taq dna polymerase Roche Search Results


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  • 99
    New England Biolabs taq polymerase
    Amplification results of three target genes using <t>Taq</t> polymerase. (A) Attempted amplification of the three <t>DNA</t> targets ( mpb83 , Mb012, and LMHCC_RS00060 ) sequences by Taq in the presence of DMSO using 3St, 2St and TD protocols; mpb83 and LMHCC_RS00060 successfully showed amplicons using the three protocols. Mb012 failed to show an amplicon. (B) Attempts of amplification of the three DNA target sequences in the absence of DMSO using 3St, 2St and TD protocols showing no amplicon. mpb83 with added enhancer in 3St PCR is used as a positive control. Mb0129 with no enhancer in 3St PCR is used as a negative control.
    Taq Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8780 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher powerup sybr green master mix
    Inhibition assays. Inhibition assays were set up as qPCR reactions using murine genomic DNA; a primer set specific to the mouse- HSD11β1 gene ( S1 Table ); and the <t>PowerUp</t> <t>SYBR</t> Green Master Mix. The reaction mixture was spiked with water (as a control) or extracted RNA or DNA from various kits. Shown are the Cq values for the control vs. reactions spiked with RNA (A) and DNA (B), in duplicate, with error bars representing standard deviations. (C) Fragment distribution of amplified RNA and DNA samples from select kits with corresponding positive controls (fresh PC-3 cells).
    Powerup Sybr Green Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9243 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher mgcl2
    Inhibition assays. Inhibition assays were set up as qPCR reactions using murine genomic DNA; a primer set specific to the mouse- HSD11β1 gene ( S1 Table ); and the <t>PowerUp</t> <t>SYBR</t> Green Master Mix. The reaction mixture was spiked with water (as a control) or extracted RNA or DNA from various kits. Shown are the Cq values for the control vs. reactions spiked with RNA (A) and DNA (B), in duplicate, with error bars representing standard deviations. (C) Fragment distribution of amplified RNA and DNA samples from select kits with corresponding positive controls (fresh PC-3 cells).
    Mgcl2, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 104037 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher superscript iii first strand synthesis system
    The smpB-ssrA Mutation Affects Levels of Yop Transcripts (A) Relative mRNA levels of the indicated Yops were determined by quantitative real-time PCR as described in Materials and Methods. Each value represents the average of <t>three</t> independent experiments. Standard deviation bars are indicated on each column. (B) Quantitative real-time PCR data were independently confirmed by Northern blot analysis of yopB mRNA. Total <t>RNA</t> samples were resolved on a 1% agarose-formaldehyde gel, transferred to nylon membranes, and probed with a biotin-labeled yopB specific probe. WT, wild type.
    Superscript Iii First Strand Synthesis System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 53767 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa sybr premix ex taq
    The smpB-ssrA Mutation Affects Levels of Yop Transcripts (A) Relative mRNA levels of the indicated Yops were determined by quantitative real-time PCR as described in Materials and Methods. Each value represents the average of <t>three</t> independent experiments. Standard deviation bars are indicated on each column. (B) Quantitative real-time PCR data were independently confirmed by Northern blot analysis of yopB mRNA. Total <t>RNA</t> samples were resolved on a 1% agarose-formaldehyde gel, transferred to nylon membranes, and probed with a biotin-labeled yopB specific probe. WT, wild type.
    Sybr Premix Ex Taq, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 49731 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher taq dna polymerase
    Use of exo+ and exo− <t>Taq</t> polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the <t>DNA</t> template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.
    Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 44901 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher superscript first strand synthesis system
    Use of exo+ and exo− <t>Taq</t> polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the <t>DNA</t> template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.
    Superscript First Strand Synthesis System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25477 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher platinum taq dna polymerase
    Characteristics and applications of the USER technique. ( a ) A comparison of the ability of <t>DNA</t> polymerases to amplify DNA fragments using uracil-free (-dU) and uracil-containing primers (+dU). Hm <t>Taq:</t> HotMaster™ Taq DNA Polymerase, Taq: Platinum ® Taq DNA Polymerase, Pwo: Pwo DNA Polymerase, Phusion: Phusion™ DNA Polymerase, PfuCx: PfuTurbo ® C x Hotstart DNA polymerase. ( b ) Functional expression of A.thaliana glucose transporter AtSTP1 in X.laevis oocytes from the Xenopus -specific USER compatible vector, pNB1u. H 2 O: control oocytes injected with water; STP1: oocytes injected with AtSTP1 cRNA. ( c ) Functional expression of the cyano fluorescence protein in leaf and root of A.thaliana from the CaMV 35S promoter using the USER compatible pCAMBIA230035Su vector (35S:CFP). Control: empty pCAMBIA230035Su.
    Platinum Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25090 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher topo ta cloning kit
    Characteristics and applications of the USER technique. ( a ) A comparison of the ability of <t>DNA</t> polymerases to amplify DNA fragments using uracil-free (-dU) and uracil-containing primers (+dU). Hm <t>Taq:</t> HotMaster™ Taq DNA Polymerase, Taq: Platinum ® Taq DNA Polymerase, Pwo: Pwo DNA Polymerase, Phusion: Phusion™ DNA Polymerase, PfuCx: PfuTurbo ® C x Hotstart DNA polymerase. ( b ) Functional expression of A.thaliana glucose transporter AtSTP1 in X.laevis oocytes from the Xenopus -specific USER compatible vector, pNB1u. H 2 O: control oocytes injected with water; STP1: oocytes injected with AtSTP1 cRNA. ( c ) Functional expression of the cyano fluorescence protein in leaf and root of A.thaliana from the CaMV 35S promoter using the USER compatible pCAMBIA230035Su vector (35S:CFP). Control: empty pCAMBIA230035Su.
    Topo Ta Cloning Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 53970 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher rt pcr
    Characteristics and applications of the USER technique. ( a ) A comparison of the ability of <t>DNA</t> polymerases to amplify DNA fragments using uracil-free (-dU) and uracil-containing primers (+dU). Hm <t>Taq:</t> HotMaster™ Taq DNA Polymerase, Taq: Platinum ® Taq DNA Polymerase, Pwo: Pwo DNA Polymerase, Phusion: Phusion™ DNA Polymerase, PfuCx: PfuTurbo ® C x Hotstart DNA polymerase. ( b ) Functional expression of A.thaliana glucose transporter AtSTP1 in X.laevis oocytes from the Xenopus -specific USER compatible vector, pNB1u. H 2 O: control oocytes injected with water; STP1: oocytes injected with AtSTP1 cRNA. ( c ) Functional expression of the cyano fluorescence protein in leaf and root of A.thaliana from the CaMV 35S promoter using the USER compatible pCAMBIA230035Su vector (35S:CFP). Control: empty pCAMBIA230035Su.
    Rt Pcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 46664 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Promega taq polymerase
    Variation of the homopolymeric cytosine (polyC) tract in the Cpn 1054 gene family in C. pneumoniae . In each panel the vertical axis indicates the number of individual clones with a specific length of polyC. The horizontal axis indicates the number of cytosines within an individual polyC tract. (A) Intrastrain variation of the length of the polyC tracts of Cpn 043, 1054,1055 within strain AR39. (B) Variation of the length of the polyC tract in Cpn 1055 within AR39, AR 458 and PS32. (C) The variation of the length of the poly C tract within Cpn 1055 of AR39 identified in recombinant clones using <t>Taq</t> and <t>Pwo</t> DNA polymerases.
    Taq Polymerase, supplied by Promega, used in various techniques. Bioz Stars score: 95/100, based on 16516 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore taq dna polymerase
    (A) The suggested effects of PtNPs on polymerase chain reaction (PCR) is based on binding of PtNPs to the <t>Taq</t> <t>DNA</t> polymerase, which leads to ceasing of PCR, (B) whereas CisPt primarily intercalates in DNA structure and stops PCR by this way. The gel electrophoregrams of PCR product mixture with particular concentration of (C) PtNPs (0.04–4 200 ng/mL of Pt) and (D) CisPt (0.04–42 000 ng/mL of Pt). (E) DNA denaturation temperature affected by the 0–200 μg/mL of Pt derivatives. Fluorescence of labelled nucleotides of DNA fragment after sequencing, which was influenced by (F) 0–20 μg/mL of PtNPs and (G) 0–0.33 μg/mL of CisPt. For all measurement n = 3.
    Taq Dna Polymerase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 3580 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher trizol reagent
    Specificity protein 1 ( SP 1) and metastasis‐associated lung adenocarcinoma transcript 1 (malat1) were remarkably increased in lung adenocarcinoma cancer tissues. A, Total <t>RNA</t> was extracted from human lung adenocarcinoma cancer tissues and adjacent normal tissues with <t>Trizol.</t> Expression of long non‐coding RNA (lnc RNA ) malat1 and sp1 was examined by qRT ‐ PCR and normalized to GAPDH . *** P
    Trizol Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 604295 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa primescript rt reagent kit
    Specificity protein 1 ( SP 1) and metastasis‐associated lung adenocarcinoma transcript 1 (malat1) were remarkably increased in lung adenocarcinoma cancer tissues. A, Total <t>RNA</t> was extracted from human lung adenocarcinoma cancer tissues and adjacent normal tissues with <t>Trizol.</t> Expression of long non‐coding RNA (lnc RNA ) malat1 and sp1 was examined by qRT ‐ PCR and normalized to GAPDH . *** P
    Primescript Rt Reagent Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 72258 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pcr buffer
    The 4% agarose gel analyses of <t>PCR</t> amplification of HIV-1 <t>DNA</t> 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .
    Pcr Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 28828 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher dntps
    The 4% agarose gel analyses of <t>PCR</t> amplification of HIV-1 <t>DNA</t> 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .
    Dntps, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 52680 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa primescript rt master mix
    The 4% agarose gel analyses of <t>PCR</t> amplification of HIV-1 <t>DNA</t> 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .
    Primescript Rt Master Mix, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 12317 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher platinum sybr green qpcr supermix udg
    The 4% agarose gel analyses of <t>PCR</t> amplification of HIV-1 <t>DNA</t> 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .
    Platinum Sybr Green Qpcr Supermix Udg, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10276 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen taq dna polymerase
    Sequences of contaminating bacterial <t>DNA</t> in three <t>Taq</t> polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.
    Taq Dna Polymerase, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 8578 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick pcr purification kit
    Sequences of contaminating bacterial <t>DNA</t> in three <t>Taq</t> polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.
    Qiaquick Pcr Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 137129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Amplification results of three target genes using Taq polymerase. (A) Attempted amplification of the three DNA targets ( mpb83 , Mb012, and LMHCC_RS00060 ) sequences by Taq in the presence of DMSO using 3St, 2St and TD protocols; mpb83 and LMHCC_RS00060 successfully showed amplicons using the three protocols. Mb012 failed to show an amplicon. (B) Attempts of amplification of the three DNA target sequences in the absence of DMSO using 3St, 2St and TD protocols showing no amplicon. mpb83 with added enhancer in 3St PCR is used as a positive control. Mb0129 with no enhancer in 3St PCR is used as a negative control.

    Journal: bioRxiv

    Article Title: PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis

    doi: 10.1101/2020.02.18.953695

    Figure Lengend Snippet: Amplification results of three target genes using Taq polymerase. (A) Attempted amplification of the three DNA targets ( mpb83 , Mb012, and LMHCC_RS00060 ) sequences by Taq in the presence of DMSO using 3St, 2St and TD protocols; mpb83 and LMHCC_RS00060 successfully showed amplicons using the three protocols. Mb012 failed to show an amplicon. (B) Attempts of amplification of the three DNA target sequences in the absence of DMSO using 3St, 2St and TD protocols showing no amplicon. mpb83 with added enhancer in 3St PCR is used as a positive control. Mb0129 with no enhancer in 3St PCR is used as a negative control.

    Article Snippet: Unsuccessful attempts were faced with Taq polymerase, OneTaq DNA Polymerase (NEB, M0480S), Platinum™ Pfx DNA Polymerase (Invitrogen, 11708039), Expand Long Template PCR System (an enzyme mix that contains thermostable Taq DNA Polymerase and a thermostable DNA polymerase with proofreading activity, Roche, 11681834001).

    Techniques: Amplification, Polymerase Chain Reaction, Positive Control, Negative Control

    Inhibition assays. Inhibition assays were set up as qPCR reactions using murine genomic DNA; a primer set specific to the mouse- HSD11β1 gene ( S1 Table ); and the PowerUp SYBR Green Master Mix. The reaction mixture was spiked with water (as a control) or extracted RNA or DNA from various kits. Shown are the Cq values for the control vs. reactions spiked with RNA (A) and DNA (B), in duplicate, with error bars representing standard deviations. (C) Fragment distribution of amplified RNA and DNA samples from select kits with corresponding positive controls (fresh PC-3 cells).

    Journal: PLoS ONE

    Article Title: Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores

    doi: 10.1371/journal.pone.0179732

    Figure Lengend Snippet: Inhibition assays. Inhibition assays were set up as qPCR reactions using murine genomic DNA; a primer set specific to the mouse- HSD11β1 gene ( S1 Table ); and the PowerUp SYBR Green Master Mix. The reaction mixture was spiked with water (as a control) or extracted RNA or DNA from various kits. Shown are the Cq values for the control vs. reactions spiked with RNA (A) and DNA (B), in duplicate, with error bars representing standard deviations. (C) Fragment distribution of amplified RNA and DNA samples from select kits with corresponding positive controls (fresh PC-3 cells).

    Article Snippet: Briefly, standard real-time PCR reactions were set up using murine genomic DNA derived from the Ep4 cell-line as the template; a primer set specific to the HSD11β1 gene ( ); and the PowerUp SYBR Green Master Mix (ThermoFisher Scientific, USA).

    Techniques: Inhibition, Real-time Polymerase Chain Reaction, SYBR Green Assay, Amplification

    Promoter methylation is involved in β4 repression during TGFβ-induced EMT. (A,B) Methylation status of the entire CpG island in the β4 promoter in the absence (A) or presence (B) of TGFβ for 11 days. Each circle represents a CpG dinucleotide from the first (1) to the last (66) CpG of randomly selected clones that were sequenced. White circles, unmethylated CpG; black circles, methylated CpG. (C) Immunoblot analysis of β4 expression in the presence of TGFβ alone or TGFβ plus 5-aza for the times indicated. (D) Analysis of β4 mRNA expression by SYBR Green qRT-PCR in the absence of TGFβ (UNT), with TGFβ alone (TGFβ) or with TGFβ and 5-aza (5aza) for 48 hours. Results are reported as the relative expression normalized to that of GAPDH. (E) Bisulfite conversion and methylation analysis of integrin α6 promoter after TGFβ treatment for 11 days as described in A.

    Journal: Journal of Cell Science

    Article Title: Regulation of ?4-integrin expression by epigenetic modifications in the mammary gland and during the epithelial-to-mesenchymal transition

    doi: 10.1242/jcs.049148

    Figure Lengend Snippet: Promoter methylation is involved in β4 repression during TGFβ-induced EMT. (A,B) Methylation status of the entire CpG island in the β4 promoter in the absence (A) or presence (B) of TGFβ for 11 days. Each circle represents a CpG dinucleotide from the first (1) to the last (66) CpG of randomly selected clones that were sequenced. White circles, unmethylated CpG; black circles, methylated CpG. (C) Immunoblot analysis of β4 expression in the presence of TGFβ alone or TGFβ plus 5-aza for the times indicated. (D) Analysis of β4 mRNA expression by SYBR Green qRT-PCR in the absence of TGFβ (UNT), with TGFβ alone (TGFβ) or with TGFβ and 5-aza (5aza) for 48 hours. Results are reported as the relative expression normalized to that of GAPDH. (E) Bisulfite conversion and methylation analysis of integrin α6 promoter after TGFβ treatment for 11 days as described in A.

    Article Snippet: To assess the expression of specific integrin subunits, E-cadherin, N-cadherin and Snai1 during the EMT by RT-PCR, total RNA (2 μg) was extracted by RNeasy (Qiagen) and reverse transcribed with SuperScriptIII Reverse Transcription system (Invitrogen), and then PCR amplified using either the HotStar Taq Master Mix system (Qiagen) or Power SYBR Green Master Mix (Applied Biosystems), as indicated in the figure legends.

    Techniques: Methylation, Clone Assay, Expressing, SYBR Green Assay, Quantitative RT-PCR

    TGFβ withdrawal reverses EMT and restores both E-cadherin and β4 integrin expression. (A) Phase-contrast photomicrographs of NMuMG cells either untreated (UNT), treated with TGFβ for 11 days (EMT) or treated with TGFβ for 11 days and subsequently in the absence of TGFβ for 13 days (MET). (B) Immunoblot analysis of E-cadherin (E-cad) and β4 integrin (β4) expression under conditions described in A. Tubulin or actin served as a loading control. (C) Analysis of β4 mRNA expression normalized to that of GAPDH in the cells described in A by SYBR Green qRT-PCR. (D) Extracts from the cells described in A were immunoprecipitated with either a nonspecific IgG or a monoclonal antibody against α6 (GOH3), and the immunoprecipitates were blotted with a polyclonal antibody against β4.

    Journal: Journal of Cell Science

    Article Title: Regulation of ?4-integrin expression by epigenetic modifications in the mammary gland and during the epithelial-to-mesenchymal transition

    doi: 10.1242/jcs.049148

    Figure Lengend Snippet: TGFβ withdrawal reverses EMT and restores both E-cadherin and β4 integrin expression. (A) Phase-contrast photomicrographs of NMuMG cells either untreated (UNT), treated with TGFβ for 11 days (EMT) or treated with TGFβ for 11 days and subsequently in the absence of TGFβ for 13 days (MET). (B) Immunoblot analysis of E-cadherin (E-cad) and β4 integrin (β4) expression under conditions described in A. Tubulin or actin served as a loading control. (C) Analysis of β4 mRNA expression normalized to that of GAPDH in the cells described in A by SYBR Green qRT-PCR. (D) Extracts from the cells described in A were immunoprecipitated with either a nonspecific IgG or a monoclonal antibody against α6 (GOH3), and the immunoprecipitates were blotted with a polyclonal antibody against β4.

    Article Snippet: To assess the expression of specific integrin subunits, E-cadherin, N-cadherin and Snai1 during the EMT by RT-PCR, total RNA (2 μg) was extracted by RNeasy (Qiagen) and reverse transcribed with SuperScriptIII Reverse Transcription system (Invitrogen), and then PCR amplified using either the HotStar Taq Master Mix system (Qiagen) or Power SYBR Green Master Mix (Applied Biosystems), as indicated in the figure legends.

    Techniques: Expressing, SYBR Green Assay, Quantitative RT-PCR, Immunoprecipitation

    The smpB-ssrA Mutation Affects Levels of Yop Transcripts (A) Relative mRNA levels of the indicated Yops were determined by quantitative real-time PCR as described in Materials and Methods. Each value represents the average of three independent experiments. Standard deviation bars are indicated on each column. (B) Quantitative real-time PCR data were independently confirmed by Northern blot analysis of yopB mRNA. Total RNA samples were resolved on a 1% agarose-formaldehyde gel, transferred to nylon membranes, and probed with a biotin-labeled yopB specific probe. WT, wild type.

    Journal: PLoS Pathogens

    Article Title: A Role for the SmpB-SsrA System in Yersinia pseudotuberculosis Pathogenesis

    doi: 10.1371/journal.ppat.0020006

    Figure Lengend Snippet: The smpB-ssrA Mutation Affects Levels of Yop Transcripts (A) Relative mRNA levels of the indicated Yops were determined by quantitative real-time PCR as described in Materials and Methods. Each value represents the average of three independent experiments. Standard deviation bars are indicated on each column. (B) Quantitative real-time PCR data were independently confirmed by Northern blot analysis of yopB mRNA. Total RNA samples were resolved on a 1% agarose-formaldehyde gel, transferred to nylon membranes, and probed with a biotin-labeled yopB specific probe. WT, wild type.

    Article Snippet: One microgram of RNA was used to synthesize cDNA using the SuperScript III first-strand synthesis system (Invitrogen).

    Techniques: Mutagenesis, Real-time Polymerase Chain Reaction, Standard Deviation, Northern Blot, Labeling

    Contribution of viral PB1-F2 protein to avian influenza promotion of apoptosis and pro-inflammation in PAM. Recombinant H5N1 (H5N1-w, H5N1-57 and H5N1-del) and mammalian influenza viruses, as indicated, were used to infect PAM at MOI of 1.0 for 6 h. ( A ) Both truncated (H5N1-57) and deleted (H5N1-del) PB1-F2 mutants showed significantly reduced activation of caspase 3/7 in PAM relative to the wild type virus (H5N1-w) but the levels were not down to the same basal levels as those from mammalian viruses. Fold changes were in relation to mock control. ( B , B’ ) The two PB1-F2 mutants conferred reduced TNF-α induction of RNA ( B ) and protein ( B’ ) in PAM compared with the wild type virus. ( C ) H5N1-del mutant also maintained elevated expression of IL-10 in PAM, unlike that of the wild type which suppressed 1L-10 expression. Hence PB1-F2 mutations in H5N1-w virus appeared to dampen apoptotic and pro-inflammatory responses. ( D – F ) The induction of IL-6 , IP-10 and IFN-β by the three recombinant H5N1 viruses, however, followed a less clear-cut pattern. ( E ) Induction of IL-6 and IP-10 was weakest with the truncated PB1-F2 mutant (H5N1-57), and was similarly high between the deleted mutant (H5N1-del) and wild type virus. H5N1-w (wild type) virus induced the strongest IFN-β response ( F ) but the induction of OAS1 ( G ) and Mx1 ( H ) did not follow the same trend. ( I ) PB1-F2 mutant viruses in PAM produced less progeny virus than the parental wild type. Data shown are the means of triplicate wells. Error bar = standard error of mean. *P

    Journal: Scientific Reports

    Article Title: Early apoptosis of porcine alveolar macrophages limits avian influenza virus replication and pro-inflammatory dysregulation

    doi: 10.1038/srep17999

    Figure Lengend Snippet: Contribution of viral PB1-F2 protein to avian influenza promotion of apoptosis and pro-inflammation in PAM. Recombinant H5N1 (H5N1-w, H5N1-57 and H5N1-del) and mammalian influenza viruses, as indicated, were used to infect PAM at MOI of 1.0 for 6 h. ( A ) Both truncated (H5N1-57) and deleted (H5N1-del) PB1-F2 mutants showed significantly reduced activation of caspase 3/7 in PAM relative to the wild type virus (H5N1-w) but the levels were not down to the same basal levels as those from mammalian viruses. Fold changes were in relation to mock control. ( B , B’ ) The two PB1-F2 mutants conferred reduced TNF-α induction of RNA ( B ) and protein ( B’ ) in PAM compared with the wild type virus. ( C ) H5N1-del mutant also maintained elevated expression of IL-10 in PAM, unlike that of the wild type which suppressed 1L-10 expression. Hence PB1-F2 mutations in H5N1-w virus appeared to dampen apoptotic and pro-inflammatory responses. ( D – F ) The induction of IL-6 , IP-10 and IFN-β by the three recombinant H5N1 viruses, however, followed a less clear-cut pattern. ( E ) Induction of IL-6 and IP-10 was weakest with the truncated PB1-F2 mutant (H5N1-57), and was similarly high between the deleted mutant (H5N1-del) and wild type virus. H5N1-w (wild type) virus induced the strongest IFN-β response ( F ) but the induction of OAS1 ( G ) and Mx1 ( H ) did not follow the same trend. ( I ) PB1-F2 mutant viruses in PAM produced less progeny virus than the parental wild type. Data shown are the means of triplicate wells. Error bar = standard error of mean. *P

    Article Snippet: RNA preparation and real-time RT-PCR Total RNA was extracted from cells using an RNeasy Plus Minikit (Qiagen). cDNA was synthesized from 1 μg of total RNA using Superscript III First Strand synthesis kit (Invitrogen).

    Techniques: Recombinant, Activation Assay, Mutagenesis, Expressing, Produced

    CH 4 accumulation and cell number dynamics during 48 h microcosm incubations . Three microcosms containing 20 L of sea water were amended as follows: B1: no amendment control; B2: amended with 100 μM glucose and 16 μM nitrate; B3: amended with 100 μM glucose, 16 μM nitrate, and 1 μM MPn. Microcosms were incubated for 48 h and subsampled at 12 h intervals for CH 4 measurements, flow cytometry, and community RNA. (A) CH 4 accumulation in amended surface seawater samples. Dissolved methane concentration increases above background only in the Glc+N+MPn microcosm starting 12 h post amendment. (B) Flow cytometric counts of SYBR-stained microbial cells from the control and treatments. (C) Green fluorescence and forward scatter plots of treatment samples. The cell number increase is largely due to the appearance of distinct high DNA-content microbial populations. The first of such populations (highlighted in red) appeared in both treatments at 24 h and represented ~30% of the cells (2.6 × 10 5 cells/ml) at that time point. The pattern remains similar between treatments at later time points with the exception of a unique large population that appears in the Glc+N+MPn microcosm 48 h after addition (circled in orange) that represents ~29% of the total cell counts at that time (~ 4 × 10 5 cells/ml). Two micrometer fluorescent beads are at the bottom right of each panel.

    Journal: Frontiers in Microbiology

    Article Title: Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria

    doi: 10.3389/fmicb.2013.00340

    Figure Lengend Snippet: CH 4 accumulation and cell number dynamics during 48 h microcosm incubations . Three microcosms containing 20 L of sea water were amended as follows: B1: no amendment control; B2: amended with 100 μM glucose and 16 μM nitrate; B3: amended with 100 μM glucose, 16 μM nitrate, and 1 μM MPn. Microcosms were incubated for 48 h and subsampled at 12 h intervals for CH 4 measurements, flow cytometry, and community RNA. (A) CH 4 accumulation in amended surface seawater samples. Dissolved methane concentration increases above background only in the Glc+N+MPn microcosm starting 12 h post amendment. (B) Flow cytometric counts of SYBR-stained microbial cells from the control and treatments. (C) Green fluorescence and forward scatter plots of treatment samples. The cell number increase is largely due to the appearance of distinct high DNA-content microbial populations. The first of such populations (highlighted in red) appeared in both treatments at 24 h and represented ~30% of the cells (2.6 × 10 5 cells/ml) at that time point. The pattern remains similar between treatments at later time points with the exception of a unique large population that appears in the Glc+N+MPn microcosm 48 h after addition (circled in orange) that represents ~29% of the total cell counts at that time (~ 4 × 10 5 cells/ml). Two micrometer fluorescent beads are at the bottom right of each panel.

    Article Snippet: In brief, roughly 10–20 ng of total RNA were amplified using MessageAmp II Bacteria kit (Ambion) and T7Bpm IdT16 VN, an oligo(dT) primer containing a promoter sequence for T7 RNA polymerase and a Bpm I recognition site. cDNA was synthesized from the amplified RNA using Superscript III (Invitrogen) and random hexamers for first-strand complementary DNA synthesis, and the SuperScript Double Stranded cDNA Synthesis kit (Invitrogen) for second-strand synthesis.

    Techniques: Incubation, Flow Cytometry, Cytometry, Concentration Assay, Gas Chromatography, Staining, Fluorescence

    Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.

    Journal: PLoS ONE

    Article Title: Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

    doi: 10.1371/journal.pone.0070942

    Figure Lengend Snippet: Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.

    Article Snippet: To test this hypothesis, we compared Eprobe 215-21 wt TO along with the shorter Eprobe 205-13 wt TO using a Taq DNA polymerase with a 5′–3′ exonuclease activity (Applied Biosystems AmpliTaq Gold) and a Taq DNA polymerase lacking the 5′–3′ exonuclease activity (Roche Genotyping Master).

    Techniques: Real-time Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Serial Dilution, Plasmid Preparation, Negative Control

    Characteristics and applications of the USER technique. ( a ) A comparison of the ability of DNA polymerases to amplify DNA fragments using uracil-free (-dU) and uracil-containing primers (+dU). Hm Taq: HotMaster™ Taq DNA Polymerase, Taq: Platinum ® Taq DNA Polymerase, Pwo: Pwo DNA Polymerase, Phusion: Phusion™ DNA Polymerase, PfuCx: PfuTurbo ® C x Hotstart DNA polymerase. ( b ) Functional expression of A.thaliana glucose transporter AtSTP1 in X.laevis oocytes from the Xenopus -specific USER compatible vector, pNB1u. H 2 O: control oocytes injected with water; STP1: oocytes injected with AtSTP1 cRNA. ( c ) Functional expression of the cyano fluorescence protein in leaf and root of A.thaliana from the CaMV 35S promoter using the USER compatible pCAMBIA230035Su vector (35S:CFP). Control: empty pCAMBIA230035Su.

    Journal: Nucleic Acids Research

    Article Title: Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments

    doi: 10.1093/nar/gkl635

    Figure Lengend Snippet: Characteristics and applications of the USER technique. ( a ) A comparison of the ability of DNA polymerases to amplify DNA fragments using uracil-free (-dU) and uracil-containing primers (+dU). Hm Taq: HotMaster™ Taq DNA Polymerase, Taq: Platinum ® Taq DNA Polymerase, Pwo: Pwo DNA Polymerase, Phusion: Phusion™ DNA Polymerase, PfuCx: PfuTurbo ® C x Hotstart DNA polymerase. ( b ) Functional expression of A.thaliana glucose transporter AtSTP1 in X.laevis oocytes from the Xenopus -specific USER compatible vector, pNB1u. H 2 O: control oocytes injected with water; STP1: oocytes injected with AtSTP1 cRNA. ( c ) Functional expression of the cyano fluorescence protein in leaf and root of A.thaliana from the CaMV 35S promoter using the USER compatible pCAMBIA230035Su vector (35S:CFP). Control: empty pCAMBIA230035Su.

    Article Snippet: PCR conditions PCR with the following DNA polymerases: HotMaster™ Taq DNA Polymerase (Eppendorf), Platinum® Taq DNA Polymerase (Invitrogen), Pwo DNA Polymerase (Roche), Phusion™ DNA Polymerase (Finnzymes), and PfuTurbo® Cx Hotstart DNA polymerase (PfuCx) (Stratagene) was performed according to manufacturers' instructions on pBAD-TOPO® (Invitrogen) containing the gene, At5g43440 (Accession no. AY143873).

    Techniques: Functional Assay, Expressing, Plasmid Preparation, Injection, Fluorescence

    Variation of the homopolymeric cytosine (polyC) tract in the Cpn 1054 gene family in C. pneumoniae . In each panel the vertical axis indicates the number of individual clones with a specific length of polyC. The horizontal axis indicates the number of cytosines within an individual polyC tract. (A) Intrastrain variation of the length of the polyC tracts of Cpn 043, 1054,1055 within strain AR39. (B) Variation of the length of the polyC tract in Cpn 1055 within AR39, AR 458 and PS32. (C) The variation of the length of the poly C tract within Cpn 1055 of AR39 identified in recombinant clones using Taq and Pwo DNA polymerases.

    Journal: BMC Microbiology

    Article Title: Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae

    doi: 10.1186/1471-2180-2-38

    Figure Lengend Snippet: Variation of the homopolymeric cytosine (polyC) tract in the Cpn 1054 gene family in C. pneumoniae . In each panel the vertical axis indicates the number of individual clones with a specific length of polyC. The horizontal axis indicates the number of cytosines within an individual polyC tract. (A) Intrastrain variation of the length of the polyC tracts of Cpn 043, 1054,1055 within strain AR39. (B) Variation of the length of the polyC tract in Cpn 1055 within AR39, AR 458 and PS32. (C) The variation of the length of the poly C tract within Cpn 1055 of AR39 identified in recombinant clones using Taq and Pwo DNA polymerases.

    Article Snippet: Both Taq polymerase (Promega, Madison, WI) and Pwo polymerase (Roche Diagnostic Corporation, Indianapolis, IN) were used in these studies.

    Techniques: Clone Assay, Recombinant

    (A) The suggested effects of PtNPs on polymerase chain reaction (PCR) is based on binding of PtNPs to the Taq DNA polymerase, which leads to ceasing of PCR, (B) whereas CisPt primarily intercalates in DNA structure and stops PCR by this way. The gel electrophoregrams of PCR product mixture with particular concentration of (C) PtNPs (0.04–4 200 ng/mL of Pt) and (D) CisPt (0.04–42 000 ng/mL of Pt). (E) DNA denaturation temperature affected by the 0–200 μg/mL of Pt derivatives. Fluorescence of labelled nucleotides of DNA fragment after sequencing, which was influenced by (F) 0–20 μg/mL of PtNPs and (G) 0–0.33 μg/mL of CisPt. For all measurement n = 3.

    Journal: PLoS ONE

    Article Title: Platinum nanoparticles induce damage to DNA and inhibit DNA replication

    doi: 10.1371/journal.pone.0180798

    Figure Lengend Snippet: (A) The suggested effects of PtNPs on polymerase chain reaction (PCR) is based on binding of PtNPs to the Taq DNA polymerase, which leads to ceasing of PCR, (B) whereas CisPt primarily intercalates in DNA structure and stops PCR by this way. The gel electrophoregrams of PCR product mixture with particular concentration of (C) PtNPs (0.04–4 200 ng/mL of Pt) and (D) CisPt (0.04–42 000 ng/mL of Pt). (E) DNA denaturation temperature affected by the 0–200 μg/mL of Pt derivatives. Fluorescence of labelled nucleotides of DNA fragment after sequencing, which was influenced by (F) 0–20 μg/mL of PtNPs and (G) 0–0.33 μg/mL of CisPt. For all measurement n = 3.

    Article Snippet: The volume of the reaction mixture was 25 μL, which was composed of 2.5 μL of 10× standard Taq reaction buffer, 0.5 μL of 1 mM deoxynucleotide solution, 0.5 μL of each of the primers (10 μM), 0.125 μL of Taq DNA polymerase; selected volume of water or drugs diluted with water (sterile, ACS purity, Sigma-Aldrich) and 0.5 μL of bacteriophage λ DNA.

    Techniques: Polymerase Chain Reaction, Binding Assay, Concentration Assay, Fluorescence, Sequencing

    Specificity protein 1 ( SP 1) and metastasis‐associated lung adenocarcinoma transcript 1 (malat1) were remarkably increased in lung adenocarcinoma cancer tissues. A, Total RNA was extracted from human lung adenocarcinoma cancer tissues and adjacent normal tissues with Trizol. Expression of long non‐coding RNA (lnc RNA ) malat1 and sp1 was examined by qRT ‐ PCR and normalized to GAPDH . *** P

    Journal: Cancer Science

    Article Title: Long non‐coding RNA metastasis‐associated lung adenocarcinoma transcript 1 promotes lung adenocarcinoma by directly interacting with specificity protein 1. Long non‐coding RNA metastasis‐associated lung adenocarcinoma transcript 1 promotes lung adenocarcinoma by directly interacting with specificity protein 1

    doi: 10.1111/cas.13587

    Figure Lengend Snippet: Specificity protein 1 ( SP 1) and metastasis‐associated lung adenocarcinoma transcript 1 (malat1) were remarkably increased in lung adenocarcinoma cancer tissues. A, Total RNA was extracted from human lung adenocarcinoma cancer tissues and adjacent normal tissues with Trizol. Expression of long non‐coding RNA (lnc RNA ) malat1 and sp1 was examined by qRT ‐ PCR and normalized to GAPDH . *** P

    Article Snippet: 2.3 RT‐PCR and RT‐qPCR analysis Total RNA was extracted from cells or tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.

    Techniques: Expressing, Quantitative RT-PCR

    The 4% agarose gel analyses of PCR amplification of HIV-1 DNA 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .

    Journal: Analytical chemistry

    Article Title: 3'-Protected 2'-Deoxynucleoside 5'-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR

    doi: 10.1021/ac8026977

    Figure Lengend Snippet: The 4% agarose gel analyses of PCR amplification of HIV-1 DNA 365 bp target at 10 copies. Each mixture contains standard dNTPs and/or 3’-THF dNTPs, 200 μM each. A, C, T, G and A, C, T, G stand for dATP, dCTP, dTTP, dGTP, and 3’-THF dATP, 3’-THF dCTP, 3’-THF dTTP, 3’-THF dGTP, respectively. Lane 1: 50 bp DNA ladder; lanes 2 and 5: empty; lane 3: standard ATCG (control 1, enzyme added as the last component); lane 4: standard ATCG (control 2, dNTP mixture was added as the last component); lane 6: ATC + G ; lane 7: AGT + C ; lane 8: GCT + A ; lane 9: ACG + T ; lane 10: AT + GC ; lane 11: CT + GA ; lane 12: GT + AC ; lane 13: AC + TG ; lane 14: AG + TC ; lane 15: GC + AT ; lane 16: T + GCA ; lane 17: G + TCA ; lane 18: C + GTA ; lane 19: A + GCT ; lane 20: TACG .

    Article Snippet: Taq DNA polymerase (recombinant), 10 × PCR buffer and 50 mM MgCl2 were purchased from Invitrogen.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification

    Anion exchange HPLC analyses of the 3’-THF dTTP after incubation in PCR buffer at different temperatures. Peak identification: (1) 3’-THF dTDP; (2) dTDP; (3) 3’-THF dTTP; (4) dTTP. Samples were analyzed by AX-HPLC on Dionex DNA Pac P-100 analytical column (4 × 250 mm) using a gradient of 1M LiCl in 25 mM Tris-base, pH 10.0 from 0 to 50% over 40 min, 1 mL/min.

    Journal: Analytical chemistry

    Article Title: 3'-Protected 2'-Deoxynucleoside 5'-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR

    doi: 10.1021/ac8026977

    Figure Lengend Snippet: Anion exchange HPLC analyses of the 3’-THF dTTP after incubation in PCR buffer at different temperatures. Peak identification: (1) 3’-THF dTDP; (2) dTDP; (3) 3’-THF dTTP; (4) dTTP. Samples were analyzed by AX-HPLC on Dionex DNA Pac P-100 analytical column (4 × 250 mm) using a gradient of 1M LiCl in 25 mM Tris-base, pH 10.0 from 0 to 50% over 40 min, 1 mL/min.

    Article Snippet: Taq DNA polymerase (recombinant), 10 × PCR buffer and 50 mM MgCl2 were purchased from Invitrogen.

    Techniques: High Performance Liquid Chromatography, Incubation, Polymerase Chain Reaction

    2% agarose gel analysis of PCR mixtures with Lambda phage DNA at 10,000 copies. Each lane contained dATP+dCTP+dGTP (200 μM each). To each reaction 3’-protected dTTP was added at 200 μM final concentration. Lane 1: control (no dTTP or 3’-protected dTTP); lane 2: 3’-Ac dTTP; lane 3: 3’-THP dTTP; lane 4: 3’-MTHP dTTP; lane 5: 3’-THF dTTP; lane 6: 3’-Pac dTTP; lanes 7 and 8: dTTP. Lanes 1-7: with Lambda DNA + HG DNA; lane 8: HG DNA only. At bottom: ratio of amplicon to off-target products estimated by integration of UV-bands.

    Journal: Analytical chemistry

    Article Title: 3'-Protected 2'-Deoxynucleoside 5'-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR

    doi: 10.1021/ac8026977

    Figure Lengend Snippet: 2% agarose gel analysis of PCR mixtures with Lambda phage DNA at 10,000 copies. Each lane contained dATP+dCTP+dGTP (200 μM each). To each reaction 3’-protected dTTP was added at 200 μM final concentration. Lane 1: control (no dTTP or 3’-protected dTTP); lane 2: 3’-Ac dTTP; lane 3: 3’-THP dTTP; lane 4: 3’-MTHP dTTP; lane 5: 3’-THF dTTP; lane 6: 3’-Pac dTTP; lanes 7 and 8: dTTP. Lanes 1-7: with Lambda DNA + HG DNA; lane 8: HG DNA only. At bottom: ratio of amplicon to off-target products estimated by integration of UV-bands.

    Article Snippet: Taq DNA polymerase (recombinant), 10 × PCR buffer and 50 mM MgCl2 were purchased from Invitrogen.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Concentration Assay, Lambda DNA Preparation, Amplification

    The 4% agarose gel analyses of PCR amplification of HIV-1 DNA template at 10 copies. Each lane contained dATP+dCTP+dGTP (200 μM each). To each reaction 3’-protected dTTP was added at 200 μM final concentration. Lanes 1 and 8: dTTP; lane 2: control (no dTTP or 3’-protected dTTP); lanes 3 and 9: 3’-Ac dTTP; lane 4: 3’-THP dTTP; lanes 5 and 10: 3’-MTHP dTTP; lanes 6 and 11: 3’-THF dTTP; lanes 7 and 12: 3’-Pac dTTP. Lanes 1-7: with HIV-1 DNA + HG DNA; lanes 8 -12: HG DNA only. At bottom: ratio of amplicon to primer dimers estimated by integration of UV-bands.

    Journal: Analytical chemistry

    Article Title: 3'-Protected 2'-Deoxynucleoside 5'-Triphosphates as a Novel Tool for Heat-Triggered Activation of PCR

    doi: 10.1021/ac8026977

    Figure Lengend Snippet: The 4% agarose gel analyses of PCR amplification of HIV-1 DNA template at 10 copies. Each lane contained dATP+dCTP+dGTP (200 μM each). To each reaction 3’-protected dTTP was added at 200 μM final concentration. Lanes 1 and 8: dTTP; lane 2: control (no dTTP or 3’-protected dTTP); lanes 3 and 9: 3’-Ac dTTP; lane 4: 3’-THP dTTP; lanes 5 and 10: 3’-MTHP dTTP; lanes 6 and 11: 3’-THF dTTP; lanes 7 and 12: 3’-Pac dTTP. Lanes 1-7: with HIV-1 DNA + HG DNA; lanes 8 -12: HG DNA only. At bottom: ratio of amplicon to primer dimers estimated by integration of UV-bands.

    Article Snippet: Taq DNA polymerase (recombinant), 10 × PCR buffer and 50 mM MgCl2 were purchased from Invitrogen.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Concentration Assay

    Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.

    Journal: PLoS ONE

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    doi: 10.1371/journal.pone.0007010

    Figure Lengend Snippet: Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.

    Article Snippet: Two polymerases not designed specifically for qPCR (no anti-Taq antibody) were also tested: Amplitaq DNA polymerase (ABI, CA; Roche lot # C00622); Qiagen Taq DNA polymerase (Qiagen, CA; Cat # 201205, lot # 127132149.

    Techniques: Sequencing, Polymerase Chain Reaction

    Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”

    Journal: PLoS ONE

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    doi: 10.1371/journal.pone.0007010

    Figure Lengend Snippet: Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”

    Article Snippet: Two polymerases not designed specifically for qPCR (no anti-Taq antibody) were also tested: Amplitaq DNA polymerase (ABI, CA; Roche lot # C00622); Qiagen Taq DNA polymerase (Qiagen, CA; Cat # 201205, lot # 127132149.

    Techniques: Concentration Assay

    Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.

    Journal: PLoS ONE

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    doi: 10.1371/journal.pone.0007010

    Figure Lengend Snippet: Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.

    Article Snippet: Two polymerases not designed specifically for qPCR (no anti-Taq antibody) were also tested: Amplitaq DNA polymerase (ABI, CA; Roche lot # C00622); Qiagen Taq DNA polymerase (Qiagen, CA; Cat # 201205, lot # 127132149.

    Techniques:

    Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.

    Journal: PLoS ONE

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    doi: 10.1371/journal.pone.0007010

    Figure Lengend Snippet: Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.

    Article Snippet: Two polymerases not designed specifically for qPCR (no anti-Taq antibody) were also tested: Amplitaq DNA polymerase (ABI, CA; Roche lot # C00622); Qiagen Taq DNA polymerase (Qiagen, CA; Cat # 201205, lot # 127132149.

    Techniques:

    Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.

    Journal: PLoS ONE

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    doi: 10.1371/journal.pone.0007010

    Figure Lengend Snippet: Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.

    Article Snippet: Two polymerases not designed specifically for qPCR (no anti-Taq antibody) were also tested: Amplitaq DNA polymerase (ABI, CA; Roche lot # C00622); Qiagen Taq DNA polymerase (Qiagen, CA; Cat # 201205, lot # 127132149.

    Techniques: Labeling