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Toyobo dna polymerase
Quantification of transcription levels by real-time <t>RT-PCR</t> ( A ) and identification of the CSS2 variant as protein ( B ). A , standard curves for the CSS2 variants and GAPDH were generated by serial dilution of each concentration-known <t>DNA</t> fragment. The expression
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1) Product Images from "Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *"

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.109553

Quantification of transcription levels by real-time RT-PCR ( A ) and identification of the CSS2 variant as protein ( B ). A , standard curves for the CSS2 variants and GAPDH were generated by serial dilution of each concentration-known DNA fragment. The expression
Figure Legend Snippet: Quantification of transcription levels by real-time RT-PCR ( A ) and identification of the CSS2 variant as protein ( B ). A , standard curves for the CSS2 variants and GAPDH were generated by serial dilution of each concentration-known DNA fragment. The expression

Techniques Used: Quantitative RT-PCR, Variant Assay, Generated, Serial Dilution, Concentration Assay, Expressing

2) Product Images from "Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *"

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.109553

Quantification of transcription levels by real-time RT-PCR ( A ) and identification of the CSS2 variant as protein ( B ). A , standard curves for the CSS2 variants and GAPDH were generated by serial dilution of each concentration-known DNA fragment. The expression
Figure Legend Snippet: Quantification of transcription levels by real-time RT-PCR ( A ) and identification of the CSS2 variant as protein ( B ). A , standard curves for the CSS2 variants and GAPDH were generated by serial dilution of each concentration-known DNA fragment. The expression

Techniques Used: Quantitative RT-PCR, Variant Assay, Generated, Serial Dilution, Concentration Assay, Expressing

3) Product Images from "Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development"

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development

Journal: PLoS ONE

doi: 10.1371/journal.pone.0043806

Generation of CSS2 −/− mice. A, Genomic structure of CSS2 gene, the targeting vector, and the genome with homologous recombination and that whose fragments were excised by flippase and Cre systems. A , The genomic structure of CSS2 gene is depicted on the top line (a). CSS2 targeting vector (b) was constructed by flanking exon 1 with loxP sites, and flanking a Neo R cassette with FRT sites. ES cell clones with homologous recombination of the vector segment (c) were obtained by positive selection, and used for generation of chimera mice, followed by germ line transmission. The FRT-flanked Neo cassette was subsequently deleted from the recombinant allele by crossing with CAG-Flp Tg mice (d). Then, a genomic fragment containing exon 1, flanked by loxP sites, was excised from the recombinant allele by crossing with CAG-Cre Tg mice (e). B , Genomic PCR. Genotyping was performed by PCR using tail DNA and primers shown in black arrows in Fig. 1A. The PCR product of wild-type allele and CSS2 mutant allele was 2.1 kb and 420 bp respectively. C , Immunoprecipitation of the CSS2, followed by western blot. The cell lysates obtained from WT MEFs were subjected to western blot analysis as described in “Experimental Procedures”. Western blot analysis shows bands of CSS2 (85 kDa) and the CSS2 variant (68 kDa).
Figure Legend Snippet: Generation of CSS2 −/− mice. A, Genomic structure of CSS2 gene, the targeting vector, and the genome with homologous recombination and that whose fragments were excised by flippase and Cre systems. A , The genomic structure of CSS2 gene is depicted on the top line (a). CSS2 targeting vector (b) was constructed by flanking exon 1 with loxP sites, and flanking a Neo R cassette with FRT sites. ES cell clones with homologous recombination of the vector segment (c) were obtained by positive selection, and used for generation of chimera mice, followed by germ line transmission. The FRT-flanked Neo cassette was subsequently deleted from the recombinant allele by crossing with CAG-Flp Tg mice (d). Then, a genomic fragment containing exon 1, flanked by loxP sites, was excised from the recombinant allele by crossing with CAG-Cre Tg mice (e). B , Genomic PCR. Genotyping was performed by PCR using tail DNA and primers shown in black arrows in Fig. 1A. The PCR product of wild-type allele and CSS2 mutant allele was 2.1 kb and 420 bp respectively. C , Immunoprecipitation of the CSS2, followed by western blot. The cell lysates obtained from WT MEFs were subjected to western blot analysis as described in “Experimental Procedures”. Western blot analysis shows bands of CSS2 (85 kDa) and the CSS2 variant (68 kDa).

Techniques Used: Mouse Assay, Plasmid Preparation, Homologous Recombination, Construct, Clone Assay, Selection, Transmission Assay, Recombinant, Polymerase Chain Reaction, Mutagenesis, Immunoprecipitation, Western Blot, Variant Assay

4) Product Images from "Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice"

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice

Journal: Rice

doi: 10.1186/s12284-014-0009-2

Plasmid construct and PCR analysis of OsAp77::GUS -transgenic lines (T 2 ) of rice. (A) Structure of T-DNA region in the expression construct for rice transformation. P nos and T nos , promoter and terminator of nopaline syntase gene, respectively. hpt , hygromycin (hyg) phosphotransferase conferring resistance to hyg; T iaaM , terminator of iaa monooxygenase gene. Arrows indicate the positions of GUS gene-specific primers (Table 1 ). (B) Gel electrophoresis of PCR-amplified GUS fragment. Lanes 1–3 are derived from line 2A; lanes 4–6, 4A; lanes 7–9, 5A; lanes 10–11, 7A; lane 12, positive control (pBI221 plasmid DNA); lane 13, negative control (non-transgenic line) .
Figure Legend Snippet: Plasmid construct and PCR analysis of OsAp77::GUS -transgenic lines (T 2 ) of rice. (A) Structure of T-DNA region in the expression construct for rice transformation. P nos and T nos , promoter and terminator of nopaline syntase gene, respectively. hpt , hygromycin (hyg) phosphotransferase conferring resistance to hyg; T iaaM , terminator of iaa monooxygenase gene. Arrows indicate the positions of GUS gene-specific primers (Table 1 ). (B) Gel electrophoresis of PCR-amplified GUS fragment. Lanes 1–3 are derived from line 2A; lanes 4–6, 4A; lanes 7–9, 5A; lanes 10–11, 7A; lane 12, positive control (pBI221 plasmid DNA); lane 13, negative control (non-transgenic line) .

Techniques Used: Plasmid Preparation, Construct, Polymerase Chain Reaction, Transgenic Assay, Expressing, Transformation Assay, Nucleic Acid Electrophoresis, Amplification, Derivative Assay, Positive Control, Negative Control

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Clone Assay:

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Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
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Amplification:

Article Title: Ursolic Acid Inhibits Na+/K+-ATPase Activity and Prevents TNF-?-Induced Gene Expression by Blocking Amino Acid Transport and Cellular Protein Synthesis
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Article Title: High-Incidence of Human Adenoviral Co-Infections in Taiwan
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Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
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Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
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Article Title: Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus
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Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
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Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
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Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
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Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
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Filtration:

Article Title: A Novel Bifunctional Amino Acid Racemase With Multiple Substrate Specificity, MalY From Lactobacillus sakei LT-13: Genome-Based Identification and Enzymological Characterization
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DNA Ligation:

Article Title: Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.)
Article Snippet: The double-digested genomic DNA was then ligated to adapters using the Liga Fast Rapid DNA Ligation System (Promega, Madison, WI, USA), and purified using Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA) to eliminate short DNA fragments ( < 300 bp). .. 2 (Toyobo, Osaka, Japan), 160 μM dNTPs, 1 mM MgSO4 , and 1 U DNA polymerase (KOD –plus–; Toyobo).

Synthesized:

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
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Quantitative RT-PCR:

Article Title: Ursolic Acid Inhibits Na+/K+-ATPase Activity and Prevents TNF-?-Induced Gene Expression by Blocking Amino Acid Transport and Cellular Protein Synthesis
Article Snippet: Paragraph title: Quantitative RT-PCR ... 2 DNA polymerase (Toyobo).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: The cDNA fragments of CSS2A, CSS2B, and CSS1 were amplified by PCR from the I.M.A.G.E cDNA clones (Invitrogen) and cDNA from a C57/Bl6 mouse, as described for “Quantitative Real Time RT-PCR,” as templates, respectively. .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) with a program of 35 cycles of 98 °C for 10 s, 75 °C for 30 s, and 68 °C for 5 min.

Real-time Polymerase Chain Reaction:

Article Title: Ursolic Acid Inhibits Na+/K+-ATPase Activity and Prevents TNF-?-Induced Gene Expression by Blocking Amino Acid Transport and Cellular Protein Synthesis
Article Snippet: Quantitative RT-PCR Total RNA was extracted from A549 cells using Sepasol® -RNA I super (Nacalai Tesque, Kyoto, Japan) and reverse-transcribed to cDNA using ReverTra Ace® (Toyobo, Osaka, Japan) and oligo(dT)20 according to the manufacturer's instructions. cDNA was amplified with a 7000 Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) using SYBR® Premix Ex Taq™ (Takara Bio, Otsu, Japan) and KOD -Plus- Ver. .. 2 DNA polymerase (Toyobo).

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: Paragraph title: RNA isolation, reverse-transcriptase (RT) PCR and real-time PCR ... Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin.

cDNA Library Assay:

Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
Article Snippet: The cDNA fragment of a truncated form of CSS3 (ChSy-2), lacking the first 129 N-terminal amino acids of CSS3, was amplified by RT (reverse transcriptase)-PCR with the Marathon-Ready™ cDNA library derived from human brain (Clontech) as a template using a 5′-primer (5′-CCCTCGAGGGCCGAGGGGGAGCCCGA-3′) containing an in-frame XhoI site and a 3′-primer (5′-CCCTCGAGCTGTCAGGAGAGAGTTCGATT-3′) containing a XhoI site located 3 bp downstream of the stop codon. .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) for 30 cycles of 94 °C for 30 s, 58 °C for 30 s and 68 °C for 150 s in 5% (v/v) DMSO.

Expressing:

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: Paragraph title: Construction of Expression Plasmids of CSS2A Variants and CSS1 ... PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert.

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The resulting PCR products were cloned via pENTR/D-TOPO (Invitrogen) into a pDEST 8 vector to generate insect cell baculovirus expression clones.

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin. .. Real-time PCR was performed for a quantitative analysis of iNOS, IL-1β and TNF-α mRNA expression using SYBR Green real-time PCR Master Mix (Toyobo) on an MX3000P real-time PCR system (Stratagene).

Transformation Assay:

Article Title: Purification and Characterization of Thermostable Endo-1,5-?-l-Arabinase from a Strain of Bacillus thermodenitrificans
Article Snippet: The composition of the PCR mixture (50 μl) was 120 mM Tris-HCl (pH 8.0), 10 mM KCl, 6 mM (NH4 )2 SO4 , 0.1% Triton X-100, 10 μg of bovine serum albumin per ml, 1 mM MgCl2 , 200 mM deoxynucleoside triphosphates, 250 ng of genomic DNA, 50 pmol of each primer, and 2.5 units of DNA polymerase from Pyrococcus kodakaraensis strain KOD1 (Toyobo, Tokyo, Japan). .. The amplified DNA (approximately 1,500 bp) was phosphorylated with T4 DNA kinase, ligated into the Sma I site of pUC18 (Amersham Pharmacia Biotec, Buckinghamshire, United Kingdom), and transformed into Escherichia coli JM109 cells by the method of Hanahan ( ).

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: Paragraph title: Plasmid constructs and rice transformation ... The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv.

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The resulting constructs were used to generate the recombinant bacmid DNAs by transformation of Escherichia coli strain DH10Bac (Invitrogen).

Derivative Assay:

Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
Article Snippet: The cDNA fragment of a truncated form of CSS3 (ChSy-2), lacking the first 129 N-terminal amino acids of CSS3, was amplified by RT (reverse transcriptase)-PCR with the Marathon-Ready™ cDNA library derived from human brain (Clontech) as a template using a 5′-primer (5′-CCCTCGAGGGCCGAGGGGGAGCCCGA-3′) containing an in-frame XhoI site and a 3′-primer (5′-CCCTCGAGCTGTCAGGAGAGAGTTCGATT-3′) containing a XhoI site located 3 bp downstream of the stop codon. .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) for 30 cycles of 94 °C for 30 s, 58 °C for 30 s and 68 °C for 150 s in 5% (v/v) DMSO.

Chromatography:

Article Title: A Novel Bifunctional Amino Acid Racemase With Multiple Substrate Specificity, MalY From Lactobacillus sakei LT-13: Genome-Based Identification and Enzymological Characterization
Article Snippet: 2 DNA polymerase was from Toyobo, Co., Ltd. (Japan). .. Molecular weight standards for gel filtration chromatography were from GE Healthcare Japan.

Polymerase Chain Reaction:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively. .. The sequence analysis of the PCR product was performed using an ABI PRISM® 3130 Genetic Analyzer (Applied Biosystems) to confirm the lack of exon 1 of CSS2 in genomic DNA.

Article Title: Purification and Characterization of Thermostable Endo-1,5-?-l-Arabinase from a Strain of Bacillus thermodenitrificans
Article Snippet: .. The composition of the PCR mixture (50 μl) was 120 mM Tris-HCl (pH 8.0), 10 mM KCl, 6 mM (NH4 )2 SO4 , 0.1% Triton X-100, 10 μg of bovine serum albumin per ml, 1 mM MgCl2 , 200 mM deoxynucleoside triphosphates, 250 ng of genomic DNA, 50 pmol of each primer, and 2.5 units of DNA polymerase from Pyrococcus kodakaraensis strain KOD1 (Toyobo, Tokyo, Japan). .. The amplified DNA (approximately 1,500 bp) was phosphorylated with T4 DNA kinase, ligated into the Sma I site of pUC18 (Amersham Pharmacia Biotec, Buckinghamshire, United Kingdom), and transformed into Escherichia coli JM109 cells by the method of Hanahan ( ).

Article Title: High-Incidence of Human Adenoviral Co-Infections in Taiwan
Article Snippet: .. PCR mixtures consisted of 1 U of DNA polymerase (KOD plus polymerase, Toyobo), 1 mM MgSO4 , 0.2 mM dNTP, 300 pM of each primer and 1 to 2 μl of template from the original purified DNA solution in a 50-μl reaction volume. .. PCR cycling consisted of initial denaturation at 95°C for 5 minutes, followed by 40 cycles of 94°C for 20 seconds, 54°C or 56°C for 20 seconds, depending on primers used, and 72°C for 40 or 80 seconds, depending on the length of PCR products.

Article Title: Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.)
Article Snippet: The PCR mixture (50 μL) contained 0.4 ng DNA, 0.2 μM of each indexed primer (one pair per mixture), 1× PCR buffer of KOD –plus– Ver. .. 2 (Toyobo, Osaka, Japan), 160 μM dNTPs, 1 mM MgSO4 , and 1 U DNA polymerase (KOD –plus–; Toyobo).

Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
Article Snippet: .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) for 30 cycles of 94 °C for 30 s, 58 °C for 30 s and 68 °C for 150 s in 5% (v/v) DMSO. .. The PCR fragments were digested with XhoI, and both ends of the fragments were partially filled by a Klenow fragment (New England Biolabs) with dCTP and dTTP.

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: .. The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv. ..

Article Title: Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus
Article Snippet: .. PCR was performed with a PTC-100™ Programmable Thermal Controller (MJ Research Inc., Quebec, Canada) using KOD -plus- DNA polymerase (TOYOBO Co., Ltd, Kita-ku, Osaka, Japan). .. PCR products were confirmed with 1% agarose gel electrophoresis and purified by the GENECLEAN II kit (MP Biomedicals Japan, Chuo-ku, Tokyo, Japan).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: .. PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert. .. Expression plasmids for Myc-tagged CSS1 and the CSS2 variants were constructed as follows.

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: .. Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The open reading frame of each licorice ( Glycyrrhiza uralensis ) CYP72A gene was amplified by RT-PCR using primers 1 and 2 for CYP72A154, primers 3 and 4 for CYP72A153, and primers 5 and 6 for CYP72A155 (for primer sequences, see online).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) with a program of 35 cycles of 98 °C for 10 s, 75 °C for 30 s, and 68 °C for 5 min. .. The amplified fragments were inserted using EcoRV and XbaI sites of the pFLAG-CMV3 vector (Sigma), which contains a secretion signal of preprotrypsin and a FLAG tag.

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
Article Snippet: .. Template cDNA was amplified by PCR using DNA polymerase (KOD-Plus-Ver.2; TOYOBO, Osaka, Japan) with primer pairs specific for the NS3 region of the HCV genome (NS3-F1 (5′-ACACCGCGGCGTGTGGGGACAT-3′; nucleotides 3295–3316) and NS3-AS2 (5′-GCTCTTGCCGCTGCCAGTGGGA-3′; 4040–4019)) or primer pairs specific for the NS5B region (NS5B-F (5′-GCGTCCAACCAGAGAAAGGA-3′; 8023–8042) and NS5B-R (5′-TGCGCTAAGACCATGGAGTC-3′; 8999–8980)); this region was also amplified by nested PCR using DNA polymerase (KOD-Plus-Ver.2; Toyobo) with primers pairs specific for the NS5A region of the HCV genome (NS5A-F1 (5′-AAGAGGCTCCACCAGTGGAT-3′: 6213-6232) and NS5A-AS1 (5′-CGCCGGAGCGTACCTGTGCA-3′: 6730-6749) as the first primer pair and NS5A-F2 (5′-AATGAGGACTGCTCCACGCC-3′: 6234-6253) and NS5A-AS2 (5′-GTGAAGAATTCGGGGGCCGG-3′: 6690–6709) as the second primer pair). .. The amplified products were purified with a QIAquick PCR purification kit (QIAGEN) and subjected to sequencing PCR using a BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions with the primer pairs NS3-F3 (5′-CAGGGGTGGCGGCTCCTT-3′: 3390–3407) and NS3-AS2, NS5A-F3 and NS5A-AS3, or NS5B-SeqF (5′-TTTACGACGTGGTCTCCACC-3′: 8110–8129) and NS5B-SeqR (5′-ACCTAGTCATAGCCTCCGTGA-3′: 8622–8602).

Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
Article Snippet: .. A 1.53-kbp blunt-ended DNA fragment containing the bchU gene was amplified from the genomic DNA of C. limnaeum using KOD -plus- DNA polymerase (TOYOBO, Osaka, Japan), and primers Uaround F and Uaround R. The PCR product was digested at the Eco RI restriction enzyme site designed in Uaround R primer, and cloned into the Sma I and Eco RI sites of pUC118 (TAKARA, Shiga, Japan), yielding pUCbchU plasmid. .. To disrupt the unique Eco RI and Bam HI sites in pUCbchU for after cloning step, this plasmid was digested by Eco RI, blunted, and self-ligated, and the resulting plasmid was in turn treated with Bam HI, blunted, and self-ligated, producing pUCbchUEB.

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: .. Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin. ..

DNA Sequencing:

Article Title: High-Incidence of Human Adenoviral Co-Infections in Taiwan
Article Snippet: PCR mixtures consisted of 1 U of DNA polymerase (KOD plus polymerase, Toyobo), 1 mM MgSO4 , 0.2 mM dNTP, 300 pM of each primer and 1 to 2 μl of template from the original purified DNA solution in a 50-μl reaction volume. .. DNA sequencing of PCR products was carried out with the primers used in PCR by Sanger’s method.

Transmission Assay:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: Germline transmission of CSS2flox allele was attained by crossing these chimeric mice with C57BL6. .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively.

Sequencing:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively. .. The sequence analysis of the PCR product was performed using an ABI PRISM® 3130 Genetic Analyzer (Applied Biosystems) to confirm the lack of exon 1 of CSS2 in genomic DNA.

Article Title: Purification and Characterization of Thermostable Endo-1,5-?-l-Arabinase from a Strain of Bacillus thermodenitrificans
Article Snippet: Paragraph title: Cloning of 16S rRNA gene and nucleotide sequencing. ... The composition of the PCR mixture (50 μl) was 120 mM Tris-HCl (pH 8.0), 10 mM KCl, 6 mM (NH4 )2 SO4 , 0.1% Triton X-100, 10 μg of bovine serum albumin per ml, 1 mM MgCl2 , 200 mM deoxynucleoside triphosphates, 250 ng of genomic DNA, 50 pmol of each primer, and 2.5 units of DNA polymerase from Pyrococcus kodakaraensis strain KOD1 (Toyobo, Tokyo, Japan).

Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
Article Snippet: The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) for 30 cycles of 94 °C for 30 s, 58 °C for 30 s and 68 °C for 150 s in 5% (v/v) DMSO. .. The resultant fragments were subcloned into pGIR201protA, resulting in the fusion of CSS3 (ChSy-2) with the insulin signal sequence and the Protein A sequence present in the vector.

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv. .. The fragment with the accurate sequence for OsAP77 promoter was then digested with Sbf I and Xba I and cloned into to a binary vector pSMAHdN627-M2GUS (Hakata et al. [ ]) treated with the same restriction enzymes followed by dephosphorylation (Figure ).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: .. PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert. .. Expression plasmids for Myc-tagged CSS1 and the CSS2 variants were constructed as follows.

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
Article Snippet: Paragraph title: 4.2. RNA Extraction, cDNA Synthesis, and Direct Sequencing of the NS3/4A, NS5A, and NS5B Regions of the HCV Genome ... Template cDNA was amplified by PCR using DNA polymerase (KOD-Plus-Ver.2; TOYOBO, Osaka, Japan) with primer pairs specific for the NS3 region of the HCV genome (NS3-F1 (5′-ACACCGCGGCGTGTGGGGACAT-3′; nucleotides 3295–3316) and NS3-AS2 (5′-GCTCTTGCCGCTGCCAGTGGGA-3′; 4040–4019)) or primer pairs specific for the NS5B region (NS5B-F (5′-GCGTCCAACCAGAGAAAGGA-3′; 8023–8042) and NS5B-R (5′-TGCGCTAAGACCATGGAGTC-3′; 8999–8980)); this region was also amplified by nested PCR using DNA polymerase (KOD-Plus-Ver.2; Toyobo) with primers pairs specific for the NS5A region of the HCV genome (NS5A-F1 (5′-AAGAGGCTCCACCAGTGGAT-3′: 6213-6232) and NS5A-AS1 (5′-CGCCGGAGCGTACCTGTGCA-3′: 6730-6749) as the first primer pair and NS5A-F2 (5′-AATGAGGACTGCTCCACGCC-3′: 6234-6253) and NS5A-AS2 (5′-GTGAAGAATTCGGGGGCCGG-3′: 6690–6709) as the second primer pair).

Injection:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: By blastocyst injection, chimeric mice were obtained. .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively.

Recombinant:

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The resulting constructs were used to generate the recombinant bacmid DNAs by transformation of Escherichia coli strain DH10Bac (Invitrogen).

Molecular Weight:

Article Title: A Novel Bifunctional Amino Acid Racemase With Multiple Substrate Specificity, MalY From Lactobacillus sakei LT-13: Genome-Based Identification and Enzymological Characterization
Article Snippet: 2 DNA polymerase was from Toyobo, Co., Ltd. (Japan). .. Molecular weight standards for gel filtration chromatography were from GE Healthcare Japan.

Mutagenesis:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively. .. The sequence analysis of the PCR product was performed using an ABI PRISM® 3130 Genetic Analyzer (Applied Biosystems) to confirm the lack of exon 1 of CSS2 in genomic DNA.

Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
Article Snippet: To construct the C. limnaeum mutant lacking bchU , the plasmid pUCbchUGm ( ) was produced as follows. .. A 1.53-kbp blunt-ended DNA fragment containing the bchU gene was amplified from the genomic DNA of C. limnaeum using KOD -plus- DNA polymerase (TOYOBO, Osaka, Japan), and primers Uaround F and Uaround R. The PCR product was digested at the Eco RI restriction enzyme site designed in Uaround R primer, and cloned into the Sma I and Eco RI sites of pUC118 (TAKARA, Shiga, Japan), yielding pUCbchU plasmid.

Isolation:

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: Plasmid constructs and rice transformation To generate OsAP77::GUS chimeric gene, which contains the GUS reporter gene under the control of the 5′-flanking region of OsAP77 , the OsAP77 promoter region was isolated using a pair of gene-specific primers designated AP77 pro-5′ and AP77 pro-3′ (Table ) that carry the extra sequences for Sbf I and Xba I recognition sites, respectively. .. The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv.

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: Paragraph title: RNA isolation, reverse-transcriptase (RT) PCR and real-time PCR ... Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin.

Labeling:

Article Title: Purification and Characterization of Thermostable Endo-1,5-?-l-Arabinase from a Strain of Bacillus thermodenitrificans
Article Snippet: The composition of the PCR mixture (50 μl) was 120 mM Tris-HCl (pH 8.0), 10 mM KCl, 6 mM (NH4 )2 SO4 , 0.1% Triton X-100, 10 μg of bovine serum albumin per ml, 1 mM MgCl2 , 200 mM deoxynucleoside triphosphates, 250 ng of genomic DNA, 50 pmol of each primer, and 2.5 units of DNA polymerase from Pyrococcus kodakaraensis strain KOD1 (Toyobo, Tokyo, Japan). .. The nucleotide sequences were analyzed by the dideoxy chain termination method using a Thermo Sequenase fluorescently labeled primer cycle sequencing kit (Amersham Pharmacia Biotec) on an A.L.F.

Mouse Assay:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively. .. The sequence analysis of the PCR product was performed using an ABI PRISM® 3130 Genetic Analyzer (Applied Biosystems) to confirm the lack of exon 1 of CSS2 in genomic DNA.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The open reading frame of each licorice ( Glycyrrhiza uralensis ) CYP72A gene was amplified by RT-PCR using primers 1 and 2 for CYP72A154, primers 3 and 4 for CYP72A153, and primers 5 and 6 for CYP72A155 (for primer sequences, see online).

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: Paragraph title: RNA isolation, reverse-transcriptase (RT) PCR and real-time PCR ... Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin.

Construct:

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: Paragraph title: Plasmid constructs and rice transformation ... The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv.

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: Expression plasmids for CSS2 variants that initiate at the start codon were constructed as follows. .. PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert.

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The resulting constructs were used to generate the recombinant bacmid DNAs by transformation of Escherichia coli strain DH10Bac (Invitrogen).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: Expression plasmids for soluble forms of CSS2A, CSS2B, and CSS1 were constructed as follows. .. The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) with a program of 35 cycles of 98 °C for 10 s, 75 °C for 30 s, and 68 °C for 5 min.

Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
Article Snippet: To construct the C. limnaeum mutant lacking bchU , the plasmid pUCbchUGm ( ) was produced as follows. .. A 1.53-kbp blunt-ended DNA fragment containing the bchU gene was amplified from the genomic DNA of C. limnaeum using KOD -plus- DNA polymerase (TOYOBO, Osaka, Japan), and primers Uaround F and Uaround R. The PCR product was digested at the Eco RI restriction enzyme site designed in Uaround R primer, and cloned into the Sma I and Eco RI sites of pUC118 (TAKARA, Shiga, Japan), yielding pUCbchU plasmid.

De-Phosphorylation Assay:

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv. .. The fragment with the accurate sequence for OsAP77 promoter was then digested with Sbf I and Xba I and cloned into to a binary vector pSMAHdN627-M2GUS (Hakata et al. [ ]) treated with the same restriction enzymes followed by dephosphorylation (Figure ).

Nested PCR:

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
Article Snippet: .. Template cDNA was amplified by PCR using DNA polymerase (KOD-Plus-Ver.2; TOYOBO, Osaka, Japan) with primer pairs specific for the NS3 region of the HCV genome (NS3-F1 (5′-ACACCGCGGCGTGTGGGGACAT-3′; nucleotides 3295–3316) and NS3-AS2 (5′-GCTCTTGCCGCTGCCAGTGGGA-3′; 4040–4019)) or primer pairs specific for the NS5B region (NS5B-F (5′-GCGTCCAACCAGAGAAAGGA-3′; 8023–8042) and NS5B-R (5′-TGCGCTAAGACCATGGAGTC-3′; 8999–8980)); this region was also amplified by nested PCR using DNA polymerase (KOD-Plus-Ver.2; Toyobo) with primers pairs specific for the NS5A region of the HCV genome (NS5A-F1 (5′-AAGAGGCTCCACCAGTGGAT-3′: 6213-6232) and NS5A-AS1 (5′-CGCCGGAGCGTACCTGTGCA-3′: 6730-6749) as the first primer pair and NS5A-F2 (5′-AATGAGGACTGCTCCACGCC-3′: 6234-6253) and NS5A-AS2 (5′-GTGAAGAATTCGGGGGCCGG-3′: 6690–6709) as the second primer pair). .. The amplified products were purified with a QIAquick PCR purification kit (QIAGEN) and subjected to sequencing PCR using a BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions with the primer pairs NS3-F3 (5′-CAGGGGTGGCGGCTCCTT-3′: 3390–3407) and NS3-AS2, NS5A-F3 and NS5A-AS3, or NS5B-SeqF (5′-TTTACGACGTGGTCTCCACC-3′: 8110–8129) and NS5B-SeqR (5′-ACCTAGTCATAGCCTCCGTGA-3′: 8622–8602).

Purification:

Article Title: High-Incidence of Human Adenoviral Co-Infections in Taiwan
Article Snippet: .. PCR mixtures consisted of 1 U of DNA polymerase (KOD plus polymerase, Toyobo), 1 mM MgSO4 , 0.2 mM dNTP, 300 pM of each primer and 1 to 2 μl of template from the original purified DNA solution in a 50-μl reaction volume. .. PCR cycling consisted of initial denaturation at 95°C for 5 minutes, followed by 40 cycles of 94°C for 20 seconds, 54°C or 56°C for 20 seconds, depending on primers used, and 72°C for 40 or 80 seconds, depending on the length of PCR products.

Article Title: Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.)
Article Snippet: Purified restriction-digested DNA was diluted with water and amplified with PCR using indexed primers (see Additional file ). .. 2 (Toyobo, Osaka, Japan), 160 μM dNTPs, 1 mM MgSO4 , and 1 U DNA polymerase (KOD –plus–; Toyobo).

Article Title: Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus
Article Snippet: PCR was performed with a PTC-100™ Programmable Thermal Controller (MJ Research Inc., Quebec, Canada) using KOD -plus- DNA polymerase (TOYOBO Co., Ltd, Kita-ku, Osaka, Japan). .. PCR products were confirmed with 1% agarose gel electrophoresis and purified by the GENECLEAN II kit (MP Biomedicals Japan, Chuo-ku, Tokyo, Japan).

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
Article Snippet: Template cDNA was amplified by PCR using DNA polymerase (KOD-Plus-Ver.2; TOYOBO, Osaka, Japan) with primer pairs specific for the NS3 region of the HCV genome (NS3-F1 (5′-ACACCGCGGCGTGTGGGGACAT-3′; nucleotides 3295–3316) and NS3-AS2 (5′-GCTCTTGCCGCTGCCAGTGGGA-3′; 4040–4019)) or primer pairs specific for the NS5B region (NS5B-F (5′-GCGTCCAACCAGAGAAAGGA-3′; 8023–8042) and NS5B-R (5′-TGCGCTAAGACCATGGAGTC-3′; 8999–8980)); this region was also amplified by nested PCR using DNA polymerase (KOD-Plus-Ver.2; Toyobo) with primers pairs specific for the NS5A region of the HCV genome (NS5A-F1 (5′-AAGAGGCTCCACCAGTGGAT-3′: 6213-6232) and NS5A-AS1 (5′-CGCCGGAGCGTACCTGTGCA-3′: 6730-6749) as the first primer pair and NS5A-F2 (5′-AATGAGGACTGCTCCACGCC-3′: 6234-6253) and NS5A-AS2 (5′-GTGAAGAATTCGGGGGCCGG-3′: 6690–6709) as the second primer pair). .. The amplified products were purified with a QIAquick PCR purification kit (QIAGEN) and subjected to sequencing PCR using a BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions with the primer pairs NS3-F3 (5′-CAGGGGTGGCGGCTCCTT-3′: 3390–3407) and NS3-AS2, NS5A-F3 and NS5A-AS3, or NS5B-SeqF (5′-TTTACGACGTGGTCTCCACC-3′: 8110–8129) and NS5B-SeqR (5′-ACCTAGTCATAGCCTCCGTGA-3′: 8622–8602).

Plasmid Preparation:

Article Title: Purification and Characterization of Thermostable Endo-1,5-?-l-Arabinase from a Strain of Bacillus thermodenitrificans
Article Snippet: The composition of the PCR mixture (50 μl) was 120 mM Tris-HCl (pH 8.0), 10 mM KCl, 6 mM (NH4 )2 SO4 , 0.1% Triton X-100, 10 μg of bovine serum albumin per ml, 1 mM MgCl2 , 200 mM deoxynucleoside triphosphates, 250 ng of genomic DNA, 50 pmol of each primer, and 2.5 units of DNA polymerase from Pyrococcus kodakaraensis strain KOD1 (Toyobo, Tokyo, Japan). .. Plasmids of randomly selected clones with inserts of the correct size were then recovered with a plasmid Midi kit (Qiagen, GmbH, Hilden, Germany).

Article Title: Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor
Article Snippet: The PCR was carried out using KOD -Plus DNA polymerase (Toyobo Biochemicals) for 30 cycles of 94 °C for 30 s, 58 °C for 30 s and 68 °C for 150 s in 5% (v/v) DMSO. .. The pGIR201protA [ ] vector digested with BamHI was also partially filled with dATP and dGTP.

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: Paragraph title: Plasmid constructs and rice transformation ... The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv.

Article Title: Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus
Article Snippet: Paragraph title: Construction of a plasmid library containing putative RND-type multidrug efflux transporter ORFs ... PCR was performed with a PTC-100™ Programmable Thermal Controller (MJ Research Inc., Quebec, Canada) using KOD -plus- DNA polymerase (TOYOBO Co., Ltd, Kita-ku, Osaka, Japan).

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: The amplified fragments were inserted using EcoRV and XbaI sites of the pFLAG-CMV3 vector (Sigma), which contains a secretion signal of preprotrypsin and a FLAG tag. .. PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert.

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions. .. The resulting PCR products were cloned via pENTR/D-TOPO (Invitrogen) into a pDEST 8 vector to generate insect cell baculovirus expression clones.

Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
Article Snippet: .. A 1.53-kbp blunt-ended DNA fragment containing the bchU gene was amplified from the genomic DNA of C. limnaeum using KOD -plus- DNA polymerase (TOYOBO, Osaka, Japan), and primers Uaround F and Uaround R. The PCR product was digested at the Eco RI restriction enzyme site designed in Uaround R primer, and cloned into the Sma I and Eco RI sites of pUC118 (TAKARA, Shiga, Japan), yielding pUCbchU plasmid. .. To disrupt the unique Eco RI and Bam HI sites in pUCbchU for after cloning step, this plasmid was digested by Eco RI, blunted, and self-ligated, and the resulting plasmid was in turn treated with Bam HI, blunted, and self-ligated, producing pUCbchUEB.

SYBR Green Assay:

Article Title: Aspirin-triggered lipoxin A4 attenuates LPS-induced pro-inflammatory responses by inhibiting activation of NF-?B and MAPKs in BV-2 microglial cells
Article Snippet: Semi-quantitative PCR was carried out with DNA polymerase (Toyobo) by using specific primers (Invitrogen): 5'-GGCAACTCTGTTGAGGAAAG-3' and 5'-GGCTCTCGGTAGACGAGA-3', which amplify the 423 bp product for ALX1/FPR-rs1; and 5'-GTCAAGATCAACAGAAGAAACC-3' and 5'-GGGCTCTCTCAAGACTATAAGG-3', which amplify 298 bp product for ALX2/FPR2; and 5'-TGGAATCCTGTGGCATCCATGAAAC-3' and 5'-TAAAACGCAGCTCAGTAACAGTCCG-3', which amplify 349 bp product for β-actin. .. Real-time PCR was performed for a quantitative analysis of iNOS, IL-1β and TNF-α mRNA expression using SYBR Green real-time PCR Master Mix (Toyobo) on an MX3000P real-time PCR system (Stratagene).

RNA Extraction:

Article Title: Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed
Article Snippet: Paragraph title: 4.2. RNA Extraction, cDNA Synthesis, and Direct Sequencing of the NS3/4A, NS5A, and NS5B Regions of the HCV Genome ... Template cDNA was amplified by PCR using DNA polymerase (KOD-Plus-Ver.2; TOYOBO, Osaka, Japan) with primer pairs specific for the NS3 region of the HCV genome (NS3-F1 (5′-ACACCGCGGCGTGTGGGGACAT-3′; nucleotides 3295–3316) and NS3-AS2 (5′-GCTCTTGCCGCTGCCAGTGGGA-3′; 4040–4019)) or primer pairs specific for the NS5B region (NS5B-F (5′-GCGTCCAACCAGAGAAAGGA-3′; 8023–8042) and NS5B-R (5′-TGCGCTAAGACCATGGAGTC-3′; 8999–8980)); this region was also amplified by nested PCR using DNA polymerase (KOD-Plus-Ver.2; Toyobo) with primers pairs specific for the NS5A region of the HCV genome (NS5A-F1 (5′-AAGAGGCTCCACCAGTGGAT-3′: 6213-6232) and NS5A-AS1 (5′-CGCCGGAGCGTACCTGTGCA-3′: 6730-6749) as the first primer pair and NS5A-F2 (5′-AATGAGGACTGCTCCACGCC-3′: 6234-6253) and NS5A-AS2 (5′-GTGAAGAATTCGGGGGCCGG-3′: 6690–6709) as the second primer pair).

Agarose Gel Electrophoresis:

Article Title: Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus
Article Snippet: PCR was performed with a PTC-100™ Programmable Thermal Controller (MJ Research Inc., Quebec, Canada) using KOD -plus- DNA polymerase (TOYOBO Co., Ltd, Kita-ku, Osaka, Japan). .. PCR products were confirmed with 1% agarose gel electrophoresis and purified by the GENECLEAN II kit (MP Biomedicals Japan, Chuo-ku, Tokyo, Japan).

In Vitro:

Article Title: Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W]Triterpene Functional Genomics in Licorice for Identification of CYP72A154 Involved in the Biosynthesis of Glycyrrhizin [C] [W] [OA]
Article Snippet: Paragraph title: In Vitro Enzyme Assays ... Thermococcus kodakaraensis -plus DNA polymerase (TOYOBO) was used for PCR, according to the manufacturer’s instructions.

Transgenic Assay:

Article Title: Chondroitin Sulfate Synthase-2 Is Necessary for Chain Extension of Chondroitin Sulfate but Not Critical for Skeletal Development
Article Snippet: Then, by crossing with CAG-flippase transgenic (Tg) mice , CSS2+/flox mice, whose genome lacked the Neo cassette, were obtained. .. Genotyping of mice was performed by PCR using KOD -Plus DNA polymerase (TOYOBO), genomic DNA from a tail biopsy as template, and primers: 5′-GTGTAGAAGCATACGGCATAGTGG-3′ and 5′-AGTGCCTGATACCTGCGCTCCAGAGG-3′ , with a program of 35 cycles at 98°C for 10 s, 67°C for 30 s, and 72°C for 180 s, generating a PCR product of 2.1 kb in the WT allele and 420 bp in the mutant allele, respectively.

Produced:

Article Title: A seventh bacterial chlorophyll driving a large light-harvesting antenna
Article Snippet: To construct the C. limnaeum mutant lacking bchU , the plasmid pUCbchUGm ( ) was produced as follows. .. A 1.53-kbp blunt-ended DNA fragment containing the bchU gene was amplified from the genomic DNA of C. limnaeum using KOD -plus- DNA polymerase (TOYOBO, Osaka, Japan), and primers Uaround F and Uaround R. The PCR product was digested at the Eco RI restriction enzyme site designed in Uaround R primer, and cloned into the Sma I and Eco RI sites of pUC118 (TAKARA, Shiga, Japan), yielding pUCbchU plasmid.

FLAG-tag:

Article Title: Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function *
Article Snippet: The amplified fragments were inserted using EcoRV and XbaI sites of the pFLAG-CMV3 vector (Sigma), which contains a secretion signal of preprotrypsin and a FLAG tag. .. PCR was carried out using KOD -Plus DNA polymerase (TOYOBO) with a program of 35 cycles at 98 °C for 10 s, 60 °C for 30 s, and 68 °C for 180 s. The amplified fragments were inserted to p3×FLAG-CMV14 vectors (Sigma) using the EcoRV or EcoRI and XbaI sites, which contains a 3×FLAG tag sequence at the C terminus of the insert.

Hood:

Article Title: Response of an aspartic protease gene OsAP77 to fungal, bacterial and viral infections in rice
Article Snippet: The OsAP77 promoter fragment was amplified by PCR with a DNA polymerase (KOD -Plus-, Toyobo, Osaka, Japan), and the genomic DNA from (O. sativa cv. .. The resulting construct was introduced into Agrobacterium tumefaciens strain EHA101 (Hood et al. [ ]) and used to transform rice (O. sativa cv.

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  • 91
    Toyobo fidelity dna polymerases
    <t>PCR</t> product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) <t>DNA</t> marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).
    Fidelity Dna Polymerases, supplied by Toyobo, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fidelity dna polymerases/product/Toyobo
    Average 91 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    fidelity dna polymerases - by Bioz Stars, 2020-02
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    99
    Toyobo kod plus dna polymerase
    The G/C-rich sequence associated with a meiosis-specific DSB on chromosome IV of S. cerevisiae folds into intramolecular G-quadruplex or i-motif structures and blocks <t>DNA</t> synthesis. ( A ) Here is a schematic diagram showing the nucleotide sequence of G-rich (WT) and its corresponding mutant template. ( B ) The Taq polymerase stop assay was performed in the absence (lanes 1 and 6 ) or presence of increasing concentrations of KCl (10, 25, 50, and 100 mM; lanes 2 – 5 and lanes 7 – 10 , respectively). The solid triangle on top of the gel denotes increasing concentrations of KCl. ( C ) Here we show a diagram of C-rich (WT) and its corresponding mutant DNA template. ( D ) Given here is the <t>KOD-Plus</t> DNA polymerase (from Thermococcus kodakaraensis ) stop assay performed with WT i-motif and its corresponding mutant template at the indicated pH values. Lane 1 is the primer used in this study. ( E ) SWNTs stabilize the i-motif DNA structure at neutral pH, which, in turn, blocks primer extension by DNA polymerase.
    Kod Plus Dna Polymerase, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kod plus dna polymerase/product/Toyobo
    Average 99 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    kod plus dna polymerase - by Bioz Stars, 2020-02
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    80
    Toyobo wild type kod dna polymerase
    Successive incorporation of 2′,4′-bridged nucleotides using analogue 3 with various <t>DNA</t> polymerases; <t>KOD</t> Dash (lane 2), wild type KOD (lane 3), KOD 1 (lane 4), KOD 2 (lane 5), KOD 3 (lane 6), KOD 4 (lane 7), KOD 5 (lane 8), KOD 6 (lane 9), KOD 7 (lane 10), KOD 8 (lane 11), and Vent(exo-) (lane 12). Primer extension reactions were performed for 1 h at 74°C under enzyme concentration of 0.4 U/μL. Primer P2 only migrated in lane 1.
    Wild Type Kod Dna Polymerase, supplied by Toyobo, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 80 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    wild type kod dna polymerase - by Bioz Stars, 2020-02
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    Image Search Results


    PCR product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) DNA marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).

    Journal: PLoS ONE

    Article Title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation

    doi: 10.1371/journal.pone.0170126

    Figure Lengend Snippet: PCR product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) DNA marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).

    Article Snippet: The same result was observed when one-step RT-PCR tests (AccessQuick RT-PCR System kit, Promega Corp, WI, USA) were performed from extracted RNA and PCR tests using other kits containing high fidelity DNA polymerases (KOD FX, KOD FX neo, and Blend–Tag Plus Kits, Toyobo Co., Japan) were performed from cDNA templates to amplify the CS1 fragment.

    Techniques: Polymerase Chain Reaction, Amplification, Marker

    RT-PCR analysis of PPO gene expression. Numbers represent weeks after flowering: g, genomic DNA control. Markers (M) are 100 bp ladder, and arrowheads and arrows, respectively, indicate 1000 bp and 500 bp.

    Journal: Journal of Experimental Botany

    Article Title: Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains

    doi: 10.1093/jxb/erq211

    Figure Lengend Snippet: RT-PCR analysis of PPO gene expression. Numbers represent weeks after flowering: g, genomic DNA control. Markers (M) are 100 bp ladder, and arrowheads and arrows, respectively, indicate 1000 bp and 500 bp.

    Article Snippet: For cDNA cloning, the first-strand cDNA was used as a template, and cDNA was amplified using PCR with gene-specific primer pairs and DNA polymerases [KOD-Plus (Toyobo Co. Ltd.) for PPO1 and ExTaq (Takara Bio Inc.) for PPO2 ], according to the manufacturer's recommended protocol.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing

    Analysis of barley BAC clones containing either the PPO1 or the PPO2 gene. (A) After digestion with eight-base cutters, BAC DNA was separated by pulsed-field gel electrophoresis. (B) BAC DNA containing the PPO1 gene was digested with various six-base cutters and separated using electrophoresis on a 1% agarose gel (left). Southern blot was probed with the PPO1 fragment (right). M1: DNA molecular weight marker III (Roche). M2: λ Hin dIII digest.

    Journal: Journal of Experimental Botany

    Article Title: Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains

    doi: 10.1093/jxb/erq211

    Figure Lengend Snippet: Analysis of barley BAC clones containing either the PPO1 or the PPO2 gene. (A) After digestion with eight-base cutters, BAC DNA was separated by pulsed-field gel electrophoresis. (B) BAC DNA containing the PPO1 gene was digested with various six-base cutters and separated using electrophoresis on a 1% agarose gel (left). Southern blot was probed with the PPO1 fragment (right). M1: DNA molecular weight marker III (Roche). M2: λ Hin dIII digest.

    Article Snippet: For cDNA cloning, the first-strand cDNA was used as a template, and cDNA was amplified using PCR with gene-specific primer pairs and DNA polymerases [KOD-Plus (Toyobo Co. Ltd.) for PPO1 and ExTaq (Takara Bio Inc.) for PPO2 ], according to the manufacturer's recommended protocol.

    Techniques: BAC Assay, Clone Assay, Pulsed-Field Gel, Electrophoresis, Agarose Gel Electrophoresis, Southern Blot, Molecular Weight, Marker

    Isolation of barley PPO homologues and their molecular mapping. (A) PCR amplicons of barley were amplified using a primer pair that was designed on the copper binding domains of wheat PPO genes. 100 bp ladder (M), template DNA of I677 (1), Haruna Nijo (HA2) (2), and J239 (3). Arrowheads and arrows, respectively, indicate 1000 bp and 500 bp. (B) A molecular map of PPO1 and PPO2 in 111 F 2 plants of the cross between HA2 and I677.

    Journal: Journal of Experimental Botany

    Article Title: Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains

    doi: 10.1093/jxb/erq211

    Figure Lengend Snippet: Isolation of barley PPO homologues and their molecular mapping. (A) PCR amplicons of barley were amplified using a primer pair that was designed on the copper binding domains of wheat PPO genes. 100 bp ladder (M), template DNA of I677 (1), Haruna Nijo (HA2) (2), and J239 (3). Arrowheads and arrows, respectively, indicate 1000 bp and 500 bp. (B) A molecular map of PPO1 and PPO2 in 111 F 2 plants of the cross between HA2 and I677.

    Article Snippet: For cDNA cloning, the first-strand cDNA was used as a template, and cDNA was amplified using PCR with gene-specific primer pairs and DNA polymerases [KOD-Plus (Toyobo Co. Ltd.) for PPO1 and ExTaq (Takara Bio Inc.) for PPO2 ], according to the manufacturer's recommended protocol.

    Techniques: Isolation, Polymerase Chain Reaction, Amplification, Binding Assay

    The G/C-rich sequence associated with a meiosis-specific DSB on chromosome IV of S. cerevisiae folds into intramolecular G-quadruplex or i-motif structures and blocks DNA synthesis. ( A ) Here is a schematic diagram showing the nucleotide sequence of G-rich (WT) and its corresponding mutant template. ( B ) The Taq polymerase stop assay was performed in the absence (lanes 1 and 6 ) or presence of increasing concentrations of KCl (10, 25, 50, and 100 mM; lanes 2 – 5 and lanes 7 – 10 , respectively). The solid triangle on top of the gel denotes increasing concentrations of KCl. ( C ) Here we show a diagram of C-rich (WT) and its corresponding mutant DNA template. ( D ) Given here is the KOD-Plus DNA polymerase (from Thermococcus kodakaraensis ) stop assay performed with WT i-motif and its corresponding mutant template at the indicated pH values. Lane 1 is the primer used in this study. ( E ) SWNTs stabilize the i-motif DNA structure at neutral pH, which, in turn, blocks primer extension by DNA polymerase.

    Journal: Biophysical Journal

    Article Title: Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

    doi: 10.1016/j.bpj.2017.04.028

    Figure Lengend Snippet: The G/C-rich sequence associated with a meiosis-specific DSB on chromosome IV of S. cerevisiae folds into intramolecular G-quadruplex or i-motif structures and blocks DNA synthesis. ( A ) Here is a schematic diagram showing the nucleotide sequence of G-rich (WT) and its corresponding mutant template. ( B ) The Taq polymerase stop assay was performed in the absence (lanes 1 and 6 ) or presence of increasing concentrations of KCl (10, 25, 50, and 100 mM; lanes 2 – 5 and lanes 7 – 10 , respectively). The solid triangle on top of the gel denotes increasing concentrations of KCl. ( C ) Here we show a diagram of C-rich (WT) and its corresponding mutant DNA template. ( D ) Given here is the KOD-Plus DNA polymerase (from Thermococcus kodakaraensis ) stop assay performed with WT i-motif and its corresponding mutant template at the indicated pH values. Lane 1 is the primer used in this study. ( E ) SWNTs stabilize the i-motif DNA structure at neutral pH, which, in turn, blocks primer extension by DNA polymerase.

    Article Snippet: The annealing mixture was mixed with a reaction buffer (1 μ L) containing 1.5 mg/mL bovine serum albumin, 0.2 mM dNTPs, and 0.5 U of KOD-Plus DNA polymerase (Toyobo, Osaka, Japan).

    Techniques: Sequencing, DNA Synthesis, Mutagenesis

    Successive incorporation of 2′,4′-bridged nucleotides using analogue 3 with various DNA polymerases; KOD Dash (lane 2), wild type KOD (lane 3), KOD 1 (lane 4), KOD 2 (lane 5), KOD 3 (lane 6), KOD 4 (lane 7), KOD 5 (lane 8), KOD 6 (lane 9), KOD 7 (lane 10), KOD 8 (lane 11), and Vent(exo-) (lane 12). Primer extension reactions were performed for 1 h at 74°C under enzyme concentration of 0.4 U/μL. Primer P2 only migrated in lane 1.

    Journal: Molecules

    Article Title: Study on Suitability of KOD DNA Polymerase for Enzymatic Production of Artificial Nucleic Acids Using Base/Sugar Modified Nucleoside Triphosphates

    doi: 10.3390/molecules15118229

    Figure Lengend Snippet: Successive incorporation of 2′,4′-bridged nucleotides using analogue 3 with various DNA polymerases; KOD Dash (lane 2), wild type KOD (lane 3), KOD 1 (lane 4), KOD 2 (lane 5), KOD 3 (lane 6), KOD 4 (lane 7), KOD 5 (lane 8), KOD 6 (lane 9), KOD 7 (lane 10), KOD 8 (lane 11), and Vent(exo-) (lane 12). Primer extension reactions were performed for 1 h at 74°C under enzyme concentration of 0.4 U/μL. Primer P2 only migrated in lane 1.

    Article Snippet: We have previously reported [ ] that incorporation of this type of bridged nucleotide (2′,4′-BNANC ) [ ] is more difficult than that of the prototype 2′-O ,4′-C -methylene bridged/locked nucleotide (BNA/LNA), which can be incorporated successively using wild-type KOD DNA polymerase [ ].

    Techniques: Concentration Assay