la taq polymerase  (TaKaRa)

 
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    Name:
    LA Taq polymerase
    Description:

    Catalog Number:
    LTP1360476
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    Score:
    85
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    Structured Review

    TaKaRa la taq polymerase
    PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the <t>Taq</t> DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; <t>Takara-bio).</t> PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    https://www.bioz.com/result/la taq polymerase/product/TaKaRa
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    Images

    1) Product Images from "Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products"

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gni111

    PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.
    Figure Legend Snippet: PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Techniques Used: Polymerase Chain Reaction, Genomic Sequencing, Sequencing, Staining

    PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.
    Figure Legend Snippet: PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Techniques Used: Polymerase Chain Reaction

    Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).
    Figure Legend Snippet: Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).

    Techniques Used: Polymerase Chain Reaction, Staining, Molecular Weight

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    Amplification:

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    Positive Control:

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    Synthesized:

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    TA Cloning:

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    Construct:

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    Real-time Polymerase Chain Reaction:

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    Nested PCR:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
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    Incubation:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: The DNA was digested overnight with Not I restriction enzyme and then denatured with 0.3 M NaOH. .. Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. The primer sequences are shown in Table S3.

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
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    Activity Assay:

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: The functional region and activity sites were identified with PROSITE ( http://prosite.expasy.org/ ). .. PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer.

    Transformation Assay:

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: Top 10 competent cells (Invitrogen, C404003) were transformed with the clones and were seeded on Xgal/IPTG containing LB/ampicillin plates. .. The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ).

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer. .. A touchdown PCR procedure was employed as follows: initial denaturation at 95°C for 5 min, followed by 10 amplification cycles of 35 s at 95°C, 35 s at 63°C with a decrease of 0.5°C per cycle and 2 min at 72°C, followed by 30 amplification cycles of 30 s at 95°C, 45 s at 59°C and 2 min at 72°C, and a final extension step at 72°C for 10 min.

    Hybridization:

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: Paragraph title: Subtractive Hybridization and TA-cloning ... The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ).

    Transfection:

    Article Title: Expression of OsCAS (Calcium-Sensing Receptor) in an Arabidopsis Mutant Increases Drought Tolerance
    Article Snippet: Paragraph title: Construction of the pcDNA3 -OsCAS vector and transfection into human embryonic kidney (HEK293) cells ... Specific primers were used in a polymerase chain reaction (PCR) to amplify the 1164-bp full-length cDNA of OsCAS by using LA-Taq DNA Polymerase (TaKaRa), according to the manufacturer’s protocols.

    Genomic Sequencing:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Paragraph title: Bisulfite Genomic Sequencing ... Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa).

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: The genome-specific primer pairs for TaSnRK2 .10-3-4AF/R , TaSnRK2 .10-3-4BF/R and TaSnRK2 .10-3-4DF/R ( ) were designed based on DNA sequence variations among the genomic sequences to identify homoeologs as well as specific alleles at individual loci. .. PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer.

    Generated:

    Article Title: MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity
    Article Snippet: Targeted regions were amplified in a PCR reaction using LA Taq® DNA Polymerase (TaKaRa RR002A). .. Targeted regions were amplified in a PCR reaction using LA Taq® DNA Polymerase (TaKaRa RR002A).

    Article Title: Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma
    Article Snippet: The MED12 forward (5′-TTCTCCTGCCCTACTCTCCC-3′) and reverse (5′-GGACCTGGATGGACATTGCA-3′) primers generated a 721 bp polymerase chain reaction (PCR) product; while the MED12L forward (5′-TGAAGCTTTTACATCCTTCTGCT-3′) and reverse (5′-GGGCAGGACGGTATACATGG-3′) primers generated a 296 bp PCR product. .. For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl.

    Imaging:

    Article Title: Expression of OsCAS (Calcium-Sensing Receptor) in an Arabidopsis Mutant Increases Drought Tolerance
    Article Snippet: Specific primers were used in a polymerase chain reaction (PCR) to amplify the 1164-bp full-length cDNA of OsCAS by using LA-Taq DNA Polymerase (TaKaRa), according to the manufacturer’s protocols. .. HEK293 cells were then transiently transfected with empty pcDNA3 vector, OsCAS, and Arabidopsis CAS.

    Sequencing:

    Article Title: A nonsense nucleotide substitution in the oculocutaneous albinism II gene underlies the original pink-eyed dilution allele (Oca2p) in mice
    Article Snippet: These primers were designed based on the reported sequence for the mouse Oca2 (NM_021879). .. PCR amplification was performed using TaKaRa LA Taq DNA polymerase in 25 µ l reactions according to the manufacturer’s instructions.

    Article Title: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs
    Article Snippet: Sequencing of TP53 was performed on exons 5, 6, 7, and 8 of the TP53 gene in all NSCLC patients included in this study. .. The fragment between exons 2 and 11 of the TP53 gene was amplified with the primers F2 and R11 (listed in Supplementary Table ), at an annealing temperature of 68 °C with the LA Taq® DNA Polymerase (Takara).

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. PCR products were subcloned into pGEM-T Easy vector (Promega Corp., Madison, WI) to analyze the methylation pattern of each clone.

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: Paragraph title: Cloning, sequence analysis and development of genome-specific primers ... PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer.

    Article Title: Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma
    Article Snippet: For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl. .. For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl.

    Article Title: Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
    Article Snippet: Paragraph title: DNA Extraction, Polymerase Chain Reaction (PCR) Amplification, and Sequencing ... To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan).

    Article Title: A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al3+ and UV-C radiation
    Article Snippet: Paragraph title: Isolation of MYB14 / 15 promoter fragments and sequence analysis ... Fragments were amplified using LA Taq DNA Polymerase (TaKaRa) following the manufacturer’s recommended reaction conditions.

    Injection:

    Article Title: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs
    Article Snippet: The fragment between exons 2 and 11 of the TP53 gene was amplified with the primers F2 and R11 (listed in Supplementary Table ), at an annealing temperature of 68 °C with the LA Taq® DNA Polymerase (Takara). .. Exons 5–8 were sequenced with the BigDye® Terminator v3.1 Cycle Sequencing kit (Life Technologies) at 56 °C annealing temperature, using primers 5F, 5R, 6F, 6R, 7F, 7R, 8F, and 8R listed in Supplementary Table .

    Binding Assay:

    Article Title: ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
    Article Snippet: To determine the binding of IRF9-related protein complexes to the promoter regions of ISGs, a ChIP assay was performed using a CST kit according to the manufacturer’s instructions. .. PCR analysis of the immunoprecipitates was performed by a standard protocol using LA-Taq polymerase (Takara, Shiga, Japan), 3 μL of the appropriate DNA sample, and the following primers: IFI27 (forward: 5′-CTTCTGGACTGCGCATGAGG-3′, reverse: 5′-CCACCCCGACTGAAGCACTG-3′) and Mx1 (forward: 5′-GGGACAGGCA & CAACAAAGCC-3′, reverse: 5′-GCCCTCTCTTCTTCCAGGCAAC-3′).

    DNA Sequencing:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. PCR products were subcloned into pGEM-T Easy vector (Promega Corp., Madison, WI) to analyze the methylation pattern of each clone.

    DNA Extraction:

    Article Title: Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
    Article Snippet: Paragraph title: DNA Extraction, Polymerase Chain Reaction (PCR) Amplification, and Sequencing ... To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan).

    Article Title: A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al3+ and UV-C radiation
    Article Snippet: Genomic DNA was extracted from the leaves of both grapevine genotypes using a new rapid plant genomic DNA extraction kit (BioTeke, Beijing, China) according to the manufacturer’s protocol. .. Fragments were amplified using LA Taq DNA Polymerase (TaKaRa) following the manufacturer’s recommended reaction conditions.

    Multiplex Assay:

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products
    Article Snippet: The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega). .. The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega).

    Methylation:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa).

    Mutagenesis:

    Article Title: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs
    Article Snippet: Paragraph title: Study of the TP53 gene mutation status in primary NSCLC samples ... The fragment between exons 2 and 11 of the TP53 gene was amplified with the primers F2 and R11 (listed in Supplementary Table ), at an annealing temperature of 68 °C with the LA Taq® DNA Polymerase (Takara).

    Isolation:

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: 5 × 107 PBMCs from single donor were suspended in 5 mL of serum free RPMI1640 medium (Invitrogen, 31800) and incubated with or without 0.01 μg/mL of rHE4 (Abcam, ab184603) for 6 h, and total RNA was isolated using TRIzol™ Reagent (Invitrogen, 15596018). .. The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ).

    Article Title: A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al3+ and UV-C radiation
    Article Snippet: Paragraph title: Isolation of MYB14 / 15 promoter fragments and sequence analysis ... Fragments were amplified using LA Taq DNA Polymerase (TaKaRa) following the manufacturer’s recommended reaction conditions.

    Functional Assay:

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: The functional region and activity sites were identified with PROSITE ( http://prosite.expasy.org/ ). .. PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer.

    Mouse Assay:

    Article Title: A nonsense nucleotide substitution in the oculocutaneous albinism II gene underlies the original pink-eyed dilution allele (Oca2p) in mice
    Article Snippet: Paragraph title: Reverse transcription-PCR analysis of Oca2 in the skin of mice ... PCR amplification was performed using TaKaRa LA Taq DNA polymerase in 25 µ l reactions according to the manufacturer’s instructions.

    Polymerase Chain Reaction:

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products
    Article Snippet: Paragraph title: PCR ... The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega).

    Article Title: Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples
    Article Snippet: This was used as a template for full-length EV amplification PCR, to test the efficiency of three commercially available long amplifying polymerases in comparison to KlenTaq LA (Clontech), which discontinued production in late 2015 . .. The following enzymes were tested: Takara LA Taq DNA Polymerase (Clontech), AccuTaq LA DNA Polymerase (Sigma) and PrimeSTAR GXL DNA Polymerase (Clontech).

    Article Title: Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples
    Article Snippet: Paragraph title: Optimisation of Near Full-Length Genome PCR ... In search of an alternative enzyme, three different long amplifying polymerases, including the Takara LA Taq DNA Polymerase (Clontech), AccuTaq LA DNA Polymerase (Sigma) and PrimeSTAR GXL DNA Polymerase (Clontech) were compared against KlenTaq for their efficiency in amplifying two American Type Culture Collection (ATCC) EV prototype strains, CVB3 (Nancy; JX312064.1) and CVB5 (Faulkner; AF114383.1) (Fig. ).

    Article Title: A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis
    Article Snippet: The presence of a CEL duplication was originally inferred by the DNA fragment analysis method of Torsvik et al., 2010 . .. Its allelic structure was worked out by PCR walking, using LA Taq polymerase (TaKaRa Bio) as described by the manufacturer. .. For mapping of the CEL-CELP recombination site, PCR products were verified by agarose gel electrophoresis, cloned into the pCR2.1-TOPO vector (Invitrogen), and analyzed by sequencing.

    Article Title: A nonsense nucleotide substitution in the oculocutaneous albinism II gene underlies the original pink-eyed dilution allele (Oca2p) in mice
    Article Snippet: The primer set 2 was designed to amplify a downstream region of the nonsense substitution. .. PCR amplification was performed using TaKaRa LA Taq DNA polymerase in 25 µ l reactions according to the manufacturer’s instructions. .. PCR reactions were carried out using the following conditions: initial denaturation at 94°C for 1 min, followed by 40 cycles at 94°C for 20 s, 55°C for 15 s, and 72°C for 1 min. A 10 µ l aliquot of each PCR product was subjected to agarose gel electrophoresis.

    Article Title: Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria
    Article Snippet: In the following step DNA isolation and Southern blot analysis were performed as des cribed above. .. Mouse mtDNA was amplified from 2 ng of total DNA with the following primers (P1:488-510, P2:4021-4040) using LA Taq polymerase (TAKARA, Japan) and following PCR conditions: 98 °C for 10 s, 58 °C for 30 s, and 60 °C for 10 min, 35 cycles. .. Northern blot transcript analysis was performed as previously described .

    Article Title: Sepsis induces long-term metabolic and mitochondrial muscle stem cell dysfunction amenable by mesenchymal stem cell therapy
    Article Snippet: The study of inflammatory cytokines was conducted on control, septic and septic mice injected with MSCs. .. Total genomic DNA samples were subjected to PCR amplification with LA Taq DNA polymerase (Takara) to amplify two large mtDNA fragments that together span the whole mtDNA genome. .. PCR products were subjected to 0.8% agarose electrophoresis gel.

    Article Title: DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families
    Article Snippet: var exon 1 sequences were amplified using primers listed in Supplementary Table S1c . .. PCR reactions were done using TaKaRa LA Taq™ polymerase (Fisher) following the manufacturer’s recommendations. .. Two-step PCR conditions were one cycle of 94°C for 1 min, followed by 33 cycles of 98°C for 10 s and an annealing/extension at 60°C for 5 min.

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa).

    Article Title: Genetic regulation of mitotic competence in G0 quiescent cells
    Article Snippet: Similarly, the 3′ deletion was checked with cp3, as an outside primer, and either CPC3 or CPC1, as inside primers (fig. S6B). .. LA Taq DNA polymerase (Takara Bio Inc.) was used for PCR following the manufacturer’s instructions. .. Nine strains failed to show amplification bands, confirming deletion, and were removed (fig. S6).

    Article Title: MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity
    Article Snippet: Cells were analyzed by flow cytometry. .. Targeted regions were amplified in a PCR reaction using LA Taq® DNA Polymerase (TaKaRa RR002A). .. PCR products were purified (Qiagen) and analyzed by Sanger sequencing.

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: The genome-specific primer pairs for TaSnRK2 .10-3-4AF/R , TaSnRK2 .10-3-4BF/R and TaSnRK2 .10-3-4DF/R ( ) were designed based on DNA sequence variations among the genomic sequences to identify homoeologs as well as specific alleles at individual loci. .. PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer. .. A touchdown PCR procedure was employed as follows: initial denaturation at 95°C for 5 min, followed by 10 amplification cycles of 35 s at 95°C, 35 s at 63°C with a decrease of 0.5°C per cycle and 2 min at 72°C, followed by 30 amplification cycles of 30 s at 95°C, 45 s at 59°C and 2 min at 72°C, and a final extension step at 72°C for 10 min.

    Article Title: Expression of OsCAS (Calcium-Sensing Receptor) in an Arabidopsis Mutant Increases Drought Tolerance
    Article Snippet: After RNase-free DNase I treatment, 1 μg of total RNA was used to synthesize cDNA using SuperScript III reverse transcriptase (TaKaRa Bio Inc., Dalian, China). .. Specific primers were used in a polymerase chain reaction (PCR) to amplify the 1164-bp full-length cDNA of OsCAS by using LA-Taq DNA Polymerase (TaKaRa), according to the manufacturer’s protocols. .. Primer pairs (1) and (2) used for PCR, designed using Primer Premier 5.0, are shown in .

    Article Title: Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma
    Article Snippet: The MED12 forward (5′-TTCTCCTGCCCTACTCTCCC-3′) and reverse (5′-GGACCTGGATGGACATTGCA-3′) primers generated a 721 bp polymerase chain reaction (PCR) product; while the MED12L forward (5′-TGAAGCTTTTACATCCTTCTGCT-3′) and reverse (5′-GGGCAGGACGGTATACATGG-3′) primers generated a 296 bp PCR product. .. For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl.

    Article Title: Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
    Article Snippet: Total genomic DNA of each individual was extracted using the CTAB method ( ). .. To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan). .. Additionally, two chloroplast fragments (trn L – trn F and trn V – trn M) and five nuclear genes (rpl9, cpi, ppi, phi , and nhx2 ) were amplified from each individual of S. lanceolata and S. caseolaris to assess the patterns of genetic diversity between and within the two species.

    Article Title: Three IgH isotypes, IgM, IgA and IgY are expressed in Gentoo penguin and zebra finch
    Article Snippet: Total RNA from Gentoo penguin whole blood and zebra finch spleen was reverse-transcribed using the primer NotI-d(T)18 ( 5’ AAC TGG AAG AAT TCG CGG CCG CAG GAA TTT TTT TTT TTT TTT TTT 3’ ). .. The 3’ RACE PCR parameters were as follows: 94°C for 5 min; followed by 40 cycles at 94°C for 30 s, 60°C for 30 s, 72°C for 90 s; and a final extension at 72°C for 5 min with LA-Taq DNA Polymerase (Takara, Dalian, Liaoning Province, China). .. The primers used were based on the conserved JH region as follows: Gentoo penguin JH GSP1 ( 5’ ATC GAC GCG TGG GGC AGC 3’ ) and GSP2 ( 5’ GCA GCG GGA CCT CCG TCA CCG TCT CCT C 3’ ); zebra finch JH GSP1 ( 5’ ATT GAC GCC TGG GGC AGC 3’ ) and GSP2 ( 5’ ACC GTC GTC ACC GTC AGC 3’ ).

    Article Title: A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al3+ and UV-C radiation
    Article Snippet: PCR primers were used to amplify the full length MYB14 and MYB15 genes respectively, using genomic DNA as a template. .. Fragments were amplified using LA Taq DNA Polymerase (TaKaRa) following the manufacturer’s recommended reaction conditions.

    Article Title: ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
    Article Snippet: As a positive control, 10 μL of rabbit polyclonal anti-Histone H3 was used; as a negative control, 1 μL of normal rabbit IgG was used (both antibodies were included with the CST kit). .. PCR analysis of the immunoprecipitates was performed by a standard protocol using LA-Taq polymerase (Takara, Shiga, Japan), 3 μL of the appropriate DNA sample, and the following primers: IFI27 (forward: 5′-CTTCTGGACTGCGCATGAGG-3′, reverse: 5′-CCACCCCGACTGAAGCACTG-3′) and Mx1 (forward: 5′-GGGACAGGCA & CAACAAAGCC-3′, reverse: 5′-GCCCTCTCTTCTTCCAGGCAAC-3′). .. The significance of differences between groups was determined by Student’s t test when the variances were equal.

    CRISPR:

    Article Title: MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity
    Article Snippet: Paragraph title: Genotyping of cells with CRISPR/Cas9-induced mutations ... Targeted regions were amplified in a PCR reaction using LA Taq® DNA Polymerase (TaKaRa RR002A).

    cDNA Library Assay:

    Article Title: Three IgH isotypes, IgM, IgA and IgY are expressed in Gentoo penguin and zebra finch
    Article Snippet: Paragraph title: 3’ RACE using JH-derived primers and cDNA library construction ... The 3’ RACE PCR parameters were as follows: 94°C for 5 min; followed by 40 cycles at 94°C for 30 s, 60°C for 30 s, 72°C for 90 s; and a final extension at 72°C for 5 min with LA-Taq DNA Polymerase (Takara, Dalian, Liaoning Province, China).

    Purification:

    Article Title: A nonsense nucleotide substitution in the oculocutaneous albinism II gene underlies the original pink-eyed dilution allele (Oca2p) in mice
    Article Snippet: PCR amplification was performed using TaKaRa LA Taq DNA polymerase in 25 µ l reactions according to the manufacturer’s instructions. .. PCR reactions were carried out using the following conditions: initial denaturation at 94°C for 1 min, followed by 40 cycles at 94°C for 20 s, 55°C for 15 s, and 72°C for 1 min. A 10 µ l aliquot of each PCR product was subjected to agarose gel electrophoresis.

    Article Title: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs
    Article Snippet: Tumor DNA from each patient was extracted with the QIAamp DNA Mini Kit (Qiagen) and purified with the QIAamp DNA Micro Kit (Qiagen). .. The fragment between exons 2 and 11 of the TP53 gene was amplified with the primers F2 and R11 (listed in Supplementary Table ), at an annealing temperature of 68 °C with the LA Taq® DNA Polymerase (Takara).

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: Next, mRNA was purified using Magnosphere™ UltraPure mRNA Purification Kit (Takara-Clontech, 9186). .. The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ).

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer. .. A touchdown PCR procedure was employed as follows: initial denaturation at 95°C for 5 min, followed by 10 amplification cycles of 35 s at 95°C, 35 s at 63°C with a decrease of 0.5°C per cycle and 2 min at 72°C, followed by 30 amplification cycles of 30 s at 95°C, 45 s at 59°C and 2 min at 72°C, and a final extension step at 72°C for 10 min.

    Article Title: Expression of OsCAS (Calcium-Sensing Receptor) in an Arabidopsis Mutant Increases Drought Tolerance
    Article Snippet: Specific primers were used in a polymerase chain reaction (PCR) to amplify the 1164-bp full-length cDNA of OsCAS by using LA-Taq DNA Polymerase (TaKaRa), according to the manufacturer’s protocols. .. Primer pairs (1) and (2) used for PCR, designed using Primer Premier 5.0, are shown in .

    Chromatin Immunoprecipitation:

    Article Title: ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
    Article Snippet: Paragraph title: ChIP assay ... PCR analysis of the immunoprecipitates was performed by a standard protocol using LA-Taq polymerase (Takara, Shiga, Japan), 3 μL of the appropriate DNA sample, and the following primers: IFI27 (forward: 5′-CTTCTGGACTGCGCATGAGG-3′, reverse: 5′-CCACCCCGACTGAAGCACTG-3′) and Mx1 (forward: 5′-GGGACAGGCA & CAACAAAGCC-3′, reverse: 5′-GCCCTCTCTTCTTCCAGGCAAC-3′).

    Plasmid Preparation:

    Article Title: Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter
    Article Snippet: Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa). .. Freshly prepared hydroquinone and sodium bisulfite were added to final concentrations of 0.5 mM and 3.1 M, respectively, and then the resulting mixture was incubated at 55 °C for 16 h. The CpG islands of target genes in the treated DNA were amplified by nested PCR using LA Taq DNA polymerase (TaKaRa).

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: PCR products of the differentially expressed genes were cloned into a pUC19-TA vector. .. The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ).

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer. .. A touchdown PCR procedure was employed as follows: initial denaturation at 95°C for 5 min, followed by 10 amplification cycles of 35 s at 95°C, 35 s at 63°C with a decrease of 0.5°C per cycle and 2 min at 72°C, followed by 30 amplification cycles of 30 s at 95°C, 45 s at 59°C and 2 min at 72°C, and a final extension step at 72°C for 10 min.

    Article Title: Expression of OsCAS (Calcium-Sensing Receptor) in an Arabidopsis Mutant Increases Drought Tolerance
    Article Snippet: Paragraph title: Construction of the pcDNA3 -OsCAS vector and transfection into human embryonic kidney (HEK293) cells ... Specific primers were used in a polymerase chain reaction (PCR) to amplify the 1164-bp full-length cDNA of OsCAS by using LA-Taq DNA Polymerase (TaKaRa), according to the manufacturer’s protocols.

    Article Title: Three IgH isotypes, IgM, IgA and IgY are expressed in Gentoo penguin and zebra finch
    Article Snippet: The 3’ RACE PCR parameters were as follows: 94°C for 5 min; followed by 40 cycles at 94°C for 30 s, 60°C for 30 s, 72°C for 90 s; and a final extension at 72°C for 5 min with LA-Taq DNA Polymerase (Takara, Dalian, Liaoning Province, China). .. The 3’ RACE PCR parameters were as follows: 94°C for 5 min; followed by 40 cycles at 94°C for 30 s, 60°C for 30 s, 72°C for 90 s; and a final extension at 72°C for 5 min with LA-Taq DNA Polymerase (Takara, Dalian, Liaoning Province, China).

    Software:

    Article Title: Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)
    Article Snippet: The primer pairs for TaSnRK2 .10-1F/R and TaSnRK2 .10-2F/R ( ) were designed based on the putative sequence using Primer Premier Version 5.0 software ( http://www.premierbiosoft.com/ ) and were used for isolating the cDNA and gDNA sequences of TaSnRK2 .10 . .. PCR assays were performed using LA Taq polymerase (TaKaRa Biotechnology Co., Ltd., Dalian, China) in a 20 μL reaction mixture containing 80 ng of gDNA or cDNA, 5 pM of TaSnRK2 .10-1F/R or TaSnRK2 .10-2F/R , 200 μM of each dNTP, 1 unit of LA Taq and 2 μL of 10× PCR buffer.

    Article Title: Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma
    Article Snippet: For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl. .. The PCR products were subsequently sequenced on an ABI Prism 3730 DNA sequencer (Applied Biosystems; Thermo Fisher Scientific, Inc.).

    Article Title: A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al3+ and UV-C radiation
    Article Snippet: Fragments were amplified using LA Taq DNA Polymerase (TaKaRa) following the manufacturer’s recommended reaction conditions. .. The PCR products were respectively linked to T-Vector pMD™19 to produce pMD- pVvMYB14 / 15 and pMD- pVlMYB14 / 15 , which were then sequenced.

    Negative Control:

    Article Title: ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
    Article Snippet: As a positive control, 10 μL of rabbit polyclonal anti-Histone H3 was used; as a negative control, 1 μL of normal rabbit IgG was used (both antibodies were included with the CST kit). .. PCR analysis of the immunoprecipitates was performed by a standard protocol using LA-Taq polymerase (Takara, Shiga, Japan), 3 μL of the appropriate DNA sample, and the following primers: IFI27 (forward: 5′-CTTCTGGACTGCGCATGAGG-3′, reverse: 5′-CCACCCCGACTGAAGCACTG-3′) and Mx1 (forward: 5′-GGGACAGGCA & CAACAAAGCC-3′, reverse: 5′-GCCCTCTCTTCTTCCAGGCAAC-3′).

    Selection:

    Article Title: Human Epididymis Secretory Protein 4 (HE4) Compromises Cytotoxic Mononuclear Cells via Inducing Dual Specificity Phosphatase 6
    Article Snippet: Top 10 competent cells (Invitrogen, C404003) were transformed with the clones and were seeded on Xgal/IPTG containing LB/ampicillin plates. .. The colonies of clones containing the inserts were selected by blue/white selection and were amplified by direct colony PCR using LA Taq® DNA polymerase (Takara-Clontech, RR002A) and M13 primers ( ). .. PCR products in the range of 200 to 3000 bp were then subjected to direct sequencing ( ).

    Agarose Gel Electrophoresis:

    Article Title: Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
    Article Snippet: To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan). .. To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan).

    Size-exclusion Chromatography:

    Article Title: Prevalence and clinical significance of mediator complex subunit 12 mutations in 362 Han Chinese samples with uterine leiomyoma
    Article Snippet: The MED12 forward (5′-TTCTCCTGCCCTACTCTCCC-3′) and reverse (5′-GGACCTGGATGGACATTGCA-3′) primers generated a 721 bp polymerase chain reaction (PCR) product; while the MED12L forward (5′-TGAAGCTTTTACATCCTTCTGCT-3′) and reverse (5′-GGGCAGGACGGTATACATGG-3′) primers generated a 296 bp PCR product. .. For each sample, 50 ng genomic DNA and 2 U LA Taq DNA polymerase (Takara Biotechnology Co., Ltd., Dalian, China) underwent 35 cycles of denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec and extension at 72°C for 20 sec, in a total volume of 25 µl. .. These reactions were performed in a Thermal Cycler 2720 (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA).

    Immunoprecipitation:

    Article Title: ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
    Article Snippet: Briefly, 1× 107 cells were processed according to the manufacturer’s protocol, and protein-DNA complexes were immunoprecipitated with 1 μg of anti-IRF9 antibodies. .. PCR analysis of the immunoprecipitates was performed by a standard protocol using LA-Taq polymerase (Takara, Shiga, Japan), 3 μL of the appropriate DNA sample, and the following primers: IFI27 (forward: 5′-CTTCTGGACTGCGCATGAGG-3′, reverse: 5′-CCACCCCGACTGAAGCACTG-3′) and Mx1 (forward: 5′-GGGACAGGCA & CAACAAAGCC-3′, reverse: 5′-GCCCTCTCTTCTTCCAGGCAAC-3′).

    Gel Extraction:

    Article Title: Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
    Article Snippet: To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan). .. To resolve the phylogenetic position of S. lanceolata within the genus Sonneratia , nrITS and one nuclear gene rpl9 were amplified from two randomly chosen individuals from each population of S. caseolaris and S. lanceolata by polymerase chain reaction (PCR) with LA Taq DNA polymerase (Takara Bio, Inc., Shiga, Japan).

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  • 99
    TaKaRa la taq polymerase
    PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the <t>Taq</t> DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; <t>Takara-bio).</t> PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.
    La Taq Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 798 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/la taq polymerase/product/TaKaRa
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    TaKaRa la pcr buffer ll
    Variation in 3DPCR <t>Taq</t> polymerase background mutation rate across the <t>PCR</t> block. ( A ) White spots correspond to PCR-positive samples for a 176 bp fragment of human TP53 . Those samples indicated by an asterisk were cloned and sequenced. ( B ) Mutation matrices for A10- and D8-derived sequences; transitions were invariably of the type N- > T,A; the number of bases sequenced is given by n. ( C ) Distribution of the number of CG- > TA transitions per clone. ( D ) A collection of the most highly mutated sequences. To compact the data, only variable sites are shown, their positions being identified above. Nucleotide positions should be read from top to bottom. To the right are the numbers of mutations per clone (mut) and the minimum number of recombination events (rec) to explain the complexity. Zones of recombination are highlighted in grey shading when possible. ( E ) 5′ Dinucleotide context for the G- > A and C- > T transitions, with the expected values shown as horizontal bars.
    La Pcr Buffer Ll, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa high fidelity pcr
    The loss of <t>MEF2A/D</t> does not alter basal synaptic transmission. ( A ) mEPSC frequency is unchanged upon deletion of Mef2a/d in hippocampal culture neurons using lentivirus expressing Cre recombinase (p > 0.05). The number of recordings is shown in the bar graph for the GFP and Cre infected neurons. Data is shown as mean ± SEM. ( B ) Lentivirus containing either GFP or Cre was infected at 4 DIV in hippocampal culture neurons and cells were harvested at 15–18 DIV, in parallel with the time of recordings. Quantitative <t>PCR</t> was used to confirm the deletion of Mef2a/d (*p
    High Fidelity Pcr, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Journal: Nucleic Acids Research

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products

    doi: 10.1093/nar/gni111

    Figure Lengend Snippet: PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Article Snippet: The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega).

    Techniques: Polymerase Chain Reaction, Genomic Sequencing, Sequencing, Staining

    PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Journal: Nucleic Acids Research

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products

    doi: 10.1093/nar/gni111

    Figure Lengend Snippet: PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

    Article Snippet: The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega).

    Techniques: Polymerase Chain Reaction

    Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).

    Journal: Nucleic Acids Research

    Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products

    doi: 10.1093/nar/gni111

    Figure Lengend Snippet: Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).

    Article Snippet: The same results were obtained by the other polymerase systems: LA Taq polymerase (Takara-bio), Tth polymerase (Applied-boisystems); Expand High Fidelity, Expand High FidelityPLUS and Expand Long Template polymerase (Roche-diagnostics); TITANIUM Taq polymerase (Becton-Dickinson-Clontech); and Taq polymerase (Promega).

    Techniques: Polymerase Chain Reaction, Staining, Molecular Weight

    ( A ) Gel electrophoresis of near full-length genome PCR products produced from four long amplifying DNA polymerases; KlenTaq LA (discontinued), AccuTaq LA, PrimeSTAR GXL and Takara LA Taq (separate gel) per manufacturer’s instructions for samples with high GC/secondary structures. M, HyperLadder 1 kb; 1, CVB3 Nancy; 2, CVB5 Faulkner; 3, H 2 O control. ( B ) Gel electrophoresis of near full-length genome PCR products produced from Takara LA Taq DNA polymerase. M, HyperLadder 1 kb; 1–4, known EV positives from NSW Health Pathology East virology diagnostic lab; 5, CVB3 Nancy; 6, H 2 O control. Full-length gels are presented in Supplementary Fig. 1 .

    Journal: Scientific Reports

    Article Title: Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

    doi: 10.1038/s41598-018-30322-y

    Figure Lengend Snippet: ( A ) Gel electrophoresis of near full-length genome PCR products produced from four long amplifying DNA polymerases; KlenTaq LA (discontinued), AccuTaq LA, PrimeSTAR GXL and Takara LA Taq (separate gel) per manufacturer’s instructions for samples with high GC/secondary structures. M, HyperLadder 1 kb; 1, CVB3 Nancy; 2, CVB5 Faulkner; 3, H 2 O control. ( B ) Gel electrophoresis of near full-length genome PCR products produced from Takara LA Taq DNA polymerase. M, HyperLadder 1 kb; 1–4, known EV positives from NSW Health Pathology East virology diagnostic lab; 5, CVB3 Nancy; 6, H 2 O control. Full-length gels are presented in Supplementary Fig. 1 .

    Article Snippet: The following enzymes were tested: Takara LA Taq DNA Polymerase (Clontech), AccuTaq LA DNA Polymerase (Sigma) and PrimeSTAR GXL DNA Polymerase (Clontech).

    Techniques: Nucleic Acid Electrophoresis, Polymerase Chain Reaction, Produced, Gas Chromatography, Diagnostic Assay

    Variation in 3DPCR Taq polymerase background mutation rate across the PCR block. ( A ) White spots correspond to PCR-positive samples for a 176 bp fragment of human TP53 . Those samples indicated by an asterisk were cloned and sequenced. ( B ) Mutation matrices for A10- and D8-derived sequences; transitions were invariably of the type N- > T,A; the number of bases sequenced is given by n. ( C ) Distribution of the number of CG- > TA transitions per clone. ( D ) A collection of the most highly mutated sequences. To compact the data, only variable sites are shown, their positions being identified above. Nucleotide positions should be read from top to bottom. To the right are the numbers of mutations per clone (mut) and the minimum number of recombination events (rec) to explain the complexity. Zones of recombination are highlighted in grey shading when possible. ( E ) 5′ Dinucleotide context for the G- > A and C- > T transitions, with the expected values shown as horizontal bars.

    Journal: British Journal of Cancer

    Article Title: Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics

    doi: 10.1038/bjc.2014.176

    Figure Lengend Snippet: Variation in 3DPCR Taq polymerase background mutation rate across the PCR block. ( A ) White spots correspond to PCR-positive samples for a 176 bp fragment of human TP53 . Those samples indicated by an asterisk were cloned and sequenced. ( B ) Mutation matrices for A10- and D8-derived sequences; transitions were invariably of the type N- > T,A; the number of bases sequenced is given by n. ( C ) Distribution of the number of CG- > TA transitions per clone. ( D ) A collection of the most highly mutated sequences. To compact the data, only variable sites are shown, their positions being identified above. Nucleotide positions should be read from top to bottom. To the right are the numbers of mutations per clone (mut) and the minimum number of recombination events (rec) to explain the complexity. Zones of recombination are highlighted in grey shading when possible. ( E ) 5′ Dinucleotide context for the G- > A and C- > T transitions, with the expected values shown as horizontal bars.

    Article Snippet: The buffer conditions were 2.5 mM MgCl2 , 1 × LA PCR Buffer ll (TaKaRa LA Taq ; TaKaRa, Otsu, Japan), 400 μ M each deoxynucleoside triphosphate (TaKaRa LA Taq ; TaKaRa), 100 μ M each primer and 1.5 U of Taq (EurobioTaq+ Eurobio AbCys).

    Techniques: Mutagenesis, Polymerase Chain Reaction, Blocking Assay, Clone Assay, Derivative Assay

    Variation in 3DPCR long-range Taq polymerase background mutation rate across the PCR block. ( A ) White spots correspond to PCR-positive samples for TP53 DNA. Those samples indicated by an asterisk were cloned and sequenced. ( B ) Mutation matrices for A6-, B3- and C2-derived sequences; transitions were invariably of the type N- > T,A; the number of bases sequenced is given by n. ( C ) 5′ Dinucleotide context for the G- > A and C- > T transitions, with the expected values shown as horizontal bars. ( D ) A collection of the most highly mutated sequences. To compact the data, only variable sites are shown, their positions being identified above. Nucleotide positions should be read from top to bottom. To the right are the numbers of mutations per clone (mut) and the minimum number of recombination events (rec) to explain the complexity. Zones of recombination are highlighted in grey shading when possible.

    Journal: British Journal of Cancer

    Article Title: Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics

    doi: 10.1038/bjc.2014.176

    Figure Lengend Snippet: Variation in 3DPCR long-range Taq polymerase background mutation rate across the PCR block. ( A ) White spots correspond to PCR-positive samples for TP53 DNA. Those samples indicated by an asterisk were cloned and sequenced. ( B ) Mutation matrices for A6-, B3- and C2-derived sequences; transitions were invariably of the type N- > T,A; the number of bases sequenced is given by n. ( C ) 5′ Dinucleotide context for the G- > A and C- > T transitions, with the expected values shown as horizontal bars. ( D ) A collection of the most highly mutated sequences. To compact the data, only variable sites are shown, their positions being identified above. Nucleotide positions should be read from top to bottom. To the right are the numbers of mutations per clone (mut) and the minimum number of recombination events (rec) to explain the complexity. Zones of recombination are highlighted in grey shading when possible.

    Article Snippet: The buffer conditions were 2.5 mM MgCl2 , 1 × LA PCR Buffer ll (TaKaRa LA Taq ; TaKaRa, Otsu, Japan), 400 μ M each deoxynucleoside triphosphate (TaKaRa LA Taq ; TaKaRa), 100 μ M each primer and 1.5 U of Taq (EurobioTaq+ Eurobio AbCys).

    Techniques: Mutagenesis, Polymerase Chain Reaction, Blocking Assay, Clone Assay, Derivative Assay

    The loss of MEF2A/D does not alter basal synaptic transmission. ( A ) mEPSC frequency is unchanged upon deletion of Mef2a/d in hippocampal culture neurons using lentivirus expressing Cre recombinase (p > 0.05). The number of recordings is shown in the bar graph for the GFP and Cre infected neurons. Data is shown as mean ± SEM. ( B ) Lentivirus containing either GFP or Cre was infected at 4 DIV in hippocampal culture neurons and cells were harvested at 15–18 DIV, in parallel with the time of recordings. Quantitative PCR was used to confirm the deletion of Mef2a/d (*p

    Journal: PLoS ONE

    Article Title: In Vivo Analysis of MEF2 Transcription Factors in Synapse Regulation and Neuronal Survival

    doi: 10.1371/journal.pone.0034863

    Figure Lengend Snippet: The loss of MEF2A/D does not alter basal synaptic transmission. ( A ) mEPSC frequency is unchanged upon deletion of Mef2a/d in hippocampal culture neurons using lentivirus expressing Cre recombinase (p > 0.05). The number of recordings is shown in the bar graph for the GFP and Cre infected neurons. Data is shown as mean ± SEM. ( B ) Lentivirus containing either GFP or Cre was infected at 4 DIV in hippocampal culture neurons and cells were harvested at 15–18 DIV, in parallel with the time of recordings. Quantitative PCR was used to confirm the deletion of Mef2a/d (*p

    Article Snippet: Genomic regions of the Mef2a locus were isolated from 129SvEv genomic DNA by high-fidelity PCR (Takara LA taq PCR system) and cloned into a pGKneoF2L2DTA vector, which contains a neomycin resistance gene, flanked by FRT and loxP sites, and a diphtheria toxin gene cassette.

    Techniques: Transmission Assay, Expressing, Infection, Real-time Polymerase Chain Reaction

    Mef2a KO mice show normal behavior. ( A ) Left, PCR genotyping to distinguish different Mef2a alleles. Right, the bar graph shows expression levels of Mef2 isoforms in the hippocampus of 4 week old animals (n=3/genotype), detected by quantitative PCR. The fold change in RNA was calculated using the comparative Ct method, normalizing to GAPDH as a control. ( B ) Nissl staining of brain cross-sections from littermate control (CTL) and Mef2a KO mice at 2 months of age. Brain-specific deletion of MEF2A was achieved by crossing MEF2A loxP/loxP mice with mice harboring a transgene for hGFAP-Cre. ( C ) Mef2a KO (KO) mice show no significant differences in locomotor activity compared to littermate CTL mice as assessed by consecutive beam breaks over a two-hour period, although the number of beam breaks significantly decreased over time (F 23,184 =41.84, P

    Journal: PLoS ONE

    Article Title: In Vivo Analysis of MEF2 Transcription Factors in Synapse Regulation and Neuronal Survival

    doi: 10.1371/journal.pone.0034863

    Figure Lengend Snippet: Mef2a KO mice show normal behavior. ( A ) Left, PCR genotyping to distinguish different Mef2a alleles. Right, the bar graph shows expression levels of Mef2 isoforms in the hippocampus of 4 week old animals (n=3/genotype), detected by quantitative PCR. The fold change in RNA was calculated using the comparative Ct method, normalizing to GAPDH as a control. ( B ) Nissl staining of brain cross-sections from littermate control (CTL) and Mef2a KO mice at 2 months of age. Brain-specific deletion of MEF2A was achieved by crossing MEF2A loxP/loxP mice with mice harboring a transgene for hGFAP-Cre. ( C ) Mef2a KO (KO) mice show no significant differences in locomotor activity compared to littermate CTL mice as assessed by consecutive beam breaks over a two-hour period, although the number of beam breaks significantly decreased over time (F 23,184 =41.84, P

    Article Snippet: Genomic regions of the Mef2a locus were isolated from 129SvEv genomic DNA by high-fidelity PCR (Takara LA taq PCR system) and cloned into a pGKneoF2L2DTA vector, which contains a neomycin resistance gene, flanked by FRT and loxP sites, and a diphtheria toxin gene cassette.

    Techniques: Gene Knockout, Mouse Assay, Polymerase Chain Reaction, Expressing, Real-time Polymerase Chain Reaction, Staining, CTL Assay, Activity Assay

    Brain-specific deletion of Mef2a and Mef2d causes impairments in motor coordination, as well as presynaptic release probability. ( A ) Detection of Mef2a and Mef2d transcripts by in situ hybridization in littermate CTL and Mef2a/d DKO (DKO) mice. Arrow indicates hippocampus. ( B ) Expression level of MEF2 transcription factors in the hippocampus of Mef2a/d DKO mice as detected by quantitative RT-PCR. RNA was isolated from the hippocampus of 4 week old animals (n=3/genotype), and then expression determined by quantitative PCR. The fold change in RNA was calculated using the comparative Ct method, normalizing to GAPDH as a control. ( C ) Mef2a/d DKO mice exhibit impaired motor coordination as assessed by falling off the accelerating rotarod faster than littermate CTLs (F 1,7 =27.64, P

    Journal: PLoS ONE

    Article Title: In Vivo Analysis of MEF2 Transcription Factors in Synapse Regulation and Neuronal Survival

    doi: 10.1371/journal.pone.0034863

    Figure Lengend Snippet: Brain-specific deletion of Mef2a and Mef2d causes impairments in motor coordination, as well as presynaptic release probability. ( A ) Detection of Mef2a and Mef2d transcripts by in situ hybridization in littermate CTL and Mef2a/d DKO (DKO) mice. Arrow indicates hippocampus. ( B ) Expression level of MEF2 transcription factors in the hippocampus of Mef2a/d DKO mice as detected by quantitative RT-PCR. RNA was isolated from the hippocampus of 4 week old animals (n=3/genotype), and then expression determined by quantitative PCR. The fold change in RNA was calculated using the comparative Ct method, normalizing to GAPDH as a control. ( C ) Mef2a/d DKO mice exhibit impaired motor coordination as assessed by falling off the accelerating rotarod faster than littermate CTLs (F 1,7 =27.64, P

    Article Snippet: Genomic regions of the Mef2a locus were isolated from 129SvEv genomic DNA by high-fidelity PCR (Takara LA taq PCR system) and cloned into a pGKneoF2L2DTA vector, which contains a neomycin resistance gene, flanked by FRT and loxP sites, and a diphtheria toxin gene cassette.

    Techniques: In Situ, Hybridization, CTL Assay, Mouse Assay, Expressing, Quantitative RT-PCR, Isolation, Real-time Polymerase Chain Reaction