hha i New England Biolabs Search Results


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  • 95
    New England Biolabs hha i
    PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with <t>Taq</t> I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .
    Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 628 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Millipore 5 aza 2
    PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with <t>Taq</t> I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .
    5 Aza 2, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 863 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    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: 94/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs restriction enzymes
    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
    Restriction Enzymes, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1648 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    New England Biolabs hha ι
    Genotyping of individuals for C/T <t>-13910</t> and G/A -22018 single-nucleotide polymorphisms by restriction digestion with Bsm F1 and <t>Hha</t> Ι. Lane M DNA molecular weight marker (100 bp, Banglore Genei, India). Lane U Undigested PCR product. C/C,
    Hha ι, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 79/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    New England Biolabs restriction enzyme hha i
    Restriction fragment length polymorphism (RFLP) with restriction enzyme <t>Hha</t> I of selected pvmsp -3α alleles in eight different Plasmodium vivax samples from Sri Lanka. With exclusion of bands above 600 bp, and below 150 bp, the estimated allele
    Restriction Enzyme Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    New England Biolabs tetranucleotide recognizing enzymes hha i
    Restriction fragment length polymorphism (RFLP) with restriction enzyme <t>Hha</t> I of selected pvmsp -3α alleles in eight different Plasmodium vivax samples from Sri Lanka. With exclusion of bands above 600 bp, and below 150 bp, the estimated allele
    Tetranucleotide Recognizing Enzymes Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 77/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    New England Biolabs hha i restriction endonucleases
    RFLP patterns of  Helicobacter  sp. monkey taxon 4,  H. macacae  and  Helicobacter  sp. monkey taxon 2 generated by  Alu I and  Hha I.
    Hha I Restriction Endonucleases, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 76/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    New England Biolabs enzyme hha i
    RFLP patterns of  Helicobacter  sp. monkey taxon 4,  H. macacae  and  Helicobacter  sp. monkey taxon 2 generated by  Alu I and  Hha I.
    Enzyme Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 76/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    New England Biolabs hha 1 enzyme
    RFLP patterns of  Helicobacter  sp. monkey taxon 4,  H. macacae  and  Helicobacter  sp. monkey taxon 2 generated by  Alu I and  Hha I.
    Hha 1 Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 76/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    New England Biolabs restrictive enzyme hha i
    RFLP patterns of  Helicobacter  sp. monkey taxon 4,  H. macacae  and  Helicobacter  sp. monkey taxon 2 generated by  Alu I and  Hha I.
    Restrictive Enzyme Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    New England Biolabs m hha
    In vitro methylation silences Foxl2 promoter reporter activity in NIH3T3 cells. The -432/+7 murine Foxl2 -luciferase reporter in pCpGL-Basic was treated in vitro with A) M . <t>Sss</t> I or B) M. <t>Hha</t> I. Mock methylated plasmid was exposed to the identical treatment but without enzyme. Plasmids were transfected in triplicate into NIH3T3 cells. For A (n=6) and B (n=4), the data reflect the means of independent experiments (+SEM) and are presented with empty vector activity set to 1. Data were analyzed by one-way ANOVA followed by Tukey post-hoc tests. Bars with different letters were statistically different, whereas those sharing letters did not differ.
    M Hha, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 79/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    New England Biolabs m hha i gene
    Fig. 4. De novo methylation catalyzed by the hybrid MTases. ( A ) Total DNA from High Five cells expressing Dnmt1– <t>Hha</t> I, Dnmt1– Hpa II, Dnmt1– Sss I or Dnmt1 was extracted 48 h post-infection. Each lane represents DNA digested with the restriction enzymes indicated (+) above each lane. Lane M contains a Hin dIII digest of λ DNA molecular weight marker. ( B ) De novo methylation of the hybrid MTase genes. Southern blots of total DNA probed with the Bam HI 2100 bp N-terminal fragment of the mouse Dnmt1 cDNA. Each lane represents either a single or double restriction digest as indicated (+). The 2100 bp band is indicated by an arrow. ( C ) De novo methylation of viral upstream and polyhedrin promoter sequences. Southern blots of total DNA probed with a 2200 bp Nsi I fragment consisting of the viral upstream sequences, polyhedrin promoter and a part of the N-terminus of the mouse Dnmt1. Each lane represents either a single or double restriction digest as indicated (+). The 2200 bp band is shown by an arrow. ( D ) Key features of the hybrid MTase and conceptual restriction maps of the Bam HI (2100 bp) and Nsi I (2200 bp) fragments. Features of the hybrid MTase are presented schematically. A 3400 bp cDNA containing the mouse Dnmt1, indicated by black shading, was fused to the N-terminus of the prokaryotic MTase, as shown in grey. The hatched line represents the upstream baculovirus ORF. pPH marks the polyhedrin promoter. Fragments analyzed by restriction enzyme digests [ Bam HI (∼2100 bp) and Nsi I (∼2200 bp)] are indicated by B and N. Restriction enzymes used for methylation analysis are listed on the left. The numbers of target sites and sequences are on the right. Restriction sites are indicated by vertical black lines.
    M Hha I Gene, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 76/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs endonucleases hha i
    Fig. 4. De novo methylation catalyzed by the hybrid MTases. ( A ) Total DNA from High Five cells expressing Dnmt1– <t>Hha</t> I, Dnmt1– Hpa II, Dnmt1– Sss I or Dnmt1 was extracted 48 h post-infection. Each lane represents DNA digested with the restriction enzymes indicated (+) above each lane. Lane M contains a Hin dIII digest of λ DNA molecular weight marker. ( B ) De novo methylation of the hybrid MTase genes. Southern blots of total DNA probed with the Bam HI 2100 bp N-terminal fragment of the mouse Dnmt1 cDNA. Each lane represents either a single or double restriction digest as indicated (+). The 2100 bp band is indicated by an arrow. ( C ) De novo methylation of viral upstream and polyhedrin promoter sequences. Southern blots of total DNA probed with a 2200 bp Nsi I fragment consisting of the viral upstream sequences, polyhedrin promoter and a part of the N-terminus of the mouse Dnmt1. Each lane represents either a single or double restriction digest as indicated (+). The 2200 bp band is shown by an arrow. ( D ) Key features of the hybrid MTase and conceptual restriction maps of the Bam HI (2100 bp) and Nsi I (2200 bp) fragments. Features of the hybrid MTase are presented schematically. A 3400 bp cDNA containing the mouse Dnmt1, indicated by black shading, was fused to the N-terminus of the prokaryotic MTase, as shown in grey. The hatched line represents the upstream baculovirus ORF. pPH marks the polyhedrin promoter. Fragments analyzed by restriction enzyme digests [ Bam HI (∼2100 bp) and Nsi I (∼2200 bp)] are indicated by B and N. Restriction enzymes used for methylation analysis are listed on the left. The numbers of target sites and sequences are on the right. Restriction sites are indicated by vertical black lines.
    Endonucleases Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs hha i sau 961
    Fig. 4. De novo methylation catalyzed by the hybrid MTases. ( A ) Total DNA from High Five cells expressing Dnmt1– <t>Hha</t> I, Dnmt1– Hpa II, Dnmt1– Sss I or Dnmt1 was extracted 48 h post-infection. Each lane represents DNA digested with the restriction enzymes indicated (+) above each lane. Lane M contains a Hin dIII digest of λ DNA molecular weight marker. ( B ) De novo methylation of the hybrid MTase genes. Southern blots of total DNA probed with the Bam HI 2100 bp N-terminal fragment of the mouse Dnmt1 cDNA. Each lane represents either a single or double restriction digest as indicated (+). The 2100 bp band is indicated by an arrow. ( C ) De novo methylation of viral upstream and polyhedrin promoter sequences. Southern blots of total DNA probed with a 2200 bp Nsi I fragment consisting of the viral upstream sequences, polyhedrin promoter and a part of the N-terminus of the mouse Dnmt1. Each lane represents either a single or double restriction digest as indicated (+). The 2200 bp band is shown by an arrow. ( D ) Key features of the hybrid MTase and conceptual restriction maps of the Bam HI (2100 bp) and Nsi I (2200 bp) fragments. Features of the hybrid MTase are presented schematically. A 3400 bp cDNA containing the mouse Dnmt1, indicated by black shading, was fused to the N-terminus of the prokaryotic MTase, as shown in grey. The hatched line represents the upstream baculovirus ORF. pPH marks the polyhedrin promoter. Fragments analyzed by restriction enzyme digests [ Bam HI (∼2100 bp) and Nsi I (∼2200 bp)] are indicated by B and N. Restriction enzymes used for methylation analysis are listed on the left. The numbers of target sites and sequences are on the right. Restriction sites are indicated by vertical black lines.
    Hha I Sau 961, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher bst ui
    Schematic of the primers and probe used for RE-dMSP of the RASSF1A promoter. The location of the primers and probe, and the recognition sites of three methylation-sensitive restriction enzymes ( Hpa II, <t>Hha</t> I and <t>Bst</t> UI) are presented. RE-dMSP, PCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1.
    Bst Ui, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs hin diii
    Schematic of the primers and probe used for RE-dMSP of the RASSF1A promoter. The location of the primers and probe, and the recognition sites of three methylation-sensitive restriction enzymes ( Hpa II, <t>Hha</t> I and <t>Bst</t> UI) are presented. RE-dMSP, PCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1.
    Hin Diii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1921 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    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: 95/100, based on 914 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs mcr bc
    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.
    Mcr Bc, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 91 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Toyobo rsa i
    Amplified products of the 16S rDNA of various Alex-CFPB (A) and digestion of the PCR products with <t>Rsa</t> I (B), Bst UI (C), <t>Mbo</t> I (D), and Hha I (E). Lane M, 100-bp ladder markers; lane 1, CFPB-A9; lane 2, CFPB-B1; lane 3, CFPB-C1; lane 4, CFPB-D1; lane 5, CFPB-E1; lane 6, CFPB-F1; lane 7, CFPB-G1; lane 8, CFPB-H1; lane 9, CFPB-I1; lane 10, CFPB-J1; lane 11, CFPB-K1; lane 12, CFPB-L1; lane 13, CFPB-M1; lane 14, CFPB-N1.
    Rsa I, supplied by Toyobo, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    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: 95/100, based on 605 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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: 95/100, based on 321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs bseri
    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.
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    New England Biolabs bstu i
    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 <t>Hha</t> I , Mbo I , and <t>BstU</t> 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.
    Bstu I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 193 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs fsp i
    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 <t>Hha</t> I , Mbo I , and <t>BstU</t> 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.
    Fsp I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    New England Biolabs bsg i
    Restriction endonuclease map and construction of plasmids used to make allelic exchange mutants and to complement LOS genes in H. somnus ). pCAAT was digested with Eco RI to obtain the 3.9-kb fragment, and pGEM-3Z was digested with Hin cII to obtain a 2.7-kb fragment. These fragments were ligated together to obtain 6.6-kb plasmid pCAAT-SalI, which was further digested with Sal I- <t>Bsg</t> I to obtain a 6.1-kb fragment with a 630-bp deletion in lob-2A . The 1.2-kb Sma I fragment from pUC4-kixx containing the Tn 5 Km r cassette was then ligated into the Sal I- Bsg I site of pCAAT-SalI to obtain 7.3-kb plasmid pCAATΔlob2A. The 8.8-kb plasmid pLSGA was constructed by digesting pCAAT with Eco RI and cloning the 3.9-kb fragment into the Sma I site of pLS88. pLSGA was then cut with Xba I and Hpa I to remove part of lob-1 and the non-LOS afu -like genes, and the 6.84-kb plasmid was ligated to itself. All ligations were done following blunt ending of the plasmids.
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    95
    New England Biolabs pvu ii
    Restriction endonuclease map and construction of plasmids used to make allelic exchange mutants and to complement LOS genes in H. somnus ). pCAAT was digested with Eco RI to obtain the 3.9-kb fragment, and pGEM-3Z was digested with Hin cII to obtain a 2.7-kb fragment. These fragments were ligated together to obtain 6.6-kb plasmid pCAAT-SalI, which was further digested with Sal I- <t>Bsg</t> I to obtain a 6.1-kb fragment with a 630-bp deletion in lob-2A . The 1.2-kb Sma I fragment from pUC4-kixx containing the Tn 5 Km r cassette was then ligated into the Sal I- Bsg I site of pCAAT-SalI to obtain 7.3-kb plasmid pCAATΔlob2A. The 8.8-kb plasmid pLSGA was constructed by digesting pCAAT with Eco RI and cloning the 3.9-kb fragment into the Sma I site of pLS88. pLSGA was then cut with Xba I and Hpa I to remove part of lob-1 and the non-LOS afu -like genes, and the 6.84-kb plasmid was ligated to itself. All ligations were done following blunt ending of the plasmids.
    Pvu Ii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 368 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Valiant restriction endonucleases hha i
    Restriction endonuclease map and construction of plasmids used to make allelic exchange mutants and to complement LOS genes in H. somnus ). pCAAT was digested with Eco RI to obtain the 3.9-kb fragment, and pGEM-3Z was digested with Hin cII to obtain a 2.7-kb fragment. These fragments were ligated together to obtain 6.6-kb plasmid pCAAT-SalI, which was further digested with Sal I- <t>Bsg</t> I to obtain a 6.1-kb fragment with a 630-bp deletion in lob-2A . The 1.2-kb Sma I fragment from pUC4-kixx containing the Tn 5 Km r cassette was then ligated into the Sal I- Bsg I site of pCAAT-SalI to obtain 7.3-kb plasmid pCAATΔlob2A. The 8.8-kb plasmid pLSGA was constructed by digesting pCAAT with Eco RI and cloning the 3.9-kb fragment into the Sma I site of pLS88. pLSGA was then cut with Xba I and Hpa I to remove part of lob-1 and the non-LOS afu -like genes, and the 6.84-kb plasmid was ligated to itself. All ligations were done following blunt ending of the plasmids.
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    New England Biolabs nhe i
    Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA <t>EcoR</t> V, <t>Nhe</t> I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.
    Nhe I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs antarctic phosphatase
    Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA <t>EcoR</t> V, <t>Nhe</t> I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.
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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: 95/100, based on 1003 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with Taq I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .

    Journal: Journal of Clinical Microbiology

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California

    doi: 10.1128/JCM.39.4.1221-1226.2001

    Figure Lengend Snippet: PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with Taq I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .

    Article Snippet: Taq I (Promega, Madison, Wis.), Hha I (New England Biolabs, Beverly, Mass.), and Mse I (New England Biolabs) restriction endonucleases were used for PCR-RFLP analysis of the gltA gene.

    Techniques: Polymerase Chain Reaction

    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

    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: By using conditions recommended by the manufacturer, plasmid DNA (a hybrid replacement plasmid recovered from E. coli DH10B) was methylated in vitro by HhaI methyltransferase (New England Biolabs) using S -adenosylmethionine as the methyl donor.

    Techniques: Plasmid Preparation, In Vitro, Methylation

    DNA methylation at the Slc17a6 promoter. a Schematic representation of the Slc17a6 gene. Solid boxes represent the 5′ and 3′UTRs and open boxes represent exons. A region spanning −255 to +90 bp relative to the transcriptional start site (TSS) is drawn below. The region (BS1, −144 to −20 bp) and CpG sites ( vertical arrows , CpGs 1–9) examined by clonal bisulphite sequencing are indicated, as is the region used in in vitro reporter assays (CpGs 1–10, −144 bp to +68 bp). Four different CpG methylation patterns were generated for reporter assays using three bacterial methyltransferases (MTs), M.SssI MT, Hha I MT and Hpa II MT either alone or in combination. Filled and open circles represent methylated and unmethylated CpGs, respectively. b DNA methylation in the adult hippocampus (P87 and 120). Each line of nine CpGs represents the DNA methylation state of one allele in one cell. Clones from controls (total n = 42 from 16 mice) as well as basal (total n = 33 from 16 mice) and high (total n = 34 from 17 mice) Slc17a6 expressors in the ethanol-exposed (EtOH) group are shown. A graph of % DNA methylation per clone is also shown. c The impact of Slc17a6 promoter methylation (CpGs 1–10, −144 to +68 bp) on luciferase activity in vitro. The results of three independent experiments in CAD cells are shown. Data are presented as mean and standard deviation. ** P

    Journal: Epigenetics & Chromatin

    Article Title: Prenatal ethanol exposure alters adult hippocampal VGLUT2 expression with concomitant changes in promoter DNA methylation, H3K4 trimethylation and miR-467b-5p levels

    doi: 10.1186/s13072-015-0032-6

    Figure Lengend Snippet: DNA methylation at the Slc17a6 promoter. a Schematic representation of the Slc17a6 gene. Solid boxes represent the 5′ and 3′UTRs and open boxes represent exons. A region spanning −255 to +90 bp relative to the transcriptional start site (TSS) is drawn below. The region (BS1, −144 to −20 bp) and CpG sites ( vertical arrows , CpGs 1–9) examined by clonal bisulphite sequencing are indicated, as is the region used in in vitro reporter assays (CpGs 1–10, −144 bp to +68 bp). Four different CpG methylation patterns were generated for reporter assays using three bacterial methyltransferases (MTs), M.SssI MT, Hha I MT and Hpa II MT either alone or in combination. Filled and open circles represent methylated and unmethylated CpGs, respectively. b DNA methylation in the adult hippocampus (P87 and 120). Each line of nine CpGs represents the DNA methylation state of one allele in one cell. Clones from controls (total n = 42 from 16 mice) as well as basal (total n = 33 from 16 mice) and high (total n = 34 from 17 mice) Slc17a6 expressors in the ethanol-exposed (EtOH) group are shown. A graph of % DNA methylation per clone is also shown. c The impact of Slc17a6 promoter methylation (CpGs 1–10, −144 to +68 bp) on luciferase activity in vitro. The results of three independent experiments in CAD cells are shown. Data are presented as mean and standard deviation. ** P

    Article Snippet: A CpG methyltransferase (M.SssI ), Hpa II methyltransferase or Hha I methyltransferase (New England Biolabs, USA) were used either alone or in combination to methylate the promoter-containing construct and vector only according to the manufacturer’s instructions. pGL4.14-based plasmids (45 ng) and pGL4.74[hRluc /TK] (5 ng) were transiently transfected into CAD cells using Lipofectamine 2000 (Life Technologies, USA) according to the manufacturer’s protocol.

    Techniques: DNA Methylation Assay, Bisulfite Sequencing, In Vitro, CpG Methylation Assay, Generated, Methylation, Clone Assay, Mouse Assay, Luciferase, Activity Assay, Standard Deviation

    Genotyping of individuals for C/T -13910 and G/A -22018 single-nucleotide polymorphisms by restriction digestion with Bsm F1 and Hha Ι. Lane M DNA molecular weight marker (100 bp, Banglore Genei, India). Lane U Undigested PCR product. C/C,

    Journal: Genes & Nutrition

    Article Title: Correlation of G/A -22018 single-nucleotide polymorphism with lactase activity and its usefulness in improving the diagnosis of adult-type hypolactasia among North Indian children

    doi: 10.1007/s12263-012-0305-7

    Figure Lengend Snippet: Genotyping of individuals for C/T -13910 and G/A -22018 single-nucleotide polymorphisms by restriction digestion with Bsm F1 and Hha Ι. Lane M DNA molecular weight marker (100 bp, Banglore Genei, India). Lane U Undigested PCR product. C/C,

    Article Snippet: PCR products were quantitated and 500 ng of DNA was digested with 1 unit of Bsm FΙ restriction enzyme (New England Biolabs, Foster City, CA) for C/T -13910 SNP and 2 units Hha Ι (New England Biolabs, Foster City, CA) for G/A -22018 SNP in a 15 μL reaction containing 1 × reaction buffer and BSA.

    Techniques: Molecular Weight, Marker, Polymerase Chain Reaction

    Restriction fragment length polymorphism (RFLP) with restriction enzyme Hha I of selected pvmsp -3α alleles in eight different Plasmodium vivax samples from Sri Lanka. With exclusion of bands above 600 bp, and below 150 bp, the estimated allele

    Journal: The American Journal of Tropical Medicine and Hygiene

    Article Title: Analysis of Polymorphisms in the Merozoite Surface Protein-3? Gene and Two Microsatellite Loci in Sri Lankan Plasmodium vivax: Evidence of Population Substructure in Sri Lanka

    doi: 10.4269/ajtmh.2011.11-0338

    Figure Lengend Snippet: Restriction fragment length polymorphism (RFLP) with restriction enzyme Hha I of selected pvmsp -3α alleles in eight different Plasmodium vivax samples from Sri Lanka. With exclusion of bands above 600 bp, and below 150 bp, the estimated allele

    Article Snippet: A refinement of the allelic diversity was obtained by digestion with restriction enzyme Hha I which subdivided the A-type alleles into nine allelic variants named A1–A9 ( , ).

    Techniques:

    C43G variant site and the Hha I recognition site in the promoter region of the XIST gene.

    Journal: Clinical and Experimental Reproductive Medicine

    Article Title: Analysis of C43G mutation in the promoter region of the XIST gene in patients with idiopathic primary ovarian insufficiency

    doi: 10.5653/cerm.2015.42.2.58

    Figure Lengend Snippet: C43G variant site and the Hha I recognition site in the promoter region of the XIST gene.

    Article Snippet: PCR products were digested with 2 U of restriction enzyme Hha I (New England Biolabs, Ipswich, MA, USA) at 37℃ for 3 hours, separated by 3% agarose gel electrophoresis, and identified by using ethidium bromide staining.

    Techniques: Variant Assay

    Detection of the G13964C variant by PCR-RFLP assay. The C→G nucleotide substitution creates a Hha I site, and the G allele is detected by Hha I digestion of the 131-bp product to 98-bp and 33-bp products (the 33-bp product is not adequately resolved on this gel). Lanes 1 and 2, GG; lane 3, CG; lane 4, CC; lanes 5 and 6, no template control; and lane 7, BRL 1-kb ladder size marker.

    Journal: Breast Cancer Research : BCR

    Article Title: The intronic G13964C variant in p53 is not a high-risk mutation in familial breast cancer in Australia

    doi:

    Figure Lengend Snippet: Detection of the G13964C variant by PCR-RFLP assay. The C→G nucleotide substitution creates a Hha I site, and the G allele is detected by Hha I digestion of the 131-bp product to 98-bp and 33-bp products (the 33-bp product is not adequately resolved on this gel). Lanes 1 and 2, GG; lane 3, CG; lane 4, CC; lanes 5 and 6, no template control; and lane 7, BRL 1-kb ladder size marker.

    Article Snippet: Cycling conditions were 94°C for 4 min; followed by four cycles of 94°C for 20 s, 60°C for 20 s and 72°C for 20 s; and 30 cycles of 94°C for 20 s, 58°C for 20 s, and 72°C for 20 s, with a final extension of 72°C for 7 min. Of the 131-bp amplified product, 3 μl was digested with 4 U of Hha I restriction enzyme (New England Biolabs) in a 12 μl reaction with 1 × NEB Buffer 4 and 1 × bovine serum albumin (New England Biolabs, Beverley, MA, USA) at 37°C for 1–2 h. The digested products were separated on a 4% NuSieve agarose gel (Bio Whittacker Molecular Applications, Rockland, ME, USA) and the genotype determined by the banding pattern observed.

    Techniques: Variant Assay, Polymerase Chain Reaction, RFLP Assay, Marker

    RFLP patterns of  Helicobacter  sp. monkey taxon 4,  H. macacae  and  Helicobacter  sp. monkey taxon 2 generated by  Alu I and  Hha I.

    Journal: Journal of Medical Microbiology

    Article Title: Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma

    doi: 10.1099/jmm.0.072462-0

    Figure Lengend Snippet: RFLP patterns of Helicobacter sp. monkey taxon 4, H. macacae and Helicobacter sp. monkey taxon 2 generated by Alu I and Hha I.

    Article Snippet: The RFLPs generated by using Alu I and Hha I restriction endonucleases corresponding to each EHS are shown in and were consistent with our previous report ( ).

    Techniques: Generated

    In vitro methylation silences Foxl2 promoter reporter activity in NIH3T3 cells. The -432/+7 murine Foxl2 -luciferase reporter in pCpGL-Basic was treated in vitro with A) M . Sss I or B) M. Hha I. Mock methylated plasmid was exposed to the identical treatment but without enzyme. Plasmids were transfected in triplicate into NIH3T3 cells. For A (n=6) and B (n=4), the data reflect the means of independent experiments (+SEM) and are presented with empty vector activity set to 1. Data were analyzed by one-way ANOVA followed by Tukey post-hoc tests. Bars with different letters were statistically different, whereas those sharing letters did not differ.

    Journal: PLoS ONE

    Article Title: The CpG Island in the Murine Foxl2 Proximal Promoter Is Differentially Methylated in Primary and Immortalized Cells

    doi: 10.1371/journal.pone.0076642

    Figure Lengend Snippet: In vitro methylation silences Foxl2 promoter reporter activity in NIH3T3 cells. The -432/+7 murine Foxl2 -luciferase reporter in pCpGL-Basic was treated in vitro with A) M . Sss I or B) M. Hha I. Mock methylated plasmid was exposed to the identical treatment but without enzyme. Plasmids were transfected in triplicate into NIH3T3 cells. For A (n=6) and B (n=4), the data reflect the means of independent experiments (+SEM) and are presented with empty vector activity set to 1. Data were analyzed by one-way ANOVA followed by Tukey post-hoc tests. Bars with different letters were statistically different, whereas those sharing letters did not differ.

    Article Snippet: Enzymes Hha I, Hpa II, McrBC, M .Sss I and M.Hha I were from New England Biolabs Inc. (Ipswich, MA).

    Techniques: In Vitro, Methylation, Activity Assay, Luciferase, Plasmid Preparation, Transfection

    Fig. 4. De novo methylation catalyzed by the hybrid MTases. ( A ) Total DNA from High Five cells expressing Dnmt1– Hha I, Dnmt1– Hpa II, Dnmt1– Sss I or Dnmt1 was extracted 48 h post-infection. Each lane represents DNA digested with the restriction enzymes indicated (+) above each lane. Lane M contains a Hin dIII digest of λ DNA molecular weight marker. ( B ) De novo methylation of the hybrid MTase genes. Southern blots of total DNA probed with the Bam HI 2100 bp N-terminal fragment of the mouse Dnmt1 cDNA. Each lane represents either a single or double restriction digest as indicated (+). The 2100 bp band is indicated by an arrow. ( C ) De novo methylation of viral upstream and polyhedrin promoter sequences. Southern blots of total DNA probed with a 2200 bp Nsi I fragment consisting of the viral upstream sequences, polyhedrin promoter and a part of the N-terminus of the mouse Dnmt1. Each lane represents either a single or double restriction digest as indicated (+). The 2200 bp band is shown by an arrow. ( D ) Key features of the hybrid MTase and conceptual restriction maps of the Bam HI (2100 bp) and Nsi I (2200 bp) fragments. Features of the hybrid MTase are presented schematically. A 3400 bp cDNA containing the mouse Dnmt1, indicated by black shading, was fused to the N-terminus of the prokaryotic MTase, as shown in grey. The hatched line represents the upstream baculovirus ORF. pPH marks the polyhedrin promoter. Fragments analyzed by restriction enzyme digests [ Bam HI (∼2100 bp) and Nsi I (∼2200 bp)] are indicated by B and N. Restriction enzymes used for methylation analysis are listed on the left. The numbers of target sites and sequences are on the right. Restriction sites are indicated by vertical black lines.

    Journal: The EMBO Journal

    Article Title: Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain

    doi: 10.1093/emboj/19.9.2103

    Figure Lengend Snippet: Fig. 4. De novo methylation catalyzed by the hybrid MTases. ( A ) Total DNA from High Five cells expressing Dnmt1– Hha I, Dnmt1– Hpa II, Dnmt1– Sss I or Dnmt1 was extracted 48 h post-infection. Each lane represents DNA digested with the restriction enzymes indicated (+) above each lane. Lane M contains a Hin dIII digest of λ DNA molecular weight marker. ( B ) De novo methylation of the hybrid MTase genes. Southern blots of total DNA probed with the Bam HI 2100 bp N-terminal fragment of the mouse Dnmt1 cDNA. Each lane represents either a single or double restriction digest as indicated (+). The 2100 bp band is indicated by an arrow. ( C ) De novo methylation of viral upstream and polyhedrin promoter sequences. Southern blots of total DNA probed with a 2200 bp Nsi I fragment consisting of the viral upstream sequences, polyhedrin promoter and a part of the N-terminus of the mouse Dnmt1. Each lane represents either a single or double restriction digest as indicated (+). The 2200 bp band is shown by an arrow. ( D ) Key features of the hybrid MTase and conceptual restriction maps of the Bam HI (2100 bp) and Nsi I (2200 bp) fragments. Features of the hybrid MTase are presented schematically. A 3400 bp cDNA containing the mouse Dnmt1, indicated by black shading, was fused to the N-terminus of the prokaryotic MTase, as shown in grey. The hatched line represents the upstream baculovirus ORF. pPH marks the polyhedrin promoter. Fragments analyzed by restriction enzyme digests [ Bam HI (∼2100 bp) and Nsi I (∼2200 bp)] are indicated by B and N. Restriction enzymes used for methylation analysis are listed on the left. The numbers of target sites and sequences are on the right. Restriction sites are indicated by vertical black lines.

    Article Snippet: The plasmid (pHSHW5), containing the M. Hha I gene, was obtained from Dr S.Kumar [New England Biolabs (NEB)].

    Techniques: Methylation, Expressing, Infection, Molecular Weight, Marker

    Fig. 6. Time course of methylation catalyzed by the hybrid Dnmt1– Hha I. ( A ) Reactions contained 30 nM hybrid Dnmt1– Hha I, 50 µM CG [poly (dG-dC)·poly (dG-dC)] and 1, 5 or 10 µM AdoMet and were incubated at 37°C. Duplicate 25 µl samples of each reaction were spotted onto DE81 paper, processed as described in Materials and methods, and 3 H incorporation was measured. The mean values, with standard deviation, for the time points are plotted as filled diamonds (1 µM AdoMet), open circles (5 µM AdoMet) or filled circles (10 µM AdoMet). ( B ) Linearity of methyltransfer reaction as a function of enzyme concentration. Duplicate reactions in 25 µl contained 50 µM CG, 5 µM AdoMet and various mouse Dnmt1– Hha I concentrations (5, 10, 20, 30, 40 and 50 µM) and were incubated at 37°C for 30 min and processed. The solid circles depict the mean values of the [ 3 H]methyl group incorporation.

    Journal: The EMBO Journal

    Article Title: Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain

    doi: 10.1093/emboj/19.9.2103

    Figure Lengend Snippet: Fig. 6. Time course of methylation catalyzed by the hybrid Dnmt1– Hha I. ( A ) Reactions contained 30 nM hybrid Dnmt1– Hha I, 50 µM CG [poly (dG-dC)·poly (dG-dC)] and 1, 5 or 10 µM AdoMet and were incubated at 37°C. Duplicate 25 µl samples of each reaction were spotted onto DE81 paper, processed as described in Materials and methods, and 3 H incorporation was measured. The mean values, with standard deviation, for the time points are plotted as filled diamonds (1 µM AdoMet), open circles (5 µM AdoMet) or filled circles (10 µM AdoMet). ( B ) Linearity of methyltransfer reaction as a function of enzyme concentration. Duplicate reactions in 25 µl contained 50 µM CG, 5 µM AdoMet and various mouse Dnmt1– Hha I concentrations (5, 10, 20, 30, 40 and 50 µM) and were incubated at 37°C for 30 min and processed. The solid circles depict the mean values of the [ 3 H]methyl group incorporation.

    Article Snippet: The plasmid (pHSHW5), containing the M. Hha I gene, was obtained from Dr S.Kumar [New England Biolabs (NEB)].

    Techniques: Methylation, Incubation, Standard Deviation, Concentration Assay

    Fig. 2. Expression and purification of hybrid MTases. ( A ) Western blot analysis of High Five cell extracts expressing the hybrid methyltransferases using a mouse Dnmt1 specific Ab 334. The relative positions of biotinylated mol. wt markers (165, 105, 76) are in kDa. His-MMT3 is a His 6 ). An uninfected High Five cell extract was used as a control (C). The MTase bands are indicated by the arrow. The hybrid proteins are indicated above each lane. ( B ) Two purified hybrid MTases, Dnmt1– Hpa II and Dnmt1– Hha I resolved on SDS–PAGE and stained with Coomassie Blue. The broad range molecular weight markers are indicated on the left in kDa. The hybrid MTases are indicated by the arrow.

    Journal: The EMBO Journal

    Article Title: Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain

    doi: 10.1093/emboj/19.9.2103

    Figure Lengend Snippet: Fig. 2. Expression and purification of hybrid MTases. ( A ) Western blot analysis of High Five cell extracts expressing the hybrid methyltransferases using a mouse Dnmt1 specific Ab 334. The relative positions of biotinylated mol. wt markers (165, 105, 76) are in kDa. His-MMT3 is a His 6 ). An uninfected High Five cell extract was used as a control (C). The MTase bands are indicated by the arrow. The hybrid proteins are indicated above each lane. ( B ) Two purified hybrid MTases, Dnmt1– Hpa II and Dnmt1– Hha I resolved on SDS–PAGE and stained with Coomassie Blue. The broad range molecular weight markers are indicated on the left in kDa. The hybrid MTases are indicated by the arrow.

    Article Snippet: The plasmid (pHSHW5), containing the M. Hha I gene, was obtained from Dr S.Kumar [New England Biolabs (NEB)].

    Techniques: Expressing, Purification, Western Blot, SDS Page, Staining, Molecular Weight

    Schematic of the primers and probe used for RE-dMSP of the RASSF1A promoter. The location of the primers and probe, and the recognition sites of three methylation-sensitive restriction enzymes ( Hpa II, Hha I and Bst UI) are presented. RE-dMSP, PCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1.

    Journal: Oncology Reports

    Article Title: Highly sensitive detection of sentinel lymph node metastasis of breast cancer by digital PCR for RASSF1A methylation

    doi: 10.3892/or.2019.7363

    Figure Lengend Snippet: Schematic of the primers and probe used for RE-dMSP of the RASSF1A promoter. The location of the primers and probe, and the recognition sites of three methylation-sensitive restriction enzymes ( Hpa II, Hha I and Bst UI) are presented. RE-dMSP, PCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1.

    Article Snippet: DNA solution (6.6 µl) was incubated for 16 h at 37°C in a final volume of 20 µl, containing 1X ddPCR Supermix for probes (Bio-Rad Laboratories, Inc.), 900 nM each primer, 250 nM probe and 10 U Hha I, Hpa II (New England BioLabs, Inc.) and Bst UI (Thermo Fisher Scientific, Inc.) each.

    Techniques: Methylation, Polymerase Chain Reaction

    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

    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

    Amplified products of the 16S rDNA of various Alex-CFPB (A) and digestion of the PCR products with Rsa I (B), Bst UI (C), Mbo I (D), and Hha I (E). Lane M, 100-bp ladder markers; lane 1, CFPB-A9; lane 2, CFPB-B1; lane 3, CFPB-C1; lane 4, CFPB-D1; lane 5, CFPB-E1; lane 6, CFPB-F1; lane 7, CFPB-G1; lane 8, CFPB-H1; lane 9, CFPB-I1; lane 10, CFPB-J1; lane 11, CFPB-K1; lane 12, CFPB-L1; lane 13, CFPB-M1; lane 14, CFPB-N1.

    Journal: Applied and Environmental Microbiology

    Article Title: Population Structure of Alexandrium (Dinophyceae) Cyst Formation-Promoting Bacteria in Hiroshima Bay, Japan

    doi: 10.1128/AEM.69.11.6560-6568.2003

    Figure Lengend Snippet: Amplified products of the 16S rDNA of various Alex-CFPB (A) and digestion of the PCR products with Rsa I (B), Bst UI (C), Mbo I (D), and Hha I (E). Lane M, 100-bp ladder markers; lane 1, CFPB-A9; lane 2, CFPB-B1; lane 3, CFPB-C1; lane 4, CFPB-D1; lane 5, CFPB-E1; lane 6, CFPB-F1; lane 7, CFPB-G1; lane 8, CFPB-H1; lane 9, CFPB-I1; lane 10, CFPB-J1; lane 11, CFPB-K1; lane 12, CFPB-L1; lane 13, CFPB-M1; lane 14, CFPB-N1.

    Article Snippet: Two micrograms of the DNA was then digested with one of four restriction endonucleases, Mbo I, Hha I (TaKaRa Biomedicals, Osaka, Japan), Rsa I (Toyobo, Osaka, Japan), and Bst UI (New England Biolabs, Inc., Beverly, Mass.) according to the protocols of each manufacturer.

    Techniques: Amplification, Polymerase Chain Reaction

    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

    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

    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

    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

    Restriction endonuclease map and construction of plasmids used to make allelic exchange mutants and to complement LOS genes in H. somnus ). pCAAT was digested with Eco RI to obtain the 3.9-kb fragment, and pGEM-3Z was digested with Hin cII to obtain a 2.7-kb fragment. These fragments were ligated together to obtain 6.6-kb plasmid pCAAT-SalI, which was further digested with Sal I- Bsg I to obtain a 6.1-kb fragment with a 630-bp deletion in lob-2A . The 1.2-kb Sma I fragment from pUC4-kixx containing the Tn 5 Km r cassette was then ligated into the Sal I- Bsg I site of pCAAT-SalI to obtain 7.3-kb plasmid pCAATΔlob2A. The 8.8-kb plasmid pLSGA was constructed by digesting pCAAT with Eco RI and cloning the 3.9-kb fragment into the Sma I site of pLS88. pLSGA was then cut with Xba I and Hpa I to remove part of lob-1 and the non-LOS afu -like genes, and the 6.84-kb plasmid was ligated to itself. All ligations were done following blunt ending of the plasmids.

    Journal: Infection and Immunity

    Article Title: Molecular Cloning and Mutagenesis of a DNA Locus Involved in Lipooligosaccharide Biosynthesis in Haemophilus somnus

    doi:

    Figure Lengend Snippet: Restriction endonuclease map and construction of plasmids used to make allelic exchange mutants and to complement LOS genes in H. somnus ). pCAAT was digested with Eco RI to obtain the 3.9-kb fragment, and pGEM-3Z was digested with Hin cII to obtain a 2.7-kb fragment. These fragments were ligated together to obtain 6.6-kb plasmid pCAAT-SalI, which was further digested with Sal I- Bsg I to obtain a 6.1-kb fragment with a 630-bp deletion in lob-2A . The 1.2-kb Sma I fragment from pUC4-kixx containing the Tn 5 Km r cassette was then ligated into the Sal I- Bsg I site of pCAAT-SalI to obtain 7.3-kb plasmid pCAATΔlob2A. The 8.8-kb plasmid pLSGA was constructed by digesting pCAAT with Eco RI and cloning the 3.9-kb fragment into the Sma I site of pLS88. pLSGA was then cut with Xba I and Hpa I to remove part of lob-1 and the non-LOS afu -like genes, and the 6.84-kb plasmid was ligated to itself. All ligations were done following blunt ending of the plasmids.

    Article Snippet: Bsg I and Hha I methylase were purchased from New England Biolabs (Beverly, Mass.).

    Techniques: Plasmid Preparation, Construct, Clone Assay

    Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA EcoR V, Nhe I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.

    Journal: Scientific Reports

    Article Title: Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

    doi: 10.1038/s41598-019-55855-8

    Figure Lengend Snippet: Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA EcoR V, Nhe I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.

    Article Snippet: Triple digestion with EcoR V, Nhe I and Spe I (New England Biolabs) was performed in the same reaction using 10, 5 and 5 units of each enzyme, respectively, with 1x NEB2 buffer.

    Techniques: Polymerase Chain Reaction, Northern Blot

    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