exonuclease i  (New England Biolabs)


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    Name:
    Exonuclease I E coli
    Description:
    Exonuclease I E coli 15 000 units
    Catalog Number:
    m0293l
    Price:
    276
    Size:
    15 000 units
    Category:
    Exonucleases
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    New England Biolabs exonuclease i
    Exonuclease I E coli
    Exonuclease I E coli 15 000 units
    https://www.bioz.com/result/exonuclease i/product/New England Biolabs
    Average 90 stars, based on 487 article reviews
    Price from $9.99 to $1999.99
    exonuclease i - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "Role of the RAD51–SWI5–SFR1 Ensemble in homologous recombination"

    Article Title: Role of the RAD51–SWI5–SFR1 Ensemble in homologous recombination

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw375

    Functional characterization of SWI5–SFR1 dN202 complex. ( A ) To map the minimal complex unit of SWI5–SFR1, purified SWI5–SFR1 was incubated with proteinase K for the indicated times. The proteolytic products were resolved by 15% SDS-PAGE and stained by Coomassie Blue staining. The asterisk denotes the SFR1 dN202 . ( B ) Purified SWI5–SFR1 dN202 complex (3 μg) was subjected to 15% SDS-PAGE and Coomassie Blue staining. ( C ) SWI5–SFR1 dN202 was tested for RAD51 interaction by affinity pulldown as described in Figure 1D . ( D ) DNA strand exchange assay to monitor the stimulatory effect of SWI5–SFR1 by RAD51. ( I ) Schematic of the DNA strand exchange assay. The radiolabeled substrate and product are visualized and quantified by phosphorimaging analysis after PAGE. The asterisk denotes the 32 P label. ( II ) DNA strand exchange was conducted with the indicated amounts of SWI5–SFR1 or SWI5–SFR1 dN202 . The results were graphed. ( E ) Exonuclease I protection assay to monitor the influence of SWI5–SFR1 on the stability of RAD51 filament. ( I ) Schematic of the exonuclease I protection assay. The RAD51 filament harboring 5′- 32 P-labeled DNA is challenged with exonuclease I. The radiolabeled DNA and product are visualized and quantified by phosphorimaging analysis after PAGE. The 32 P label is denoted by the asterisk. ( II ) Treatment of the RAD51 presynaptic filament with exonuclease I in the presence of the indicated concentrations of SWI5–SFR1 or SWI5–SFR1 dN202 . The results were graphed. (D-E) Error bars represent the standard deviation (±SD) calculated based on at least three independent experiments.
    Figure Legend Snippet: Functional characterization of SWI5–SFR1 dN202 complex. ( A ) To map the minimal complex unit of SWI5–SFR1, purified SWI5–SFR1 was incubated with proteinase K for the indicated times. The proteolytic products were resolved by 15% SDS-PAGE and stained by Coomassie Blue staining. The asterisk denotes the SFR1 dN202 . ( B ) Purified SWI5–SFR1 dN202 complex (3 μg) was subjected to 15% SDS-PAGE and Coomassie Blue staining. ( C ) SWI5–SFR1 dN202 was tested for RAD51 interaction by affinity pulldown as described in Figure 1D . ( D ) DNA strand exchange assay to monitor the stimulatory effect of SWI5–SFR1 by RAD51. ( I ) Schematic of the DNA strand exchange assay. The radiolabeled substrate and product are visualized and quantified by phosphorimaging analysis after PAGE. The asterisk denotes the 32 P label. ( II ) DNA strand exchange was conducted with the indicated amounts of SWI5–SFR1 or SWI5–SFR1 dN202 . The results were graphed. ( E ) Exonuclease I protection assay to monitor the influence of SWI5–SFR1 on the stability of RAD51 filament. ( I ) Schematic of the exonuclease I protection assay. The RAD51 filament harboring 5′- 32 P-labeled DNA is challenged with exonuclease I. The radiolabeled DNA and product are visualized and quantified by phosphorimaging analysis after PAGE. The 32 P label is denoted by the asterisk. ( II ) Treatment of the RAD51 presynaptic filament with exonuclease I in the presence of the indicated concentrations of SWI5–SFR1 or SWI5–SFR1 dN202 . The results were graphed. (D-E) Error bars represent the standard deviation (±SD) calculated based on at least three independent experiments.

    Techniques Used: Functional Assay, Purification, Incubation, SDS Page, Staining, Polyacrylamide Gel Electrophoresis, Labeling, Standard Deviation

    SWI5 F83A/L85A-SFR1 is functionally impaired. ( A ) The effect of SWI5–SFR1 or SWI5 FL/AA –SFR1 on RAD51-mediated DNA strand exchange was examined. The results were graphed. ( B ) Exonuclease I protection assay was conducted with the indicated concentrations of SWI5–SFR1 and SWI5 FL/AA –SFR1. The results were graphed. ( C ) The average length of RAD51 filaments with negative staining was determined by electron microscopy (see Supplementary Figure S5). RAD51 was examined alone or with SWI5–SFR1 or SWI5 FL/AA –SFR1. The total 225 filaments were counted in each reaction. We note that the average length of the presynaptic filament in the presence of SWI5–SFR1 is much longer than expected. This could be due to the end-to-end association between two DNA molecules by RAD51 as described by Baumann et al. ( 35 ). ( D ) Thin-layer chromatography to monitor the hydrolysis of [γ- 32 P] ATP by RAD51 in the absence or presence of indicated concentrations of SWI5–SFR1 or SWI5 FL/AA –SFR1. The results were graphed. (A, B and D) Error bars represent the standard deviation (±SD) calculated based on at least three independent experiments.
    Figure Legend Snippet: SWI5 F83A/L85A-SFR1 is functionally impaired. ( A ) The effect of SWI5–SFR1 or SWI5 FL/AA –SFR1 on RAD51-mediated DNA strand exchange was examined. The results were graphed. ( B ) Exonuclease I protection assay was conducted with the indicated concentrations of SWI5–SFR1 and SWI5 FL/AA –SFR1. The results were graphed. ( C ) The average length of RAD51 filaments with negative staining was determined by electron microscopy (see Supplementary Figure S5). RAD51 was examined alone or with SWI5–SFR1 or SWI5 FL/AA –SFR1. The total 225 filaments were counted in each reaction. We note that the average length of the presynaptic filament in the presence of SWI5–SFR1 is much longer than expected. This could be due to the end-to-end association between two DNA molecules by RAD51 as described by Baumann et al. ( 35 ). ( D ) Thin-layer chromatography to monitor the hydrolysis of [γ- 32 P] ATP by RAD51 in the absence or presence of indicated concentrations of SWI5–SFR1 or SWI5 FL/AA –SFR1. The results were graphed. (A, B and D) Error bars represent the standard deviation (±SD) calculated based on at least three independent experiments.

    Techniques Used: Negative Staining, Electron Microscopy, Thin Layer Chromatography, Standard Deviation

    Related Articles

    Amplification:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: .. Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold. .. High throughput real time PCR was then conducted on the Fluidigm BioMark HD system using SsoFast EvaGreen Supermix with Low ROX (Bio-Rad) and Fluidigm 48.48 Dynamic Array integrated fluidic circuits.

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: Initial fragment amplification was carried out using primers kdr CL-F (5′-AAA TGT CTC GCC CAA ATC AG-3′) and kdr CL-R (5′-GCA CCT GCA AAA CAA TGT CA-3′) described previously [ ]. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: The first-strand cDNA, synthesized using the qScript cDNA Synthesis kit, was first amplified for specific target amplification (STA). .. Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs).

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: .. Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs). .. Cycle sequencing was carried out using the BigDye Terminator v. 1.1 Cycle Sequencing Kit on ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: Amplification of the fragments was verified by agarose gel electrophoresis, simultaneously running a Generuler 100bp Plus DNA Ladder (Fermentas). .. To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used.

    Article Title: Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing
    Article Snippet: Prior to DNA sequencing, enzymatic cleanup of each PCR was performed using a combination of Exonuclease I (Exo; New England BioLabs, Ipswich, MA) and shrimp alkaline phosphatase (SAP; USB, Affymetrix, Cleveland, OH) as described previously ( ). .. For the sequencing of specific PCR products, 1 μl of the ExoSAP-treated DNA was mixed with 6 μl of 5× sequencing buffer and 2 μl of sequencing reaction mix from a BigDye Terminator cycle sequencing kit, version 1.1 (Applied Biosystems, Foster City, CA), 2 μl of amplicon-specific primer (2 μmol/μl), and 9 μl of PCR-grade water for a final volume of 20 μl.

    Article Title: Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella
    Article Snippet: .. The successfully amplified double-stranded PCR products, treated with Exonuclease I (New England Biolabs, Ipswich MA, USA) and Shrimp Alkaline Phosphatase (Promega) to inactivate remaining primers and dNTPs, were directly used for the cycle-sequencing reaction using dye-labeled dideoxy terminators (Applied Biosystems, Foster City, CA, USA) with the amplification primers on an ABI 3130xl automated DNA sequencer. ..

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: Paragraph title: Multiplex PCR amplification and purification. ... To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: .. The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs). .. The templates were directly used for sequencing on an ABI 3130xl automated sequencer (Applied Biosystems), using the BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems).

    Stable Transfection:

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR
    Article Snippet: HepG2, HepaRG, Hepa1-6, Hepa56D, and HeLa cells stably expressing hNTCP were cultivated as described previously ( , ). .. T5 Exo (M0363), BAL-31 nuclease (M0213), exonuclease I (M0293), exonuclease III (M0206), exonuclease V (RecBCD, M0345), mung bean nuclease (M0250), EcoRI (R0101), and Nb.BtsI (R0707) were purchased from New England Biolabs.

    Synthesized:

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: The first-strand cDNA, synthesized using the qScript cDNA Synthesis kit, was first amplified for specific target amplification (STA). .. Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs).

    Quantitative RT-PCR:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Paragraph title: RNA Isolation and Fluidigm BioMark RT-qPCR Analysis ... Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold.

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Paragraph title: High-throughput quantitative RT-PCR analysis ... Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs).

    Real-time Polymerase Chain Reaction:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold. .. High throughput real time PCR was then conducted on the Fluidigm BioMark HD system using SsoFast EvaGreen Supermix with Low ROX (Bio-Rad) and Fluidigm 48.48 Dynamic Array integrated fluidic circuits.

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: The assay was performed on an Agilent MX3005 real-time PCR machine with cycling conditions of 95 °C for 10 min, followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min. To assess the genetic diversity and detect potential signatures of selection acting on the voltage-gated sodium channel, a portion of this gene spanning exon 20 was sequenced in 15 An. coluzzii and 14 An. arabiensis females. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    Incubation:

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs). .. Briefly, 2 µL of diluted Exo I at 4 units/µL was added to each 5-µL STA reaction, and then incubated for 30 min at 37°C and 15 min at 80°C.

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: DNA was extracted from feathers in 300 μl of 6% Chelex 100 (Biorad) containing 3 μl proteinase K (0.5 mg ml−1 ), incubated at 65°C for 2 hours and at 95°C for 5 min. A 971 bp fragment of the mtDNA cytochrome b gene was amplified using primers and H15938, as in . .. Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs).

    Article Title: Rapid Identification of Pseudallescheria and Scedosporium Strains by Using Rolling Circle Amplification
    Article Snippet: Unbound padlock probes and ITS templates were removed by exonucleolysis in 20-μl volumes containing 10 U exonuclease I and 10 U exonuclease III (New England BioLabs, Leusden, The Netherlands) for 30 min at 37°C. .. Lytic activity was stopped by incubation at 94°C for 30 min.

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA). .. The samples were incubated in the 9800 Fast Thermal Cycler (Applied Biosystems) for 30 min at 37°C and then for 20 min at 80°C to inactivate the enzymes.

    Activity Assay:

    Article Title: Rapid Identification of Pseudallescheria and Scedosporium Strains by Using Rolling Circle Amplification
    Article Snippet: Unbound padlock probes and ITS templates were removed by exonucleolysis in 20-μl volumes containing 10 U exonuclease I and 10 U exonuclease III (New England BioLabs, Leusden, The Netherlands) for 30 min at 37°C. .. Lytic activity was stopped by incubation at 94°C for 30 min.

    Expressing:

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR
    Article Snippet: HepG2, HepaRG, Hepa1-6, Hepa56D, and HeLa cells stably expressing hNTCP were cultivated as described previously ( , ). .. T5 Exo (M0363), BAL-31 nuclease (M0213), exonuclease I (M0293), exonuclease III (M0206), exonuclease V (RecBCD, M0345), mung bean nuclease (M0250), EcoRI (R0101), and Nb.BtsI (R0707) were purchased from New England Biolabs.

    Modification:

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR
    Article Snippet: HepG2hNTCP , Hepa1-6hNTCP , Hepa56DhNTCP , and HeLahNTCP cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 2 mM l -glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, and 1 mM nonessential amino acids. .. T5 Exo (M0363), BAL-31 nuclease (M0213), exonuclease I (M0293), exonuclease III (M0206), exonuclease V (RecBCD, M0345), mung bean nuclease (M0250), EcoRI (R0101), and Nb.BtsI (R0707) were purchased from New England Biolabs.

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: DNA isolation, PCR amplification and sequencing Genomic DNA was extracted from a pool of leaves from three plants per accession using a modified CTAB procedure [ ]. .. The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs).

    Gel Purification:

    Article Title: Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA
    Article Snippet: .. After gel purification and reverse transcription as described above using the RT primer 5′-CAAGCAGAAGACGGCATACGAGC-3′, first-strand cDNA was treated with Exonuclease I (New England Biolabs Inc.) as described to remove excess RT primers. ..

    Cell Culture:

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR
    Article Snippet: HepG2hNTCP , Hepa1-6hNTCP , Hepa56DhNTCP , and HeLahNTCP cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 2 mM l -glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, and 1 mM nonessential amino acids. .. T5 Exo (M0363), BAL-31 nuclease (M0213), exonuclease I (M0293), exonuclease III (M0206), exonuclease V (RecBCD, M0345), mung bean nuclease (M0250), EcoRI (R0101), and Nb.BtsI (R0707) were purchased from New England Biolabs.

    other:

    Article Title: Construction and electrophoretic migration of single-stranded DNA knots and catenanes
    Article Snippet: T4 DNA ligase and exonuclease I, exonuclease III and T4 polynucleotide kinase were supplied by New England Biolabs.

    DNA Sequencing:

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used. .. The BigDye XTerminator purification kit was used as purification method for DNA sequencing with the purpose of removing unincorporated BigDye terminators.

    Article Title: Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing
    Article Snippet: .. Prior to DNA sequencing, enzymatic cleanup of each PCR was performed using a combination of Exonuclease I (Exo; New England BioLabs, Ipswich, MA) and shrimp alkaline phosphatase (SAP; USB, Affymetrix, Cleveland, OH) as described previously ( ). .. For the sequencing of specific PCR products, 1 μl of the ExoSAP-treated DNA was mixed with 6 μl of 5× sequencing buffer and 2 μl of sequencing reaction mix from a BigDye Terminator cycle sequencing kit, version 1.1 (Applied Biosystems, Foster City, CA), 2 μl of amplicon-specific primer (2 μmol/μl), and 9 μl of PCR-grade water for a final volume of 20 μl.

    Sequencing:

    Article Title: Visual short-term memory deficits associated with GBA mutation and Parkinson’s disease
    Article Snippet: Briefly, DNA was treated with an ExoSAP reaction as follows: 1 × SAP buffer, shrimp alkaline phosphatase (500 U; SAP, Promega), Exonuclease I (2 U; NEB). .. The sequencing reaction was performed according to BigDye® Terminator v3.1 Cycle Sequencing protocol (Applied Biosystems).

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: .. Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs). .. Cycle sequencing was carried out using the BigDye Terminator v. 1.1 Cycle Sequencing Kit on ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: Paragraph title: Direct Sequencing of PCR-amplified LRP4 DNA ... To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used.

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: .. Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Article Title: Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing
    Article Snippet: Prior to DNA sequencing, enzymatic cleanup of each PCR was performed using a combination of Exonuclease I (Exo; New England BioLabs, Ipswich, MA) and shrimp alkaline phosphatase (SAP; USB, Affymetrix, Cleveland, OH) as described previously ( ). .. For the sequencing of specific PCR products, 1 μl of the ExoSAP-treated DNA was mixed with 6 μl of 5× sequencing buffer and 2 μl of sequencing reaction mix from a BigDye Terminator cycle sequencing kit, version 1.1 (Applied Biosystems, Foster City, CA), 2 μl of amplicon-specific primer (2 μmol/μl), and 9 μl of PCR-grade water for a final volume of 20 μl.

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: For this purpose, primers for the amplification and sequencing of 13 targets per strain (Table ) were divided into four amplification groups (AGs), taking into account the PCR product length and amplification efficiency for all targets. .. To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: Paragraph title: DNA isolation, PCR amplification and sequencing ... The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs).

    Cellular Antioxidant Activity Assay:

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: Initial fragment amplification was carried out using primers kdr CL-F (5′-AAA TGT CTC GCC CAA ATC AG-3′) and kdr CL-R (5′-GCA CCT GCA AAA CAA TGT CA-3′) described previously [ ]. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    DNA Extraction:

    Article Title: Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella
    Article Snippet: Paragraph title: 2.1. Tissue Sampling, DNA Extraction, and Amplification ... The successfully amplified double-stranded PCR products, treated with Exonuclease I (New England Biolabs, Ipswich MA, USA) and Shrimp Alkaline Phosphatase (Promega) to inactivate remaining primers and dNTPs, were directly used for the cycle-sequencing reaction using dye-labeled dideoxy terminators (Applied Biosystems, Foster City, CA, USA) with the amplification primers on an ABI 3130xl automated DNA sequencer.

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: Paragraph title: DNA isolation, PCR amplification and sequencing ... The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs).

    Mutagenesis:

    Article Title: Visual short-term memory deficits associated with GBA mutation and Parkinson’s disease
    Article Snippet: For the L444P mutation primers used were: 5’-GGAGGACCCAATTGGGTGCGT-3’ and 5’-ACGCTGTCTTCAGCCCACTTC-3’. .. Briefly, DNA was treated with an ExoSAP reaction as follows: 1 × SAP buffer, shrimp alkaline phosphatase (500 U; SAP, Promega), Exonuclease I (2 U; NEB).

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: Paragraph title: Investigation of the role of the 1014F knockdown resistance mutation in pyrethroid/DDT resistance ... Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    Isolation:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Paragraph title: RNA Isolation and Fluidigm BioMark RT-qPCR Analysis ... Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold.

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR
    Article Snippet: PHH were isolated from liver specimens obtained after partial hepatectomy and following written informed consent of the patients (approved by the ethics commission of Hannover Medical School/Ethik-Kommission der MHH, no. 252-2008). .. T5 Exo (M0363), BAL-31 nuclease (M0213), exonuclease I (M0293), exonuclease III (M0206), exonuclease V (RecBCD, M0345), mung bean nuclease (M0250), EcoRI (R0101), and Nb.BtsI (R0707) were purchased from New England Biolabs.

    Polymerase Chain Reaction:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold. .. PCR was performed using the thermal protocol GE Fast 96 × 96 PCR + Melt v2.pcl.

    Article Title: Visual short-term memory deficits associated with GBA mutation and Parkinson’s disease
    Article Snippet: The resulting PCR products were digested with XhoI (NEB) for N370S and NciI (NEB) for L444P and resolved by agarose gel electrophoresis. .. Briefly, DNA was treated with an ExoSAP reaction as follows: 1 × SAP buffer, shrimp alkaline phosphatase (500 U; SAP, Promega), Exonuclease I (2 U; NEB).

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA). ..

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: .. Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs). .. Cycle sequencing was carried out using the BigDye Terminator v. 1.1 Cycle Sequencing Kit on ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: Paragraph title: Direct Sequencing of PCR-amplified LRP4 DNA ... To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used.

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: .. Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Article Title: Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing
    Article Snippet: .. Prior to DNA sequencing, enzymatic cleanup of each PCR was performed using a combination of Exonuclease I (Exo; New England BioLabs, Ipswich, MA) and shrimp alkaline phosphatase (SAP; USB, Affymetrix, Cleveland, OH) as described previously ( ). .. For the sequencing of specific PCR products, 1 μl of the ExoSAP-treated DNA was mixed with 6 μl of 5× sequencing buffer and 2 μl of sequencing reaction mix from a BigDye Terminator cycle sequencing kit, version 1.1 (Applied Biosystems, Foster City, CA), 2 μl of amplicon-specific primer (2 μmol/μl), and 9 μl of PCR-grade water for a final volume of 20 μl.

    Article Title: Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella
    Article Snippet: .. The successfully amplified double-stranded PCR products, treated with Exonuclease I (New England Biolabs, Ipswich MA, USA) and Shrimp Alkaline Phosphatase (Promega) to inactivate remaining primers and dNTPs, were directly used for the cycle-sequencing reaction using dye-labeled dideoxy terminators (Applied Biosystems, Foster City, CA, USA) with the amplification primers on an ABI 3130xl automated DNA sequencer. ..

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: .. To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA). .. The samples were incubated in the 9800 Fast Thermal Cycler (Applied Biosystems) for 30 min at 37°C and then for 20 min at 80°C to inactivate the enzymes.

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: Paragraph title: DNA isolation, PCR amplification and sequencing ... The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs).

    Purification:

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used. .. Sequencing was carried out directly on purified fragments with the ABI 310 Genetic Analyzer (Applied Biosystems), using an ABI Prism BigDye terminator cycle sequencing ready reaction kit, version 1.1 (Applied Biosystems).

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: .. Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: Paragraph title: Multiplex PCR amplification and purification. ... To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

    Article Title: Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
    Article Snippet: .. The fragments of 30 worldwide distributed accessions (An-2, Bl-1, Bsch-2, Bur-0, C24, Can-0, Cha-0, Col-0, Ct-1, Cvi-0, Edi-0, El-0, Er-0, Est-1, Gre-0, Ler-1, Mt-0, Nok-2, Oy-0, Ra-0, Rsch-0, Sap-0, Sha(kdara), Stw-0, Te-0, Tsu-1, Van-0, Wil, Ws-3, Yo-0) were amplified with the proof-reading polymerase Phusion (Finnzymes) and purified enzymatically by using Exonuclease I and Antarctic Phosphatase (New England Biolabs). .. The templates were directly used for sequencing on an ABI 3130xl automated sequencer (Applied Biosystems), using the BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems).

    High Throughput Screening Assay:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold. .. High throughput real time PCR was then conducted on the Fluidigm BioMark HD system using SsoFast EvaGreen Supermix with Low ROX (Bio-Rad) and Fluidigm 48.48 Dynamic Array integrated fluidic circuits.

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Paragraph title: High-throughput quantitative RT-PCR analysis ... Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs).

    Activated Clotting Time Assay:

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: Probes were labelled with two specific fluorophores, FAM and HEX: FAM to detect the resistant allele [(5′-ACG ACA AAA TTT C-3′ for 1014F kdr ), (5′-ACG ACT GAA TTT C-3′ for 1014S kdr )] and HEX (5′-CTT ACG ACT AAA TTT C-3′) to detect the susceptible allele. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    Chromatin Immunoprecipitation:

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs). .. High-throughput qPCRs were performed on the Biomark HD (Fluidigm) in a microfluidic multiplex 48.48 dynamic array chip according to the Fluidigm Advanced Development Protocol with EvaGreen.

    Plasmid Preparation:

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: .. Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Software:

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs). .. PCR was performed in a 15 μl reaction containing the same concentrations as listed above; the products were sent for genotyping to GATCBiotech AG, Germany and scored with the Gene Marker v. 5.1 software package (SoftGenetics LLC 2004).

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Multiplex Assay:

    Article Title: Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei *
    Article Snippet: Reference , never edited, pre-edited, and edited ( , ) transcript cDNAs were then preamplified in multiplex specific target amplification reactions using TaqMan PreAmp Master Mix (Life Technologies). .. Specific target amplification reactions were performed with the following thermocycling conditions: one cycle at 95 °C for 10 min, and 14 cycles of 95 °C for 15 s and 60 °C for 4 min. Preamplified cDNA was treated with exonuclease I (New England Biolabs) and diluted 10-fold.

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs). .. High-throughput qPCRs were performed on the Biomark HD (Fluidigm) in a microfluidic multiplex 48.48 dynamic array chip according to the Fluidigm Advanced Development Protocol with EvaGreen.

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: Paragraph title: Multiplex PCR amplification and purification. ... To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

    Selection:

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: The assay was performed on an Agilent MX3005 real-time PCR machine with cycling conditions of 95 °C for 10 min, followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min. To assess the genetic diversity and detect potential signatures of selection acting on the voltage-gated sodium channel, a portion of this gene spanning exon 20 was sequenced in 15 An. coluzzii and 14 An. arabiensis females. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    Agarose Gel Electrophoresis:

    Article Title: Visual short-term memory deficits associated with GBA mutation and Parkinson’s disease
    Article Snippet: The resulting PCR products were digested with XhoI (NEB) for N370S and NciI (NEB) for L444P and resolved by agarose gel electrophoresis. .. Briefly, DNA was treated with an ExoSAP reaction as follows: 1 × SAP buffer, shrimp alkaline phosphatase (500 U; SAP, Promega), Exonuclease I (2 U; NEB).

    Article Title: Bone Overgrowth-associated Mutations in the LRP4 Gene Impair Sclerostin Facilitator Function *
    Article Snippet: Amplification of the fragments was verified by agarose gel electrophoresis, simultaneously running a Generuler 100bp Plus DNA Ladder (Fermentas). .. To remove primers and unincorporated dNTPs, exonuclease I (New England Biolabs) and calf intestine alkaline phosphatase (Roche Applied Science) were used.

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: Each PCR was run in a 9800 Fast Thermal Cycler (Applied Biosystems, Foster City, CA) under the following universal conditions: 3 min of denaturation at 94°C, followed by 35 cycles of 30 s at 94°C, 30 s at 56°C, and 1 min at 72°C and a final extension step at 72°C for 7 min. Multiplex PCR products (3.0 μl from each AG) were analyzed on a 1.5% agarose gel stained with 0.3 μg/ml ethidium bromide. .. To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

    Sampling:

    Article Title: Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella
    Article Snippet: Paragraph title: 2.1. Tissue Sampling, DNA Extraction, and Amplification ... The successfully amplified double-stranded PCR products, treated with Exonuclease I (New England Biolabs, Ipswich MA, USA) and Shrimp Alkaline Phosphatase (Promega) to inactivate remaining primers and dNTPs, were directly used for the cycle-sequencing reaction using dye-labeled dideoxy terminators (Applied Biosystems, Foster City, CA, USA) with the amplification primers on an ABI 3130xl automated DNA sequencer.

    Concentration Assay:

    Article Title: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
    Article Snippet: Briefly, a 12-cycle preamplification reaction was performed for each sample in 5 µL by pooling all primer pairs (final concentration, 50 nM), 1.25 µL cDNA, and 2.5 µL 2× PreAmp Master Mix (Applied Biosystems) following the manufacturer’s protocol. .. Unincorporated primers were then cleaned up using Exonuclease I (New England Biolabs).

    CTG Assay:

    Article Title: A combination of metabolic resistance and high frequency of the 1014F kdr mutation is driving pyrethroid resistance in Anopheles coluzzii population from Guinea savanna of Cameroon
    Article Snippet: The primers kdr _F (5′-CAT TTT TCT TGG CCA CTG TAG TGA T-3′) and kdr _R (5′-CGA TCT TGG TCC ATG TTA ATT TGC A-3′) were used without modififcation. .. Cycling condition were as follows: 95 °C for 5min, followed by 35 cycles of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 45 s, followed by a final extension step at 72 °C for 10 min. PCR products were cleaned up using Exonuclease I (Exo I) and Shrimp Alkaline Phosphate (Exo-SAP protocol) according to the protocol of New England Biolabs (NEB, MA, USA).

    BAC Assay:

    Article Title: Subtypes of the Plasmid-Encoded Serine Protease EspP in Shiga Toxin-Producing Escherichia coli: Distribution, Secretion, and Proteolytic Activity ▿
    Article Snippet: .. Plasmid DNA purified with NucleoBond BAC 100 cartridges (Macherey-Nagel, Düren, Germany) or the 3,760-bp espP PCR product (Table ) purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (GE Healthcare, München, Germany) was used as a template for bidirectional sequencing with an automated ABI Prism 3130 Avant Genetic Analyzer (Perkin-Elmer Applied Biosystems, Weiterstadt, Germany), ABI Prism BigDye Terminator Ready Reaction Cycle Sequencing kit (Perkin-Elmer Applied Biosystems), and customized primers. .. Sequences were analyzed using MEGA software, version 3.1 , and aligned with ClustalW , and homology was determined using the EMBL-GenBank database ( ).

    Marker:

    Article Title: Hybridization of glaucous gull (Larus hyperboreus) and herring gull (Larus argentatus) in Iceland: mitochondrial and microsatellite data
    Article Snippet: Prior to sequencing, excess primers and nucleotides were enzymatically removed from PCR amplification products using a mixture of exonuclease I and Antarctic phosphatase (New England BioLabs). .. PCR was performed in a 15 μl reaction containing the same concentrations as listed above; the products were sent for genotyping to GATCBiotech AG, Germany and scored with the Gene Marker v. 5.1 software package (SoftGenetics LLC 2004).

    Staining:

    Article Title: Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland ▿
    Article Snippet: Each PCR was run in a 9800 Fast Thermal Cycler (Applied Biosystems, Foster City, CA) under the following universal conditions: 3 min of denaturation at 94°C, followed by 35 cycles of 30 s at 94°C, 30 s at 56°C, and 1 min at 72°C and a final extension step at 72°C for 7 min. Multiplex PCR products (3.0 μl from each AG) were analyzed on a 1.5% agarose gel stained with 0.3 μg/ml ethidium bromide. .. To enzymatically purify the samples from residual deoxynucleotides and excess primers, 8.0 μl of the AG1, AG2, or AG3 PCR product and 4.0 μl of the AG4 PCR product was transferred into new reaction tubes, followed by the addition of 1.0 μl rAPid Alkaline Phosphatase (1 U/μl; Roche Diagnostics), 0.2 μl of the corresponding buffer, and 0.05 μl exonuclease I ( Exo I; 20 U/μl; New England Biolabs, Ipswich, MA).

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