplicon contains both methylated and unmethylated alleles (i.e., composite methylation), it is amplified from both whole-genome-amplified templates. If an amplicon is partially methylated on both alleles (i.e., incomplete methylation), it is amplified from neither whole-genome-amplified template.

    Article Snippet: HM-WGA-PCR Genomic DNA (500 ng) was digested with 50 U of Hpa II, Hha I, Msp I (TaKaRa), or McrBC (New England Biolabs) overnight at 37°C in 50 μl of the recommended buffers.

    Techniques: Whole Genome Amplification, Polymerase Chain Reaction, Methylation, Amplification, Staining

    PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by Alu I (a) or Hha I (b) and analysed by electrophoresis on a 6 % Visigel matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588

    Journal: Journal of Medical Microbiology

    Article Title: Helicobactermarmotae and novel Helicobacter and Campylobacter species isolated from the livers and intestines of prairie dogs

    doi: 10.1099/jmm.0.032144-0

    Figure Lengend Snippet: PCR products of 1.2 kb produced using Helicobacter genus-specific primers were digested by Alu I (a) or Hha I (b) and analysed by electrophoresis on a 6 % Visigel matrix. Lanes 1–4, prairie dog isolates MIT 07-5168, MIT 07-5167, MIT 04-8588

    Article Snippet: Restriction patterns were compared after the digested PCR products had been separated on a 6 % Visigel separation matrix (Stratagene).

    Techniques: Polymerase Chain Reaction, Produced, Electrophoresis