exonuclease i e coli  (New England Biolabs)


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    Name:
    Exonuclease I (E.coli) - 1
    Description:

    Catalog Number:
    M0293L
    Price:
    None
    Score:
    85
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    New England Biolabs exonuclease i e coli

    https://www.bioz.com/result/exonuclease i e coli/product/New England Biolabs
    Average 99 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    exonuclease i e coli - by Bioz Stars, 2019-12
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: Paragraph title: Cloning and sequencing ... Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing.

    Amplification:

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: PCR was performed using an appropriate dilution of cDNA generated from the cerebral cortex of F1 (B6×BALB) animals. .. Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega). .. Purified PCR products were used in combination with a conventional primer designed to sit at the nucleotide to the immediate 5′ position of a coding SNPs in the transcript.

    Article Title: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes
    Article Snippet: Paragraph title: Mitochondrial DNA control region and Zfy intron amplification and sequencing ... We purified polymerase chain reaction (PCR) products using Exosap-IT (USB Corporation, Cleveland, OH), or Exonuclease I and Antarctic Phosphatase (New England BioLabs Inc., Ipswich, MA), prior to sequencing on a MegaBACE 1000 (GE Healthcare) or an AB3730 (Applied Biosystems).

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: Amplicon lengths ranged from 120 to 190 bp in size depending on the amplicon ( Supplementary Table S2 ). .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers.

    Article Title: Magnetic resonance imaging and genetic investigation of a case of rottweiler leukoencephalomyelopathy
    Article Snippet: For the DARS2 mutation analysis, suitable PCR products were amplified using AmpliTaq Gold 360 (Life Technologies). .. The PCR products were resequenced after rAPid alkaline phosphatase (Roche) and exonuclease I (New England Biolabs) treatment using both PCR primers and the ABI BigDye Terminator Sequencing Kit 3.1 (Life Technologies) in an ABI 3730 sequencer (see Additional file : Table S1).

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Primers 8817–8878 at 300 nM concentration were used in amplification of the genes 1–31 with 35 cycles. .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    Article Title: Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization
    Article Snippet: Specific Target Amplification (STA) was performed on cDNA samples using TaqMan® PreAmp Master Mix (Life Technologies™) and standard protocols provided by manufacturer. .. Samples were treated with Exonuclease I (New England BioLabs, Ipswich, MA) to remove unincorporated primers by adding 2 μl (at 4 U/μl) to each STA reaction.

    Article Title: A recombineering based approach for high-throughput conditional knockout targeting vector construction
    Article Snippet: PCR amplification was carried out using Extensor Hi-Fidelity PCR Master Mix 2 (2X, ABgene). .. This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min.

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: The reaction conditions were as follows: 95° for 2 min, followed by 35 cycles of 95° for 30 s, annealing temperature (Table ) for 30 s, and 72° for 30 s, with final extension of 72° for 5 min. Amplification was performed in an MJ Research Tetrad Thermal Cycler (MJ Research, Waltham, MA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    Article Title: Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1
    Article Snippet: Genomic DNA was amplified by yeast colony polymerase chain reaction (PCR), using a blend of Pwo and Taq polymerase. .. The resulting 2 kb PCR products were treated with exonuclease I and Antarctic phosphatase (NEB) and directly used in sequencing reactions.

    Article Title: A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3
    Article Snippet: Products were amplified using a ‘touch-down’ PCR programme, decreasing the annealing temperature from 67.5 to 61°C over 13 cycles, with a further 29 cycles at 61°C. .. PCR product clean-up was carried out using ExoI (NEB, Ipswich, MA, USA) and SAP (USB, part of Affymetrix, Santa Clara, CA, USA) with standard protocols, and sequencing reactions, using BigDye Terminator v3.1 Cycle Sequencing kits, were run on a 3730xl DNA Analyzer (Applied Biosystems).

    Filtration:

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: DNA was precipitated with EtOH, washed with 70% EtOH and resuspended in 100 µl of water. .. To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above. .. Following proteinase K and RNAse I incubations, DNA fragments were extracted twice with phenol and once with phenol–chloroform, precipitated with EtOH, washed with 70% EtOH and resuspended in 100 µl of water.

    Positive Control:

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: One three-spined stickleback individual from the Baltic Sea (60°12' N, 25°11' E) was used as a positive control. .. PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs.

    Synthesized:

    Article Title: Genetic variants of FZD4 and LRP5 genes in patients with advanced retinopathy of prematurity
    Article Snippet: To identify variants in all coding exons of the FZD4 , LRP5, TSPAN12, and NDP genes, oligonucleotide primers on the flanking intron/untranslated region (UTR) sequences were designed and synthesized as described [ - ]. .. The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA).

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Synthesized universal fragments were gel-purified (QIAquick Gel Extraction Kit, Qiagen). .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    TA Cloning:

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: PCR products from rhizosphere soils were cloned using INVα F' competent cells and the pCR®2.1 vector from the TA Cloning® Kit (Life Technologies, Grand Island, NY) according to the manufacturer's directions. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing.

    Construct:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: The “pooled” gene assay mix was constructed by combining 1μl of all 96 primers (forward and reverse combined) with DNA suspension buffer (104 μl) (Teknova #T0223). .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    Gene Assay:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: The “pooled” gene assay mix was constructed by combining 1μl of all 96 primers (forward and reverse combined) with DNA suspension buffer (104 μl) (Teknova #T0223). .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    Incubation:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: The “pooled” gene assay mix was constructed by combining 1μl of all 96 primers (forward and reverse combined) with DNA suspension buffer (104 μl) (Teknova #T0223). .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes. .. Samples were then diluted 5-fold using 18 μl DNA suspension buffer (Sigma-Aldrich #W1754-1VL).

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: This step not only makes the eluted DNA double stranded to be precisely size-selected by SPRI beads, but also synthesizes the sequence required for bridge PCR. .. We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min. .. Following incubation at 70°C for 10 min to inactivate Exonuclease I, we purified the double-stranded template DNAs with 50 μl of AMPure XP twice as described above, except for reducing the volume of final elution to 20 μl.

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: Amplicon lengths ranged from 120 to 190 bp in size depending on the amplicon ( Supplementary Table S2 ). .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers. .. Probe design and preparation .

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: Transformants were transferred to Luria-Bertani (LB) broth containing kanamycin (50 μ g/mL) in 96-well tissue culture plates, incubated for 16 h at 37°C at 225 rpm, then screened with PCR using the M13f and M13r primers ( ) to check for the presence of an insert. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing.

    Article Title: A recombineering based approach for high-throughput conditional knockout targeting vector construction
    Article Snippet: PCR was performed using PTC-225 PCR machine (Peltier Thermal Cycler) with the following settings: 94°C for 4 min, this was followed by 35 cycles of 94°C for 30 s, 60°C for 30 s and 68°C for 1 min (Bsd ) or 2–3 min (Neo and retrieval backbone). .. This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min. .. The PCR products were then purified using Qiagen mini-preparation columns and eluted in 50 μl of PCR-grade water.

    Article Title: A molecular inversion probe assay for detecting alternative splicing
    Article Snippet: The wash buffer was removed from the beads and 10 μl of ligation mix (1 μl Ampligase, 1 μl 10× ligation buffer and 8 μl water) was added; the ligation reaction was incubated at 58°C for 30 minutes. .. The ligated MIPs were further purified and fully eluted from the immobilized cDNA by digesting all linear DNA with exonucleases; 4 μl of exonuclease mix (3.5 μl 10× Exonuclease Buffer, 0.5 μl Exo I (NEB catalog no. M0293S.

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: Following an overnight incubation at 37°C with proteinase K and RNAse I, the lysates were extracted twice with phenol and once with phenol–chloroform. .. To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above.

    Article Title: Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing
    Article Snippet: Protection of ssDNA against the action of E. coli Exo I by DMC1 with and without Hop2–Mnd1 was conducted as described ( ). .. Presynaptic filaments were assembled with DMC1 (0.3 µM) and 5' 32 P-labeled 100-mer ssDNA (3 µM nucleotides) and then incubated with ExoI (2–6 U, as indicated in the figures; New England Biolabs). .. Duplex capture by the Hop2-Mnd1-DMC1-ssDNA ensemble was examined as described ( ).

    Article Title: Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis
    Article Snippet: One-cell stage embryos were microinjected with 1–2 nl of the mixture, and cultured until shield to 80% epiboly stages. .. To extract genomic DNA, individual embryos were placed into 25 μl of ice-cold DNA extraction buffer (10 mM Tris–HCl, pH 8.0, 2 mM EDTA, 0.2% Triton X-100, 200 μg/ml Proteinase K) and incubated at 50°C for 16 h, then at 95°C for 10 min. To remove remaining targeting oligonucleotide, 25 μl of Exonuclease I mixture [0.04 U/μl Exonuclease I (New England Biolabs), 134 mM Glycine-KOH, pH 9.5, 13.4 mM MgCl2 , 20 mM 2-mercaptoethanol] was added, and incubated at 37°C for 1 h and at 80°C for 20 min. .. Mutant template was detected with a pair of PCR primers (BrulATRFO: 5′-AAGCTGAACAGTCAGAGTTGGTC-3′ (T m = 55°C) and BrulMutMcAsR: 5′-TGATTTCATAAACTGCACCC-3′ (T m = 48°C).

    Expressing:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: Paragraph title: Single-cell gene expression analysis ... Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min).

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: Paragraph title: Allele-specific SNapShot gene expression analysis ... Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega).

    Article Title: Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization
    Article Snippet: Paragraph title: Measurement of gene expression on BioMark™ HD system ... Samples were treated with Exonuclease I (New England BioLabs, Ipswich, MA) to remove unincorporated primers by adding 2 μl (at 4 U/μl) to each STA reaction.

    Modification:

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: The genomic PCR was performed similarly to the plasmid-programmed reaction with the modification in the annealing step (temperature decrement of 1° from 68°C to 60°C on the first eight cycles was used, then 27 cycles at 60°C, annealing for 50 seconds) and prolonged to 40 seconds elongation step. .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    Ligation:

    Article Title: A molecular inversion probe assay for detecting alternative splicing
    Article Snippet: Following ligation, the beads were washed three times with Dynabead wash buffer: twice at 58°C and once at room temperature. .. The ligated MIPs were further purified and fully eluted from the immobilized cDNA by digesting all linear DNA with exonucleases; 4 μl of exonuclease mix (3.5 μl 10× Exonuclease Buffer, 0.5 μl Exo I (NEB catalog no. M0293S.

    Generated:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min). .. Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min).

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: PCR was performed using an appropriate dilution of cDNA generated from the cerebral cortex of F1 (B6×BALB) animals. .. Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega).

    Cell Culture:

    Article Title: Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis
    Article Snippet: One-cell stage embryos were microinjected with 1–2 nl of the mixture, and cultured until shield to 80% epiboly stages. .. To extract genomic DNA, individual embryos were placed into 25 μl of ice-cold DNA extraction buffer (10 mM Tris–HCl, pH 8.0, 2 mM EDTA, 0.2% Triton X-100, 200 μg/ml Proteinase K) and incubated at 50°C for 16 h, then at 95°C for 10 min. To remove remaining targeting oligonucleotide, 25 μl of Exonuclease I mixture [0.04 U/μl Exonuclease I (New England Biolabs), 134 mM Glycine-KOH, pH 9.5, 13.4 mM MgCl2 , 20 mM 2-mercaptoethanol] was added, and incubated at 37°C for 1 h and at 80°C for 20 min.

    Bridge PCR:

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: This step not only makes the eluted DNA double stranded to be precisely size-selected by SPRI beads, but also synthesizes the sequence required for bridge PCR. .. We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min.

    Overlap Extension Polymerase Chain Reaction:

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Paragraph title: Preparation of PCR products for OE-PCR ... Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    DNA Sequencing:

    Article Title: Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1
    Article Snippet: Paragraph title: Genomic DNA sequencing ... The resulting 2 kb PCR products were treated with exonuclease I and Antarctic phosphatase (NEB) and directly used in sequencing reactions.

    Sequencing:

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: This step not only makes the eluted DNA double stranded to be precisely size-selected by SPRI beads, but also synthesizes the sequence required for bridge PCR. .. We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min.

    Article Title: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes
    Article Snippet: For a subsample of males we amplified a 658 bp fragment of the last intron of the Zfy gene with published primers (LGL-331: Shaw et al. ; Yint-2-335: Wilson et al. ) as in Wilson et al. ( ). .. We purified polymerase chain reaction (PCR) products using Exosap-IT (USB Corporation, Cleveland, OH), or Exonuclease I and Antarctic Phosphatase (New England BioLabs Inc., Ipswich, MA), prior to sequencing on a MegaBACE 1000 (GE Healthcare) or an AB3730 (Applied Biosystems). .. We edited and aligned sequences in Bioedit (v7.0.9, Hall ) or MEGA (v5, Tamura et al. ).

    Article Title: Genetic variants of FZD4 and LRP5 genes in patients with advanced retinopathy of prematurity
    Article Snippet: The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA). .. The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA).

    Article Title: Magnetic resonance imaging and genetic investigation of a case of rottweiler leukoencephalomyelopathy
    Article Snippet: For the DARS2 mutation analysis, suitable PCR products were amplified using AmpliTaq Gold 360 (Life Technologies). .. The PCR products were resequenced after rAPid alkaline phosphatase (Roche) and exonuclease I (New England Biolabs) treatment using both PCR primers and the ABI BigDye Terminator Sequencing Kit 3.1 (Life Technologies) in an ABI 3730 sequencer (see Additional file : Table S1). .. The sequence data were analysed using Sequencer 4.9 software (GeneCodes).

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: Transformants were transferred to Luria-Bertani (LB) broth containing kanamycin (50 μ g/mL) in 96-well tissue culture plates, incubated for 16 h at 37°C at 225 rpm, then screened with PCR using the M13f and M13r primers ( ) to check for the presence of an insert. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing. .. Purified plasmid DNA was mixed with the M13f primer then submitted to the Cornell University Life Sciences Core Laboratories Center.

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: Alternatively, the PCR products were separated using an HDA-GT12 DNA analyzer and scored by Biocalculator software (both from eGene, Irvine, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs). .. DNA sequencing was performed using ABI BigDye Terminator (v3.1; Applied Biosystems, Foster City, CA) according to the manufacturer's protocol, except that 5-μl reactions were performed with 0.25 μl of BigDye on an ABI 3730xl DNA sequencing machine with 50 cm arrays.

    Article Title: Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1
    Article Snippet: Genomic DNA was amplified by yeast colony polymerase chain reaction (PCR), using a blend of Pwo and Taq polymerase. .. The resulting 2 kb PCR products were treated with exonuclease I and Antarctic phosphatase (NEB) and directly used in sequencing reactions. .. Lasergene (DNAStar) was used to assemble and analyse the sequences.

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs. .. The sequencing reactions were performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to manufacture's instructions.

    Article Title: A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3
    Article Snippet: All primer sequences can be found in Supporting Information, . .. PCR product clean-up was carried out using ExoI (NEB, Ipswich, MA, USA) and SAP (USB, part of Affymetrix, Santa Clara, CA, USA) with standard protocols, and sequencing reactions, using BigDye Terminator v3.1 Cycle Sequencing kits, were run on a 3730xl DNA Analyzer (Applied Biosystems). .. Base calling and quality assessment were carried out using the Contig Express programme from the Vector NTI package (Invitrogen Life Technologies, Carlsbad, CA, USA).

    Injection:

    Article Title: Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis
    Article Snippet: Paragraph title: Microinjection of targeting oligonucleotides/Rad52 mixtures and DNA extraction from injected embryos ... To extract genomic DNA, individual embryos were placed into 25 μl of ice-cold DNA extraction buffer (10 mM Tris–HCl, pH 8.0, 2 mM EDTA, 0.2% Triton X-100, 200 μg/ml Proteinase K) and incubated at 50°C for 16 h, then at 95°C for 10 min. To remove remaining targeting oligonucleotide, 25 μl of Exonuclease I mixture [0.04 U/μl Exonuclease I (New England Biolabs), 134 mM Glycine-KOH, pH 9.5, 13.4 mM MgCl2 , 20 mM 2-mercaptoethanol] was added, and incubated at 37°C for 1 h and at 80°C for 20 min.

    Binding Assay:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min). .. Distinct primer assays were generated by adding individual primer pairs (5μM) together with a mix of 2x Assay Loading Reagent (Fluidigm) and 1x DNA suspension buffer to each well of a new plate.

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes. .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    Article Title: Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization
    Article Snippet: Samples were treated with Exonuclease I (New England BioLabs, Ipswich, MA) to remove unincorporated primers by adding 2 μl (at 4 U/μl) to each STA reaction. .. Operation of instruments and handling and processing of the IFC controller HX were performed using standardized protocol for gene expression analysis provided by Fluidigm®.

    Staining:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: Using the same staining protocol and gating strategy outlined above, 10 cells in triplicate were sorted from selected cTfh subsets of 5 normal subjects and 4 MZL patients. .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: PCR samples were stained prior to electrophoresis with 1× GelRed (Biotium, Hayward, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    DNA Extraction:

    Article Title: Genetic variants of FZD4 and LRP5 genes in patients with advanced retinopathy of prematurity
    Article Snippet: DNA samples were extracted from peripheral blood using a DNA extraction kit (QiaAmp; Qiagen, Chatsworth, CA). .. The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA).

    Article Title: Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis
    Article Snippet: One-cell stage embryos were microinjected with 1–2 nl of the mixture, and cultured until shield to 80% epiboly stages. .. To extract genomic DNA, individual embryos were placed into 25 μl of ice-cold DNA extraction buffer (10 mM Tris–HCl, pH 8.0, 2 mM EDTA, 0.2% Triton X-100, 200 μg/ml Proteinase K) and incubated at 50°C for 16 h, then at 95°C for 10 min. To remove remaining targeting oligonucleotide, 25 μl of Exonuclease I mixture [0.04 U/μl Exonuclease I (New England Biolabs), 134 mM Glycine-KOH, pH 9.5, 13.4 mM MgCl2 , 20 mM 2-mercaptoethanol] was added, and incubated at 37°C for 1 h and at 80°C for 20 min. .. Mutant template was detected with a pair of PCR primers (BrulATRFO: 5′-AAGCTGAACAGTCAGAGTTGGTC-3′ (T m = 55°C) and BrulMutMcAsR: 5′-TGATTTCATAAACTGCACCC-3′ (T m = 48°C).

    In Vivo:

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: Paragraph title: In vivo TMP–DNA PB and selection of DNA-crosslinked fragments ... To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above.

    Mutagenesis:

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: These regions contain a mutant count of greater than 1 for any single point mutation. .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers.

    Article Title: Magnetic resonance imaging and genetic investigation of a case of rottweiler leukoencephalomyelopathy
    Article Snippet: For the DARS2 mutation analysis, suitable PCR products were amplified using AmpliTaq Gold 360 (Life Technologies). .. The PCR products were resequenced after rAPid alkaline phosphatase (Roche) and exonuclease I (New England Biolabs) treatment using both PCR primers and the ABI BigDye Terminator Sequencing Kit 3.1 (Life Technologies) in an ABI 3730 sequencer (see Additional file : Table S1).

    Isolation:

    Article Title: A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3
    Article Snippet: Sequencing was performed on DNA samples isolated from three of the most severely affected family members (II-3, III-4 and III-6). .. PCR product clean-up was carried out using ExoI (NEB, Ipswich, MA, USA) and SAP (USB, part of Affymetrix, Santa Clara, CA, USA) with standard protocols, and sequencing reactions, using BigDye Terminator v3.1 Cycle Sequencing kits, were run on a 3730xl DNA Analyzer (Applied Biosystems).

    Size-exclusion Chromatography:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: Next, pre-amplification mix, consisting of pooled mixture of all primer assays (500nM), 5× PreAmp Master Mix (Fluidigm) and H2 O, was added to each well and run on a thermocycler (95°C for 5 min followed by 18 cycles: 96°C for 5 sec 60°C for 6 min). .. Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min).

    Labeling:

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega). .. Purified PCR products were used in combination with a conventional primer designed to sit at the nucleotide to the immediate 5′ position of a coding SNPs in the transcript.

    Purification:

    Article Title: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes
    Article Snippet: For a subsample of males we amplified a 658 bp fragment of the last intron of the Zfy gene with published primers (LGL-331: Shaw et al. ; Yint-2-335: Wilson et al. ) as in Wilson et al. ( ). .. We purified polymerase chain reaction (PCR) products using Exosap-IT (USB Corporation, Cleveland, OH), or Exonuclease I and Antarctic Phosphatase (New England BioLabs Inc., Ipswich, MA), prior to sequencing on a MegaBACE 1000 (GE Healthcare) or an AB3730 (Applied Biosystems). .. We edited and aligned sequences in Bioedit (v7.0.9, Hall ) or MEGA (v5, Tamura et al. ).

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: Transformants were transferred to Luria-Bertani (LB) broth containing kanamycin (50 μ g/mL) in 96-well tissue culture plates, incubated for 16 h at 37°C at 225 rpm, then screened with PCR using the M13f and M13r primers ( ) to check for the presence of an insert. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing. .. Purified plasmid DNA was mixed with the M13f primer then submitted to the Cornell University Life Sciences Core Laboratories Center.

    Article Title: A recombineering based approach for high-throughput conditional knockout targeting vector construction
    Article Snippet: This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min. .. This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min.

    Article Title: A molecular inversion probe assay for detecting alternative splicing
    Article Snippet: Circularized MIPs were dissociated from the cDNA by holding the sample at 95°C for 5 minutes and chilled on ice. .. The ligated MIPs were further purified and fully eluted from the immobilized cDNA by digesting all linear DNA with exonucleases; 4 μl of exonuclease mix (3.5 μl 10× Exonuclease Buffer, 0.5 μl Exo I (NEB catalog no. M0293S. .. 1 μl Exo III (NEB catalog no. M0206S)) was added to the MIP reaction and samples were incubated at 37°C for 45 minutes.

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: DNA was precipitated with EtOH, washed with 70% EtOH and resuspended in 100 µl of water. .. To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above. .. Following proteinase K and RNAse I incubations, DNA fragments were extracted twice with phenol and once with phenol–chloroform, precipitated with EtOH, washed with 70% EtOH and resuspended in 100 µl of water.

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: Approximate size of the PCR amplicons was determined by electrophoresis on 1.5% agarose gel with a DNA ladder (GeneRuler™ DNA Ladder Mix, Fermentas). .. PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs. .. The sequencing reactions were performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to manufacture's instructions.

    Polymerase Chain Reaction:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: Similar to before [ ], PCR plates were thawed and pre-heated for 90 seconds at 65°C. .. Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min).

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: PCR was performed using an appropriate dilution of cDNA generated from the cerebral cortex of F1 (B6×BALB) animals. .. Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega). .. Purified PCR products were used in combination with a conventional primer designed to sit at the nucleotide to the immediate 5′ position of a coding SNPs in the transcript.

    Article Title: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes
    Article Snippet: For a subsample of males we amplified a 658 bp fragment of the last intron of the Zfy gene with published primers (LGL-331: Shaw et al. ; Yint-2-335: Wilson et al. ) as in Wilson et al. ( ). .. We purified polymerase chain reaction (PCR) products using Exosap-IT (USB Corporation, Cleveland, OH), or Exonuclease I and Antarctic Phosphatase (New England BioLabs Inc., Ipswich, MA), prior to sequencing on a MegaBACE 1000 (GE Healthcare) or an AB3730 (Applied Biosystems). .. We edited and aligned sequences in Bioedit (v7.0.9, Hall ) or MEGA (v5, Tamura et al. ).

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: Multiplex PCR cycling was performed according to the manufacturer’s recommendations (Kapa Biosystems) for a total of 15–25 PCR cycles using 63°C as optimal annealing temperature. .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers.

    Article Title: Genetic variants of FZD4 and LRP5 genes in patients with advanced retinopathy of prematurity
    Article Snippet: Polymerase chain reaction (PCR) was performed with optimized annealing temperatures. .. The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA). .. The samples were denatured and analyzed with a DNA sequencer (3100 or 3730 Genetic Analyzer; Applied Biosystems).

    Article Title: Magnetic resonance imaging and genetic investigation of a case of rottweiler leukoencephalomyelopathy
    Article Snippet: For the DARS2 mutation analysis, suitable PCR products were amplified using AmpliTaq Gold 360 (Life Technologies). .. The PCR products were resequenced after rAPid alkaline phosphatase (Roche) and exonuclease I (New England Biolabs) treatment using both PCR primers and the ABI BigDye Terminator Sequencing Kit 3.1 (Life Technologies) in an ABI 3730 sequencer (see Additional file : Table S1). .. The sequence data were analysed using Sequencer 4.9 software (GeneCodes).

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: Transformants were transferred to Luria-Bertani (LB) broth containing kanamycin (50 μ g/mL) in 96-well tissue culture plates, incubated for 16 h at 37°C at 225 rpm, then screened with PCR using the M13f and M13r primers ( ) to check for the presence of an insert. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing.

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Synthesized universal fragments were gel-purified (QIAquick Gel Extraction Kit, Qiagen). .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes. .. To obtain the libraries of DNA templates two universal fragments (1, 2 or 3, 4, ) were combined with one of the 31 variable PCR fragments using OE-PCR.

    Article Title: Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization
    Article Snippet: The PCR plate was transferred to a thermal cycler and subjected to the following thermal protocol: 95°C, 10 min; 14 cycles (95°C ,15 s; 60°C, 4 min); 4°C hold. .. Samples were treated with Exonuclease I (New England BioLabs, Ipswich, MA) to remove unincorporated primers by adding 2 μl (at 4 U/μl) to each STA reaction.

    Article Title: A recombineering based approach for high-throughput conditional knockout targeting vector construction
    Article Snippet: PCR was performed using PTC-225 PCR machine (Peltier Thermal Cycler) with the following settings: 94°C for 4 min, this was followed by 35 cycles of 94°C for 30 s, 60°C for 30 s and 68°C for 1 min (Bsd ) or 2–3 min (Neo and retrieval backbone). .. This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min. .. The PCR products were then purified using Qiagen mini-preparation columns and eluted in 50 μl of PCR-grade water.

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: Alternatively, the PCR products were separated using an HDA-GT12 DNA analyzer and scored by Biocalculator software (both from eGene, Irvine, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs). .. DNA sequencing was performed using ABI BigDye Terminator (v3.1; Applied Biosystems, Foster City, CA) according to the manufacturer's protocol, except that 5-μl reactions were performed with 0.25 μl of BigDye on an ABI 3730xl DNA sequencing machine with 50 cm arrays.

    Article Title: Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1
    Article Snippet: Genomic DNA was amplified by yeast colony polymerase chain reaction (PCR), using a blend of Pwo and Taq polymerase. .. The resulting 2 kb PCR products were treated with exonuclease I and Antarctic phosphatase (NEB) and directly used in sequencing reactions. .. Lasergene (DNAStar) was used to assemble and analyse the sequences.

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: Approximate size of the PCR amplicons was determined by electrophoresis on 1.5% agarose gel with a DNA ladder (GeneRuler™ DNA Ladder Mix, Fermentas). .. PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs. .. The sequencing reactions were performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to manufacture's instructions.

    Article Title: A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3
    Article Snippet: All primer sequences can be found in Supporting Information, . .. PCR product clean-up was carried out using ExoI (NEB, Ipswich, MA, USA) and SAP (USB, part of Affymetrix, Santa Clara, CA, USA) with standard protocols, and sequencing reactions, using BigDye Terminator v3.1 Cycle Sequencing kits, were run on a 3730xl DNA Analyzer (Applied Biosystems). .. Base calling and quality assessment were carried out using the Contig Express programme from the Vector NTI package (Invitrogen Life Technologies, Carlsbad, CA, USA).

    Quantitative RT-PCR:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: Paragraph title: Microfluidic RT-qPCR ... Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    FACS:

    Article Title: Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease
    Article Snippet: After FACS sorting, PCR plates were frozen and kept in -80°C until usage. .. Exonuclease mixture, containing of Exonuclease I (New England BioLabs), 10× Exonuclease I Reaction Buffer (New England BioLabs) and H2 O was added to each well to remove excessive primers and the plate was run on a thermocycler (37°C for 30 min, 80°C for 15 min).

    Activated Clotting Time Assay:

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: We suspended the collected beads in 50 μl of 1× Phusion HF buffer containing 0.25 mM dNTPs, 2 U Phusion Hot Start High-Fidelity DNA Polymerase (Finnzyme) and 0.8 μM Primer-3 (5′-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3′). .. We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min.

    Helicase-dependent Amplification:

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: Alternatively, the PCR products were separated using an HDA-GT12 DNA analyzer and scored by Biocalculator software (both from eGene, Irvine, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    Plasmid Preparation:

    Article Title: Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands
    Article Snippet: PCR products from rhizosphere soils were cloned using INVα F' competent cells and the pCR®2.1 vector from the TA Cloning® Kit (Life Technologies, Grand Island, NY) according to the manufacturer's directions. .. Proper-sized transformants were purified with exonuclease 1 and antarctic phosphatase (New England BioLabs, Inc., Ipswich, MA) for 45 min at 37°C then at 95°C for 15 min prior to sequencing.

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: In addition, the fragment encoding for PP1 phosphatase catalytic subunit (GeneBank ID NP_002699) was amplified from PP1-encoding plasmid with primers 9176 and 9177 using PCR conditions as given for genomic PCR. .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    Software:

    Article Title: Natural Genetic Variation of Integrin Alpha L (Itgal) Modulates Ischemic Brain Injury in Stroke
    Article Snippet: Amplicons containing coding SNPs were amplified by conventional PCR, and 15 ul of PCR products were treated with 1 U exonuclease I (New England Biolabs) and 5 U of Shrimp Alkaline Phosphatase (SAP) (Promega). .. Cycling conditions were as follows: 40 cycles of 95C° for 10 s, 50C° for 5 s, and 60C° for 30 s. The primer is then labeled with a fluorescently tagged dideoxynucleotide through a single base pair extension (SNaPshot kit from ABI).

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: Alternatively, the PCR products were separated using an HDA-GT12 DNA analyzer and scored by Biocalculator software (both from eGene, Irvine, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    Irradiation:

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above. .. To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above.

    Multiplex Assay:

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: Amplicon lengths ranged from 120 to 190 bp in size depending on the amplicon ( Supplementary Table S2 ). .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers. .. Probe design and preparation .

    Selection:

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min. .. Following incubation at 70°C for 10 min to inactivate Exonuclease I, we purified the double-stranded template DNAs with 50 μl of AMPure XP twice as described above, except for reducing the volume of final elution to 20 μl.

    Article Title: A recombineering based approach for high-throughput conditional knockout targeting vector construction
    Article Snippet: The restriction maps of the selection cassettes and PL611 are depicted in Supplementary Figures 2–6. .. This was then followed by 68°C for 5 min. After PCR reactions, 0.5 μl of exonuclease I (10 U, from either New England Biolabs or Epicentre) was added per 50 μl of PCR products and incubated at 37°C for 1 h followed by heat inactivation at 80°C for 20 min.

    Article Title: A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Article Snippet: Paragraph title: In vivo TMP–DNA PB and selection of DNA-crosslinked fragments ... To select the crosslinked fragments, DNA samples were boiled for 2 min, chilled on ice and then digested with excess Exonuclease I (NE BioLabs) during 4 h. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess λ Exonuclease (NE BioLabs) during 6 h. The reaction terminated by inactivation of the enzyme at 80°C during 10 min. To examine TMP PB to purified yeast DNA, unreacted cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier, as above.

    Agarose Gel Electrophoresis:

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: Approximate size of the PCR amplicons was determined by electrophoresis on 1.5% agarose gel with a DNA ladder (GeneRuler™ DNA Ladder Mix, Fermentas). .. PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs.

    Electrophoresis:

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: PCR samples were stained prior to electrophoresis with 1× GelRed (Biotium, Hayward, CA). .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: Approximate size of the PCR amplicons was determined by electrophoresis on 1.5% agarose gel with a DNA ladder (GeneRuler™ DNA Ladder Mix, Fermentas). .. PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs.

    Ethanol Precipitation:

    Article Title: Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)
    Article Snippet: PCR products were purified using exonuclease I (New England Biolabs) and shrimp alkaline phosphatase (Roche) and directly sequenced in both forward and reverse directions with the same primers as those used in the PCRs. .. The sequencing reactions were performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) according to manufacture's instructions.

    Concentration Assay:

    Article Title: Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
    Article Snippet: Multiplex pre-amplification from ∼20 ng genomic DNA or 10 ng plasma-circulating DNA was performed in a total volume of 25 µl using a mixture of 100 primers (50 paired sets) at a final concentration of 0.3 µM for each primer with 0.3 mM dNTPs, 3 mM MgCl2 , 1× Kapa HiFi buffer and 0.5 U of Kapa HiFi HotStart DNA polymerase (Kapa Biosystems, Woburn, MA, USA) reported to have an error rate of 2.8 × 10−7 mis-incorporations/bp. .. Following multiplex cycling, 1 µl of exonuclease I (New England Biolabs, Ipswich, MA, USA) was added to each reaction and incubated at 37°C for 30 min and 80°C for 15 min to remove unincorporated primers.

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Primers 8817–8878 at 300 nM concentration were used in amplification of the genes 1–31 with 35 cycles. .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    Article Title: Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
    Article Snippet: The polymerase chain reaction (PCR) was performed in a 20 μl volume containing 10 ng of genomic DNA as a template, 200 μmol/L of each dNTP, 1× Standard Taq PCR buffer with 1.5 mmol/L MgCl2 , 1.2 U Taq polymerase (all from New England Biolabs, Ipswich, MA), and forward and reverse primers at a concentration of 0.25 μmol/L each. .. If sequencing was needed, PCR products were first treated with Exonuclease I and subsequently with Antarctic Phosphatase (both from New England Biolabs).

    Fractionation:

    Article Title: Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    Article Snippet: Paragraph title: Elution and size fractionation ... We transferred the supernatant to a new tube, added 1 μl of 20 U/μl Exonuclease I (NEB) and incubated the tube at 37°C for 15 min.

    Migration:

    Article Title: Circulating Tfh1 (cTfh1) cell numbers and PD1 expression are elevated in low-grade B-cell non-Hodgkin’s lymphoma and cTfh gene expression is perturbed in marginal zone lymphoma
    Article Snippet: A custom panel of 96 genes (including 4 candidate reference genes) implicated in CD4+ T-cell biology (migration, differentiation, effector function and cell signalling pathways) was created, and primers designed using the D3 Assay Design service (Fluidigm, ) ( ). .. Following pre-amplification unincorporated primers were removed by exonuclease I digestion (2 μl of 4 U/μl exonuclease I (New England Biolabs Inc., #M0293S) by incubation in a thermal cycler at 37°C for 30 minutes followed by 80°C for 15 minutes.

    Gel Extraction:

    Article Title: Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System
    Article Snippet: Synthesized universal fragments were gel-purified (QIAquick Gel Extraction Kit, Qiagen). .. Variable ORF-encoded fragments were freed from residual primers by treatment with 15 U/ml Exonuclease I (NEB), which was added directly to the final PCR reaction mixture, for 30 minutes at 37°C followed by nuclease inactivation at 85°C for 30 minutes.

    Variant Assay:

    Article Title: Genetic variants of FZD4 and LRP5 genes in patients with advanced retinopathy of prematurity
    Article Snippet: The PCR products were treated with shrimp alkaline phosphatase (Roche Applied Science, Indianapolis, IN) and exonuclease I (NEB, Ipswich, MA), and then sequenced with the BigDye Terminator ver.1.1 (Applied Biosystems, Foster City, CA). .. Each sequence change was evaluated by two examiners using the Phred/Phrap/Consed program [ ].

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    New England Biolabs e coli exoi
    <t>DNA</t> with 3′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) DNA substrates bearing different types of 3′ ends and labeled by 32 P at the third nucleotide from the 3′ end were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with four sets of data. ( C ) Assay for detecting biotin at the 3′ end of ss-DNA. The 32 P-labeled 3′ ddC or biotin DNA with short 3′ ss-overhangs was pre-incubated with buffer or avidin and then treated with E. coli <t>ExoI.</t> The products were analyzed on a 1% TAE-agarose gel. ( D ) Avidin was not removed from the 3′ end of resection intermediates. 3′ avidin DNA was incubated in extracts for the indicated times, isolated, supplemented with buffer or avidin, and treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel.
    E Coli Exoi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli exoi/product/New England Biolabs
    Average 99 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    e coli exoi - by Bioz Stars, 2019-12
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    99
    New England Biolabs exonuclease 1 recombinant shrimp alkaline phosphatase
    <t>DNA</t> with 3′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) DNA substrates bearing different types of 3′ ends and labeled by 32 P at the third nucleotide from the 3′ end were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with four sets of data. ( C ) Assay for detecting biotin at the 3′ end of ss-DNA. The 32 P-labeled 3′ ddC or biotin DNA with short 3′ ss-overhangs was pre-incubated with buffer or avidin and then treated with E. coli <t>ExoI.</t> The products were analyzed on a 1% TAE-agarose gel. ( D ) Avidin was not removed from the 3′ end of resection intermediates. 3′ avidin DNA was incubated in extracts for the indicated times, isolated, supplemented with buffer or avidin, and treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel.
    Exonuclease 1 Recombinant Shrimp Alkaline Phosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease 1 recombinant shrimp alkaline phosphatase/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    exonuclease 1 recombinant shrimp alkaline phosphatase - by Bioz Stars, 2019-12
    99/100 stars
      Buy from Supplier

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    DNA with 3′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) DNA substrates bearing different types of 3′ ends and labeled by 32 P at the third nucleotide from the 3′ end were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with four sets of data. ( C ) Assay for detecting biotin at the 3′ end of ss-DNA. The 32 P-labeled 3′ ddC or biotin DNA with short 3′ ss-overhangs was pre-incubated with buffer or avidin and then treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel. ( D ) Avidin was not removed from the 3′ end of resection intermediates. 3′ avidin DNA was incubated in extracts for the indicated times, isolated, supplemented with buffer or avidin, and treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel.

    Journal: Nucleic Acids Research

    Article Title: The structure of ends determines the pathway choice and Mre11 nuclease dependency of DNA double-strand break repair

    doi: 10.1093/nar/gkw274

    Figure Lengend Snippet: DNA with 3′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) DNA substrates bearing different types of 3′ ends and labeled by 32 P at the third nucleotide from the 3′ end were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with four sets of data. ( C ) Assay for detecting biotin at the 3′ end of ss-DNA. The 32 P-labeled 3′ ddC or biotin DNA with short 3′ ss-overhangs was pre-incubated with buffer or avidin and then treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel. ( D ) Avidin was not removed from the 3′ end of resection intermediates. 3′ avidin DNA was incubated in extracts for the indicated times, isolated, supplemented with buffer or avidin, and treated with E. coli ExoI. The products were analyzed on a 1% TAE-agarose gel.

    Article Snippet: To detect the presence of 3′ biotin on 3′ ss-overhangs or resection intermediates, the DNA was pre-incubated with ELB buffer or avidin on ice for 5 min, and then treated with Escherichia coli ExoI (NEB, MA) at 22ºC for 60 min. To analyze the intermediates of the 5′ biotin-avidin DNA, DNA was treated with E. coli ExoI (0.2 u/μl, NEB, MA) or RecJ (0.3 u/μl; NEB, MA) at 22°C for 60 min. To detect the presence of 5′ biotin, DNA was pre-incubated with ELB buffer or avidin on ice for 5 min, and then treated with T7 Exo (0.6 unit/μl; NEB, MA) at 22°C for 60 min.

    Techniques: Labeling, Incubation, Agarose Gel Electrophoresis, Avidin-Biotin Assay, Isolation

    DNA with 5′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) 32 P -labeled DNA substrates bearing different types of 5′ ends were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel and detected by exposing the dried gel to X-ray film. Avidin is bound to DNA ends via biotin. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with five sets of data. ( C ) Resection of 5′ avidin DNA proceeds in the 5′→3′ direction. 5′ avidin DNA was incubated with extracts for 30 min and re-isolated. They were incubated with buffer or avidin and then treated with E. coli ExoI or RecJ. The products were analyzed on a 1% TAE-agarose gel.

    Journal: Nucleic Acids Research

    Article Title: The structure of ends determines the pathway choice and Mre11 nuclease dependency of DNA double-strand break repair

    doi: 10.1093/nar/gkw274

    Figure Lengend Snippet: DNA with 5′ damaged nucleotides or bulky adducts is channeled to resection. ( A ) 32 P -labeled DNA substrates bearing different types of 5′ ends were incubated with Xenopus egg extracts for the indicated times. The products were analyzed on a 1% TAE-agarose gel and detected by exposing the dried gel to X-ray film. Avidin is bound to DNA ends via biotin. ( B ) Plot of the percentages of substrates converted into supercoiled monomer products at 180′. The averages and standard deviations were calculated with five sets of data. ( C ) Resection of 5′ avidin DNA proceeds in the 5′→3′ direction. 5′ avidin DNA was incubated with extracts for 30 min and re-isolated. They were incubated with buffer or avidin and then treated with E. coli ExoI or RecJ. The products were analyzed on a 1% TAE-agarose gel.

    Article Snippet: To detect the presence of 3′ biotin on 3′ ss-overhangs or resection intermediates, the DNA was pre-incubated with ELB buffer or avidin on ice for 5 min, and then treated with Escherichia coli ExoI (NEB, MA) at 22ºC for 60 min. To analyze the intermediates of the 5′ biotin-avidin DNA, DNA was treated with E. coli ExoI (0.2 u/μl, NEB, MA) or RecJ (0.3 u/μl; NEB, MA) at 22°C for 60 min. To detect the presence of 5′ biotin, DNA was pre-incubated with ELB buffer or avidin on ice for 5 min, and then treated with T7 Exo (0.6 unit/μl; NEB, MA) at 22°C for 60 min.

    Techniques: Labeling, Incubation, Agarose Gel Electrophoresis, Avidin-Biotin Assay, Isolation

    The extended G-overhang is not due to the collapse of replication fork. ( A ) No 5′ C-rich overhang was detected during the cell cycle. Genomic DNA isolated from synchronized HeLa cells were hybridized to an 18-mer G-rich probe for detecting C-rich overhangs and hybridized to an 18-mer C-rich probe for detecting G-overhangs under native conditions. To determine the hybridization signals contributed by G- or C-rich overhangs, DNA was digested with 3′ → 5′ exonuclease ExoI, which specifically removes 3′ G-overhangs, or the 5′ → 3′ exonuclease RecJf , which specifically removes 5′ C-rich overhangs before hybridization. The same gels were then denatured to determine the total telomere signal. Asyn, asynchronized HeLa cells. ( B ) Quantitation of relative amount of G-overhangs from ( A ). ( C ) Hybridization of G-rich probe to (C3 TA2 )4 oligo. The ss (C3 TA2 )4 oligo was hybridized to G-rich probe under the native condition identical to ( A ) and separated in 20% native 0.5 × TBE polyacrylamide gel.

    Journal:

    Article Title: Molecular steps of G-overhang generation at human telomeres and its function in chromosome end protection

    doi: 10.1038/emboj.2010.156

    Figure Lengend Snippet: The extended G-overhang is not due to the collapse of replication fork. ( A ) No 5′ C-rich overhang was detected during the cell cycle. Genomic DNA isolated from synchronized HeLa cells were hybridized to an 18-mer G-rich probe for detecting C-rich overhangs and hybridized to an 18-mer C-rich probe for detecting G-overhangs under native conditions. To determine the hybridization signals contributed by G- or C-rich overhangs, DNA was digested with 3′ → 5′ exonuclease ExoI, which specifically removes 3′ G-overhangs, or the 5′ → 3′ exonuclease RecJf , which specifically removes 5′ C-rich overhangs before hybridization. The same gels were then denatured to determine the total telomere signal. Asyn, asynchronized HeLa cells. ( B ) Quantitation of relative amount of G-overhangs from ( A ). ( C ) Hybridization of G-rich probe to (C3 TA2 )4 oligo. The ss (C3 TA2 )4 oligo was hybridized to G-rich probe under the native condition identical to ( A ) and separated in 20% native 0.5 × TBE polyacrylamide gel.

    Article Snippet: To remove the 3′ G-rich overhang, total DNA was treated with the 3′ → 5′ exonuclease Escherichia coli ExoI (0.3 U/μg DNA, NEB) in 15 μl buffer (10 mM HEPES pH 7.5, 100 mM LiCl, 2.5 mM MgCl2 , 5 mM CaCl2 , 20 mM β-mercaptoethanol, 0.067 μg/μl DNase-free RNaseA) at 37°C for 1 h to overnight.

    Techniques: Isolation, Hybridization, Quantitation Assay

    ( A ) The nascent base pair binding pocket at the active site of Taq DNA pol I. Amino acids of Taq DNA pol I that interact with the incoming nucleotide ( red ) and the templating base ( magenta ) that are conserved in pol ν are colored in blue . Amino

    Journal:

    Article Title: A unique error signature for human DNA polymerase ?

    doi: 10.1016/j.dnarep.2006.09.012

    Figure Lengend Snippet: ( A ) The nascent base pair binding pocket at the active site of Taq DNA pol I. Amino acids of Taq DNA pol I that interact with the incoming nucleotide ( red ) and the templating base ( magenta ) that are conserved in pol ν are colored in blue . Amino

    Article Snippet: The exonuclease-deficient, large Klenow fragment of E. coli DNA pol I and T4 polynucleotide kinase were purchased from New England BioLabs.

    Techniques: Binding Assay