taq polymerase binding Search Results


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  • 99
    New England Biolabs taq dna polymerase
    Taq Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 12425 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq dna polymerase/product/New England Biolabs
    Average 99 stars, based on 12425 article reviews
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    taq dna polymerase - by Bioz Stars, 2020-07
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    99
    Thermo Fisher taq dna polymerase
    Effect of various ribonucleotide substitutions on iLock probe RNA detection assay with PBCV-1 ligase. Recognition of the invader structure and structure-specific endonucleolytic activity of <t>Taq</t> <t>DNA</t> polymerase can vary for different RNA substitutions. ( A ) Targeting let-7a with iLock probe. Ribonucleotides were introduced: at a terminal 3′ base (3); base in the 5′ arm, that an invading 3′ arm competes with for target binding (displaced base, 3D); base in the 5′ arm, that becomes a 5′-phosphorylated donor after iLock probe activation (3D5); in the flap sequence (3DF/DF). ( B ) iLocks were modified according to A , except nonchimeric iLock (DNA). The total number of RCPs for each probe is shown on y -axis. ( C ) PAGE of three selected iLock probes (DNA, 3, 3D) after activation and ligation, without (first three lanes) and with Taq DNA polymerase (last three lanes). Nonactivated iLock probe (79) is shortened upon activation by 14 nt (65) and ligated (seen as high molecular weight band at the top of the gel). (22) let-7a miRNA.
    Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 44913 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    taq dna polymerase - by Bioz Stars, 2020-07
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    99
    Qiagen taq polymerase
    TALEN-induced mutations in the Platynereis estrogen receptor . (A) Schematic of the er locus showing target exons 2 and 3 with TALEN target sites (yellow). Blue arrows, primer positions; red double-ended arrow, region of sequence deleted in E; green, <t>DNA-binding</t> domain. Primer combinations used for screening are shown above in B–E. (B–E) <t>PCR,</t> undigested PCR product; NI, non-injected. (B) Restriction digest screening of larvae injected with er Ex3_L2/R2 TALENs (mRNA concentration: 267 ng/µl/TALEN mRNA). Arrowhead indicates uncut PCR product following AflI II digestion (asterisk). (C) Mutation evidence at exon 2 site: uncut band adult worm +3 vs. fully digested product from mutation-negative (−) TALEN-injected worm. (D) Adult worms er+31 and er+37 with mutations at exon 3 site. (E) Deletions (red arrow) detected in larvae and adult worms resulting from simultaneous cleavage at exons 2 and 3 using 300 ng/µl/TALEN mRNA: deletion positive (+); deletion negative (−). Please note different primer pairs used for larval vs. adult samples. (F) Mutant sequences obtained from digest screening for exons 1, 2, and long deletions. Numbers in brackets indicate the sample or worm from which the sequence was obtained; all other sequences are from injected larvae shown in B. Length of mutations are indicated by ∆ with “−” indicating deletions and “+” indicating insertions. Restriction site is shown in boldface type; asterisks indicate frameshift mutations. Shading key: yellow, TALEN binding sites; gray, spacer; blue, nucleotides differing from wild type; green, inserted nucleotides.
    Taq Polymerase, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 6473 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 6473 article reviews
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    taq polymerase - by Bioz Stars, 2020-07
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    99
    Qiagen hotstar taq polymerase
    TALEN-induced mutations in the Platynereis estrogen receptor . (A) Schematic of the er locus showing target exons 2 and 3 with TALEN target sites (yellow). Blue arrows, primer positions; red double-ended arrow, region of sequence deleted in E; green, <t>DNA-binding</t> domain. Primer combinations used for screening are shown above in B–E. (B–E) <t>PCR,</t> undigested PCR product; NI, non-injected. (B) Restriction digest screening of larvae injected with er Ex3_L2/R2 TALENs (mRNA concentration: 267 ng/µl/TALEN mRNA). Arrowhead indicates uncut PCR product following AflI II digestion (asterisk). (C) Mutation evidence at exon 2 site: uncut band adult worm +3 vs. fully digested product from mutation-negative (−) TALEN-injected worm. (D) Adult worms er+31 and er+37 with mutations at exon 3 site. (E) Deletions (red arrow) detected in larvae and adult worms resulting from simultaneous cleavage at exons 2 and 3 using 300 ng/µl/TALEN mRNA: deletion positive (+); deletion negative (−). Please note different primer pairs used for larval vs. adult samples. (F) Mutant sequences obtained from digest screening for exons 1, 2, and long deletions. Numbers in brackets indicate the sample or worm from which the sequence was obtained; all other sequences are from injected larvae shown in B. Length of mutations are indicated by ∆ with “−” indicating deletions and “+” indicating insertions. Restriction site is shown in boldface type; asterisks indicate frameshift mutations. Shading key: yellow, TALEN binding sites; gray, spacer; blue, nucleotides differing from wild type; green, inserted nucleotides.
    Hotstar Taq Polymerase, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 3297 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 3297 article reviews
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    hotstar taq polymerase - by Bioz Stars, 2020-07
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    92
    PerkinElmer taq polymerase
    Identification of MalE-GadX binding sites in gadA and gadBC promoters. (A) Gel retardation assays of in vitro binding of the purified MalE-GadX protein to the promoter regions of gadA (P gadA , left) and gadBC (P gadB , right) genes. The <t>DNA</t> fragments were labeled with [α- 32 P]dATP by fill-in of 5′ protruding ends. In each binding reaction, 10 fmol of the DNA probe was incubated in a 10-μl volume with increasing amounts (0.5 to 10 pmol) of the MalE-GadX protein, under the conditions described in Materials and Methods. MalE-GadX-bound DNA fragments (forms I, II, and III) were separated from the unbound probe on a 5% polyacrylamide gel run in 0.5× TAE buffer. (B) DNase I footprinting assays. The 265-bp DNA fragments carrying the promoter regions of gadA (left) and gadBC (right) were incubated with the indicated amounts (picomoles) of MalE-GadX. Samples were processed as described in Materials and Methods using gadAfrw (left panel) and gadABrev (right panel) as the primers. Lanes G and A represent <t>Taq</t> I polymerase sequencing reactions using the same primers. The MalE-GadX-protected sites are indicated with vertical lines and labeled with roman numbers from I to IV. Arrows indicate DNase I-hypersensitive sites. (C) Sequence alignment of gadA and gadBC promoter regions showing the DNase I-protected sites on the coding (full line) and noncoding (dotted line) DNA strands. Sites are indicated above the corresponding sequence. The −35 and −10 hexamers for both gadA and gadBC are shown in bold type.
    Taq Polymerase, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 92/100, based on 4381 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 4381 article reviews
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    taq polymerase - by Bioz Stars, 2020-07
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    92
    Roche taq dna polymerase
    Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of <t>Taq</t> <t>DNA</t> polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.
    Taq Dna Polymerase, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 8839 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 8839 article reviews
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    taq dna polymerase - by Bioz Stars, 2020-07
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    92
    Fisher Scientific taq polymerase
    Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of <t>Taq</t> <t>DNA</t> polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.
    Taq Polymerase, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 92/100, based on 349 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Promega taq dna polymerase
    Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of <t>Taq</t> <t>DNA</t> polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.
    Taq Dna Polymerase, supplied by Promega, used in various techniques. Bioz Stars score: 95/100, based on 19543 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher accuprime taq dna polymerase
    Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of <t>Taq</t> <t>DNA</t> polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.
    Accuprime Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1644 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    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: 96/100, based on 3580 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher platinum taq dna polymerase
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
    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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    85
    Affibody taq polymerase binding affibody
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
    Taq Polymerase Binding Affibody, supplied by Affibody, used in various techniques. Bioz Stars score: 85/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 24 article reviews
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    93
    Meridian Life Science taq dna polymerase
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
    Taq Dna Polymerase, supplied by Meridian Life Science, used in various techniques. Bioz Stars score: 93/100, based on 2073 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq dna polymerase/product/Meridian Life Science
    Average 93 stars, based on 2073 article reviews
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    taq dna polymerase - by Bioz Stars, 2020-07
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    90
    Fisher Bioreagents standard taq polymerase
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
    Standard Taq Polymerase, supplied by Fisher Bioreagents, used in various techniques. Bioz Stars score: 90/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa takara taq polymerase
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
    Takara Taq Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 802 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/takara taq polymerase/product/TaKaRa
    Average 99 stars, based on 802 article reviews
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    takara taq polymerase - by Bioz Stars, 2020-07
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    99
    TaKaRa la taq dna polymerase
    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) <t>Taq</t> Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized <t>DNA</t> template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).
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    Effect of various ribonucleotide substitutions on iLock probe RNA detection assay with PBCV-1 ligase. Recognition of the invader structure and structure-specific endonucleolytic activity of Taq DNA polymerase can vary for different RNA substitutions. ( A ) Targeting let-7a with iLock probe. Ribonucleotides were introduced: at a terminal 3′ base (3); base in the 5′ arm, that an invading 3′ arm competes with for target binding (displaced base, 3D); base in the 5′ arm, that becomes a 5′-phosphorylated donor after iLock probe activation (3D5); in the flap sequence (3DF/DF). ( B ) iLocks were modified according to A , except nonchimeric iLock (DNA). The total number of RCPs for each probe is shown on y -axis. ( C ) PAGE of three selected iLock probes (DNA, 3, 3D) after activation and ligation, without (first three lanes) and with Taq DNA polymerase (last three lanes). Nonactivated iLock probe (79) is shortened upon activation by 14 nt (65) and ligated (seen as high molecular weight band at the top of the gel). (22) let-7a miRNA.

    Journal: RNA

    Article Title: Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection

    doi: 10.1261/rna.066753.118

    Figure Lengend Snippet: Effect of various ribonucleotide substitutions on iLock probe RNA detection assay with PBCV-1 ligase. Recognition of the invader structure and structure-specific endonucleolytic activity of Taq DNA polymerase can vary for different RNA substitutions. ( A ) Targeting let-7a with iLock probe. Ribonucleotides were introduced: at a terminal 3′ base (3); base in the 5′ arm, that an invading 3′ arm competes with for target binding (displaced base, 3D); base in the 5′ arm, that becomes a 5′-phosphorylated donor after iLock probe activation (3D5); in the flap sequence (3DF/DF). ( B ) iLocks were modified according to A , except nonchimeric iLock (DNA). The total number of RCPs for each probe is shown on y -axis. ( C ) PAGE of three selected iLock probes (DNA, 3, 3D) after activation and ligation, without (first three lanes) and with Taq DNA polymerase (last three lanes). Nonactivated iLock probe (79) is shortened upon activation by 14 nt (65) and ligated (seen as high molecular weight band at the top of the gel). (22) let-7a miRNA.

    Article Snippet: Duplicate reactions were incubated in a heated-lid thermocycler at 51°C for 30 min, in a 10 µL volume containing 0.1 U/µL of Taq DNA polymerase (ThermoFisher Scientific), 0.4 U/µL U RNase Inhibitor (Blirt) and 1× Taq polymerase buffer supplied with 8 mM MgCl2.

    Techniques: RNA Detection, Activity Assay, Binding Assay, Activation Assay, Sequencing, Modification, Polyacrylamide Gel Electrophoresis, Ligation, Molecular Weight

    An overview of the experimental design and procedure. A shows the role of the selector probe and complementary vector. The target DNA fragment containing the insertion/deletion is cut with restriction enzymes and ligated to a complementary probe to form a circle. The circular ligation product is again cut to form a linear fragment with universal primer binding site. B shows the MLGA reaction scheme. Genomic DNA is restriction digested; ligated to specific selector probes and these products are amplified by multiplex PCR using fluorescent labels. The fragments can then be separated by capillary electrophoresis and analyzed. C is a schematic representation of the process, from design to analysis.

    Journal: PLoS ONE

    Article Title: Automated Genotyping of Biobank Samples by Multiplex Amplification of Insertion/Deletion Polymorphisms

    doi: 10.1371/journal.pone.0052750

    Figure Lengend Snippet: An overview of the experimental design and procedure. A shows the role of the selector probe and complementary vector. The target DNA fragment containing the insertion/deletion is cut with restriction enzymes and ligated to a complementary probe to form a circle. The circular ligation product is again cut to form a linear fragment with universal primer binding site. B shows the MLGA reaction scheme. Genomic DNA is restriction digested; ligated to specific selector probes and these products are amplified by multiplex PCR using fluorescent labels. The fragments can then be separated by capillary electrophoresis and analyzed. C is a schematic representation of the process, from design to analysis.

    Article Snippet: The enzymes were subsequently inactivated at 80°C for 20 min. Circularization and ligation of restriction digested fragments was performed in a 20 µl reaction by adding 2.2 nM vector oligonucleotide, 0.1 nM of each Selector probe, 9.67 mM MgCl2 , 0.8 mM NAD, 4 U Ampligase (Epicentre) and 1× Taq DNA Polymerase PCR Buffer (Invitrogen) to the DNA.

    Techniques: Plasmid Preparation, Ligation, Binding Assay, Amplification, Multiplex Assay, Polymerase Chain Reaction, Electrophoresis

    TALEN-induced mutations in the Platynereis estrogen receptor . (A) Schematic of the er locus showing target exons 2 and 3 with TALEN target sites (yellow). Blue arrows, primer positions; red double-ended arrow, region of sequence deleted in E; green, DNA-binding domain. Primer combinations used for screening are shown above in B–E. (B–E) PCR, undigested PCR product; NI, non-injected. (B) Restriction digest screening of larvae injected with er Ex3_L2/R2 TALENs (mRNA concentration: 267 ng/µl/TALEN mRNA). Arrowhead indicates uncut PCR product following AflI II digestion (asterisk). (C) Mutation evidence at exon 2 site: uncut band adult worm +3 vs. fully digested product from mutation-negative (−) TALEN-injected worm. (D) Adult worms er+31 and er+37 with mutations at exon 3 site. (E) Deletions (red arrow) detected in larvae and adult worms resulting from simultaneous cleavage at exons 2 and 3 using 300 ng/µl/TALEN mRNA: deletion positive (+); deletion negative (−). Please note different primer pairs used for larval vs. adult samples. (F) Mutant sequences obtained from digest screening for exons 1, 2, and long deletions. Numbers in brackets indicate the sample or worm from which the sequence was obtained; all other sequences are from injected larvae shown in B. Length of mutations are indicated by ∆ with “−” indicating deletions and “+” indicating insertions. Restriction site is shown in boldface type; asterisks indicate frameshift mutations. Shading key: yellow, TALEN binding sites; gray, spacer; blue, nucleotides differing from wild type; green, inserted nucleotides.

    Journal: Genetics

    Article Title: TALENs Mediate Efficient and Heritable Mutation of Endogenous Genes in the Marine Annelid Platynereis dumerilii

    doi: 10.1534/genetics.113.161091

    Figure Lengend Snippet: TALEN-induced mutations in the Platynereis estrogen receptor . (A) Schematic of the er locus showing target exons 2 and 3 with TALEN target sites (yellow). Blue arrows, primer positions; red double-ended arrow, region of sequence deleted in E; green, DNA-binding domain. Primer combinations used for screening are shown above in B–E. (B–E) PCR, undigested PCR product; NI, non-injected. (B) Restriction digest screening of larvae injected with er Ex3_L2/R2 TALENs (mRNA concentration: 267 ng/µl/TALEN mRNA). Arrowhead indicates uncut PCR product following AflI II digestion (asterisk). (C) Mutation evidence at exon 2 site: uncut band adult worm +3 vs. fully digested product from mutation-negative (−) TALEN-injected worm. (D) Adult worms er+31 and er+37 with mutations at exon 3 site. (E) Deletions (red arrow) detected in larvae and adult worms resulting from simultaneous cleavage at exons 2 and 3 using 300 ng/µl/TALEN mRNA: deletion positive (+); deletion negative (−). Please note different primer pairs used for larval vs. adult samples. (F) Mutant sequences obtained from digest screening for exons 1, 2, and long deletions. Numbers in brackets indicate the sample or worm from which the sequence was obtained; all other sequences are from injected larvae shown in B. Length of mutations are indicated by ∆ with “−” indicating deletions and “+” indicating insertions. Restriction site is shown in boldface type; asterisks indicate frameshift mutations. Shading key: yellow, TALEN binding sites; gray, spacer; blue, nucleotides differing from wild type; green, inserted nucleotides.

    Article Snippet: PCR and restriction digest screening assays PCR reaction mixes contained DNA polymerase [either HotStar Taq Plus (Qiagen) or Phusion Polymerase (Fermentas)], 1.5–3 mM MgCl2 , 400 μM dNTPs, 200 μM of each primer, 1× reaction buffer (according to the enzyme used), 1–2 µl of DNA template in final volume of 25 or 50 µl.

    Techniques: Sequencing, Binding Assay, Polymerase Chain Reaction, Injection, TALENs, Concentration Assay, Mutagenesis

    Identification of MalE-GadX binding sites in gadA and gadBC promoters. (A) Gel retardation assays of in vitro binding of the purified MalE-GadX protein to the promoter regions of gadA (P gadA , left) and gadBC (P gadB , right) genes. The DNA fragments were labeled with [α- 32 P]dATP by fill-in of 5′ protruding ends. In each binding reaction, 10 fmol of the DNA probe was incubated in a 10-μl volume with increasing amounts (0.5 to 10 pmol) of the MalE-GadX protein, under the conditions described in Materials and Methods. MalE-GadX-bound DNA fragments (forms I, II, and III) were separated from the unbound probe on a 5% polyacrylamide gel run in 0.5× TAE buffer. (B) DNase I footprinting assays. The 265-bp DNA fragments carrying the promoter regions of gadA (left) and gadBC (right) were incubated with the indicated amounts (picomoles) of MalE-GadX. Samples were processed as described in Materials and Methods using gadAfrw (left panel) and gadABrev (right panel) as the primers. Lanes G and A represent Taq I polymerase sequencing reactions using the same primers. The MalE-GadX-protected sites are indicated with vertical lines and labeled with roman numbers from I to IV. Arrows indicate DNase I-hypersensitive sites. (C) Sequence alignment of gadA and gadBC promoter regions showing the DNase I-protected sites on the coding (full line) and noncoding (dotted line) DNA strands. Sites are indicated above the corresponding sequence. The −35 and −10 hexamers for both gadA and gadBC are shown in bold type.

    Journal: Journal of Bacteriology

    Article Title: Functional Characterization and Regulation of gadX, a Gene Encoding an AraC/XylS-Like Transcriptional Activator of the Escherichia coli Glutamic Acid Decarboxylase System †

    doi: 10.1128/JB.184.10.2603-2613.2002

    Figure Lengend Snippet: Identification of MalE-GadX binding sites in gadA and gadBC promoters. (A) Gel retardation assays of in vitro binding of the purified MalE-GadX protein to the promoter regions of gadA (P gadA , left) and gadBC (P gadB , right) genes. The DNA fragments were labeled with [α- 32 P]dATP by fill-in of 5′ protruding ends. In each binding reaction, 10 fmol of the DNA probe was incubated in a 10-μl volume with increasing amounts (0.5 to 10 pmol) of the MalE-GadX protein, under the conditions described in Materials and Methods. MalE-GadX-bound DNA fragments (forms I, II, and III) were separated from the unbound probe on a 5% polyacrylamide gel run in 0.5× TAE buffer. (B) DNase I footprinting assays. The 265-bp DNA fragments carrying the promoter regions of gadA (left) and gadBC (right) were incubated with the indicated amounts (picomoles) of MalE-GadX. Samples were processed as described in Materials and Methods using gadAfrw (left panel) and gadABrev (right panel) as the primers. Lanes G and A represent Taq I polymerase sequencing reactions using the same primers. The MalE-GadX-protected sites are indicated with vertical lines and labeled with roman numbers from I to IV. Arrows indicate DNase I-hypersensitive sites. (C) Sequence alignment of gadA and gadBC promoter regions showing the DNase I-protected sites on the coding (full line) and noncoding (dotted line) DNA strands. Sites are indicated above the corresponding sequence. The −35 and −10 hexamers for both gadA and gadBC are shown in bold type.

    Article Snippet: To generate the isopropyl-β- d -thiogalactopyranoside (IPTG)-inducible p malE :: gadX construct, the 838-bp DNA fragment encompassing the entire gadX gene was amplified by PCR using Taq polymerase (Perkin Elmer) from pBsAX with the primers 5′-GGCAT ATG CAATCACTACATGGGA-3′ and 5′-CCGGATCC CTA TAATCTTATTCCTTCCG-3′ (the gadX start and stop codons are underlined).

    Techniques: Binding Assay, Electrophoretic Mobility Shift Assay, In Vitro, Purification, Labeling, Incubation, Footprinting, Sequencing

    Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of Taq DNA polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.

    Journal: Applied and Environmental Microbiology

    Article Title: Multiplex PCR for Detection and Identification of Lactococcal Bacteriophages

    doi:

    Figure Lengend Snippet: Multiplex PCR competition assay for different combinations of phage species in the same sample. Phage Q7 represents the 936 species, Q30 represents the P335 species, and Q38 represents the c2 species. Reactions were carried out with 1.25 (A and C) and 2.50 (B and D) U of Taq DNA polymerase. Lanes (boldface, phage concentration of 10 8 PFU/ml; lightface, phage concentration of 10 7 PFU/ml): 1, 14, 15, and 28, 100-bp DNA ladder (Gibco/BRL, Burlington, Ontario, Canada); 2, 936 plus c2 ; 3, 936 plus P335 ; 4, c2 plus P335 ; 5, 936 plus c2 plus P335 ; 6, 936 plus c2; 7, 936 plus P335; 8, 936 plus P335 ; 9, c2 plus P335; 10, 936 plus P335 ; 11, c2 plus P335 ; 12, 936 plus c2 plus P335; 13, 936 plus c2 plus P335 ; 16, 936 plus c2 plus P335 ; 17, 936 plus c2 plus P335; 18, 936 plus c2 plus P335; 19, 936 plus c2 plus P335 ; 20, 936 plus c2 plus P335; 21, 936 ; 22, c2 ; 23, P335 ; 24, 10 pg of 936 DNA; 25, 10 pg of c2 DNA; 26, 10 pg of P335 DNA; 27, negative control.

    Article Snippet: PCRs were performed in 50 μl containing 125 mM deoxynucleoside triphosphate (Pharmacia Biotech, Baie d'Urfé, Québec, Canada), 5 mM concentrations of the six primers, 1.25 U of Taq DNA polymerase (Roche Diagnostic), Taq buffer (10 mM Tris-HCl, 1.5 mM magnesium chloride, 50 mM potassium chloride, pH 8.3), and 1 μl of the template.

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Competitive Binding Assay, Concentration Assay, Negative Control

    (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

    The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) Taq Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized DNA template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).

    Journal: PLoS ONE

    Article Title: Melt Analysis of Mismatch Amplification Mutation Assays (Melt-MAMA): A Functional Study of a Cost-Effective SNP Genotyping Assay in Bacterial Models

    doi: 10.1371/journal.pone.0032866

    Figure Lengend Snippet: The principle of the Melt-MAMA PCR reaction. Four different scenarios involving two alternate SNP allele templates (I II vs. III IV) and the interaction of Allele-Specific (AS) PCR amplification using MAMA primers. The annealing of AS-MAMA primers to their allelic templates is shown with one primer labeled with a 5′ GC-clamp (Ia) whereas the other is not (IVa). (Ib and IVb) Taq Polymerase extends from the 3′ matched AS-MAMA primer despite the antepenultimate destabilizing nucleotide. (Ic and IVc) The second PCR cycle replicates from a newly synthesized DNA template made in the previous step (Ib and IVb). With the synthesized DNA serving as the template, a perfect primer-template complex is formed eliminating the antepenultimate destabilizing mismatch observed in Iab and IVab. At PCR endpoint (Id and IVd), the amplicons generated from the 3′ matched AS-MAMA primer greatly outnumbers the amplicons generated by the mismatched AS-MAMA primer. Temperature-dissociation curve plots (Ie and IVe) of each AS-PCR product (Iabcd, IIab and IIIab, IVabcd), showing the fluorescent intensity and the rate of fluorescent intensity change (derivative) as a function of temperature. For each allelic template reaction (I II vs. III IV), the melt profiles (Ie and IVe) show only a single change in fluorescent intensity. This indicates the amplification of the perfect-matched amplicon and little to no amplification of the mismatched amplicon. The GC –clamp “labeled” amplicons dissociate at higher temperatures (∼3°C to 5°C) than non-GC amplicons. Nonproductive primer annealing is shown for an AS-MAMA primer (IIa) and a GC-clamp AS-MAMA primer (IIIa) binding with their respective corresponding mismatched templates. The lack of Watson-Crick base pairing at two 3′ positions (the antepenultimate nucleotide at the 3′ end) of the AS primer introduces instability at this region (IIb and IIIb). This prevents efficient extension by the polymerase, which retards or prevents product amplification (Ie and IVe).

    Article Snippet: The conventional PCR master mix comprised two forward AS primers and a common reverse primer starting at 0.2 µM (IDT, San Diego, CA), 1x PCR buffer without MgCl2 (Invitrogen, Carlsbad, CA), 2 mM MgCl2 (Invitrogen, Carlsbad, CA), 200 µM of each dNTPs (Invitrogen, Carlsbad, CA), 0.8 units of Platinum Taq DNA polymerase (Invitrogen, Carlsbad, CA), 1 µl of template at ∼1ng/µl, and molecular grade water to a final volume of 10 µl.

    Techniques: Polymerase Chain Reaction, Amplification, Labeling, Synthesized, Generated, Binding Assay