taq polymerase binding Search Results


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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 5491 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs taq dna 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 Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8662 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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 33236 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 2726 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher taq dna polymerase pcr
    Model <t>DNA-encoded</t> library bead structures. Lysine, linker (gray), photocleavable linker, and Glu were sequentially coupled to 10-μm-diameter TentaGel resin. (A) Positive control inhibitor beads 1 display pepstatin A (red) coupled to Glu. The linker is labeled with 5(6)-carboxy TMR fluorophore (orange). Negative control beads 2 were prepared by acetylating the Glu α amine and linker amine (cyan). Bead sets were substoichiometrically functionalized with azido DNA headpiece (HDNA) via CuAAC. The DNA encoding sequence was installed by split-and-pool combinatorial enzymatic ligation. The BSB region contained 10 unique sequence modules at each of 4 positions (1—4, 10 4 possible BSBs). The encoding regions (ER, 5—10) contained either 729 (Glu-pepstatin A positive control beads, 1 ) or 1728 (N-acetyl-Glu negative control beads, 2 ) possible sequences. The DNA sequence terminates with ligation of a reverse primer module containing the reverse <t>PCR</t> primer binding site flanking an internal unique molecular identifier (UMI, green, inset). The UMI is a random 8-mer (65 536 possible sequences). (B) Micrographs of a model library containing positive and negative control beads 1 and 2 visualized in brightfield (left) and brightfield overlay with TMR fluorescence emission (λ ex = 550 nm; λ em = 570 nm; right) illustrate facile differentiation between the two bead types. Scale = 100 μm.
    Taq Dna Polymerase Pcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 127 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher accuprime taq dna polymerase
    Model <t>DNA-encoded</t> library bead structures. Lysine, linker (gray), photocleavable linker, and Glu were sequentially coupled to 10-μm-diameter TentaGel resin. (A) Positive control inhibitor beads 1 display pepstatin A (red) coupled to Glu. The linker is labeled with 5(6)-carboxy TMR fluorophore (orange). Negative control beads 2 were prepared by acetylating the Glu α amine and linker amine (cyan). Bead sets were substoichiometrically functionalized with azido DNA headpiece (HDNA) via CuAAC. The DNA encoding sequence was installed by split-and-pool combinatorial enzymatic ligation. The BSB region contained 10 unique sequence modules at each of 4 positions (1—4, 10 4 possible BSBs). The encoding regions (ER, 5—10) contained either 729 (Glu-pepstatin A positive control beads, 1 ) or 1728 (N-acetyl-Glu negative control beads, 2 ) possible sequences. The DNA sequence terminates with ligation of a reverse primer module containing the reverse <t>PCR</t> primer binding site flanking an internal unique molecular identifier (UMI, green, inset). The UMI is a random 8-mer (65 536 possible sequences). (B) Micrographs of a model library containing positive and negative control beads 1 and 2 visualized in brightfield (left) and brightfield overlay with TMR fluorescence emission (λ ex = 550 nm; λ em = 570 nm; right) illustrate facile differentiation between the two bead types. Scale = 100 μm.
    Accuprime Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1259 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa taq dna polymerase
    Model <t>DNA-encoded</t> library bead structures. Lysine, linker (gray), photocleavable linker, and Glu were sequentially coupled to 10-μm-diameter TentaGel resin. (A) Positive control inhibitor beads 1 display pepstatin A (red) coupled to Glu. The linker is labeled with 5(6)-carboxy TMR fluorophore (orange). Negative control beads 2 were prepared by acetylating the Glu α amine and linker amine (cyan). Bead sets were substoichiometrically functionalized with azido DNA headpiece (HDNA) via CuAAC. The DNA encoding sequence was installed by split-and-pool combinatorial enzymatic ligation. The BSB region contained 10 unique sequence modules at each of 4 positions (1—4, 10 4 possible BSBs). The encoding regions (ER, 5—10) contained either 729 (Glu-pepstatin A positive control beads, 1 ) or 1728 (N-acetyl-Glu negative control beads, 2 ) possible sequences. The DNA sequence terminates with ligation of a reverse primer module containing the reverse <t>PCR</t> primer binding site flanking an internal unique molecular identifier (UMI, green, inset). The UMI is a random 8-mer (65 536 possible sequences). (B) Micrographs of a model library containing positive and negative control beads 1 and 2 visualized in brightfield (left) and brightfield overlay with TMR fluorescence emission (λ ex = 550 nm; λ em = 570 nm; right) illustrate facile differentiation between the two bead types. Scale = 100 μm.
    Taq Dna Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 10265 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    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: 93/100, based on 4139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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: 99/100, based on 6706 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    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: 93/100, based on 343 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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: 99/100, based on 15477 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 18784 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa ex 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).
    Ex Taq Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 6171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    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: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    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: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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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    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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    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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    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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    Neq SSB-like dsDNA and mRNA binding properties. A Binding to 2.5 pmol of 100 bp PCR product. Lanes 1–6 contain 0, 10, 20, 40, 80 and 160 pmoles of Neq SSB-like, respectively. B Binding to 0.132 pmol of Escherichia coli genomic <t>DNA.</t> Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. C Binding to 0.2 pmol of pDONR201 plasmid DNA (4470 bp). Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. D Binding to 0.1 pmol of pDONR201 plasmid DNA + 0.05 pmol of linearized pDONR201 plasmid DNA. Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. E Control binding reaction with 0.2 pmol of pDONR201 plasmid DNA. Lanes 1–4 contain 0, 10, 20 and 40 pmoles of <t>Taq</t> SSB, respectively. F Binding to 980 ng of mRNA. Lanes 1–5 contain 0, 10, 20, 40, 80 pmoles of Neq SSB-like, respectively.
    Maxima Hot Start Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 481 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Affibody taq polymerase binding affibody molecule ztaq
    PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z <t>Taq:3638</t> -ST-CH 3 . Comparison B illustrates uptake of the targeting <t>Affibody</t> increasing as the tumors grow from time from inoculation
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    PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z <t>Taq:3638</t> -ST-CH 3 . Comparison B illustrates uptake of the targeting <t>Affibody</t> increasing as the tumors grow from time from inoculation
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    PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z <t>Taq:3638</t> -ST-CH 3 . Comparison B illustrates uptake of the targeting <t>Affibody</t> increasing as the tumors grow from time from inoculation
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    PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z <t>Taq:3638</t> -ST-CH 3 . Comparison B illustrates uptake of the targeting <t>Affibody</t> increasing as the tumors grow from time from inoculation
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    An overview of the experimental design and procedure. A shows the role of the selector probe and complementary vector. The target <t>DNA</t> 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 <t>PCR</t> 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.
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    An overview of the experimental design and procedure. A shows the role of the selector probe and complementary vector. The target <t>DNA</t> 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 <t>PCR</t> 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.
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    <t>Smad4</t> mutagenesis. (A) Schematic of mutations introduced into wild-type HA-tagged murine Smad4; DBD, DNA-binding domain; NES, nuclear export signal. Briefly, WT HA-Smad4 was used as a template for PCR reactions using Platinum High Fidelity <t>Taq</t> polymerase
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    <t>Smad4</t> mutagenesis. (A) Schematic of mutations introduced into wild-type HA-tagged murine Smad4; DBD, DNA-binding domain; NES, nuclear export signal. Briefly, WT HA-Smad4 was used as a template for PCR reactions using Platinum High Fidelity <t>Taq</t> polymerase
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    Image Search Results


    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

    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

    (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

    Model DNA-encoded library bead structures. Lysine, linker (gray), photocleavable linker, and Glu were sequentially coupled to 10-μm-diameter TentaGel resin. (A) Positive control inhibitor beads 1 display pepstatin A (red) coupled to Glu. The linker is labeled with 5(6)-carboxy TMR fluorophore (orange). Negative control beads 2 were prepared by acetylating the Glu α amine and linker amine (cyan). Bead sets were substoichiometrically functionalized with azido DNA headpiece (HDNA) via CuAAC. The DNA encoding sequence was installed by split-and-pool combinatorial enzymatic ligation. The BSB region contained 10 unique sequence modules at each of 4 positions (1—4, 10 4 possible BSBs). The encoding regions (ER, 5—10) contained either 729 (Glu-pepstatin A positive control beads, 1 ) or 1728 (N-acetyl-Glu negative control beads, 2 ) possible sequences. The DNA sequence terminates with ligation of a reverse primer module containing the reverse PCR primer binding site flanking an internal unique molecular identifier (UMI, green, inset). The UMI is a random 8-mer (65 536 possible sequences). (B) Micrographs of a model library containing positive and negative control beads 1 and 2 visualized in brightfield (left) and brightfield overlay with TMR fluorescence emission (λ ex = 550 nm; λ em = 570 nm; right) illustrate facile differentiation between the two bead types. Scale = 100 μm.

    Journal: ACS Combinatorial Science

    Article Title: An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening

    doi: 10.1021/acscombsci.6b00192

    Figure Lengend Snippet: Model DNA-encoded library bead structures. Lysine, linker (gray), photocleavable linker, and Glu were sequentially coupled to 10-μm-diameter TentaGel resin. (A) Positive control inhibitor beads 1 display pepstatin A (red) coupled to Glu. The linker is labeled with 5(6)-carboxy TMR fluorophore (orange). Negative control beads 2 were prepared by acetylating the Glu α amine and linker amine (cyan). Bead sets were substoichiometrically functionalized with azido DNA headpiece (HDNA) via CuAAC. The DNA encoding sequence was installed by split-and-pool combinatorial enzymatic ligation. The BSB region contained 10 unique sequence modules at each of 4 positions (1—4, 10 4 possible BSBs). The encoding regions (ER, 5—10) contained either 729 (Glu-pepstatin A positive control beads, 1 ) or 1728 (N-acetyl-Glu negative control beads, 2 ) possible sequences. The DNA sequence terminates with ligation of a reverse primer module containing the reverse PCR primer binding site flanking an internal unique molecular identifier (UMI, green, inset). The UMI is a random 8-mer (65 536 possible sequences). (B) Micrographs of a model library containing positive and negative control beads 1 and 2 visualized in brightfield (left) and brightfield overlay with TMR fluorescence emission (λ ex = 550 nm; λ em = 570 nm; right) illustrate facile differentiation between the two bead types. Scale = 100 μm.

    Article Snippet: PCR mixture contained Taq DNA polymerase (0.05 U/μL), oligonucleotide primer 5′-CCTCTCTATGGGCAGTCGGTGATGCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ (0.3 μM), SYBR Green (0.2×, Life Technologies), DMSO (6%), betaine (1 M), MgCl2 (1 mM), and PCR buffer (1×).

    Techniques: Positive Control, Labeling, Negative Control, Sequencing, Ligation, Polymerase Chain Reaction, Binding Assay, Fluorescence

    Identification of Jdp2 intron 2 mRNAs. ( A ) Ethidium bromide-stained agarose gel showing representative PCR products with linker-specific forward primer on 5′ RACE cDNA from tumor 1161 using different reverse primers in Jdp2 (oligos 96, 46 and 86, lanes 2, 3 and 4, respectively) and Actb exon 3 (lane 5); in lane 1 no cDNA template was added. ( B ) and ( C ) Schematic structure of the alternative Jdp2 exon 1e through 1k as found by 5′ RACE in tumor tissue (B) and normal tissue (C). Positions of exon 1-specific splice donor sites relative to exon 3 are given in base pairs. Putative start codons (M) in frame with the ORF of Jdp2 are indicated, while an asterisk indicates that no ORF is present in frame with Jdp2. ( D ) Protein structure of Jdp2 as generated from exon 1a through 1d, and predicted Jdp2 isoforms generated from exon 1e, 1f, 1i and 1j. The INHAT domain as well as the basic DNA binding domain (DBD) and the leucine zipper (ZIP) regions are indicated. Methionines are indicated (M) and the N-terminal peptides are shown for the isoforms.

    Journal: Nucleic Acids Research

    Article Title: Activation of alternative Jdp2 promoters and functional protein isoforms in T-cell lymphomas by retroviral insertion mutagenesis

    doi: 10.1093/nar/gkp469

    Figure Lengend Snippet: Identification of Jdp2 intron 2 mRNAs. ( A ) Ethidium bromide-stained agarose gel showing representative PCR products with linker-specific forward primer on 5′ RACE cDNA from tumor 1161 using different reverse primers in Jdp2 (oligos 96, 46 and 86, lanes 2, 3 and 4, respectively) and Actb exon 3 (lane 5); in lane 1 no cDNA template was added. ( B ) and ( C ) Schematic structure of the alternative Jdp2 exon 1e through 1k as found by 5′ RACE in tumor tissue (B) and normal tissue (C). Positions of exon 1-specific splice donor sites relative to exon 3 are given in base pairs. Putative start codons (M) in frame with the ORF of Jdp2 are indicated, while an asterisk indicates that no ORF is present in frame with Jdp2. ( D ) Protein structure of Jdp2 as generated from exon 1a through 1d, and predicted Jdp2 isoforms generated from exon 1e, 1f, 1i and 1j. The INHAT domain as well as the basic DNA binding domain (DBD) and the leucine zipper (ZIP) regions are indicated. Methionines are indicated (M) and the N-terminal peptides are shown for the isoforms.

    Article Snippet: To look for alternative splicing between published exons 1a through 1d, PCR reactions were done with forward primers Exon1a-154 (5′-tgggcaccgcgcctgcagcag-3′), Exon1b-148 (5′-ggaggagcgcgagcat-3′), Exon1c-70 (5′-gctctggctgggttaggagggaac-3′) or Exon1d-150 (5′-cagctgcctctctccatctt-3′) and reverse primer Intron2-87 (5′-tccttcgctcttcttcctcgtctagctt-3′) using 1/500 of the cDNA (corresponding to 4 ng of total RNA) per PCR reaction (Taq polymerase, Invitrogen).

    Techniques: Staining, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Generated, Binding Assay

    Jdp2 isoforms are differentially expressed in the normal tissue. ( A – C ) QRT-PCR was done in triplicates as described for Figure 5 on the indicated BALB/c mouse tissues to detect full length (A), exon 1e-3-4 (B) and exon 1f-3-4 (C) mRNA. Expression signal is shown as normalized to the geometric mean of Actb and Tbp (black bars) or normalized to total RNA (white bars) and is shown as fold difference to thymus. The figures are representative of two–three experiments. ( D ) Western blotting on 0.2 μM PVDF membranes using polyclonal anti-Jdp2 and, subsequently, anti-β-Actin and anti-H2B antibody on crude protein extracts from the same panel of BALB/c tissue. Open and closed arrows indicate the position of full length and isoform Jdp2.

    Journal: Nucleic Acids Research

    Article Title: Activation of alternative Jdp2 promoters and functional protein isoforms in T-cell lymphomas by retroviral insertion mutagenesis

    doi: 10.1093/nar/gkp469

    Figure Lengend Snippet: Jdp2 isoforms are differentially expressed in the normal tissue. ( A – C ) QRT-PCR was done in triplicates as described for Figure 5 on the indicated BALB/c mouse tissues to detect full length (A), exon 1e-3-4 (B) and exon 1f-3-4 (C) mRNA. Expression signal is shown as normalized to the geometric mean of Actb and Tbp (black bars) or normalized to total RNA (white bars) and is shown as fold difference to thymus. The figures are representative of two–three experiments. ( D ) Western blotting on 0.2 μM PVDF membranes using polyclonal anti-Jdp2 and, subsequently, anti-β-Actin and anti-H2B antibody on crude protein extracts from the same panel of BALB/c tissue. Open and closed arrows indicate the position of full length and isoform Jdp2.

    Article Snippet: To look for alternative splicing between published exons 1a through 1d, PCR reactions were done with forward primers Exon1a-154 (5′-tgggcaccgcgcctgcagcag-3′), Exon1b-148 (5′-ggaggagcgcgagcat-3′), Exon1c-70 (5′-gctctggctgggttaggagggaac-3′) or Exon1d-150 (5′-cagctgcctctctccatctt-3′) and reverse primer Intron2-87 (5′-tccttcgctcttcttcctcgtctagctt-3′) using 1/500 of the cDNA (corresponding to 4 ng of total RNA) per PCR reaction (Taq polymerase, Invitrogen).

    Techniques: Quantitative RT-PCR, Expressing, Western Blot

    Correlation of intragenic provirus insertion and appearance of Jdp2 intron 2 including transcripts. ( A ) Schematic representation of the localization of the Northern blot probe and QRT-PCR amplicons E2-E3, E2-E4, I2-E4, E1e-E4 and E1f-E4 for Jdp2 mRNA detection with exons shown as boxes and coding sequence in black. ( B and C ) Northern blotting on total RNA from thymus tumors from a subset of animals with integration in clusters D (B) and B (C) according to the retroviral tagging data. Control samples (Ctrl) are thymic tumors from retrovirus-infected animals of the same cohort in which no integrations were found by retroviral tagging. The distance between integration and the beginning of Jdp2 exon 3 for each tumor is shown above the lanes. Ethidium bromide staining of ribosomal bands 28S and 18S was used to evaluate even loading and RNA integrity. ( D and E ) QRT-PCR on a subset of D tumors and B tumors amplifying either Refseq Jdp2 mRNA (E2-E3) (D) or intron 2-including alternative mRNA (I2-E4) (E). The signal was normalized to Tbp and shown as fold difference to the average of control tumor samples (Ctrl).

    Journal: Nucleic Acids Research

    Article Title: Activation of alternative Jdp2 promoters and functional protein isoforms in T-cell lymphomas by retroviral insertion mutagenesis

    doi: 10.1093/nar/gkp469

    Figure Lengend Snippet: Correlation of intragenic provirus insertion and appearance of Jdp2 intron 2 including transcripts. ( A ) Schematic representation of the localization of the Northern blot probe and QRT-PCR amplicons E2-E3, E2-E4, I2-E4, E1e-E4 and E1f-E4 for Jdp2 mRNA detection with exons shown as boxes and coding sequence in black. ( B and C ) Northern blotting on total RNA from thymus tumors from a subset of animals with integration in clusters D (B) and B (C) according to the retroviral tagging data. Control samples (Ctrl) are thymic tumors from retrovirus-infected animals of the same cohort in which no integrations were found by retroviral tagging. The distance between integration and the beginning of Jdp2 exon 3 for each tumor is shown above the lanes. Ethidium bromide staining of ribosomal bands 28S and 18S was used to evaluate even loading and RNA integrity. ( D and E ) QRT-PCR on a subset of D tumors and B tumors amplifying either Refseq Jdp2 mRNA (E2-E3) (D) or intron 2-including alternative mRNA (I2-E4) (E). The signal was normalized to Tbp and shown as fold difference to the average of control tumor samples (Ctrl).

    Article Snippet: To look for alternative splicing between published exons 1a through 1d, PCR reactions were done with forward primers Exon1a-154 (5′-tgggcaccgcgcctgcagcag-3′), Exon1b-148 (5′-ggaggagcgcgagcat-3′), Exon1c-70 (5′-gctctggctgggttaggagggaac-3′) or Exon1d-150 (5′-cagctgcctctctccatctt-3′) and reverse primer Intron2-87 (5′-tccttcgctcttcttcctcgtctagctt-3′) using 1/500 of the cDNA (corresponding to 4 ng of total RNA) per PCR reaction (Taq polymerase, Invitrogen).

    Techniques: Northern Blot, Quantitative RT-PCR, Sequencing, Infection, Staining

    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

    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

    Neq SSB-like dsDNA and mRNA binding properties. A Binding to 2.5 pmol of 100 bp PCR product. Lanes 1–6 contain 0, 10, 20, 40, 80 and 160 pmoles of Neq SSB-like, respectively. B Binding to 0.132 pmol of Escherichia coli genomic DNA. Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. C Binding to 0.2 pmol of pDONR201 plasmid DNA (4470 bp). Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. D Binding to 0.1 pmol of pDONR201 plasmid DNA + 0.05 pmol of linearized pDONR201 plasmid DNA. Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. E Control binding reaction with 0.2 pmol of pDONR201 plasmid DNA. Lanes 1–4 contain 0, 10, 20 and 40 pmoles of Taq SSB, respectively. F Binding to 980 ng of mRNA. Lanes 1–5 contain 0, 10, 20, 40, 80 pmoles of Neq SSB-like, respectively.

    Journal: PLoS ONE

    Article Title: Characterization of a Single-Stranded DNA-Binding-Like Protein from Nanoarchaeum equitans—A Nucleic Acid Binding Protein with Broad Substrate Specificity

    doi: 10.1371/journal.pone.0126563

    Figure Lengend Snippet: Neq SSB-like dsDNA and mRNA binding properties. A Binding to 2.5 pmol of 100 bp PCR product. Lanes 1–6 contain 0, 10, 20, 40, 80 and 160 pmoles of Neq SSB-like, respectively. B Binding to 0.132 pmol of Escherichia coli genomic DNA. Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. C Binding to 0.2 pmol of pDONR201 plasmid DNA (4470 bp). Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. D Binding to 0.1 pmol of pDONR201 plasmid DNA + 0.05 pmol of linearized pDONR201 plasmid DNA. Lanes 1–7 contain 0, 10, 20, 40, 80, 160 and 320 pmoles of Neq SSB-like, respectively. E Control binding reaction with 0.2 pmol of pDONR201 plasmid DNA. Lanes 1–4 contain 0, 10, 20 and 40 pmoles of Taq SSB, respectively. F Binding to 980 ng of mRNA. Lanes 1–5 contain 0, 10, 20, 40, 80 pmoles of Neq SSB-like, respectively.

    Article Snippet: The PCR reaction solution consisted of 0.2 μg of Nanoarchaeum equitans Kin4-M genome DNA, 1 μl (10 μM) of each primer, 2.5 μl (10 mM) dNTPs, 2 μl (25 mM) MgCl2 , 2.5 μl of 10 x Hot Start Buffer (200 mM Tris-HCl pH 8.3, 200 mM KCl, 50 mM (NH4 )2 SO4 ), and 2 U of Maxima Hot Start Taq DNA Polymerase (Fermentas, Lithuania).

    Techniques: Binding Assay, Polymerase Chain Reaction, Plasmid Preparation

    PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z Taq:3638 -ST-CH 3 . Comparison B illustrates uptake of the targeting Affibody increasing as the tumors grow from time from inoculation

    Journal: EJNMMI Research

    Article Title: Preclinical PET imaging of EGFR levels: pairing a targeting with a non-targeting Sel-tagged Affibody-based tracer to estimate the specific uptake

    doi: 10.1186/s13550-016-0213-8

    Figure Lengend Snippet: PET images, summed 30–60 min, and TACs from a Balbc nu/nu mouse (prone) bearing tumors ( white arrows ): a one A431 xenograft (1 × 10 7 cells, 15 days) or b two A431 xenografts ( left : 1 × 10 7 cells, 28 days; right : 1 × 10 7 cells, 25 days). Comparison A shows a 7-times higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 compared to the non-targeting [methyl- 11 C]-Z Taq:3638 -ST-CH 3 . Comparison B illustrates uptake of the targeting Affibody increasing as the tumors grow from time from inoculation

    Article Snippet: DNA constructions and expression of Sel-tagged Affibody molecules The EGFR-binding Affibody molecule ZEGFR:2377 [ , ] and the irrelevant Taq polymerase-binding Affibody molecule ZTaq:3638 [ ] were fused with a C-terminal ST as previously described [ , ].

    Techniques: Positron Emission Tomography

    PET images, summed 30–60 min, and TACs from a SCID mouse (prone) bearing tumors ( white arrows ): a one FaDu xenograft (1 × 10 6 cells, 12 days) or b two FaDu xenografts ( left : (1 × 10 6 cells, 12 days); right : (0.5 × 10 6 cells, 12 days). Comparison A illustrates the higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 but with a ≈60 % non-targeting uptake of [methyl- 11 C]-Z Taq:3638 -ST-CH 3 . Comparison B illustrates the visually discernable heterogeneous uptake of the targeting Affibody in the larger tumor on the left. SUV mean is affected by whether the entire (1) or only central ROI (2) of the left tumor is used

    Journal: EJNMMI Research

    Article Title: Preclinical PET imaging of EGFR levels: pairing a targeting with a non-targeting Sel-tagged Affibody-based tracer to estimate the specific uptake

    doi: 10.1186/s13550-016-0213-8

    Figure Lengend Snippet: PET images, summed 30–60 min, and TACs from a SCID mouse (prone) bearing tumors ( white arrows ): a one FaDu xenograft (1 × 10 6 cells, 12 days) or b two FaDu xenografts ( left : (1 × 10 6 cells, 12 days); right : (0.5 × 10 6 cells, 12 days). Comparison A illustrates the higher uptake with targeting [methyl- 11 C]-Z EGFR:2377 -ST-CH 3 but with a ≈60 % non-targeting uptake of [methyl- 11 C]-Z Taq:3638 -ST-CH 3 . Comparison B illustrates the visually discernable heterogeneous uptake of the targeting Affibody in the larger tumor on the left. SUV mean is affected by whether the entire (1) or only central ROI (2) of the left tumor is used

    Article Snippet: DNA constructions and expression of Sel-tagged Affibody molecules The EGFR-binding Affibody molecule ZEGFR:2377 [ , ] and the irrelevant Taq polymerase-binding Affibody molecule ZTaq:3638 [ ] were fused with a C-terminal ST as previously described [ , ].

    Techniques: Positron Emission Tomography

    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

    Smad4 mutagenesis. (A) Schematic of mutations introduced into wild-type HA-tagged murine Smad4; DBD, DNA-binding domain; NES, nuclear export signal. Briefly, WT HA-Smad4 was used as a template for PCR reactions using Platinum High Fidelity Taq polymerase

    Journal: Journal of Cell Science

    Article Title: Postnatal ablation of osteoblast Smad4 enhances proliferative responses to canonical Wnt signaling through interactions with β-catenin

    doi: 10.1242/jcs.132233

    Figure Lengend Snippet: Smad4 mutagenesis. (A) Schematic of mutations introduced into wild-type HA-tagged murine Smad4; DBD, DNA-binding domain; NES, nuclear export signal. Briefly, WT HA-Smad4 was used as a template for PCR reactions using Platinum High Fidelity Taq polymerase

    Article Snippet: Briefly, WT HA-Smad4 was used as a template for PCR reaction using Platinum High Fidelity Taq polymerase (Invitrogen) and the following primers: (ΔDBD F) 5′-phospho-CATGTGATCTATGCCCGTC-3′ and (ΔDBD R) 5′-phospho-TCCATCCAATGTTCTCTGTAT-3′; (ΔNES F) 5′-phospho-AGTAATGCTCCAAGTATGTTA-3′ and (ΔNES R) 5′-phospho-GACAACCCGCTCATAGTG-3′; (ΔMH2 F) 5′-phospho-TGCTGGATTGAGATTCACCT-3′ and (ΔMH2 R) 5′-phospho-AGGATGATTGGAAATGGGAG-3′; (ΔMH1 F) 5′-phospho-TCACCTGGAATTGATCTCTC-3′ and (ΔMH1 R) 5′-phospho-GCTCAGACAGGCATCGTT-3′; (ΔLinker F) 5′-phospho-CATCCTGCTCCTGAGTAC-3′ and (ΔLinker R) 5′-phospho-CTGCAGTGTTAATCCTGA G-3′; (R100T F) 5′-phospho-ACGTGGCCTGATCTACACAAGAATG-3′ and (R100T R) 5′-phospho-CGTCCACAGACGGGCATAGATCAC-3′.

    Techniques: Mutagenesis, Binding Assay, Polymerase Chain Reaction

    Development of a TA cloning- and RE digestion-based method to examine genetic rearrangements of TALE repeat arrays. ( a ) Work flow chart. A fusion expression cassette bearing both left and right TALEN arms (TALEN L-R) is amplified with forward and reverse PCR primers (FP and RP) designed to amplify the full-length of tandem repeat arrays. The PCR products are inserted into a TA cloning vector. EcoRI digestion of individual clones followed by agarose gel electrophoresis is used to detect the size change of the TALE repeat arrays. The detection of a 1.76 kb DNA fragment indicates that the number of the tandem repeat units remains correct in the TALEN expression cassette. To further classify the genetic rearrangement events, the clones with no obvious size changes are subjected to DNA sequencing. ( b ) The use of an enzyme mixture allows PCR amplification of single band. Left: Platinum Taq DNA Polymerase High Fidelity. Right: Platinum Taq DNA Polymerase High Fidelity mixed with Elongase (1:2). ( c ) TA cloning and EcoRI digestion detect no change in the size of the TALE repeat arrays in plasmid vector samples. The band at 3 kb after EcoRI digestion is the linearized cloning vector, while the DNA band at 1.76 kb is the DNA insert bearing a TALE repeat array. “–“ and “+”: Without and with EcoRI. One kb DNA ladder was used as a molecular weight standard. ( d ) DNA sequencing analysis confirms no change in DNA recognition specificity by RVDs in left (top panel) and right (bottom panel) TALEN arms in the above plasmid samples. Amino acid sequence alignment was performed after translating DNA sequences into amino acids. The pair letters in the sequence represent a RVD (HD, NI, NG, and NN) for each TALE repeat unit in a TALEN arm.

    Journal: Molecular Therapy. Methods & Clinical Development

    Article Title: Genetic rearrangements of variable di-residue (RVD)-containing repeat arrays in a baculoviral TALEN system

    doi: 10.1038/mtm.2014.50

    Figure Lengend Snippet: Development of a TA cloning- and RE digestion-based method to examine genetic rearrangements of TALE repeat arrays. ( a ) Work flow chart. A fusion expression cassette bearing both left and right TALEN arms (TALEN L-R) is amplified with forward and reverse PCR primers (FP and RP) designed to amplify the full-length of tandem repeat arrays. The PCR products are inserted into a TA cloning vector. EcoRI digestion of individual clones followed by agarose gel electrophoresis is used to detect the size change of the TALE repeat arrays. The detection of a 1.76 kb DNA fragment indicates that the number of the tandem repeat units remains correct in the TALEN expression cassette. To further classify the genetic rearrangement events, the clones with no obvious size changes are subjected to DNA sequencing. ( b ) The use of an enzyme mixture allows PCR amplification of single band. Left: Platinum Taq DNA Polymerase High Fidelity. Right: Platinum Taq DNA Polymerase High Fidelity mixed with Elongase (1:2). ( c ) TA cloning and EcoRI digestion detect no change in the size of the TALE repeat arrays in plasmid vector samples. The band at 3 kb after EcoRI digestion is the linearized cloning vector, while the DNA band at 1.76 kb is the DNA insert bearing a TALE repeat array. “–“ and “+”: Without and with EcoRI. One kb DNA ladder was used as a molecular weight standard. ( d ) DNA sequencing analysis confirms no change in DNA recognition specificity by RVDs in left (top panel) and right (bottom panel) TALEN arms in the above plasmid samples. Amino acid sequence alignment was performed after translating DNA sequences into amino acids. The pair letters in the sequence represent a RVD (HD, NI, NG, and NN) for each TALE repeat unit in a TALEN arm.

    Article Snippet: An enzyme mixture containing Platinum Taq DNA Polymerase High Fidelity (Invitrogen) and Elongase (Invitrogen) was used to amplify the full length of TALE DNA binding domains.

    Techniques: TA Cloning, Flow Cytometry, Expressing, Amplification, Polymerase Chain Reaction, Plasmid Preparation, Clone Assay, Agarose Gel Electrophoresis, DNA Sequencing, Molecular Weight, Sequencing