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  • 95
    Millipore single stranded dna templates
    Single Stranded Dna Templates, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher template dna puc57 tff1
    Template Dna Puc57 Tff1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATUM template dna
    <t>PCR</t> amplification of the nuc gene of S. aureus . Lane 1: 100 bp <t>DNA</t> ladder. Lane 5: Amplified PCR product
    Template Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 96/100, based on 1683 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kaneka Corp dna template
    <t>PCR</t> amplification of the nuc gene of S. aureus . Lane 1: 100 bp <t>DNA</t> ladder. Lane 5: Amplified PCR product
    Dna Template, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 94/100, based on 68 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pharmingen dna template
    <t>PCR</t> amplification of the nuc gene of S. aureus . Lane 1: 100 bp <t>DNA</t> ladder. Lane 5: Amplified PCR product
    Dna Template, supplied by Pharmingen, used in various techniques. Bioz Stars score: 90/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pharmingen dna templates
    <t>PCR</t> amplification of the nuc gene of S. aureus . Lane 1: 100 bp <t>DNA</t> ladder. Lane 5: Amplified PCR product
    Dna Templates, supplied by Pharmingen, used in various techniques. Bioz Stars score: 88/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dna templates
    RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with <t>RNA</t> and <t>DNA</t> templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .
    Dna Templates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3027 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    DSMZ template dna
    RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with <t>RNA</t> and <t>DNA</t> templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .
    Template Dna, supplied by DSMZ, used in various techniques. Bioz Stars score: 92/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare template dna
    Kinetic analysis of the inhibition of calf thymus pol α by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying <t>DNA</t> template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., <t>dTTP)</t>
    Template Dna, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 95/100, based on 692 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega template dna
    Kinetic analysis of the inhibition of calf thymus pol α by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying <t>DNA</t> template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., <t>dTTP)</t>
    Template Dna, supplied by Promega, used in various techniques. Bioz Stars score: 96/100, based on 3578 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa template dna
    Sensitivity of <t>RE-dMSP</t> for the detection of methylated RASSF1A. (A) Detection sensitivity of RE-dMSP was assessed using 0, 1, 3, 10, 30 and 100 copies of methylated genomic <t>DNA,</t> spiked in 10,000 copies of unmethylated genomic DNA extracted from the peripheral blood leukocytes of a healthy individual. Methylated RASSF1A was quantified by RE-dMSP with restriction enzymes (solid line, with REs), and the total inputs of methylated and unmethylated DNA were measured without restriction enzymes (dotted line, without REs). Error bars indicate the standard deviation of eight experiments. (B) Positive detection rate in eight experiments for each sample, compared between RE-dMSP and qPCR with bisulfite modification. RE-dMSP, dPCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1; RE, restriction enzyme; qPCR, quantitative PCR.
    Template Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 3940 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dna template
    Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per <t>PCR</t> reaction volume (1.5 µL of <t>DNA).</t> The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.
    Dna Template, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7577 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore template dna
    Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per <t>PCR</t> reaction volume (1.5 µL of <t>DNA).</t> The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.
    Template Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 1154 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Templates, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 832 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Addgene inc template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Template Dna, supplied by Addgene inc, used in various techniques. Bioz Stars score: 95/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriGene template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Template Dna, supplied by OriGene, used in various techniques. Bioz Stars score: 93/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Glen Research dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Templates, supplied by Glen Research, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriGene dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Templates, supplied by OriGene, used in various techniques. Bioz Stars score: 88/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    5 PRIME template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Template Dna, supplied by 5 PRIME, used in various techniques. Bioz Stars score: 92/100, based on 131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Templates, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 78 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Microsynth dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Templates, supplied by Microsynth, used in various techniques. Bioz Stars score: 88/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pacific Biosciences template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Template Dna, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Microbiologics Inc dna template
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Dna Template, supplied by Microbiologics Inc, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Integrated DNA Technologies template hairpin dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Template Hairpin Dna, supplied by Integrated DNA Technologies, 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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    Sangon Biotech control dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Control Dna Templates, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 86/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abbott Laboratories ic dna template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Ic Dna Template Dna, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 78/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATUM genomiphi dna template dna
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Genomiphi Dna Template Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 78/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pharmingen riboquant dna templates
    Effect of the mutated AP-1 sites on the regulation of the TF promoter by <t>PML/RARα.</t> EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled <t>DNA</t> probes spanning from position −250 to −196
    Riboquant Dna Templates, supplied by Pharmingen, used in various techniques. Bioz Stars score: 76/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATUM template mrho dna
    Validation of <t>mRho</t> -specific CRISPRd-mediated gene deletion in vivo A , Schematic of experimental (AAVs-Cas9+GR) and control (AAVs-Cas9+SR) AAV2/8 vector pairs. B , Conventional gene replacement therapy vs CRISPRd plus gene replacement, compound therapy for a heterozygous loci. C , gRNA1 and gRNA2 sequences, their targeting sites on m Rho , and the corresponding sites on hRHO – showing the 12 and 4 mismatches, respectively. D , Representative data of in vitro SpCas9/gRNA cutting. In a cell-free assay, mRho vs hRHO <t>DNA</t> template was mixed with recombinant SpCas9 protein and a single gRNA: gRNA1, gRNA2, or control (scrambled gRNA). (n=3) E , Experimental scheme and timeline for subretinal injection of dual AAV vectors in right eyes of wild-type C57BL/6J mice (using a unique, posterior approach); respecting IACUC protocols, left eyes were uninjected. F , Representative data of Cas9-immunostaining in retinal flat mount. 14 days after Cas9+GR subretinal injection, the retinas were collected and stained for anti-Cas9 antibogy (n=3). Image was assembled from multiple pictures. G , Representative data of PCR analysis of retinal genomic DNA from AAVs-Cas9+GR-injected right eyes and uninjected, fellow (left) eyes. (n=4, two mice data are shown). H , Representative data of mRho gene ablation validated by Sanger sequencing of PCR amplicon from Fig. 2G.
    Template Mrho Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 81/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    N/A
    NEBNext Enzymatic Methyl seq EM seq provides a high performance enzyme based alternative to bisulfite conversion for methylome analysis The consistently high conversion performance and minimized DNA damage with the
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    Human DNA Standards and No Template Control 1 8 for use with Femto Human DNA Quantification Kit for detecting femtogram levels of human DNA
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    Image Search Results


    PCR amplification of the nuc gene of S. aureus . Lane 1: 100 bp DNA ladder. Lane 5: Amplified PCR product

    Journal: Iranian Journal of Veterinary Research

    Article Title: Isolation, characterization and therapeutic potential assessment of bacteriophages virulent to Staphylococcus aureus associated with goat mastitis

    doi:

    Figure Lengend Snippet: PCR amplification of the nuc gene of S. aureus . Lane 1: 100 bp DNA ladder. Lane 5: Amplified PCR product

    Article Snippet: The PCR mixture consisting of 50 ng template DNA, 20 pmol of each primer and 17 µl PCR master-mix (Qiagen, USA) was diluted up to a 25 µl volume with nuclease free water.

    Techniques: Polymerase Chain Reaction, Amplification

    PCR product in agarose gel electrophoresis. M, Marker DNA λ/ Hind III (M); lane 1 and 2, represented the DNA fragment (2,2 kb) that resulted by PCR using the genome of M. tuberculosis H37RV and INH-resistant M. tuberculosis R2 as templates respectively. The DNA fragment of 2.2 kb corresponds to the katG gene.

    Journal: Journal of Medicine and Life

    Article Title: Molecular Analysis of katG Encoding Catalase-Peroxidase from Clinical Isolate of Isoniazid-Resistant Mycobacterium tuberculosis

    doi:

    Figure Lengend Snippet: PCR product in agarose gel electrophoresis. M, Marker DNA λ/ Hind III (M); lane 1 and 2, represented the DNA fragment (2,2 kb) that resulted by PCR using the genome of M. tuberculosis H37RV and INH-resistant M. tuberculosis R2 as templates respectively. The DNA fragment of 2.2 kb corresponds to the katG gene.

    Article Snippet: The total volume for PCR was 25 µL and it was composed of 5 µL DNA template (25 ng DNA); 20 pmol of each primer; 1.25 units of Taq DNA polymerase (Roche); buffer 1x (10 mM Tris HCl pH 9; 1.5 mM MgCl2 ; 50 mM KCl) and 100 µM of dNTP mix (Roche).

    Techniques: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Marker

    Molecular modeling of UTP binding opposite dT template at pol II active site. ( A ) UTP forms a wobble bonding pair with dT template, resulting in the misalignment of its triphosphate group compared to cognate ATP recognition. ( B ) An alternative form of UTP:dT pairing In this form, the UTP shifts toward the minor groove of the RNA/DNA hybrid, leading to steric clash between pol II residues and the incoming nucleotide. The two potential base pairing behaviors were modeled based on the previously reported U:U pair ( 42 ).

    Journal: Nucleic Acids Research

    Article Title: Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution

    doi: 10.1093/nar/gkw220

    Figure Lengend Snippet: Molecular modeling of UTP binding opposite dT template at pol II active site. ( A ) UTP forms a wobble bonding pair with dT template, resulting in the misalignment of its triphosphate group compared to cognate ATP recognition. ( B ) An alternative form of UTP:dT pairing In this form, the UTP shifts toward the minor groove of the RNA/DNA hybrid, leading to steric clash between pol II residues and the incoming nucleotide. The two potential base pairing behaviors were modeled based on the previously reported U:U pair ( 42 ).

    Article Snippet: Briefly, an aliquot of 5′-32 P-labeled RNA (10 μM) was annealed with a 1.5-fold amount of template DNA (15 μM) and 2-fold amount of non-template DNA (20 μM) to form the RNA/DNA scaffold (final stock concentration: 1 μM, defined by RNA concentration) in elongation buffer (20 mM Tris–HCl (pH 7.5), 40 mM KCl, 5 mM MgCl2 ).

    Techniques: Binding Assay

    Oncogene sequence analysis. ( top ) Genomic DNA was extracted from BC and electrophoresed in agarose/ethidium bromide. Sample numbers are on top of each lane; mw: molecular weight markers. ( mid ) Exon-intron structure of the TP53 gene. ( bottom ) PCR amplification of the TP53 exons. EX: exon number; multiplex: simultaneous amplification of all exons with optimized primers and amplification procedure; mw: molecular weight markers

    Journal: BMC Cancer

    Article Title: p53, cathepsin D, Bcl-2 are joint prognostic indicators of breast cancer metastatic spreading

    doi: 10.1186/s12885-016-2713-3

    Figure Lengend Snippet: Oncogene sequence analysis. ( top ) Genomic DNA was extracted from BC and electrophoresed in agarose/ethidium bromide. Sample numbers are on top of each lane; mw: molecular weight markers. ( mid ) Exon-intron structure of the TP53 gene. ( bottom ) PCR amplification of the TP53 exons. EX: exon number; multiplex: simultaneous amplification of all exons with optimized primers and amplification procedure; mw: molecular weight markers

    Article Snippet: Reactions were performed in 30 μl total volume (15 μl KapaBlood PCR Kit B, 0.5 μl of template pretreated DNA, 20 pmol primer forward, 20 pmol primer reverse).

    Techniques: Sequencing, Molecular Weight, Polymerase Chain Reaction, Amplification, Multiplex Assay

    RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with RNA and DNA templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: RT progression assay determining G-quartet formation in the Sp1 binding region. Cation-dependent pausing of reverse transcription at the guanine-rich elements in the U3 region was analyzed with RNA and DNA templates. A fragment of the RNA/DNA sequence of the Sp1 binding region is shown (top) with G-rich elements (shaded). Strong pauses of the RT near G-rich elements were observed in the presence of 50 mM of KCl, but not LiCl, indicating that these elements are involved in the formation of structure, which is stabilized by potassium ions but destabilized by lithium ions. This is indicative of a G-quadruplex. The cation-independent RT pauses are likely caused by hairpin structures. DNA primer, P; DNA marker, M; KCl, K + ; LiCl, Li + .

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: Binding Assay, Sequencing, Marker

    Formation of the structure stabilized by potassium ions in the HIV-1 U3 region facilitates RT template switching during reverse transcription. (A) Reconstituted system to analyze the influence of G-rich elements on strand transfer during HIV-1 minus strand DNA synthesis in vitro . Donor and acceptor RNA templates represent two copies of the viral RNA genome; in which reverse transcription is initiated from a 32 P-labeled DNA primer annealed to the donor RNA. The acceptor RNA does not share a homology (circle) with two nucleotides at the 5′ end of the donor RNA. TP, transfer product; DE, donor extension product; and P, DNA primer. (B) A time course of strand transfer reactions performed in the presence of potassium and lithium ions. Samples were collected at 1, 5, 15, and 30 min after the reaction was initiated. Formation of a potassium-dependent structure, anticipated to be a G-quadruplex, in the RNA template paused the RT during minus strand DNA synthesis and influenced the yield of the final products. The transfer efficiency decreased about 37% in reactions with lithium ions, presumably because the templates could not form a G-quadruplex.

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: Formation of the structure stabilized by potassium ions in the HIV-1 U3 region facilitates RT template switching during reverse transcription. (A) Reconstituted system to analyze the influence of G-rich elements on strand transfer during HIV-1 minus strand DNA synthesis in vitro . Donor and acceptor RNA templates represent two copies of the viral RNA genome; in which reverse transcription is initiated from a 32 P-labeled DNA primer annealed to the donor RNA. The acceptor RNA does not share a homology (circle) with two nucleotides at the 5′ end of the donor RNA. TP, transfer product; DE, donor extension product; and P, DNA primer. (B) A time course of strand transfer reactions performed in the presence of potassium and lithium ions. Samples were collected at 1, 5, 15, and 30 min after the reaction was initiated. Formation of a potassium-dependent structure, anticipated to be a G-quadruplex, in the RNA template paused the RT during minus strand DNA synthesis and influenced the yield of the final products. The transfer efficiency decreased about 37% in reactions with lithium ions, presumably because the templates could not form a G-quadruplex.

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: DNA Synthesis, In Vitro, Labeling

    CD spectral analysis of the RNA and single stranded DNA with Sp1 binding sites in HIV-1. CD spectra indicate the formation of the parallel G-quadruplex for the RNA template and an antiparallel or hybrid G-quadruplex for single stranded DNA. For reference, a profile of the G-rich sequence (50% of Gs; GGGGGGAUUGUG UGGUACAGUGCAGAGA), which is unable to adopt G-quadruplex structure, is shown in gray.

    Journal: Biochemistry

    Article Title: U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    doi: 10.1021/bi4016692

    Figure Lengend Snippet: CD spectral analysis of the RNA and single stranded DNA with Sp1 binding sites in HIV-1. CD spectra indicate the formation of the parallel G-quadruplex for the RNA template and an antiparallel or hybrid G-quadruplex for single stranded DNA. For reference, a profile of the G-rich sequence (50% of Gs; GGGGGGAUUGUG UGGUACAGUGCAGAGA), which is unable to adopt G-quadruplex structure, is shown in gray.

    Article Snippet: Preparation of RNA Templates RNA molecules were transcribed in vitro (Ambion T7-MEGAshortscript kit; Applied Biosystems) from DNA templates amplified by PCR using Vent DNA polymerase (New England BioLabs, Inc.) and two overlapping oligomers with the sequence of the desired region.

    Techniques: Binding Assay, Sequencing

    Kinetic analysis of the inhibition of calf thymus pol α by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying DNA template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., dTTP)

    Journal: Biochemical pharmacology

    Article Title: Anti-cancer gallotannin penta-O-galloyl-beta-D-glucose is a nanomolar inhibitor of select mammalian DNA polymerases

    doi: 10.1016/j.bcp.2010.06.031

    Figure Lengend Snippet: Kinetic analysis of the inhibition of calf thymus pol α by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying DNA template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., dTTP)

    Article Snippet: Nucleotides such as [3 H]-deoxythymidine 5′-triphosphate (dTTP) (43 Ci/mmol), and chemically synthesized DNA template, such as poly(dA) were purchased from GE Healthcare Bio-Sciences (Little Chalfont, UK).

    Techniques: Inhibition

    Kinetic analysis of the inhibition of rat pol β by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying DNA template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., dTTP) concentrations

    Journal: Biochemical pharmacology

    Article Title: Anti-cancer gallotannin penta-O-galloyl-beta-D-glucose is a nanomolar inhibitor of select mammalian DNA polymerases

    doi: 10.1016/j.bcp.2010.06.031

    Figure Lengend Snippet: Kinetic analysis of the inhibition of rat pol β by PGG. (A and B) Lineweaver–Burk double-reciprocal plots obtained by varying DNA template-primer (i.e., poly(dA)/oligo(dT) 18 ) concentrations (A), and dNTP substrate (i.e., dTTP) concentrations

    Article Snippet: Nucleotides such as [3 H]-deoxythymidine 5′-triphosphate (dTTP) (43 Ci/mmol), and chemically synthesized DNA template, such as poly(dA) were purchased from GE Healthcare Bio-Sciences (Little Chalfont, UK).

    Techniques: Inhibition

    Sensitivity of RE-dMSP for the detection of methylated RASSF1A. (A) Detection sensitivity of RE-dMSP was assessed using 0, 1, 3, 10, 30 and 100 copies of methylated genomic DNA, spiked in 10,000 copies of unmethylated genomic DNA extracted from the peripheral blood leukocytes of a healthy individual. Methylated RASSF1A was quantified by RE-dMSP with restriction enzymes (solid line, with REs), and the total inputs of methylated and unmethylated DNA were measured without restriction enzymes (dotted line, without REs). Error bars indicate the standard deviation of eight experiments. (B) Positive detection rate in eight experiments for each sample, compared between RE-dMSP and qPCR with bisulfite modification. RE-dMSP, dPCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1; RE, restriction enzyme; qPCR, quantitative PCR.

    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: Sensitivity of RE-dMSP for the detection of methylated RASSF1A. (A) Detection sensitivity of RE-dMSP was assessed using 0, 1, 3, 10, 30 and 100 copies of methylated genomic DNA, spiked in 10,000 copies of unmethylated genomic DNA extracted from the peripheral blood leukocytes of a healthy individual. Methylated RASSF1A was quantified by RE-dMSP with restriction enzymes (solid line, with REs), and the total inputs of methylated and unmethylated DNA were measured without restriction enzymes (dotted line, without REs). Error bars indicate the standard deviation of eight experiments. (B) Positive detection rate in eight experiments for each sample, compared between RE-dMSP and qPCR with bisulfite modification. RE-dMSP, dPCR with methylation-specific restriction enzymes; RASSF1A, Ras association domain-containing protein 1; RE, restriction enzyme; qPCR, quantitative PCR.

    Article Snippet: For sensitivity analysis of RE-dMSP, 0, 1, 3, 10, 30 and 100 copies of methylated DNA template (EpiScope® Methylated HeLa gDNA; Takara Bio, Inc.) spiked in 10,000 copies of unmethylated DNA from the peripheral blood leukocytes of a healthy individual were subjected to RE-dMSP with or without restriction enzymes.

    Techniques: Methylation, Standard Deviation, Real-time Polymerase Chain Reaction, Modification, Digital PCR

    Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per PCR reaction volume (1.5 µL of DNA). The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.

    Journal: Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc

    Article Title: Application of real-time quantitative PCR assays for detecting marine Brucella spp. in fish

    doi: 10.1177/1040638717733024

    Figure Lengend Snippet: Standard curve demonstrating the range of threshold cycle (Ct) values plotted versus genome equivalents (GE) of Brucella pinnipedialis strain B04-0821 per PCR reaction volume (1.5 µL of DNA). The regression line represents data that were in the linear range. Each point represents the mean value for triplicate runs at each dilution.

    Article Snippet: Total PCR reaction volumes were 15 µL with 4.5 µL of DNA template, 100 µM primers and probe, and a commercial master mix (TaqMan universal master mix II, Life Technologies, Carlsbad, CA).

    Techniques: Polymerase Chain Reaction

    Effect of the mutated AP-1 sites on the regulation of the TF promoter by PML/RARα. EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled DNA probes spanning from position −250 to −196

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: PML/RAR? fusion protein transactivates the tissue factor promoter through a GAGC-containing element without direct DNA association

    doi: 10.1073/pnas.0915006107

    Figure Lengend Snippet: Effect of the mutated AP-1 sites on the regulation of the TF promoter by PML/RARα. EMSA analysis for the interaction of PML/RARα with the TF promoter was performed using radiolabeled DNA probes spanning from position −250 to −196

    Article Snippet: PML/RARα and RARα proteins were synthesized in vitro with pSG5-RARα and pSG5-PML/RARα as DNA templates according to the manufacturer’s protocol (Promega).

    Techniques:

    Validation of mRho -specific CRISPRd-mediated gene deletion in vivo A , Schematic of experimental (AAVs-Cas9+GR) and control (AAVs-Cas9+SR) AAV2/8 vector pairs. B , Conventional gene replacement therapy vs CRISPRd plus gene replacement, compound therapy for a heterozygous loci. C , gRNA1 and gRNA2 sequences, their targeting sites on m Rho , and the corresponding sites on hRHO – showing the 12 and 4 mismatches, respectively. D , Representative data of in vitro SpCas9/gRNA cutting. In a cell-free assay, mRho vs hRHO DNA template was mixed with recombinant SpCas9 protein and a single gRNA: gRNA1, gRNA2, or control (scrambled gRNA). (n=3) E , Experimental scheme and timeline for subretinal injection of dual AAV vectors in right eyes of wild-type C57BL/6J mice (using a unique, posterior approach); respecting IACUC protocols, left eyes were uninjected. F , Representative data of Cas9-immunostaining in retinal flat mount. 14 days after Cas9+GR subretinal injection, the retinas were collected and stained for anti-Cas9 antibogy (n=3). Image was assembled from multiple pictures. G , Representative data of PCR analysis of retinal genomic DNA from AAVs-Cas9+GR-injected right eyes and uninjected, fellow (left) eyes. (n=4, two mice data are shown). H , Representative data of mRho gene ablation validated by Sanger sequencing of PCR amplicon from Fig. 2G.

    Journal: Ophthalmology

    Article Title: CRISPR-based genome surgery for the treatment of autosomal dominant retinitis pigmentosa

    doi: 10.1016/j.ophtha.2018.04.001

    Figure Lengend Snippet: Validation of mRho -specific CRISPRd-mediated gene deletion in vivo A , Schematic of experimental (AAVs-Cas9+GR) and control (AAVs-Cas9+SR) AAV2/8 vector pairs. B , Conventional gene replacement therapy vs CRISPRd plus gene replacement, compound therapy for a heterozygous loci. C , gRNA1 and gRNA2 sequences, their targeting sites on m Rho , and the corresponding sites on hRHO – showing the 12 and 4 mismatches, respectively. D , Representative data of in vitro SpCas9/gRNA cutting. In a cell-free assay, mRho vs hRHO DNA template was mixed with recombinant SpCas9 protein and a single gRNA: gRNA1, gRNA2, or control (scrambled gRNA). (n=3) E , Experimental scheme and timeline for subretinal injection of dual AAV vectors in right eyes of wild-type C57BL/6J mice (using a unique, posterior approach); respecting IACUC protocols, left eyes were uninjected. F , Representative data of Cas9-immunostaining in retinal flat mount. 14 days after Cas9+GR subretinal injection, the retinas were collected and stained for anti-Cas9 antibogy (n=3). Image was assembled from multiple pictures. G , Representative data of PCR analysis of retinal genomic DNA from AAVs-Cas9+GR-injected right eyes and uninjected, fellow (left) eyes. (n=4, two mice data are shown). H , Representative data of mRho gene ablation validated by Sanger sequencing of PCR amplicon from Fig. 2G.

    Article Snippet: To validate the targeting efficiency of our system, gRNA (25 ng/µl) was added to the reaction mixture alongside Cas9 protein (30 ng/µl, NEB) and template mRho DNA (20 ng/µl, 750 bp) covering both targeting sites of gRNA1 and gRNA2, and they were subsequently incubated at 37° C for 2 hr.

    Techniques: In Vivo, Plasmid Preparation, In Vitro, Cell-Free Assay, Recombinant, Injection, Mouse Assay, Immunostaining, Staining, Polymerase Chain Reaction, Sequencing, Amplification