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  • 99
    New England Biolabs apai
    Pulse-field gel electrophoresis patterns of ( a ) <t>XbaI-digested</t> genomic DNA of B. breve isolates and ( b ) <t>ApaI-digested</t> genomic DNA of L. plantarum isolates from human milk and infant faeces. The unedited versions of these images can be found as Supplementary Figures S3 and S4 .
    Apai, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1193 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher fastdigest apai
    Pulse-field gel electrophoresis patterns of ( a ) <t>XbaI-digested</t> genomic DNA of B. breve isolates and ( b ) <t>ApaI-digested</t> genomic DNA of L. plantarum isolates from human milk and infant faeces. The unedited versions of these images can be found as Supplementary Figures S3 and S4 .
    Fastdigest Apai, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher apai
    (a) Pulsed-field gel of <t>S1</t> nuclease-digested genomic DNA from A. bereziniae CHI-40-1, recipients, and transconjugants; (b) in-gel hybridization with a bla NDM-1 gene probe; (c) pulsed-field gel of <t>ApaI-digested</t> genomic DNA from CHI-40-1; (d) in-gel hybridization
    Apai, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 935 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    GE Healthcare apai
    (a) Pulsed-field gel of <t>S1</t> nuclease-digested genomic DNA from A. bereziniae CHI-40-1, recipients, and transconjugants; (b) in-gel hybridization with a bla NDM-1 gene probe; (c) pulsed-field gel of <t>ApaI-digested</t> genomic DNA from CHI-40-1; (d) in-gel hybridization
    Apai, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    apai  (Roche)
    92
    Roche apai
    <t>PFGE</t> dendrogram of L. monocytogenes harboring LmoJ2 and LmoJ3. PFGE with <t>ApaI</t> and AscI and profile clustering were performed as described in Materials and Methods. Isolates harboring LmoJ2 and LmoJ3 are indicated with filled and open circles, respectively.
    Apai, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Promega apai
    Structural- and chemical probing of <t>DNA</t> and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by <t>ApaI</t> then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.
    Apai, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 275 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega apai enzyme
    Structural- and chemical probing of <t>DNA</t> and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by <t>ApaI</t> then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.
    Apai Enzyme, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs apai restriction endonuclease
    Structural- and chemical probing of <t>DNA</t> and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by <t>ApaI</t> then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.
    Apai Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher apai fd
    Structural- and chemical probing of <t>DNA</t> and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by <t>ApaI</t> then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.
    Apai Fd, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore apai
    Structural- and chemical probing of <t>DNA</t> and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by <t>ApaI</t> then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.
    Apai, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Pulse-field gel electrophoresis patterns of ( a ) XbaI-digested genomic DNA of B. breve isolates and ( b ) ApaI-digested genomic DNA of L. plantarum isolates from human milk and infant faeces. The unedited versions of these images can be found as Supplementary Figures S3 and S4 .

    Journal: Scientific Reports

    Article Title: The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

    doi: 10.1038/srep40597

    Figure Lengend Snippet: Pulse-field gel electrophoresis patterns of ( a ) XbaI-digested genomic DNA of B. breve isolates and ( b ) ApaI-digested genomic DNA of L. plantarum isolates from human milk and infant faeces. The unedited versions of these images can be found as Supplementary Figures S3 and S4 .

    Article Snippet: The restriction enzyme XbaI was used to cleave bifidobacterial chromosomal DNA and ApaI (New England Biolabs, MA, United States) was used for Lactobacillus .

    Techniques: Nucleic Acid Electrophoresis

    a - d Restriction endonuclease digestion for FokI, ApaI, Bsm I and TaqI polymorphisms, M = Marker

    Journal: BMC Nephrology

    Article Title: Influence of vitamin D receptor polymorphisms on biochemical markers of mineral bone disorders in South African patients with chronic kidney disease

    doi: 10.1186/s12882-018-0831-7

    Figure Lengend Snippet: a - d Restriction endonuclease digestion for FokI, ApaI, Bsm I and TaqI polymorphisms, M = Marker

    Article Snippet: The PCR products were then digested with enzymes ApaI, BsmI, FokI, and TaqI (New England Biolabs, Beverly, MA, USA) according to the supplier’s protocol.

    Techniques: Marker

    Frequency of vitamin D deficiency according to BsmI (A), ApaI (B), and TaqI (C) SNPs in VDR gene grouped by presence of polymorphic allele. White bars express the frequency of vitamin D status ( deficiency or insufficiency/sufficiency) for the wild genotype of each VDR SNP. Gray bars express the frequency of vitamin D status for the polymorphic (in heterozygous plus homozygous) genotypes. Pearson chi-square test, * p

    Journal: BMC Pediatrics

    Article Title: Vitamin D deficiency in girls from South Brazil: a cross-sectional study on prevalence and association with vitamin D receptor gene variants

    doi: 10.1186/1471-2431-12-62

    Figure Lengend Snippet: Frequency of vitamin D deficiency according to BsmI (A), ApaI (B), and TaqI (C) SNPs in VDR gene grouped by presence of polymorphic allele. White bars express the frequency of vitamin D status ( deficiency or insufficiency/sufficiency) for the wild genotype of each VDR SNP. Gray bars express the frequency of vitamin D status for the polymorphic (in heterozygous plus homozygous) genotypes. Pearson chi-square test, * p

    Article Snippet: Protocol conditions consisted of denaturation at 95°C for 2 min followed by 35 cycles (95°C, 30sec; 59.2°C, 30sec; 72°C, 80sec) and final extension at 72°C for 5 min. PCR products were digested overnight by the restriction enzymes ApaI or TaqI (New England Biolabs, USA) at 37°C or 65°C, respectively.

    Techniques:

    Vitamin D levels according to BsmI (A), ApaI (B), and TaqI (C) SNPs in VDR gene grouped by presence of polymorphic allele. Values are expressed as means (central circle) and 95% CI (lower and upper limit). Two-tailed Student’s t -test, * p

    Journal: BMC Pediatrics

    Article Title: Vitamin D deficiency in girls from South Brazil: a cross-sectional study on prevalence and association with vitamin D receptor gene variants

    doi: 10.1186/1471-2431-12-62

    Figure Lengend Snippet: Vitamin D levels according to BsmI (A), ApaI (B), and TaqI (C) SNPs in VDR gene grouped by presence of polymorphic allele. Values are expressed as means (central circle) and 95% CI (lower and upper limit). Two-tailed Student’s t -test, * p

    Article Snippet: Protocol conditions consisted of denaturation at 95°C for 2 min followed by 35 cycles (95°C, 30sec; 59.2°C, 30sec; 72°C, 80sec) and final extension at 72°C for 5 min. PCR products were digested overnight by the restriction enzymes ApaI or TaqI (New England Biolabs, USA) at 37°C or 65°C, respectively.

    Techniques: Two Tailed Test

    Dendrogram produced by the unweighted-pair group method using average linkages showing clustering by Dice coefficient of the combined PFGE (AscI and ApaI) profiles of the 20 L. monocytogenes isolates obtained from animal cases analyzed in this study.

    Journal: Applied and Environmental Microbiology

    Article Title: Ruminant Rhombencephalitis-Associated Listeria monocytogenes Strains Constitute a Genetically Homogeneous Group Related to Human Outbreak Strains

    doi: 10.1128/AEM.00219-13

    Figure Lengend Snippet: Dendrogram produced by the unweighted-pair group method using average linkages showing clustering by Dice coefficient of the combined PFGE (AscI and ApaI) profiles of the 20 L. monocytogenes isolates obtained from animal cases analyzed in this study.

    Article Snippet: PFGE was performed by including genomic DNA in agarose plugs prior to digestion with the AscI and ApaI restriction enzymes (New England BioLabs), followed by PFGE with a Chef DR III system (Bio-Rad, Hercules, CA) , and pulsotypes were analyzed as described elsewhere ( ).

    Techniques: Produced

    a Location of TaqMan PCR Cy5 probe in the lambda genome is shown in red , FAM probes are shown in green , and the location of the ApaI restriction site is shown in black . b Representative image of multiplexed PCR emulsion on Lambda DNA. c Representative scatterplot of Cy5 and FAM intensities for Lambda DNA. d Fraction of multiplexed droplets for Lambda DNA undigested ( blue ), ApaI digested ( red ), and Fragmentase digested ( green )

    Journal: Virology Journal

    Article Title: Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry

    doi: 10.1186/s12985-016-0655-7

    Figure Lengend Snippet: a Location of TaqMan PCR Cy5 probe in the lambda genome is shown in red , FAM probes are shown in green , and the location of the ApaI restriction site is shown in black . b Representative image of multiplexed PCR emulsion on Lambda DNA. c Representative scatterplot of Cy5 and FAM intensities for Lambda DNA. d Fraction of multiplexed droplets for Lambda DNA undigested ( blue ), ApaI digested ( red ), and Fragmentase digested ( green )

    Article Snippet: For ApaI restriction enzyme digestion (NEB) or Fragmentase digest (New England Biolabs; NEB), Lambda DNA is treated enzymatically prior to the mixing with the PCR reagents.

    Techniques: Polymerase Chain Reaction, Lambda DNA Preparation

    ( A ) Sequence comparison of the human U6 promoter and the modified U6 promoter with the bacterial tetracycline operon (tetO). The modified portion is indicated in bold. (B–E) Schematic illustrations of the vector construction process. ( B ) The U6 promoter sequence with an SphI recognition sequence (GCATG|C) was ligated into a TA cloning vector. ( C ) To preserve the first transcribed nucleotide as guanosine, the plasmid was digested with SphI and blunted with Klenow fragment. ( D ), DNA oligomers were ligated in two separate ligation reactions. Oligo1 was ligated following AatII digestion. ( E ) Oligo2 including the transcriptional termination signal T 5 was ligated following AatII and ApaI digestion. (F–J) Schematic maps of vectors used in this study. ( F ) U6pro/DNMT1. DNMT1-targeting hairpin siRNA is driven by the human U6 promoter. ( G ) U6pro/Blank. As a control, the transcriptional termination signal T 5 was ligated immediately downstream of the human U6 promoter. ( H ) U6pro/tetO/DNMT1. DNMT1-targeting hairpin siRNA is driven by the modified U6 promoter regulated by tetracycline. ( I ) U6pro/tetO/DNMT1/Hygro. U6pro/tetO/DNMT1 with the hygromycin resistance gene. ( J ) tetR/Neo. The tetR coding region was ligated in an expression vector with the neomycin resistance gene.

    Journal: Nucleic Acids Research

    Article Title: Establishment of conditional vectors for hairpin siRNA knockdowns

    doi:

    Figure Lengend Snippet: ( A ) Sequence comparison of the human U6 promoter and the modified U6 promoter with the bacterial tetracycline operon (tetO). The modified portion is indicated in bold. (B–E) Schematic illustrations of the vector construction process. ( B ) The U6 promoter sequence with an SphI recognition sequence (GCATG|C) was ligated into a TA cloning vector. ( C ) To preserve the first transcribed nucleotide as guanosine, the plasmid was digested with SphI and blunted with Klenow fragment. ( D ), DNA oligomers were ligated in two separate ligation reactions. Oligo1 was ligated following AatII digestion. ( E ) Oligo2 including the transcriptional termination signal T 5 was ligated following AatII and ApaI digestion. (F–J) Schematic maps of vectors used in this study. ( F ) U6pro/DNMT1. DNMT1-targeting hairpin siRNA is driven by the human U6 promoter. ( G ) U6pro/Blank. As a control, the transcriptional termination signal T 5 was ligated immediately downstream of the human U6 promoter. ( H ) U6pro/tetO/DNMT1. DNMT1-targeting hairpin siRNA is driven by the modified U6 promoter regulated by tetracycline. ( I ) U6pro/tetO/DNMT1/Hygro. U6pro/tetO/DNMT1 with the hygromycin resistance gene. ( J ) tetR/Neo. The tetR coding region was ligated in an expression vector with the neomycin resistance gene.

    Article Snippet: Oligo2 [a mixture of DNMTO2F (5′-CCTGTTGGCATCTGCCATTCCCTTTTTGGGCC-3′) and DNMTO2R (5′-CAAAAAGGGAATGGCAGATGCCAACAGGACGT-3′)] was ligated after sequence analysis and AatII–ApaI (New England Biolabs) digestion (Fig. E).

    Techniques: Sequencing, Modification, Plasmid Preparation, TA Cloning, Ligation, Expressing

    (a) Pulsed-field gel of S1 nuclease-digested genomic DNA from A. bereziniae CHI-40-1, recipients, and transconjugants; (b) in-gel hybridization with a bla NDM-1 gene probe; (c) pulsed-field gel of ApaI-digested genomic DNA from CHI-40-1; (d) in-gel hybridization

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Characterization of Plasmids in Extensively Drug-Resistant Acinetobacter Strains Isolated in India and Pakistan

    doi: 10.1128/AAC.03242-14

    Figure Lengend Snippet: (a) Pulsed-field gel of S1 nuclease-digested genomic DNA from A. bereziniae CHI-40-1, recipients, and transconjugants; (b) in-gel hybridization with a bla NDM-1 gene probe; (c) pulsed-field gel of ApaI-digested genomic DNA from CHI-40-1; (d) in-gel hybridization

    Article Snippet: Plugs were treated with ApaI (Thermo Scientific, Waltham, MA, USA) or S1 nuclease (Thermo Scientific) and pulsed-field gel electrophoresis (PFGE) performed as described previously ( , ).

    Techniques: Pulsed-Field Gel, Hybridization

    PFGE dendrogram of L. monocytogenes harboring LmoJ2 and LmoJ3. PFGE with ApaI and AscI and profile clustering were performed as described in Materials and Methods. Isolates harboring LmoJ2 and LmoJ3 are indicated with filled and open circles, respectively.

    Journal: Applied and Environmental Microbiology

    Article Title: Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains

    doi: 10.1128/AEM.07203-11

    Figure Lengend Snippet: PFGE dendrogram of L. monocytogenes harboring LmoJ2 and LmoJ3. PFGE with ApaI and AscI and profile clustering were performed as described in Materials and Methods. Isolates harboring LmoJ2 and LmoJ3 are indicated with filled and open circles, respectively.

    Article Snippet: Pulsed-field gel electrophoresis (PFGE) was conducted with AscI (New England BioLabs, Ipswich, MA) and ApaI (Roche, Indianapolis, IN) as described previously , and BioNumerics (Applied Maths, Austin, TX) was employed for analysis of the PFGE profiles.

    Techniques:

    Structural- and chemical probing of DNA and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by ApaI then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.

    Journal: PLoS ONE

    Article Title: Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

    doi: 10.1371/journal.pone.0165788

    Figure Lengend Snippet: Structural- and chemical probing of DNA and DNA-PNA complex formation in pMP178(75 repeats). A) Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP178(75 repeats), was incubated in the absence (No PNA) or the presence of 10 μM of PNA (GAA-PNA or CTT-PNA) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Non-treated plasmid was used in a set of four different controls (C) of the PE reactions C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of GAA-PNA. C3= plasmid incubated in the presence of CTT-PNA. C4= plasmid not incubated. All samples were linearized by ApaI then subjected as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP178(75 repeats) and the PE reaction control (C4) are shown as references. The DNA fragments detected in a PE reaction using the GAA (R)-strand as template, and the right gel panel shows the DNA fragments detected in a PE reaction using the CTT (Y)-strand as template. The A 1 to A 9 nucleotides flanking the repeats of the R-strand and T 1 to T 12 flanking in the Y-strand and the middle point of the repeat sequence are indicated (M). B) Models showing the most predominant DNA and DNA-PNA structures formed at pMP178(75 repeats) in the absence or the presence of CTT-PNA or GAA-PNA respectively. They correspond to: 1. 5′3′3′-pyrimidine motif H-DNA, 2. CTT-PNA stabilized 5′3′3′-pyrimidine motif H-DNA, 3. Triplex-invasion, 4. Intermolecular triplex and 5. Duplex-invasion structure. Thin line= purine strand, thick line= pyrimidine strand, grey line= PNA. Regions modified by CAA (π) or cleaved by BQQ-OP (o) are indicated.

    Article Snippet: The isolated DNA was digested using ApaI (1 U, Promega) during 3 h at 37°C and then analyzed using 0.7% agarose gel electrophoresis (50 V, 1 h) and ethidium bromide or SYBR-safe (Life Technologies) staining.

    Techniques: Polyacrylamide Gel Electrophoresis, Cellular Antioxidant Activity Assay, Modification, Plasmid Preparation, Incubation, Sequencing

    BQQ-OP mediated DNA cleavage of H-DNA forming (GAA) 115 repeats in the presence of PNA. A) Schematic presentation of pMP179 and the H-DNA forming site. The two DNA fragments generated by triplex-specific cleavage followed by enzymatic digestion are indicated as X (3814 bp) and Y (3178 bp). B) Representative gel for pMP179(115 repeats) incubated with 10 μM PNA (CTT-PNA or GAA-PNA, lane 1 or 2, respectively), in the absence of ONs (lane 3) or with 10 μM ssDNA (CTT-DNA or GAA-DNA, lane 4 or 5, respectively) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). Triplex-specific cleavage was carried out in the presence of Cu 2+ and MPA, followed by digestion with ApaI. Reference supercoiled (SC) and linearized (Lin) pMP179(115 repeats) and a molecular weight DNA ladder (M) are also shown. C) Graph represents the percentage of BQQ-OP mediated cleavage obtained for pMP179(115 repeats) in the absence (indicate in the graph as pMP179) or in the presence of PNA- or DNA oligomers. Values indicate the ratio between the intensity of DNA double strand cleavage to the total band intensity from the respective lane and are expressed as mean±S.D. (n=3). No cleavage was obtained in the presence of GAA-PNA and therefore not included in the graph. ** P ≤0.01 in relation to plasmid in the absence of oligonucleotide (pMP179).

    Journal: PLoS ONE

    Article Title: Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

    doi: 10.1371/journal.pone.0165788

    Figure Lengend Snippet: BQQ-OP mediated DNA cleavage of H-DNA forming (GAA) 115 repeats in the presence of PNA. A) Schematic presentation of pMP179 and the H-DNA forming site. The two DNA fragments generated by triplex-specific cleavage followed by enzymatic digestion are indicated as X (3814 bp) and Y (3178 bp). B) Representative gel for pMP179(115 repeats) incubated with 10 μM PNA (CTT-PNA or GAA-PNA, lane 1 or 2, respectively), in the absence of ONs (lane 3) or with 10 μM ssDNA (CTT-DNA or GAA-DNA, lane 4 or 5, respectively) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). Triplex-specific cleavage was carried out in the presence of Cu 2+ and MPA, followed by digestion with ApaI. Reference supercoiled (SC) and linearized (Lin) pMP179(115 repeats) and a molecular weight DNA ladder (M) are also shown. C) Graph represents the percentage of BQQ-OP mediated cleavage obtained for pMP179(115 repeats) in the absence (indicate in the graph as pMP179) or in the presence of PNA- or DNA oligomers. Values indicate the ratio between the intensity of DNA double strand cleavage to the total band intensity from the respective lane and are expressed as mean±S.D. (n=3). No cleavage was obtained in the presence of GAA-PNA and therefore not included in the graph. ** P ≤0.01 in relation to plasmid in the absence of oligonucleotide (pMP179).

    Article Snippet: The isolated DNA was digested using ApaI (1 U, Promega) during 3 h at 37°C and then analyzed using 0.7% agarose gel electrophoresis (50 V, 1 h) and ethidium bromide or SYBR-safe (Life Technologies) staining.

    Techniques: Generated, Incubation, Molecular Weight, Plasmid Preparation

    Structural- and chemical probing of DNA and DNA-PNA complex formation at (GAA) 9 repeats. Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP141(9 repeats), was incubated in the absence (No PNA) or presence of 10 μM of GAA-PNA or CTT-PNA in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then either chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Untreated plasmid was used in a set of four different controls (C) of the PE reactions: C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of CTT-PNA. C3= plasmid incubated in the presence of GAA-PNA. C4= plasmid not incubated. All samples were linearized using ApaI and then used as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP141(9 repeats) and a PE reaction control (C4) are also shown. The left gel panel shows the DNA fragments obtained in a PE reaction using the GAA containing (R)-strand as template, and the right gel panel shows the DNA fragments obtained when using the CTT containing (Y)-strand as template. The A 1 to A 23 nucleotides flanking the repeats of the R-strand and T 1 to T 23 flanking in the Y-strand and the mid-point of the repeat sequence (M) are indicated.

    Journal: PLoS ONE

    Article Title: Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

    doi: 10.1371/journal.pone.0165788

    Figure Lengend Snippet: Structural- and chemical probing of DNA and DNA-PNA complex formation at (GAA) 9 repeats. Non-denaturing PAGE of DNA fragments mapped by BQQ-OP cleavage and chloroacetaldehyde (CAA) modification followed by primer extension (PE). Plasmid pMP141(9 repeats), was incubated in the absence (No PNA) or presence of 10 μM of GAA-PNA or CTT-PNA in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). The plasmid was then either chemically modified using 2% CAA or cleaved using 1 μM BQQ-OP. Untreated plasmid was used in a set of four different controls (C) of the PE reactions: C1= plasmid incubated in the absence of PNA. C2= plasmid incubated in the presence of CTT-PNA. C3= plasmid incubated in the presence of GAA-PNA. C4= plasmid not incubated. All samples were linearized using ApaI and then used as templates for the PE reaction. Sequence ladders using dideoxynucleotides (C=ddCTP, T=ddTTP, G=ddGTP and A=ddATP), linearized pMP141(9 repeats) and a PE reaction control (C4) are also shown. The left gel panel shows the DNA fragments obtained in a PE reaction using the GAA containing (R)-strand as template, and the right gel panel shows the DNA fragments obtained when using the CTT containing (Y)-strand as template. The A 1 to A 23 nucleotides flanking the repeats of the R-strand and T 1 to T 23 flanking in the Y-strand and the mid-point of the repeat sequence (M) are indicated.

    Article Snippet: The isolated DNA was digested using ApaI (1 U, Promega) during 3 h at 37°C and then analyzed using 0.7% agarose gel electrophoresis (50 V, 1 h) and ethidium bromide or SYBR-safe (Life Technologies) staining.

    Techniques: Polyacrylamide Gel Electrophoresis, Cellular Antioxidant Activity Assay, Modification, Plasmid Preparation, Incubation, Sequencing

    BQQ-OP mediated DNA cleavage of H-DNA forming (GAA) 115 repeats in the presence of LNA-PS. A) Representative gel from pMP179(115 repeats) incubated with 10 μM LNA-PS (GAA-LNA-PS 1, 2 or 3 or ER-LNA-PS or CTT-LNA-PS, lane 1, 2, 3, 4 or 7, respectively), in the absence of oligonucleotide (lane 8) or with 10 μM ssDNA (CTT-DNA or GAA-DNA, lane 5 or 6, respectively) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). Triplex-specific cleavage was carried out in the presence of Cu 2+ and MPA, and the plasmid was subsequently digested using ApaI. The two obtained DNA fragments have approximately 3814 and 3178 bp. Reference supercoiled (SC) and linearized (Lin) pMP179(115 repeats) and a molecular weight DNA ladder (M) are also shown. B) Graph represents the percentage of BQQ-OP mediated cleavage for pMP179(115 repeats) in the absence (indicate in the graph as pMP179) or in the presence of LNA- or DNA oligomers. Values indicate the ratio between the intensity of DNA double strand cleavage to the total band intensity from the respective lane and are expressed as mean±S.D. (n=3). *** P ≤0.001, **** P

    Journal: PLoS ONE

    Article Title: Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

    doi: 10.1371/journal.pone.0165788

    Figure Lengend Snippet: BQQ-OP mediated DNA cleavage of H-DNA forming (GAA) 115 repeats in the presence of LNA-PS. A) Representative gel from pMP179(115 repeats) incubated with 10 μM LNA-PS (GAA-LNA-PS 1, 2 or 3 or ER-LNA-PS or CTT-LNA-PS, lane 1, 2, 3, 4 or 7, respectively), in the absence of oligonucleotide (lane 8) or with 10 μM ssDNA (CTT-DNA or GAA-DNA, lane 5 or 6, respectively) in buffer (10 mM sodium cacodylate, 100 mM NaCl, 2 mM MgCl 2 , pH 7.5). Triplex-specific cleavage was carried out in the presence of Cu 2+ and MPA, and the plasmid was subsequently digested using ApaI. The two obtained DNA fragments have approximately 3814 and 3178 bp. Reference supercoiled (SC) and linearized (Lin) pMP179(115 repeats) and a molecular weight DNA ladder (M) are also shown. B) Graph represents the percentage of BQQ-OP mediated cleavage for pMP179(115 repeats) in the absence (indicate in the graph as pMP179) or in the presence of LNA- or DNA oligomers. Values indicate the ratio between the intensity of DNA double strand cleavage to the total band intensity from the respective lane and are expressed as mean±S.D. (n=3). *** P ≤0.001, **** P

    Article Snippet: The isolated DNA was digested using ApaI (1 U, Promega) during 3 h at 37°C and then analyzed using 0.7% agarose gel electrophoresis (50 V, 1 h) and ethidium bromide or SYBR-safe (Life Technologies) staining.

    Techniques: Incubation, Plasmid Preparation, Molecular Weight