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  • 94
    New England Biolabs taq i methyltransferase
    A total of 1225 tiled fluorescence microscopy images of a sample of E. coli genomic <t>DNA</t> labeled with Atto647N at sites reading 5′-TCGA-3′ using the M. <t>Taq</t> I DNA <t>methyltransferase</t> enzyme in order to direct labeling. The image contains approximately 500 megabases of genomic material and took of the order of 10 min to acquire.
    Taq I Methyltransferase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
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    95
    Millipore taq i
    ( A ) Conventional techniques used to clone PCR products include (1) restriction-cutback methods, in which a restriction endonuclease is used to cleave both DNA insert and vector, leaving complementary overhangs; (2) blunt-end cloning, in which both insert and vector are prepared to have blunt ends; (3) TA Cloning uses the thermophilic <t>Taq</t> I polymerase to add a single 3′A overhang to each end of a PCR product, which can then be joined to a TA Cloning vector with single 3′T overhangs. All three methods involve a second step in which the PCR product and the vector are joined by the action of DNA ligase. ( B ) During DNA relaxation, the enzyme Vaccinia DNA topoisomerase I cleaves the phosphodiester backbone of one strand at a consensus pentapyrimidine element 5′-(C/T)CCTT in the scissile strand, allowing the DNA to unwind and reduce its winding (W) number, n , to n +1 or n −1 (for DNA that was negatively or positively supercoiled, respectively). ( C ) In the cleavage reaction, bond energy is conserved by formation of a covalent adduct between the 3′ phosphate of the incised strand and a tyrosyl residue (Tyr-274) of the protein. The covalent complex can reclose across the same bond originally cleaved or it can combine with a heterologous acceptor DNA that has a 5′ hydroxyl tail complementary to that of the adduct, and thereby create a recombinant molecule. ( D ) Topoisomerase I-mediated cloning uses the reaction mediated by Vaccinia DNA topoisomerase I to join PCR-amplified DNA fragments into plasmid vectors. PCR fragments have 5′ hydroxyl residues from the primers used for the amplification reaction, and therefore are an ideal substrate for the topoisomerase ligation reaction. The topoisomerase I (solid black shape) is shown linked to the vector through the 3′ phosphate (P) of the incised strand. The PCR product has single 3′ A overhangs (A).
    Taq I, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq i/product/Millipore
    Average 95 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
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    98
    TaKaRa taq i
    The three different <t>Taq</t> I PCR-RFLP genotypes of pCISH gene. The genotypes (AA, AG, GG) are shown at the top. M: DNA molecular marker DL2000. PCR-RFLP, polymerase chain reaction–restriction fragment length polymorphism; pCISH, porcine cytokine inducible SH2-containing protein.
    Taq I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 98/100, based on 327 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 98 stars, based on 327 article reviews
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    92
    Promega taq i
    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, <t>Taq</t> I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Taq I, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher taq i
    Promoter hypermethylation of DUSP2 in human cancers. a . Combined bisulfite restriction analysis (COBRA) of DUSP2 . Bisulfite-treated DNA from the indicated cancer cell lines, normal epithelial breast cells (HB2) and in vitro methylated DNA ( ivm ) was amplified, digested with <t>Taq</t> I (+) or mock digested (-) and resolved on 2 % agarose gels with a 100 bp marker (M). Methylation levels obtained from pyrosequencing are indicated in percentage. b . Bisulfite pyrosequence analysis of DUSP2 in human cells. The mean methylation levels of five CpGs were analyzed by pyrosequencing (Seq1). The analysis included the results of three independent experiments. The dashed line marks 5 % threshold
    Taq I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 716 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    taq i  (Roche)
    92
    Roche taq i
    Consensus sequence of the SSUsat monomers from Spisula subtruncata . On the basis of the DNA sequences of the recovered SSUsat monomers from Spisula subtruncata genome, a consensus sequence was derived. Restriction sites for Msp I/ <t>Hpa</t> II, Pvu II and <t>Taq</t> I are underlined. Green and red arrows indicate the positions of PCR primers used for SSUsat amplification in related species.
    Taq I, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 62 article reviews
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    92
    GE Healthcare taq i
    Dendrogram derived from FAFLP patterns of 106 V. cholerae strains with the Apa I/ <t>Taq</t> I enzyme combination. The dendrogram was constructed by using the Pearson coefficient and the unweighted pair group method of arithmetic averages. V. mimicus LMG 7896 T was included as an out-group. The year, place, and source of isolation of strains are listed. C and E mean clinical and environmental isolates, respectively. Cophenetic correlation values are shown on the left.
    Taq I, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq i/product/GE Healthcare
    Average 92 stars, based on 21 article reviews
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    92
    Boehringer Mannheim taq i
    (A) 16S PCR-RFLP patterns observed with <t>Dde</t> I. (B) 16S PCR-RFLP patterns observed with <t>Taq</t> I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Taq I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher restrictase taq i
    (A) 16S PCR-RFLP patterns observed with <t>Dde</t> I. (B) 16S PCR-RFLP patterns observed with <t>Taq</t> I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Restrictase Taq I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher taq i polymerase
    (A) 16S PCR-RFLP patterns observed with <t>Dde</t> I. (B) 16S PCR-RFLP patterns observed with <t>Taq</t> I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Taq I Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    A total of 1225 tiled fluorescence microscopy images of a sample of E. coli genomic DNA labeled with Atto647N at sites reading 5′-TCGA-3′ using the M. Taq I DNA methyltransferase enzyme in order to direct labeling. The image contains approximately 500 megabases of genomic material and took of the order of 10 min to acquire.

    Journal: ACS Nano

    Article Title: Combing of Genomic DNA from Droplets Containing Picograms of Material

    doi: 10.1021/nn5063497

    Figure Lengend Snippet: A total of 1225 tiled fluorescence microscopy images of a sample of E. coli genomic DNA labeled with Atto647N at sites reading 5′-TCGA-3′ using the M. Taq I DNA methyltransferase enzyme in order to direct labeling. The image contains approximately 500 megabases of genomic material and took of the order of 10 min to acquire.

    Article Snippet: To the molten agarose we added 10 μL of NEB cutsmart buffer, 10 μL of M.Taq I DNA methyltransferase (New England Biolabs) and 10 μL of 1 mM AdoEnYn cofactor (5′-[(S )-[(3S )-3-amino-3-carboxylpropyl](E )-pent-2-en-4-ynylsulfonio]-5′-deoxyadenosine).

    Techniques: Fluorescence, Microscopy, Labeling

    Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Journal: Applied and Environmental Microbiology

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    doi: 10.1128/AEM.67.10.4414-4425.2001

    Figure Lengend Snippet: Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Article Snippet: To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.).

    Techniques: Amplification, Positive Control

    ( A ) Conventional techniques used to clone PCR products include (1) restriction-cutback methods, in which a restriction endonuclease is used to cleave both DNA insert and vector, leaving complementary overhangs; (2) blunt-end cloning, in which both insert and vector are prepared to have blunt ends; (3) TA Cloning uses the thermophilic Taq I polymerase to add a single 3′A overhang to each end of a PCR product, which can then be joined to a TA Cloning vector with single 3′T overhangs. All three methods involve a second step in which the PCR product and the vector are joined by the action of DNA ligase. ( B ) During DNA relaxation, the enzyme Vaccinia DNA topoisomerase I cleaves the phosphodiester backbone of one strand at a consensus pentapyrimidine element 5′-(C/T)CCTT in the scissile strand, allowing the DNA to unwind and reduce its winding (W) number, n , to n +1 or n −1 (for DNA that was negatively or positively supercoiled, respectively). ( C ) In the cleavage reaction, bond energy is conserved by formation of a covalent adduct between the 3′ phosphate of the incised strand and a tyrosyl residue (Tyr-274) of the protein. The covalent complex can reclose across the same bond originally cleaved or it can combine with a heterologous acceptor DNA that has a 5′ hydroxyl tail complementary to that of the adduct, and thereby create a recombinant molecule. ( D ) Topoisomerase I-mediated cloning uses the reaction mediated by Vaccinia DNA topoisomerase I to join PCR-amplified DNA fragments into plasmid vectors. PCR fragments have 5′ hydroxyl residues from the primers used for the amplification reaction, and therefore are an ideal substrate for the topoisomerase ligation reaction. The topoisomerase I (solid black shape) is shown linked to the vector through the 3′ phosphate (P) of the incised strand. The PCR product has single 3′ A overhangs (A).

    Journal: Genome Research

    Article Title: Genome-Scale Cloning and Expression of Individual Open Reading Frames Using Topoisomerase I-Mediated Ligation

    doi:

    Figure Lengend Snippet: ( A ) Conventional techniques used to clone PCR products include (1) restriction-cutback methods, in which a restriction endonuclease is used to cleave both DNA insert and vector, leaving complementary overhangs; (2) blunt-end cloning, in which both insert and vector are prepared to have blunt ends; (3) TA Cloning uses the thermophilic Taq I polymerase to add a single 3′A overhang to each end of a PCR product, which can then be joined to a TA Cloning vector with single 3′T overhangs. All three methods involve a second step in which the PCR product and the vector are joined by the action of DNA ligase. ( B ) During DNA relaxation, the enzyme Vaccinia DNA topoisomerase I cleaves the phosphodiester backbone of one strand at a consensus pentapyrimidine element 5′-(C/T)CCTT in the scissile strand, allowing the DNA to unwind and reduce its winding (W) number, n , to n +1 or n −1 (for DNA that was negatively or positively supercoiled, respectively). ( C ) In the cleavage reaction, bond energy is conserved by formation of a covalent adduct between the 3′ phosphate of the incised strand and a tyrosyl residue (Tyr-274) of the protein. The covalent complex can reclose across the same bond originally cleaved or it can combine with a heterologous acceptor DNA that has a 5′ hydroxyl tail complementary to that of the adduct, and thereby create a recombinant molecule. ( D ) Topoisomerase I-mediated cloning uses the reaction mediated by Vaccinia DNA topoisomerase I to join PCR-amplified DNA fragments into plasmid vectors. PCR fragments have 5′ hydroxyl residues from the primers used for the amplification reaction, and therefore are an ideal substrate for the topoisomerase ligation reaction. The topoisomerase I (solid black shape) is shown linked to the vector through the 3′ phosphate (P) of the incised strand. The PCR product has single 3′ A overhangs (A).

    Article Snippet: PCR cycling conditions were: 1 cycle of 94°C for 10 min; 25 cycles of 94°C for 1 min, 56°C for 1 min, and 72°C for 3 min; followed by 1 cycle of 72°C for 4 min. Each initial amplification was performed in a 30 μl total volume with 2 units of Taq I (Sigma, St. Louis, MO) polymerase, 0.4 μl of 50 m m dNTPs, 100 ng of each primer, in 1× PCR buffer J (Invitrogen, Carlsbad, CA) (final concentrations of 60 m m Tris-Cl, 15 m m (NH4 )2 SO4 , 2.0 m m Mg2+ , pH 9.5).

    Techniques: Polymerase Chain Reaction, Plasmid Preparation, Clone Assay, TA Cloning, Recombinant, Amplification, Ligation

    The three different Taq I PCR-RFLP genotypes of pCISH gene. The genotypes (AA, AG, GG) are shown at the top. M: DNA molecular marker DL2000. PCR-RFLP, polymerase chain reaction–restriction fragment length polymorphism; pCISH, porcine cytokine inducible SH2-containing protein.

    Journal: Asian-Australasian Journal of Animal Sciences

    Article Title: Characterization of porcine cytokine inducible SH2-containing protein gene and its association with piglet diarrhea traits

    doi: 10.5713/ajas.16.0169

    Figure Lengend Snippet: The three different Taq I PCR-RFLP genotypes of pCISH gene. The genotypes (AA, AG, GG) are shown at the top. M: DNA molecular marker DL2000. PCR-RFLP, polymerase chain reaction–restriction fragment length polymorphism; pCISH, porcine cytokine inducible SH2-containing protein.

    Article Snippet: For the PCR-RFLP profile, 8.5 μL of PCR products amplified by primer pairs CV-1 or CV-41 were digested with 5 U of Taq I or Hae III (TaKaRa, Japan) for 5 h at 65°C or 37°C, and then separated on a 1.5% agarose gel.

    Techniques: Polymerase Chain Reaction, Marker

    Identification of the duplication junction via inverse PCR. a Isolation of the junction fragment. Two distinct inverse PCR products were observed following agarose gel electrophoresis. The larger product was derived from a normal allele and the small product from a rearranged allele (left). The amplified products were purified following nested PCR (right). P, patient; C, control; H, H 2 O. b Sanger sequencing of the PCR products including the junction. The unknown sequence next to the junction was identified as intron 1 of the OTC gene in the reverse orientation. The normal exon 6 and intron 1 sequences are aligned in red and blue typeface, respectively. Underlined nucleotides indicate microhomology at the breakpoint junction. c Predicted structure of the junction. Horizontal arrows indicate the recognition sites of the primers used for inverse PCR and the vertical arrows denote the Taq I restriction sites

    Journal: BMC Medical Genetics

    Article Title: Exonic duplication of the OTC gene by a complex rearrangement that likely occurred via a replication-based mechanism: a case report

    doi: 10.1186/s12881-018-0733-3

    Figure Lengend Snippet: Identification of the duplication junction via inverse PCR. a Isolation of the junction fragment. Two distinct inverse PCR products were observed following agarose gel electrophoresis. The larger product was derived from a normal allele and the small product from a rearranged allele (left). The amplified products were purified following nested PCR (right). P, patient; C, control; H, H 2 O. b Sanger sequencing of the PCR products including the junction. The unknown sequence next to the junction was identified as intron 1 of the OTC gene in the reverse orientation. The normal exon 6 and intron 1 sequences are aligned in red and blue typeface, respectively. Underlined nucleotides indicate microhomology at the breakpoint junction. c Predicted structure of the junction. Horizontal arrows indicate the recognition sites of the primers used for inverse PCR and the vertical arrows denote the Taq I restriction sites

    Article Snippet: Inverse PCR were performed using restriction enzyme Taq I (TaKaRa, Shiga, Japan) to isolate the unknown sequences adjacent to the duplicated region of the OTC gene in the study patient.

    Techniques: Inverse PCR, Isolation, Agarose Gel Electrophoresis, Derivative Assay, Amplification, Purification, Nested PCR, Sequencing, Polymerase Chain Reaction

    Relative yield of the modified DNAs generated by PCR using various triphosphate analogs together with ( A ) Taq DNA polymerase, ( B ) Tth DNA polymerase, ( C ) Vent(exo-) DNA polymerase, ( D ) KOD Dash DNA polymerase and ( E ) KOD(exo-) DNA polymerase. The x -axis indicates the kind of triphosphate analog used, and the y -axis indicates the relative yield of the PCR product. The black and white bars indicate the relative yield of the PCR product generated from amplifying regions I and II, respectively. The relative standard deviations were less than ±6% for all reactions.

    Journal: Nucleic Acids Research

    Article Title: Systematic characterization of 2?-deoxynucleoside- 5?-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA

    doi: 10.1093/nar/gkl637

    Figure Lengend Snippet: Relative yield of the modified DNAs generated by PCR using various triphosphate analogs together with ( A ) Taq DNA polymerase, ( B ) Tth DNA polymerase, ( C ) Vent(exo-) DNA polymerase, ( D ) KOD Dash DNA polymerase and ( E ) KOD(exo-) DNA polymerase. The x -axis indicates the kind of triphosphate analog used, and the y -axis indicates the relative yield of the PCR product. The black and white bars indicate the relative yield of the PCR product generated from amplifying regions I and II, respectively. The relative standard deviations were less than ±6% for all reactions.

    Article Snippet: Materials The following commercial available thermostable DNA polymerases were purchased: Taq (Takara Bio), Tth (Toyobo), Vent(exo-) (New England Biolabs) and KOD Dash (Toyobo).

    Techniques: Modification, Generated, Polymerase Chain Reaction

    Representative ultraviolet images from ethidium bromide-stained PAGE gels of the 110 nt PCR product derived from pUC18 (amplifying region I) and the C5-modified nucleoside triphosphates. ( A–C ) The reaction mixtures containing dATP, dGTP, dCTP and T AL (lane 3), T AC (lane 4), T AF (lane 5), T PA (lane 6), T PN (lane 7), T PR (lane 8), T A2 (lane 11), T A4 (lane 12), T A6 (lane 13), T G6 (lane 14), T ME (lane 15), T CN (lane 16), or T DH (lane 17) were separated by electrophoresis on denaturing PAGE. Except for the positive control, the reaction mixtures do not contain natural TTP. The PCR product was generated by the positive control (reaction mixture containing dATP, dGTP, dCTP and TTP; lanes 2 and 10) but not by the negative control (reaction mixture containing dATP, dGTP and dCTP; lanes 1 and 9). ( D–F ) Reaction mixtures containing dATP, dGTP, TTP and C AL (lane 3), C AC (lane 4), C AF (lane 5), C PA (lane 6), C PN (lane 7), C PR (lane 8), C A2 (lane 11), C A4 (lane 12), C A6 (lane 13), C G6 (lane 14), C ME (lane 15), C CN (lane 16) or C DH (lane 17) were separated by electrophoresis on denaturing PAGE. Except for the positive control, the reaction mixtures did not contain natural dCTP. The PCR product was generated by the positive control (reaction mixture containing dATP, dGTP, dCTP and TTP; lanes 2 and 10) but not by the negative control (reaction mixture containing dATP, dGTP and TTP; lanes 1 and 9). The thermostable DNA polymerases used were Taq (A, D), Vent(exo-) (B and E), and KOD Dash (C and F).

    Journal: Nucleic Acids Research

    Article Title: Systematic characterization of 2?-deoxynucleoside- 5?-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA

    doi: 10.1093/nar/gkl637

    Figure Lengend Snippet: Representative ultraviolet images from ethidium bromide-stained PAGE gels of the 110 nt PCR product derived from pUC18 (amplifying region I) and the C5-modified nucleoside triphosphates. ( A–C ) The reaction mixtures containing dATP, dGTP, dCTP and T AL (lane 3), T AC (lane 4), T AF (lane 5), T PA (lane 6), T PN (lane 7), T PR (lane 8), T A2 (lane 11), T A4 (lane 12), T A6 (lane 13), T G6 (lane 14), T ME (lane 15), T CN (lane 16), or T DH (lane 17) were separated by electrophoresis on denaturing PAGE. Except for the positive control, the reaction mixtures do not contain natural TTP. The PCR product was generated by the positive control (reaction mixture containing dATP, dGTP, dCTP and TTP; lanes 2 and 10) but not by the negative control (reaction mixture containing dATP, dGTP and dCTP; lanes 1 and 9). ( D–F ) Reaction mixtures containing dATP, dGTP, TTP and C AL (lane 3), C AC (lane 4), C AF (lane 5), C PA (lane 6), C PN (lane 7), C PR (lane 8), C A2 (lane 11), C A4 (lane 12), C A6 (lane 13), C G6 (lane 14), C ME (lane 15), C CN (lane 16) or C DH (lane 17) were separated by electrophoresis on denaturing PAGE. Except for the positive control, the reaction mixtures did not contain natural dCTP. The PCR product was generated by the positive control (reaction mixture containing dATP, dGTP, dCTP and TTP; lanes 2 and 10) but not by the negative control (reaction mixture containing dATP, dGTP and TTP; lanes 1 and 9). The thermostable DNA polymerases used were Taq (A, D), Vent(exo-) (B and E), and KOD Dash (C and F).

    Article Snippet: Materials The following commercial available thermostable DNA polymerases were purchased: Taq (Takara Bio), Tth (Toyobo), Vent(exo-) (New England Biolabs) and KOD Dash (Toyobo).

    Techniques: Staining, Polyacrylamide Gel Electrophoresis, Polymerase Chain Reaction, Derivative Assay, Modification, Electrophoresis, Positive Control, Generated, Negative Control

    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Article Snippet: The amplified product of the gltA gene obtained with the set of primers suggested by Regnery et al. ( ) was digested with Taq I (Promega, Madison, Wis.) and Hha I (new England BioLabs, Beverly, Mass.) restriction endonucleases.

    Techniques: Polymerase Chain Reaction

    PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Article Snippet: The amplified product of the gltA gene obtained with the set of primers suggested by Regnery et al. ( ) was digested with Taq I (Promega, Madison, Wis.) and Hha I (new England BioLabs, Beverly, Mass.) restriction endonucleases.

    Techniques: Polymerase Chain Reaction

    Promoter hypermethylation of DUSP2 in human cancers. a . Combined bisulfite restriction analysis (COBRA) of DUSP2 . Bisulfite-treated DNA from the indicated cancer cell lines, normal epithelial breast cells (HB2) and in vitro methylated DNA ( ivm ) was amplified, digested with Taq I (+) or mock digested (-) and resolved on 2 % agarose gels with a 100 bp marker (M). Methylation levels obtained from pyrosequencing are indicated in percentage. b . Bisulfite pyrosequence analysis of DUSP2 in human cells. The mean methylation levels of five CpGs were analyzed by pyrosequencing (Seq1). The analysis included the results of three independent experiments. The dashed line marks 5 % threshold

    Journal: BMC Cancer

    Article Title: The dual specificity phosphatase 2 gene is hypermethylated in human cancer and regulated by epigenetic mechanisms

    doi: 10.1186/s12885-016-2087-6

    Figure Lengend Snippet: Promoter hypermethylation of DUSP2 in human cancers. a . Combined bisulfite restriction analysis (COBRA) of DUSP2 . Bisulfite-treated DNA from the indicated cancer cell lines, normal epithelial breast cells (HB2) and in vitro methylated DNA ( ivm ) was amplified, digested with Taq I (+) or mock digested (-) and resolved on 2 % agarose gels with a 100 bp marker (M). Methylation levels obtained from pyrosequencing are indicated in percentage. b . Bisulfite pyrosequence analysis of DUSP2 in human cells. The mean methylation levels of five CpGs were analyzed by pyrosequencing (Seq1). The analysis included the results of three independent experiments. The dashed line marks 5 % threshold

    Article Snippet: Products were digested with 0.5 μl Taq I (Fermentas) 1 h at 65 °C and resolved on 2 % TBE agarose gel.

    Techniques: Combined Bisulfite Restriction Analysis Assay, In Vitro, Methylation, Amplification, Marker

    Hypermethylation of DUSP2 in primary Merkel cell carcinoma (MCC). a . Structure of the DUSP2 CpG island promoter on chromosome 2q11.2. Vertical lines indicate CpGs and the transcriptional start site is marked. A CTCF motif sequence (GGCAGAGCA; CTCFBSDB2.0) is marked [ 47 ]. Primers used for COBRA and sequencing (Seq1 and Seq2) are depicted by arrows. TaqI restriction sites for COBRA and CpGs analyzed by pyrosequencing are indicated. The 454 bp DUSP2 fragment for the luciferase promoter assay is indicated. b . Methylation of DUSP2 in MCC (m = methylated). For COBRA bisulfite-treated DNA from MCC, benign nevus cell nevi (NCN) and in vitro methylated DNA ( ivm ) was amplified by semi-nested PCR. First and second PCR products are indicated (439 bp and 303 bp, respectively). Products were digested with Taq I (+) or mock digested (-) and resolved on 2 % agarose gels with a 100 bp marker (M)

    Journal: BMC Cancer

    Article Title: The dual specificity phosphatase 2 gene is hypermethylated in human cancer and regulated by epigenetic mechanisms

    doi: 10.1186/s12885-016-2087-6

    Figure Lengend Snippet: Hypermethylation of DUSP2 in primary Merkel cell carcinoma (MCC). a . Structure of the DUSP2 CpG island promoter on chromosome 2q11.2. Vertical lines indicate CpGs and the transcriptional start site is marked. A CTCF motif sequence (GGCAGAGCA; CTCFBSDB2.0) is marked [ 47 ]. Primers used for COBRA and sequencing (Seq1 and Seq2) are depicted by arrows. TaqI restriction sites for COBRA and CpGs analyzed by pyrosequencing are indicated. The 454 bp DUSP2 fragment for the luciferase promoter assay is indicated. b . Methylation of DUSP2 in MCC (m = methylated). For COBRA bisulfite-treated DNA from MCC, benign nevus cell nevi (NCN) and in vitro methylated DNA ( ivm ) was amplified by semi-nested PCR. First and second PCR products are indicated (439 bp and 303 bp, respectively). Products were digested with Taq I (+) or mock digested (-) and resolved on 2 % agarose gels with a 100 bp marker (M)

    Article Snippet: Products were digested with 0.5 μl Taq I (Fermentas) 1 h at 65 °C and resolved on 2 % TBE agarose gel.

    Techniques: Sequencing, Combined Bisulfite Restriction Analysis Assay, Luciferase, Promoter Assay, Methylation, In Vitro, Amplification, Nested PCR, Polymerase Chain Reaction, Marker

    Consensus sequence of the SSUsat monomers from Spisula subtruncata . On the basis of the DNA sequences of the recovered SSUsat monomers from Spisula subtruncata genome, a consensus sequence was derived. Restriction sites for Msp I/ Hpa II, Pvu II and Taq I are underlined. Green and red arrows indicate the positions of PCR primers used for SSUsat amplification in related species.

    Journal: Scientific Reports

    Article Title: Methylation profile of a satellite DNA constituting the intercalary G+C-rich heterochromatin of the cut trough shell Spisula subtruncata (Bivalvia, Mactridae)

    doi: 10.1038/s41598-017-07231-7

    Figure Lengend Snippet: Consensus sequence of the SSUsat monomers from Spisula subtruncata . On the basis of the DNA sequences of the recovered SSUsat monomers from Spisula subtruncata genome, a consensus sequence was derived. Restriction sites for Msp I/ Hpa II, Pvu II and Taq I are underlined. Green and red arrows indicate the positions of PCR primers used for SSUsat amplification in related species.

    Article Snippet: Southern and dot blot hybridisation Genomic DNAs were digested with Hae III (Fermentas), Hpa II (Fermentas), Msp I (Promega), Pvu II (New England Biolabs) and Taq I (Roche).

    Techniques: Sequencing, Derivative Assay, Polymerase Chain Reaction, Amplification

    Dendrogram derived from FAFLP patterns of 106 V. cholerae strains with the Apa I/ Taq I enzyme combination. The dendrogram was constructed by using the Pearson coefficient and the unweighted pair group method of arithmetic averages. V. mimicus LMG 7896 T was included as an out-group. The year, place, and source of isolation of strains are listed. C and E mean clinical and environmental isolates, respectively. Cophenetic correlation values are shown on the left.

    Journal: Journal of Clinical Microbiology

    Article Title: Genomic Diversity of Clinical and Environmental Vibrio cholerae Strains Isolated in Brazil between 1991 and 2001 as Revealed by Fluorescent Amplified Fragment Length Polymorphism Analysis

    doi: 10.1128/JCM.41.5.1946-1950.2003

    Figure Lengend Snippet: Dendrogram derived from FAFLP patterns of 106 V. cholerae strains with the Apa I/ Taq I enzyme combination. The dendrogram was constructed by using the Pearson coefficient and the unweighted pair group method of arithmetic averages. V. mimicus LMG 7896 T was included as an out-group. The year, place, and source of isolation of strains are listed. C and E mean clinical and environmental isolates, respectively. Cophenetic correlation values are shown on the left.

    Article Snippet: Briefly, 1 μg of high-molecular-mass DNA was digested with Taq I and Apa I (Amersham Pharmacia Biotech, Uppsala, Sweden) followed by ligation of restriction half-site-specific adapters to all restriction fragments with T4 ligase (Amersham Pharmacia Biotech).

    Techniques: Derivative Assay, Construct, Isolation

    (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Journal: Journal of Clinical Microbiology

    Article Title: Rapid Identification of Campylobacter, Arcobacter, and Helicobacter Isolates by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene

    doi:

    Figure Lengend Snippet: (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Article Snippet: For restriction endonuclease digestion a 20-μl reaction mixture which included 10 μl of the PCR amplicon with 10 U of the restriction endonuclease Dde I (Boehringer-Mannheim, Indianapolis, Ind.), Taq I (Boehringer-Mannheim), or Bsr I (New England Biolabs, Inc., Beverly, Mass.) was employed, following conditions recommended by the respective manufacturers.

    Techniques: Polymerase Chain Reaction