dna polymerase Thermo Fisher Search Results


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  • 95
    New England Biolabs phi29 dna polymerase
    Phi29 Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 599 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher accuprime pfx dna polymerase
    Single strand binding protein, ET SSB, only has a minor effect on the reduction of artifacts. Taq (NE Biolabs) and <t>AccuPrime</t> Pfx (Life Technologies) <t>DNA</t> polymerases were used in amplification of TALE DNA repeats. The arrows indicate the expected size of the amplification products. PCR conditions are given in the supplementary material .
    Accuprime Pfx Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2254 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher phusion high fidelity dna polymerase
    Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial <t>DNA</t> (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of <t>Phusion,</t> Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .
    Phusion High Fidelity Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 14136 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher taq dna polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 33236 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher dna polymerase
    <t>PCR</t> of human genomic <t>DNA</t>
    Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 3625 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher bsm dna polymerase
    Verification of UIMA using different <t>DNA</t> polymerases. All reactions shared the same primer (RL) and template (F*R*) and were incubated for 180 min. The sequences of RL and F*R* were shown in Table S1 . ( A ) Real-time fluorescence change in reactions using a series of Bst DNA polymerases ( Bst LF, Bst 2.0, Bst 2.0 WS, and Bst 3.0) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( B ) Real-time fluorescence change in reactions using non- Bst polymerases <t>(Bsm,</t> BcaBEST, Vent(exo-), and z-Taq) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( C ) Temperature gradients assay for the products of reactions using the polymerases with negative results in ( B ). The products were analyzed by 2.5% agarose gel electrophoresis. NTC and NPC for Bsm were performed at 56 °C. NTCs and NPCs for Vent (exo-) and z-Taq were performed at 63 °C. The groping of gels cropped from different gels. Exposure time is 5 s. ( D ) Temperature gradients assay for the products of reactions using the polymerases of Klenow(exo-) and Klenow. The products were analyzed by 2.5% agarose gel electrophoresis. Their NTCs and NPCs were performed at 43 °C. M1 and M2: DNA Marker. NTC: no-target control; NPC: no-primer control. The groping of gels cropped from different gels. Exposure time is 5 s. The full-length gels are presented in Supplementary Figure S7 .
    Bsm Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher t4 dna polymerase exonuclease
    UV damage does not affect NCP reconstitution with the 601 sequence. A , NCP reconstitution with UV-undamaged and -damaged DNA. The 147-bp 601 DNA containing both UV lesions and labeling were mixed with histone octamer at 2 m NaCl. The reconstitution was performed by stepwise salt dialysis, and the final NaCl concentration was 50 m m . The reconstituted products were resolved in 5% native polyacrylamide gel and stained with SYBR Gold. The 100-bp DNA markers are indicated on the left. B , presence of CPDs and 6-4PPs in UV-damaged DNA. The different UV-damaged DNA were blotted on the nitrocellulose and detected by lesion-specific antibodies. The same membranes were reprobed with 32 P-labeled DNA to show equal loading. C , Southern blot of the photoproduct yield of the UV-irradiated DNA fragment. The DNA was treated with or without photolyase prior to the <t>T4</t> DNA polymerase ( pol ) digestion. The digested samples were blotted on the nylon membrane and probed with with 32 P-labeled DNA. D , quantification data of the photoproduct yield by Southern blots. The CPD signals were calculated by subtracting the total signals with the 6-4PPs signals. Three independent experiments were performed to show error bars .
    T4 Dna Polymerase Exonuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 169 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher proof reading platinum pfx dnapol
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Proof Reading Platinum Pfx Dnapol, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher dreamtaq dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Dreamtaq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3323 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher phusion dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Phusion Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 8083 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher elongase dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Elongase Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher amplitaq 360 dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Amplitaq 360 Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher thermalace dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Thermalace Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 141 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Promega gotaq dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Gotaq Dna Polymerase, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 9071 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher amplitaq dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Amplitaq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4337 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher rtth dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Rtth Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 206 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher sybgreen dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Sybgreen Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher accuprimetaq dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Accuprimetaq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pfx50 dna polymerase
    <t>RT-PCR</t> of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic <t>DNA</t> (B), or a control without RT (C).
    Pfx50 Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 328 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Thermo Fisher thermosequenase dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Thermosequenase Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher pfx50tm dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Pfx50tm Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher supertaq dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Supertaq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher thermoprimeplus dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Thermoprimeplus Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher proofstart dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Proofstart Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher hifi dna polymerase
    Screening various <t>DNA</t> polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, <t>Thermosequenase;</t> lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.
    Hifi Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher phi29 dna polymerase
    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic <t>DNA</t> prepared from tumor samples is then incubated with the <t>Phi29</t> DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study
    Phi29 Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 333 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher amplitaqr dna polymerase
    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic <t>DNA</t> prepared from tumor samples is then incubated with the <t>Phi29</t> DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study
    Amplitaqr Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher ϕ29 dna polymerase
    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic <t>DNA</t> prepared from tumor samples is then incubated with the <t>Phi29</t> DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study
    ϕ29 Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher fidelitaq dna polymerase
    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic <t>DNA</t> prepared from tumor samples is then incubated with the <t>Phi29</t> DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study
    Fidelitaq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 74 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher thermostart dna polymerase
    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic <t>DNA</t> prepared from tumor samples is then incubated with the <t>Phi29</t> DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study
    Thermostart Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Single strand binding protein, ET SSB, only has a minor effect on the reduction of artifacts. Taq (NE Biolabs) and AccuPrime Pfx (Life Technologies) DNA polymerases were used in amplification of TALE DNA repeats. The arrows indicate the expected size of the amplification products. PCR conditions are given in the supplementary material .

    Journal: Scientific Reports

    Article Title: PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

    doi: 10.1038/srep05052

    Figure Lengend Snippet: Single strand binding protein, ET SSB, only has a minor effect on the reduction of artifacts. Taq (NE Biolabs) and AccuPrime Pfx (Life Technologies) DNA polymerases were used in amplification of TALE DNA repeats. The arrows indicate the expected size of the amplification products. PCR conditions are given in the supplementary material .

    Article Snippet: Better performance of AccuPrime Pfx DNA polymerase compared to other DNA polymerases on repetitive DNA templates is also likely due to its mixture of other proprietary thermostable accessory proteins in this polymerase mix ( http://tools.lifetechnologies.com/content/sfs/manuals/accuprimepfx_man.pdf ) .

    Techniques: Binding Assay, Amplification, Polymerase Chain Reaction

    Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .

    Journal: Scientific Reports

    Article Title: Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results

    doi: 10.1038/srep08056

    Figure Lengend Snippet: Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .

    Article Snippet: Taq polymerase A range of 13 high fidelity, regular, economy and premium Taq polymerase enzymes were selected: Biotaq® (Bioline, London, UK), FastStart® High Fidelity PCR System (Roche, Mannheim, Germany), AmpliTaq Gold® (Applied Biosystems, Warrington, UK), HotStarTaq® DNA Polymerase (Qiagen, Hilden, Gernamy), Phusion® High Fidelity DNA Polymerase (Finnzymes, Espoo, Finland), Taq DNA Polymerase (Roche, Maylan, France), i-MaxTM II DNA Polymerase (iNtRON Biotechnology, Seongnam, Korea), KAPA HiFi™ (Kapa Biosystems, Boston, USA), OneTaq ™ DNA Polymerase (New England Biolabs, Hitchin, UK), Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Deep Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Pwo® DNA Polymerase (Roche, Maylan, France) and Velocity DNA Polymerase (Bioline, London, UK) (abbreviated names in ).

    Techniques: Polymerase Chain Reaction, Modification

    Differential peak morphologies of androgen receptor alleles resulting from DNA dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen Taq DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )

    Journal: BMC Genetics

    Article Title: A test of somatic mosaicism in the androgen receptor gene of Canada lynx (Lynx canadensis)

    doi: 10.1186/s12863-015-0284-y

    Figure Lengend Snippet: Differential peak morphologies of androgen receptor alleles resulting from DNA dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen Taq DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )

    Article Snippet: Amplification was conducted in a 10ul reaction containing deionized water (Invitrogen), 10X PCR Reaction Buffer (Invitrogen), 50 mM MgCl2 (Invitrogen), 100 mM dNTP solution (Invitrogen), 3 mg/mL BSA, 40uM forward and reverse primers (Integrated DNA Technologies) mentioned above (forward primers labeled with the fluorescent dye HEX), 0.0375U Invitrogen Taq DNA Polymerase, and 5 ng of DNA.

    Techniques: Positive Control, Amplification

    PCR of human genomic DNA

    Journal:

    Article Title: Expression of Kir7.1 and a Novel Kir7.1 Splice Variant in Native Human Retinal Pigment Epithelium

    doi: 10.1016/j.exer.2007.09.011

    Figure Lengend Snippet: PCR of human genomic DNA

    Article Snippet: The PCR products were generated by adding DNA polymerase (Taq DNA polymerase; Gibco BRL Life Technologies, Gaithersburg, MD or SuperTaq-Plus™ ; Ambion, Austin, TX) and cycled 30 times for GAPDH or 35 times for Kir7.1, Kir7.1S, or rhodopsin (1 min at 94°C, 1 min at 54°C–64°C, 0.5 –1 min at 72°C), followed by a 7 min-extension at 72°C.

    Techniques: Polymerase Chain Reaction

    RT-PCR analysis showing that qseE , yfhG , qseF , and glnB are cotranscribed. In lanes 1 to 3, primers flanking qseE to qseF show no product when no RT is added (lane 1) and show product when either a genomic DNA control or cDNA is used (lanes 2 and 3);

    Journal:

    Article Title: A Novel Two-Component Signaling System That Activates Transcription of an Enterohemorrhagic Escherichia coli Effector Involved in Remodeling of Host Actin ▿

    doi: 10.1128/JB.01848-06

    Figure Lengend Snippet: RT-PCR analysis showing that qseE , yfhG , qseF , and glnB are cotranscribed. In lanes 1 to 3, primers flanking qseE to qseF show no product when no RT is added (lane 1) and show product when either a genomic DNA control or cDNA is used (lanes 2 and 3);

    Article Snippet: Plasmid pNR01 was constructed by amplifying the qseE gene from the EHEC strain 86-24 by use of Pfx DNA polymerase (Invitrogen) with primers YfhKFBAD and YfhKRBAD and cloning the resulting PCR product into the EcoRI-KpnI cloning site of vector pBADMycHisA (Invitrogen).

    Techniques: Reverse Transcription Polymerase Chain Reaction

    Verification of UIMA using different DNA polymerases. All reactions shared the same primer (RL) and template (F*R*) and were incubated for 180 min. The sequences of RL and F*R* were shown in Table S1 . ( A ) Real-time fluorescence change in reactions using a series of Bst DNA polymerases ( Bst LF, Bst 2.0, Bst 2.0 WS, and Bst 3.0) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( B ) Real-time fluorescence change in reactions using non- Bst polymerases (Bsm, BcaBEST, Vent(exo-), and z-Taq) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( C ) Temperature gradients assay for the products of reactions using the polymerases with negative results in ( B ). The products were analyzed by 2.5% agarose gel electrophoresis. NTC and NPC for Bsm were performed at 56 °C. NTCs and NPCs for Vent (exo-) and z-Taq were performed at 63 °C. The groping of gels cropped from different gels. Exposure time is 5 s. ( D ) Temperature gradients assay for the products of reactions using the polymerases of Klenow(exo-) and Klenow. The products were analyzed by 2.5% agarose gel electrophoresis. Their NTCs and NPCs were performed at 43 °C. M1 and M2: DNA Marker. NTC: no-target control; NPC: no-primer control. The groping of gels cropped from different gels. Exposure time is 5 s. The full-length gels are presented in Supplementary Figure S7 .

    Journal: Scientific Reports

    Article Title: Unusual isothermal multimerization and amplification by the strand-displacing DNA polymerases with reverse transcription activities

    doi: 10.1038/s41598-017-13324-0

    Figure Lengend Snippet: Verification of UIMA using different DNA polymerases. All reactions shared the same primer (RL) and template (F*R*) and were incubated for 180 min. The sequences of RL and F*R* were shown in Table S1 . ( A ) Real-time fluorescence change in reactions using a series of Bst DNA polymerases ( Bst LF, Bst 2.0, Bst 2.0 WS, and Bst 3.0) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( B ) Real-time fluorescence change in reactions using non- Bst polymerases (Bsm, BcaBEST, Vent(exo-), and z-Taq) at 63 °C. No-primer controls (NPCs) were shown in Fig. S5 . ( C ) Temperature gradients assay for the products of reactions using the polymerases with negative results in ( B ). The products were analyzed by 2.5% agarose gel electrophoresis. NTC and NPC for Bsm were performed at 56 °C. NTCs and NPCs for Vent (exo-) and z-Taq were performed at 63 °C. The groping of gels cropped from different gels. Exposure time is 5 s. ( D ) Temperature gradients assay for the products of reactions using the polymerases of Klenow(exo-) and Klenow. The products were analyzed by 2.5% agarose gel electrophoresis. Their NTCs and NPCs were performed at 43 °C. M1 and M2: DNA Marker. NTC: no-target control; NPC: no-primer control. The groping of gels cropped from different gels. Exposure time is 5 s. The full-length gels are presented in Supplementary Figure S7 .

    Article Snippet: Bsm DNA polymerase, Maxima H Minus Reverse Transcriptase (MHM), Nuclease-Free Water were purchased from Thermo Fisher Scientific.

    Techniques: Incubation, Fluorescence, Agarose Gel Electrophoresis, Marker

    UV damage does not affect NCP reconstitution with the 601 sequence. A , NCP reconstitution with UV-undamaged and -damaged DNA. The 147-bp 601 DNA containing both UV lesions and labeling were mixed with histone octamer at 2 m NaCl. The reconstitution was performed by stepwise salt dialysis, and the final NaCl concentration was 50 m m . The reconstituted products were resolved in 5% native polyacrylamide gel and stained with SYBR Gold. The 100-bp DNA markers are indicated on the left. B , presence of CPDs and 6-4PPs in UV-damaged DNA. The different UV-damaged DNA were blotted on the nitrocellulose and detected by lesion-specific antibodies. The same membranes were reprobed with 32 P-labeled DNA to show equal loading. C , Southern blot of the photoproduct yield of the UV-irradiated DNA fragment. The DNA was treated with or without photolyase prior to the T4 DNA polymerase ( pol ) digestion. The digested samples were blotted on the nylon membrane and probed with with 32 P-labeled DNA. D , quantification data of the photoproduct yield by Southern blots. The CPD signals were calculated by subtracting the total signals with the 6-4PPs signals. Three independent experiments were performed to show error bars .

    Journal: The Journal of Biological Chemistry

    Article Title: UV Damage in DNA Promotes Nucleosome Unwrapping *

    doi: 10.1074/jbc.M110.140087

    Figure Lengend Snippet: UV damage does not affect NCP reconstitution with the 601 sequence. A , NCP reconstitution with UV-undamaged and -damaged DNA. The 147-bp 601 DNA containing both UV lesions and labeling were mixed with histone octamer at 2 m NaCl. The reconstitution was performed by stepwise salt dialysis, and the final NaCl concentration was 50 m m . The reconstituted products were resolved in 5% native polyacrylamide gel and stained with SYBR Gold. The 100-bp DNA markers are indicated on the left. B , presence of CPDs and 6-4PPs in UV-damaged DNA. The different UV-damaged DNA were blotted on the nitrocellulose and detected by lesion-specific antibodies. The same membranes were reprobed with 32 P-labeled DNA to show equal loading. C , Southern blot of the photoproduct yield of the UV-irradiated DNA fragment. The DNA was treated with or without photolyase prior to the T4 DNA polymerase ( pol ) digestion. The digested samples were blotted on the nylon membrane and probed with with 32 P-labeled DNA. D , quantification data of the photoproduct yield by Southern blots. The CPD signals were calculated by subtracting the total signals with the 6-4PPs signals. Three independent experiments were performed to show error bars .

    Article Snippet: Briefly, samples were incubated with 2.5 units of T4 DNA polymerase-exonuclease (Fermentas) at 37 °C for 2 h. The reaction was stopped by heating at 65 °C for 10 min.

    Techniques: Sequencing, Labeling, Concentration Assay, Staining, Southern Blot, Irradiation

    Single-stranded DNA ligation with T4 DNA ligase and CircLigase. A pool of 60 nt acceptor oligonucleotides (‘60N’) were ligated to 10 pmol of a 3΄ biotinylated donor oligonucleotide (CL78) using either T4 DNA ligase in the presence of a splinter oligonucleotide (TL38) or CircLigase. Ligation products were visualized on a 10% denaturing polyacrylamide gel stained with SybrGold. Band shifts from 60 nt to 80 nt indicate successful ligation. Schematic overviews of the reaction schemes are shown on top. The scheme developed by Kwok et al . ( 19 ) is shown for comparison. M: Single-stranded DNA size marker.

    Journal: Nucleic Acids Research

    Article Title: Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

    doi: 10.1093/nar/gkx033

    Figure Lengend Snippet: Single-stranded DNA ligation with T4 DNA ligase and CircLigase. A pool of 60 nt acceptor oligonucleotides (‘60N’) were ligated to 10 pmol of a 3΄ biotinylated donor oligonucleotide (CL78) using either T4 DNA ligase in the presence of a splinter oligonucleotide (TL38) or CircLigase. Ligation products were visualized on a 10% denaturing polyacrylamide gel stained with SybrGold. Band shifts from 60 nt to 80 nt indicate successful ligation. Schematic overviews of the reaction schemes are shown on top. The scheme developed by Kwok et al . ( 19 ) is shown for comparison. M: Single-stranded DNA size marker.

    Article Snippet: For fill-in with T4 DNA polymerase a 50 μl reaction mix was prepared containing 1× T4 DNA polymerase buffer (ThermoFisher Scientific), 0.05% Tween-20, 100 μM each dNTP, 100 pmol primer CL130 and 2 μl 5 U/μl T4 DNA polymerase (ThermoFisher Scientific).

    Techniques: DNA Ligation, Ligation, Staining, Marker

    Library preparation methods for highly degraded DNA. ( A ) In the single-stranded library preparation method described here (ssDNA2.0), DNA fragments (black) are 5΄ and 3΄ dephosphorylated and separated into single strands by heat denaturation. 3΄ biotinylated adapter molecules (red) are attached to the 3΄ ends of the DNA fragments via hybridization to a stretch of six random nucleotides (marked as ‘N’) belonging to a splinter oligonucleotide complementary to the adapter and nick closure with T4 DNA ligase. Following the immobilization of the ligation products on streptavidin-coated beads, the splinter oligonucleotide is removed by bead wash at an elevated temperature. Synthesis of the second strand is carried out using the Klenow fragment of Escherichia coli DNA polymerase I and a primer with phosphorothioate backbone modifications (red stars) to prevent exonucleolytic degradation. Unincorporated primers are removed through a bead wash at an elevated temperature, preventing the formation of adapter dimers in the subsequent blunt-end ligation reaction, which is again catalyzed by T4 DNA ligase. Adapter self-ligation is prevented through a 3΄ dideoxy modification in the adapter. The final library strand is released from the beads by heat denaturation. ( B ) In the single-stranded library preparation method originally described in Gansauge and Meyer, ( 4 ), the first adapter was attached through true single-stranded DNA ligation using CircLigase. The large fragment of Bst DNA polymerase was used to copy the template strand, leaving overhanging 3΄ nucleotides, which had to be removed in a blunt-end repair reaction using T4 DNA polymerase. ( C ) The ‘454’ method of double-stranded library preparation in the implementation of Meyer and Kircher, ( 23 ), is based on non-directional blunt-end ligation of a mixture of two adapters to blunt-end repaired DNA fragments using T4 DNA ligase. To prevent adapter self-ligation, no phosphate groups are present at the 5΄ ends of the adapters, resulting in the ligation of the adapter strands only and necessitating subsequent nick fill-in with a strand-displacing polymerase. Intermittent DNA purification steps are required in-between enzymatic reactions. ( D ) The ‘Illumina’ method of double-stranded library preparation, shown here as implemented in New England Biolabs’ NEBNext Ultra II kit, requires the addition of A-overhangs (marked as ‘A’) to blunt-end repaired DNA fragments using a 3΄-5΄ exonuclease deletion mutant of the Klenow fragment of E. coli DNA polymerase I. Both adapter sequences are combined into one bell-shaped structure, which carries a 3΄ T overhang to allow sticky end ligation with T4 DNA ligase. Following ligation, adapter strands are separated by excision of uracil. Excess adapters and adapter dimers are removed through size-selective purification.

    Journal: Nucleic Acids Research

    Article Title: Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

    doi: 10.1093/nar/gkx033

    Figure Lengend Snippet: Library preparation methods for highly degraded DNA. ( A ) In the single-stranded library preparation method described here (ssDNA2.0), DNA fragments (black) are 5΄ and 3΄ dephosphorylated and separated into single strands by heat denaturation. 3΄ biotinylated adapter molecules (red) are attached to the 3΄ ends of the DNA fragments via hybridization to a stretch of six random nucleotides (marked as ‘N’) belonging to a splinter oligonucleotide complementary to the adapter and nick closure with T4 DNA ligase. Following the immobilization of the ligation products on streptavidin-coated beads, the splinter oligonucleotide is removed by bead wash at an elevated temperature. Synthesis of the second strand is carried out using the Klenow fragment of Escherichia coli DNA polymerase I and a primer with phosphorothioate backbone modifications (red stars) to prevent exonucleolytic degradation. Unincorporated primers are removed through a bead wash at an elevated temperature, preventing the formation of adapter dimers in the subsequent blunt-end ligation reaction, which is again catalyzed by T4 DNA ligase. Adapter self-ligation is prevented through a 3΄ dideoxy modification in the adapter. The final library strand is released from the beads by heat denaturation. ( B ) In the single-stranded library preparation method originally described in Gansauge and Meyer, ( 4 ), the first adapter was attached through true single-stranded DNA ligation using CircLigase. The large fragment of Bst DNA polymerase was used to copy the template strand, leaving overhanging 3΄ nucleotides, which had to be removed in a blunt-end repair reaction using T4 DNA polymerase. ( C ) The ‘454’ method of double-stranded library preparation in the implementation of Meyer and Kircher, ( 23 ), is based on non-directional blunt-end ligation of a mixture of two adapters to blunt-end repaired DNA fragments using T4 DNA ligase. To prevent adapter self-ligation, no phosphate groups are present at the 5΄ ends of the adapters, resulting in the ligation of the adapter strands only and necessitating subsequent nick fill-in with a strand-displacing polymerase. Intermittent DNA purification steps are required in-between enzymatic reactions. ( D ) The ‘Illumina’ method of double-stranded library preparation, shown here as implemented in New England Biolabs’ NEBNext Ultra II kit, requires the addition of A-overhangs (marked as ‘A’) to blunt-end repaired DNA fragments using a 3΄-5΄ exonuclease deletion mutant of the Klenow fragment of E. coli DNA polymerase I. Both adapter sequences are combined into one bell-shaped structure, which carries a 3΄ T overhang to allow sticky end ligation with T4 DNA ligase. Following ligation, adapter strands are separated by excision of uracil. Excess adapters and adapter dimers are removed through size-selective purification.

    Article Snippet: For fill-in with T4 DNA polymerase a 50 μl reaction mix was prepared containing 1× T4 DNA polymerase buffer (ThermoFisher Scientific), 0.05% Tween-20, 100 μM each dNTP, 100 pmol primer CL130 and 2 μl 5 U/μl T4 DNA polymerase (ThermoFisher Scientific).

    Techniques: Hybridization, Ligation, Modification, DNA Ligation, DNA Purification, Mutagenesis, Purification

    Effects of single-stranded ligation schemes on library characteristics. ( A ) Informative sequence content of libraries prepared with CircLigase and T4 DNA ligase as a function of the input volume of ancient DNA extract used for library preparation. ( B ) Average GC content of the sequences obtained with the two ligation schemes. Note that the average GC content exceeds that of a typical mammalian genome because most sequences derive from microbial DNA, which is the dominant source of DNA in most ancient bones. ( C ) Fragment size distribution in the libraries as inferred from overlap-merged paired-end reads. Short artifacts in the library prepared from extremely little input DNA (corresponding to ∼1 mg bone) are mainly due to the incorporation of splinter fragments. ( D ) Frequencies of damage-induced C to T substitutions near the 5΄ and 3΄ ends of sequences.

    Journal: Nucleic Acids Research

    Article Title: Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

    doi: 10.1093/nar/gkx033

    Figure Lengend Snippet: Effects of single-stranded ligation schemes on library characteristics. ( A ) Informative sequence content of libraries prepared with CircLigase and T4 DNA ligase as a function of the input volume of ancient DNA extract used for library preparation. ( B ) Average GC content of the sequences obtained with the two ligation schemes. Note that the average GC content exceeds that of a typical mammalian genome because most sequences derive from microbial DNA, which is the dominant source of DNA in most ancient bones. ( C ) Fragment size distribution in the libraries as inferred from overlap-merged paired-end reads. Short artifacts in the library prepared from extremely little input DNA (corresponding to ∼1 mg bone) are mainly due to the incorporation of splinter fragments. ( D ) Frequencies of damage-induced C to T substitutions near the 5΄ and 3΄ ends of sequences.

    Article Snippet: For fill-in with T4 DNA polymerase a 50 μl reaction mix was prepared containing 1× T4 DNA polymerase buffer (ThermoFisher Scientific), 0.05% Tween-20, 100 μM each dNTP, 100 pmol primer CL130 and 2 μl 5 U/μl T4 DNA polymerase (ThermoFisher Scientific).

    Techniques: Ligation, Sequencing, Ancient DNA Assay

    RT-PCR of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic DNA (B), or a control without RT (C).

    Journal: Infection and Immunity

    Article Title: An Immunoreactive 38-Kilodalton Protein of Ehrlichia canis Shares Structural Homology and Iron-Binding Capacity with the Ferric Ion-Binding Protein Family

    doi: 10.1128/IAI.73.1.62-69.2005

    Figure Lengend Snippet: RT-PCR of E. canis fbp (lanes 1), E. canis membrane permease (lanes 2), and the intergenic region spanning the area from the 3′ end of fbp to the 5′ start of membrane permease (lanes 3) with either RNA from E. canis -infected DH82 cells (A), E. canis genomic DNA (B), or a control without RT (C).

    Article Snippet: Reactions were conducted with the Superscript III one-step RT-PCR system with Platinum DNA polymerase (Invitrogen) in a total volume of 50 μl.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Infection

    Screening various DNA polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, Thermosequenase; lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.

    Journal: Molecules

    Article Title: Synthesis and Enzymatic Incorporation of Modified Deoxyuridine Triphosphates

    doi: 10.3390/molecules200813591

    Figure Lengend Snippet: Screening various DNA polymerases with compound 1A and T1 . Lane 1, primer only; lane 2, ddTTP (control); lane 3, dTTP (control); lane 4, Tth; lane 5, Tfl; lane 6, Thermosequenase; lane 7, Vent(exo-); lane 8, Therminator; lane 9, KOD DASH; lane 10, Klenow; lane 11, Sequenase v.2.0.

    Article Snippet: Sequenase v.2.0 and Thermosequenase DNA polymerase were purchased from Affymetrix (Santa Clara, CA, USA).

    Techniques:

    Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic DNA prepared from tumor samples is then incubated with the Phi29 DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study

    Journal: Acta Neuropathologica Communications

    Article Title: The level of activity of the alternative lengthening of telomeres correlates with patient age in IDH-mutant ATRX-loss-of-expression anaplastic astrocytomas

    doi: 10.1186/s40478-019-0833-0

    Figure Lengend Snippet: Measurement of the level of ALT activity levels in human diffuse gliomas. Top panels illustrate the principle of the ALT C-circle assay [ 17 ] and describe its general steps. ALT cells have very long telomeres that have been amplified mainly by homologous recombination that generates partially single-stranded extra-chromosomal circles. Genomic DNA prepared from tumor samples is then incubated with the Phi29 DNA polymerase that specifically amplifies this telomeric DNA. Middle panel illustrates ALT-specific signals measured in tumor DNA samples using this assay, which were detected here on dot blots hybridized with a telomeric 32 P-labeled probe. Genomic DNAs from HeLa (telomerase positive) and U2OS (ALT positive) cells were also probed, representing negative and posititve controls for the C-circle assay, respectively. These assays were systematically performed in duplicates and here dot blot 2, on the right, was loaded with the same tumor samples as dot blot 1, on the left, to insure for reproducibility. Bottom table illustrates examples of duplicate numbers obtained for each of the indicated tumors, real signals of which are represented in the middle panel above. The C-circle score was determined after calculating the intensity of the signal relative to that of the ALT positive U2OS cell line, designated to be 100 arbitrary units (AU). Note that the C-circle assays were performed on representative samples, including those from the two patient groups analyzed in the present study

    Article Snippet: ALT cells, but not telomerase positive cells, generate extra-chromosomal telomeric single-stranded DNA called C-circles, which can be amplified using the Phi29 DNA polymerase [ ] (Fig. ).

    Techniques: Activity Assay, Amplification, Homologous Recombination, Incubation, Labeling, Dot Blot