antartic phosphatase  (New England Biolabs)


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    Name:
    Antarctic Phosphatase
    Description:

    Catalog Number:
    M0289L
    Price:
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    Score:
    85
    Buy from Supplier
    Name:
    Antarctic Phosphatase Reaction Buffer
    Description:

    Catalog Number:
    B0289S
    Price:
    None
    Score:
    85
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    Structured Review

    New England Biolabs antartic phosphatase

    https://www.bioz.com/result/antartic phosphatase/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    antartic phosphatase - by Bioz Stars, 2019-10
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    Related Articles

    Clone Assay:

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: Paragraph title: Cloning of K. pneumoniae dedA ... For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette.

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: PTENpg1 asRNA α was PCR amplified using primers with Nhe1 or Kpn1 restriction sites ( ) and cloned into pcDNA 3.1. .. The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: PCR amplicons of 401 bp containing the entire exon 2 and exon-intron boundaries of Phox2b (188 bp) starting 112 bp upstream and finishing 101 bp downstream of Phox2b exon2 respectively. .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Constructs were transformed into competent bacteria and grown onto ampicilline agar plate to generate bacteria clones containing either the WT or the del18 construct.

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. The sequence of gB amino acids spanning 711 to 796 were deleted from pKgBΔSS by cassette PCR mutagenesis.

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product was digested by Bam HI and Kpn I, cloned into pGTP_FZ301 previously digested by Bam HI and Kpn I, and ligation was used to transform MG1363. pGTP_FZ301_NucB plasmid extracted from a chloramphenicol resistant clone was verified by digestion and sequencing. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Amplification:

    Article Title: Aire controls gene expression in the thymic epithelium with ordered stochasticity
    Article Snippet: First the fragmentation of the amplified RNA (aRNA) was performed using the Magnesium RNA Fragmentation Module (NEBNext E6150S). .. First the 5’ end of the aRNA was dephosphorylated by adding 4 µL of a mix containing 2µL of 10X Antarctic Phosphatase Reaction Buffer, 1µL of Antartic phosphatase (5U/µL stock, NEB M0289) and 1µL of RNAseOut to 16µL of each aRNA pool and incubating at 37°C for 30min and 65°C for 5min.

    Article Title: Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes
    Article Snippet: Genomic DNA was amplified by PCR using the specific primers and KAPA2G Robust Hotstart Ready Mix (KAPA Biosystems). .. PCR products were enzymatically purified with Exonuclease I and Antartic phosphatase (both New England BioLabs Inc.).

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: Since studied K. pneumoniae ST258 is resistant to ampicillin, the selection marker of both vector and clone was replaced by the apramycin resistance cassette of pIJ773. .. For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette. .. In parallel, the AprR cassette of pIJ773 was amplified using primers Apr1 and Apr2, digested with XbaI and ligated separately with the linearized plasmids described above using T4 ligase (Thermo Scientific, USA).

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: The following primers were used: 12S rDNA: 12SA 5´-AAACTGGGATTAGATACCCCACTAT-3´ and 12SB 5´-GAGGGTGACGGGCGGTGTGT-3´ [ ] amplified a ~400 base pair fragment while 16S rDNA 5´-GCCTGTTTATCAAAAACAT-3´ and 16SH 5´-CCGGTCTGAACTCAGATCACGT- 3´ [ ] amplified a ~700 base pair fragment. .. Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample.

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs).

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: PTENpg1 asRNA α was PCR amplified using primers with Nhe1 or Kpn1 restriction sites ( ) and cloned into pcDNA 3.1. .. The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: PCR products containing either the Wild type (WT) or the c.393_410del18 (del18) mutation were amplified using primers containining both of them an artificial site for Kpn1 (sequences can be asked on requests) and as template a DNA sample of the patient heterozygous for the mutation. .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.).

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: Plasmid pKΔ4B was derived by Cai et al. following engineering of linker-insertion mutants in the glycoprotein B gene. .. DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. This plasmid was designated pKgBΔSS.

    Article Title: Novel mutations of TCOF1 gene in European patients with treacher Collins syndrome
    Article Snippet: PCR amplification was performed in a 25 μl reaction volume containing 2.5 U AmpliTaq Gold™ DNA polymerase (Applied Biosystems, Foster City, CA), 1X reaction buffer (10 mM Tris HCl pH 8.3, 50 mM KCl, 2.5 mM MgCl2 ), 200 μM of each deoxyribonucleoside triphosphate (dNTPs) and 0.2 mM each of primers using a PTC 100 thermocycler (MJ Research, Inc. Waltham, MA, USA). .. PCR products were purified by digestion with Antartic Phosphatase and Exonuclease I (New England BioLabs Inc.) and were sequenced in both directions using the Applied Biosystem Big Dye Terminator v3.1 Cycle sequencing kit.

    Polyacrylamide Gel Electrophoresis:

    Article Title: CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo
    Article Snippet: To produce 5′-end-labeled sgRNAs, purified sgRNA transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BIoLabs) to 50 pmol of sgRNA in a final volume of 10 μL containing 50 mM Bis-Propane pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20U, Invitrogen). .. To produce 5′-end-labeled sgRNAs, purified sgRNA transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BIoLabs) to 50 pmol of sgRNA in a final volume of 10 μL containing 50 mM Bis-Propane pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20U, Invitrogen).

    Article Title: Investigating a New Generation of Ribozymes in Order to Target HCV
    Article Snippet: In order to generate 5′-end-labeled RNA substrate, 50 pmol of purified transcripts were dephosphorylated by adding 1 U of Antartic phosphatase (New England Biolabs) and incubating for 1 h at 37°C in a final volume of 10 µL containing 50 mM Bis-Propane, pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and 40 U of RNAGuard. .. The dephosphorylated RNAs (5 pmol) were then 5′-end labeled by incubation for 1 h at 37°C with 3 U of T4 polynucleotide kinase (USB) and 3.2 pmol of [γ-32P ]ATP (6000 Ci/mmol; New England Nuclear) in the provided reaction buffer.

    Article Title: 5?-UTR G-quadruplex structures acting as translational repressors
    Article Snippet: In order to produce 5′-end-labeled PG4s, purified transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BioLabs,) to 50 pmol of RNA and incubating the reaction mixture for 30 min at 37°C in a final volume of 10 µl containing 50 mM Bis-Propane (pH 6.0), 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20 U, Invitrogen). .. In order to produce 5′-end-labeled PG4s, purified transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BioLabs,) to 50 pmol of RNA and incubating the reaction mixture for 30 min at 37°C in a final volume of 10 µl containing 50 mM Bis-Propane (pH 6.0), 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20 U, Invitrogen).

    Article Title: A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme
    Article Snippet: Purified substrates or ribozymes (40 pmol) were dephosphorylated in a final volume of 10 µl using 10 U of Antartic phosphatase according to the manufacturer's conditions (New England Biolabs). .. Purified substrates or ribozymes (40 pmol) were dephosphorylated in a final volume of 10 µl using 10 U of Antartic phosphatase according to the manufacturer's conditions (New England Biolabs).

    Synthesized:

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.). .. Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.).

    Autoradiography:

    Article Title: CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo
    Article Snippet: To produce 5′-end-labeled sgRNAs, purified sgRNA transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BIoLabs) to 50 pmol of sgRNA in a final volume of 10 μL containing 50 mM Bis-Propane pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20U, Invitrogen). .. The reaction was stopped by adding formamide dye buffer (95% formamide, 10 mM EDTA, 0.025% bromophenol blue and 0.025% xylene cyanol), and the radiolabeled sgRNA purified by 8% polyacrylamide gel electrophoresis.

    Article Title: Investigating a New Generation of Ribozymes in Order to Target HCV
    Article Snippet: In order to generate 5′-end-labeled RNA substrate, 50 pmol of purified transcripts were dephosphorylated by adding 1 U of Antartic phosphatase (New England Biolabs) and incubating for 1 h at 37°C in a final volume of 10 µL containing 50 mM Bis-Propane, pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and 40 U of RNAGuard. .. The dephosphorylated RNAs (5 pmol) were then 5′-end labeled by incubation for 1 h at 37°C with 3 U of T4 polynucleotide kinase (USB) and 3.2 pmol of [γ-32P ]ATP (6000 Ci/mmol; New England Nuclear) in the provided reaction buffer.

    Article Title: 5?-UTR G-quadruplex structures acting as translational repressors
    Article Snippet: In order to produce 5′-end-labeled PG4s, purified transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BioLabs,) to 50 pmol of RNA and incubating the reaction mixture for 30 min at 37°C in a final volume of 10 µl containing 50 mM Bis-Propane (pH 6.0), 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20 U, Invitrogen). .. The reactions were stopped by adding formamide dye buffer (95% formamide, 10 mM EDTA, 0.025% bromophenol blue and 0.025% xylene cyanol), and the RNA molecules purified by 10% polyacrylamide gel electrophoresis.

    Article Title: A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme
    Article Snippet: Purified substrates or ribozymes (40 pmol) were dephosphorylated in a final volume of 10 µl using 10 U of Antartic phosphatase according to the manufacturer's conditions (New England Biolabs). .. The reactions were stopped by the addition of formamide dye buffer and the mixtures fractionated through denaturing 10–20% PAGE gels.

    Construct:

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: The K. pneumoniae dedA gene (KpndedA ) was amplified from RH201207 genomic DNA using primers KdedA1 and KdedA2 , digested with SacI and HindIII (New England Biolabs, UAS) and ligated with a similarly digested and dephosphorylated linearized fragment of vector pBAD-HisA (Invitrogen, USA) to construct plasmid pBAD-KpndedA . .. For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette.

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Constructs were transformed into competent bacteria and grown onto ampicilline agar plate to generate bacteria clones containing either the WT or the del18 construct.

    Incubation:

    Article Title: Aire controls gene expression in the thymic epithelium with ordered stochasticity
    Article Snippet: Samples were immediately incubated at 94°C (lid 105°C) for 2 minutes, then immediately transferred onto ice and the reaction was stopped by adding quickly 2µL of 10X RNA Fragmentation Stop Solution. .. First the 5’ end of the aRNA was dephosphorylated by adding 4 µL of a mix containing 2µL of 10X Antarctic Phosphatase Reaction Buffer, 1µL of Antartic phosphatase (5U/µL stock, NEB M0289) and 1µL of RNAseOut to 16µL of each aRNA pool and incubating at 37°C for 30min and 65°C for 5min.

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase. .. All binding experiments were performed in triplicate on 24-well plates using a Microlab Starlet automate (Hamilton).

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs).

    Expressing:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: The target site of the scarlet -targeting gRNA was 5ʹ-GGTTCACTCGTCGCCTTAATggg-3ʹ (protospacer adjacent motif shown in lowercase). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. A pair of scarlet- targeting oligonucleotides were then annealed and ligated into the linearized pDR274 vector using a ligation mix (TaKaRa Bio, Shiga, Japan).

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: E.coli TOP 10 electrocompetent cells (Invitrogen, Carlsbad, U.S.A.) were utilized as gene expression and production of recombinant amylosucrase variants. .. Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.).

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PZn zitR SPExp4 expression and secretion cassette was PCR-amplified from pGTPb_PZn zitR- SPExp4 using primers 7 and 8. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Transformation Assay:

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: Ligation reaction was transformed into NEB 5-α competent cells. pGTPb_PZn zitR- SPExp4 from an ampicillin-resistant clone was verified by digestion and sequencing, revealing three silent mutations in zitR sequence. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Derivative Assay:

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: Plasmid pGST‐amylosucrase (pGST‐AS) derived from the pGEX‐6P‐3 (GE Healthcare Biosciences, Piscataway, U.S.A) encoding GST fused to N. polysaccharea amylosucrase, was used for the construction of semi‐rational libraries. .. Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.).

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: Plasmid pKΔ4B was derived by Cai et al. following engineering of linker-insertion mutants in the glycoprotein B gene. .. DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ).

    Flow Cytometry:

    Article Title: Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS
    Article Snippet: Nucleobond AXR-80 gravity flow columns were purchased from Machery-Nagel (Bethlehem, PA). .. Snake venom phosphodiesterase I was purchased from Worthington Biochemicals (Lakewood, NJ) and antartic phosphatase from New England Biolabs (Ipswich, MA).

    Ligation:

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: PCR amplicons of 401 bp containing the entire exon 2 and exon-intron boundaries of Phox2b (188 bp) starting 112 bp upstream and finishing 101 bp downstream of Phox2b exon2 respectively. .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Constructs were transformed into competent bacteria and grown onto ampicilline agar plate to generate bacteria clones containing either the WT or the del18 construct.

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product was digested by Bam HI and Kpn I, cloned into pGTP_FZ301 previously digested by Bam HI and Kpn I, and ligation was used to transform MG1363. pGTP_FZ301_NucB plasmid extracted from a chloramphenicol resistant clone was verified by digestion and sequencing. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Generated:

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: T7 transcripts were generated by linearization of pcDNA 3.1 with Kpn1 and T7 transcribed with the Durascribe T7 kit (Epicenter, Madison WI, USA) using fluorinated CTPs and UTPs (TriLink). .. The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs).

    Sequencing:

    Article Title: Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes
    Article Snippet: Paragraph title: Sanger sequencing of genomic DNA ... PCR products were enzymatically purified with Exonuclease I and Antartic phosphatase (both New England BioLabs Inc.).

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase. .. After five washings with 500 µL of culture medium, bound sequences were recovered in 200 µL of lysis buffer (50 mM Hepes PH 7.5, 150 mM NaCl, 10% glycerol, 1% Triton X100, 2 mM MgCl2 and 5 mM EGTA) and the radioactivity counted.

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Constructs were transformed into competent bacteria and grown onto ampicilline agar plate to generate bacteria clones containing either the WT or the del18 construct.

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. This plasmid was designated pKgBΔSS.

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product was digested by Bam HI and Kpn I, cloned into pGTP_FZ301 previously digested by Bam HI and Kpn I, and ligation was used to transform MG1363. pGTP_FZ301_NucB plasmid extracted from a chloramphenicol resistant clone was verified by digestion and sequencing. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Article Title: Novel mutations of TCOF1 gene in European patients with treacher Collins syndrome
    Article Snippet: A 10-minute denaturation step at 94°C was followed by 30 cycles at 94°C for 30 seconds, annealing temperature was performed, for each primer, 30 seconds at 52.5-62°C, and extending for 30 sec at 72°C; the reaction was completed by a final extension for 7 minutes at 72°C. .. PCR products were purified by digestion with Antartic Phosphatase and Exonuclease I (New England BioLabs Inc.) and were sequenced in both directions using the Applied Biosystem Big Dye Terminator v3.1 Cycle sequencing kit. .. New mutations were not found in 100 normal chromosomes by sequencing.

    Antiviral Assay:

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product digested by Ava II was cloned into pGTPb_102a_SPExp4 previously digested by Rsr II and dephosphorylated. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Binding Assay:

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: Paragraph title: Binding of Radioactive Aptamers on Adherent Cells ... First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase.

    In Vivo:

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs). .. The T7 transcripts were transfected into target cells at 25-50nM using Lipofectamine 2000 (Life Technologies).

    Radioactivity:

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase. .. Radioactive aptamers at different concentrations were incubated for 15 min at 37°C on 80% confluent cell monolayer in 200 µL of RPMI 1640 containing 100 µg/ml of tRNA as a nonspecific competitor.

    Mutagenesis:

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: PCR products containing either the Wild type (WT) or the c.393_410del18 (del18) mutation were amplified using primers containining both of them an artificial site for Kpn1 (sequences can be asked on requests) and as template a DNA sample of the patient heterozygous for the mutation. .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.).

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. This plasmid was designated pKgBΔSS.

    Transfection:

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs). .. The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.).

    Labeling:

    Article Title: CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo
    Article Snippet: Paragraph title: sgRNA labeling and in-line probing ... To produce 5′-end-labeled sgRNAs, purified sgRNA transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BIoLabs) to 50 pmol of sgRNA in a final volume of 10 μL containing 50 mM Bis-Propane pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20U, Invitrogen).

    Article Title: Investigating a New Generation of Ribozymes in Order to Target HCV
    Article Snippet: Paragraph title: RNA Substrate Labeling ... In order to generate 5′-end-labeled RNA substrate, 50 pmol of purified transcripts were dephosphorylated by adding 1 U of Antartic phosphatase (New England Biolabs) and incubating for 1 h at 37°C in a final volume of 10 µL containing 50 mM Bis-Propane, pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and 40 U of RNAGuard.

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: ACE4-specific bands were cut and analyzed by nano-LC-MS/MS. .. First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase. .. All binding experiments were performed in triplicate on 24-well plates using a Microlab Starlet automate (Hamilton).

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample. .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) in accordance with the manufacturer's instructions.

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. The sequence of gB amino acids spanning 711 to 796 were deleted from pKgBΔSS by cassette PCR mutagenesis.

    Article Title: 5?-UTR G-quadruplex structures acting as translational repressors
    Article Snippet: Paragraph title: RNA labeling ... In order to produce 5′-end-labeled PG4s, purified transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BioLabs,) to 50 pmol of RNA and incubating the reaction mixture for 30 min at 37°C in a final volume of 10 µl containing 50 mM Bis-Propane (pH 6.0), 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20 U, Invitrogen).

    Avidin-Biotin Assay:

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs). .. The T7 transcripts were transfected into target cells at 25-50nM using Lipofectamine 2000 (Life Technologies).

    Polymerase Chain Reaction:

    Article Title: Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes
    Article Snippet: Genomic DNA was amplified by PCR using the specific primers and KAPA2G Robust Hotstart Ready Mix (KAPA Biosystems). .. PCR products were enzymatically purified with Exonuclease I and Antartic phosphatase (both New England BioLabs Inc.). .. Purified PCR products were sequenced using the BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems) on a 3730xl DNA Analyzer (Applied Biosystems).

    Article Title: Social and Population Structure in the Ant Cataglyphis emmae
    Article Snippet: The thermal cycle profile was as follows: an initial denaturation step of 2 min at 94°C; 35 cycles of denaturation at 30 s at 94°C, annealing for 30 s at 52°C and extension for 45 s at 72°C; and a final extension for 5 min at 72°C. .. Following the PCR reactions, excess primers and dNTPs were removed using enzymatic reaction of E. coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: The following primers were used: 12S rDNA: 12SA 5´-AAACTGGGATTAGATACCCCACTAT-3´ and 12SB 5´-GAGGGTGACGGGCGGTGTGT-3´ [ ] amplified a ~400 base pair fragment while 16S rDNA 5´-GCCTGTTTATCAAAAACAT-3´ and 16SH 5´-CCGGTCTGAACTCAGATCACGT- 3´ [ ] amplified a ~700 base pair fragment. .. Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample. .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) in accordance with the manufacturer's instructions.

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: The thermal cycle profile was as follows: an initial denaturation step of 2min at 94°C; 35 cycles of denaturation at 30s at 94°C, annealing for 30s at 52°C and extension for 45s at 72°C; and a final extension for 5min at 72°C. .. Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Article Title: A pseudogene long noncoding RNA network regulates PTEN transcription and translation in human cells
    Article Snippet: PTENpg1 asRNA α was PCR amplified using primers with Nhe1 or Kpn1 restriction sites ( ) and cloned into pcDNA 3.1. .. The resultant transcripts were DNase treated and dephosporylation using Antartic Phosphatase (New England Biolabs).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: PCR amplicons of 401 bp containing the entire exon 2 and exon-intron boundaries of Phox2b (188 bp) starting 112 bp upstream and finishing 101 bp downstream of Phox2b exon2 respectively. .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.).

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: Plasmid pKΔ4B was derived by Cai et al. following engineering of linker-insertion mutants in the glycoprotein B gene. .. DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ). .. This plasmid was designated pKgBΔSS.

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product was digested by Bam HI and Kpn I, cloned into pGTP_FZ301 previously digested by Bam HI and Kpn I, and ligation was used to transform MG1363. pGTP_FZ301_NucB plasmid extracted from a chloramphenicol resistant clone was verified by digestion and sequencing. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Article Title: Novel mutations of TCOF1 gene in European patients with treacher Collins syndrome
    Article Snippet: A 10-minute denaturation step at 94°C was followed by 30 cycles at 94°C for 30 seconds, annealing temperature was performed, for each primer, 30 seconds at 52.5-62°C, and extending for 30 sec at 72°C; the reaction was completed by a final extension for 7 minutes at 72°C. .. PCR products were purified by digestion with Antartic Phosphatase and Exonuclease I (New England BioLabs Inc.) and were sequenced in both directions using the Applied Biosystem Big Dye Terminator v3.1 Cycle sequencing kit. .. New mutations were not found in 100 normal chromosomes by sequencing.

    Selection:

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: Since studied K. pneumoniae ST258 is resistant to ampicillin, the selection marker of both vector and clone was replaced by the apramycin resistance cassette of pIJ773. .. For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette.

    De-Phosphorylation Assay:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: The target site of the scarlet -targeting gRNA was 5ʹ-GGTTCACTCGTCGCCTTAATggg-3ʹ (protospacer adjacent motif shown in lowercase). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. A pair of scarlet- targeting oligonucleotides were then annealed and ligated into the linearized pDR274 vector using a ligation mix (TaKaRa Bio, Shiga, Japan).

    CRISPR:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: Paragraph title: Knockout of Scarlet by CRISPR/Cas9 system ... To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    Purification:

    Article Title: Aire controls gene expression in the thymic epithelium with ordered stochasticity
    Article Snippet: First the 5’ end of the aRNA was dephosphorylated by adding 4 µL of a mix containing 2µL of 10X Antarctic Phosphatase Reaction Buffer, 1µL of Antartic phosphatase (5U/µL stock, NEB M0289) and 1µL of RNAseOut to 16µL of each aRNA pool and incubating at 37°C for 30min and 65°C for 5min. .. First the 5’ end of the aRNA was dephosphorylated by adding 4 µL of a mix containing 2µL of 10X Antarctic Phosphatase Reaction Buffer, 1µL of Antartic phosphatase (5U/µL stock, NEB M0289) and 1µL of RNAseOut to 16µL of each aRNA pool and incubating at 37°C for 30min and 65°C for 5min.

    Article Title: Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes
    Article Snippet: Genomic DNA was amplified by PCR using the specific primers and KAPA2G Robust Hotstart Ready Mix (KAPA Biosystems). .. PCR products were enzymatically purified with Exonuclease I and Antartic phosphatase (both New England BioLabs Inc.). .. Purified PCR products were sequenced using the BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems) on a 3730xl DNA Analyzer (Applied Biosystems).

    Article Title: CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo
    Article Snippet: DNA was then eluted, ethanol precipitated, dissolved in water and PCR amplified as mentioned above. .. To produce 5′-end-labeled sgRNAs, purified sgRNA transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BIoLabs) to 50 pmol of sgRNA in a final volume of 10 μL containing 50 mM Bis-Propane pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20U, Invitrogen). .. Dephosphorylated sgRNAs (5 pmol) were 5′-end-rediolabeled using 3 U of T4 polynucleotide kinase (New England Biolabs) for 1 h at 37°C in the presence of 3.2 pmol of [α-32 P]ATP (6000 Ci/mmol; Perkin Elmer).

    Article Title: Investigating a New Generation of Ribozymes in Order to Target HCV
    Article Snippet: The RNA was quantified by absorbance at 260 nm. .. In order to generate 5′-end-labeled RNA substrate, 50 pmol of purified transcripts were dephosphorylated by adding 1 U of Antartic phosphatase (New England Biolabs) and incubating for 1 h at 37°C in a final volume of 10 µL containing 50 mM Bis-Propane, pH 6.0, 1 mM MgCl2 , 0.1 mM ZnCl2 and 40 U of RNAGuard. .. The dephosphorylated RNAs (5 pmol) were then 5′-end labeled by incubation for 1 h at 37°C with 3 U of T4 polynucleotide kinase (USB) and 3.2 pmol of [γ-32P ]ATP (6000 Ci/mmol; New England Nuclear) in the provided reaction buffer.

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Constructs were transformed into competent bacteria and grown onto ampicilline agar plate to generate bacteria clones containing either the WT or the del18 construct.

    Article Title: 5?-UTR G-quadruplex structures acting as translational repressors
    Article Snippet: CD melting curves were obtained by heating the samples from 25°C to 90°C at a controlled rate of 1°C min−1 and monitoring a 264-nm CD peak every 0.2 min. Melting temperature (T m ) values were calculated using ‘fraction folded’ (θ ) versus temperature plots ( ). .. In order to produce 5′-end-labeled PG4s, purified transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England BioLabs,) to 50 pmol of RNA and incubating the reaction mixture for 30 min at 37°C in a final volume of 10 µl containing 50 mM Bis-Propane (pH 6.0), 1 mM MgCl2 , 0.1 mM ZnCl2 and RNase OUT (20 U, Invitrogen). .. Dephosphorylated transcripts (5 pmol) were 5′-end-radiolabeled using 3 U of T4 polynucleotide kinase (Promega) for 1 h at 37°C in the presence of 3.2 pmol of [α-32 P]ATP (6000 Ci/mmol; New England Nuclear).

    Article Title: A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme
    Article Snippet: The bands corresponding to the correct sizes for the RNA species were cut out, the transcripts eluted and then ethanol precipitated. .. Purified substrates or ribozymes (40 pmol) were dephosphorylated in a final volume of 10 µl using 10 U of Antartic phosphatase according to the manufacturer's conditions (New England Biolabs). .. Dephosphorylated RNAs (10 pmol) were 5′-end labelled in a final volume of 10 µl containing 3.2 pmol [γ-32 P]-ATP (6000 Ci/mmol, Amersham Biosciences), 10 mM Tris–HCl, pH 7.5, 10 mM MgCl2 , 50 mM KCl and 3 U of T4 polynucleotide kinase (Amersham Biosciences) at 37°C for 90 min.

    Article Title: Novel mutations of TCOF1 gene in European patients with treacher Collins syndrome
    Article Snippet: A 10-minute denaturation step at 94°C was followed by 30 cycles at 94°C for 30 seconds, annealing temperature was performed, for each primer, 30 seconds at 52.5-62°C, and extending for 30 sec at 72°C; the reaction was completed by a final extension for 7 minutes at 72°C. .. PCR products were purified by digestion with Antartic Phosphatase and Exonuclease I (New England BioLabs Inc.) and were sequenced in both directions using the Applied Biosystem Big Dye Terminator v3.1 Cycle sequencing kit. .. New mutations were not found in 100 normal chromosomes by sequencing.

    Plasmid Preparation:

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: Since studied K. pneumoniae ST258 is resistant to ampicillin, the selection marker of both vector and clone was replaced by the apramycin resistance cassette of pIJ773. .. For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette. .. In parallel, the AprR cassette of pIJ773 was amplified using primers Apr1 and Apr2, digested with XbaI and ligated separately with the linearized plasmids described above using T4 ligase (Thermo Scientific, USA).

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: The target site of the scarlet -targeting gRNA was 5ʹ-GGTTCACTCGTCGCCTTAATggg-3ʹ (protospacer adjacent motif shown in lowercase). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. A pair of scarlet- targeting oligonucleotides were then annealed and ligated into the linearized pDR274 vector using a ligation mix (TaKaRa Bio, Shiga, Japan).

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: Plasmid pGST‐amylosucrase (pGST‐AS) derived from the pGEX‐6P‐3 (GE Healthcare Biosciences, Piscataway, U.S.A) encoding GST fused to N. polysaccharea amylosucrase, was used for the construction of semi‐rational libraries. .. Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.).

    Article Title: Contributions of PHOX2B in the Pathogenesis of Hirschsprung Disease
    Article Snippet: Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.). .. Amplicons were then digested with Asp718 (iso -schizomer of KpnI) for convenient reasons to subclone it into the Exontrap cloning system (MoBiTec) at the multiple cloning site previously digested with Asp718 and dephosphorylated using antartic phosphatase (New England Biolabs inc.) before ligation with the T4 DNA ligase (New England Biolab inc.).

    Article Title: VirD - A Virion Display Array For Profiling Functional Membrane Proteins
    Article Snippet: Plasmid pKΔ4B was derived by Cai et al. following engineering of linker-insertion mutants in the glycoprotein B gene. .. DNA sequences encoding amino acids 43 through 711 of gB were deleted and a BglII restriction site added to maintain the protein reading frame . pKΔ4B was digested with Xho1 and BglII, treated with antartic phosphatase (NEB) and ligated with an Xho1-BglII PCR fragment amplified from pKΔ4B which deletes all gB amino acids from 1–43 (gBΔSS) but retains the gB promoter sequences ( ).

    Article Title: Production and purification of staphylococcal nuclease in Lactococcus lactis using a new expression-secretion system and a pH-regulated mini-reactor
    Article Snippet: PCR product was digested by Bam HI and Kpn I, cloned into pGTP_FZ301 previously digested by Bam HI and Kpn I, and ligation was used to transform MG1363. pGTP_FZ301_NucB plasmid extracted from a chloramphenicol resistant clone was verified by digestion and sequencing. .. Restriction enzymes, T4 DNA ligase and Antartic phosphatase (New england Biolabs, Ipswich, MA), high fidelity Phusion™ DNA polymerase (Finnzymes, Espoo, Finland) were used according to recommendations.

    Recombinant:

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: E.coli TOP 10 electrocompetent cells (Invitrogen, Carlsbad, U.S.A.) were utilized as gene expression and production of recombinant amylosucrase variants. .. Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.).

    In Vitro:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    Size-exclusion Chromatography:

    Article Title: Novel mutations of TCOF1 gene in European patients with treacher Collins syndrome
    Article Snippet: A 10-minute denaturation step at 94°C was followed by 30 cycles at 94°C for 30 seconds, annealing temperature was performed, for each primer, 30 seconds at 52.5-62°C, and extending for 30 sec at 72°C; the reaction was completed by a final extension for 7 minutes at 72°C. .. PCR products were purified by digestion with Antartic Phosphatase and Exonuclease I (New England BioLabs Inc.) and were sequenced in both directions using the Applied Biosystem Big Dye Terminator v3.1 Cycle sequencing kit.

    Ethanol Precipitation:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA). .. To synthesize gRNAs in vitro , gRNA synthesis vectors were digested by Dra I (NEW ENGLAND Biolabs, Connecticut, USA) and purified by phenol/chloroform extraction.

    Knock-Out:

    Article Title: Generation of white-eyed Daphnia magna mutants lacking scarlet function
    Article Snippet: Paragraph title: Knockout of Scarlet by CRISPR/Cas9 system ... To generate the gRNA expression vectors, the plasmid pDR274 (Addgene plasmid 42250, [ ] was digested with Bsa I (NEW ENGLAND Biolabs, Connecticut, USA), followed by dephosphorylation with Antartic Phosphatase (NEW ENGLAND Biolabs, Connecticut, USA).

    DNA Purification:

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.). .. Oligonucleotides were synthesized by Eurogenetec (Liege, Belgium).

    Lysis:

    Article Title: From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors
    Article Snippet: First, 2′F-Py RNAs were dephosphorylated at the 5′-end using antartic phosphatase (New England Biolabs) before 5′-[32 P] labeling (3×103 Bq.pmole−1 ) using T4 kinase. .. Radioactive aptamers at different concentrations were incubated for 15 min at 37°C on 80% confluent cell monolayer in 200 µL of RPMI 1640 containing 100 µg/ml of tRNA as a nonspecific competitor.

    Marker:

    Article Title: The secondary resistome of multidrug-resistant Klebsiella pneumoniae
    Article Snippet: Since studied K. pneumoniae ST258 is resistant to ampicillin, the selection marker of both vector and clone was replaced by the apramycin resistance cassette of pIJ773. .. For this, both plasmids pBAD-HisA and pBAD-KpndedA were amplified using primers Bad1 and Bad2 , digested with XbaI and dephosphorylated with Antartic phosphatase (New England Biolabs, USA) resulting in the linearized plasmid minus the AmpR cassette.

    Gel Extraction:

    Article Title: Novel product specificity toward erlose and panose exhibited by multisite engineered mutants of amylosucrase
    Article Snippet: Dpn I, Eco RI HF and Not I HF restriction enzymes, T4 DNA ligase and Antartic Phosphatase were purchased from New England Biolabs (Beverly, MA, U.S.A.). .. Oligonucleotides were synthesized by Eurogenetec (Liege, Belgium).

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    New England Biolabs antarctic phosphatase anp
    RNA 3 ′ -terminal phosphate modifications with MthRnl. A , gel shift analysis of archaeal RNA ligase (MthRnl) reaction products of either FAM-RNA17p ( column I ) or FAM-RNA17(OMe)p ( column II ) followed by phosphatase treatment with either <t>AnP</t> or <t>PNK.</t>
    Antarctic Phosphatase Anp, 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/antarctic phosphatase anp/product/New England Biolabs
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    New England Biolabs antartic phosphatase
    RNA 3 ′ -terminal phosphate modifications with MthRnl. A , gel shift analysis of archaeal RNA ligase (MthRnl) reaction products of either FAM-RNA17p ( column I ) or FAM-RNA17(OMe)p ( column II ) followed by phosphatase treatment with either <t>AnP</t> or <t>PNK.</t>
    Antartic 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/antartic phosphatase/product/New England Biolabs
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    New England Biolabs phosphatase buffer
    RNA 3 ′ -terminal phosphate modifications with MthRnl. A , gel shift analysis of archaeal RNA ligase (MthRnl) reaction products of either FAM-RNA17p ( column I ) or FAM-RNA17(OMe)p ( column II ) followed by phosphatase treatment with either <t>AnP</t> or <t>PNK.</t>
    Phosphatase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    RNA 3 ′ -terminal phosphate modifications with MthRnl. A , gel shift analysis of archaeal RNA ligase (MthRnl) reaction products of either FAM-RNA17p ( column I ) or FAM-RNA17(OMe)p ( column II ) followed by phosphatase treatment with either AnP or PNK.

    Journal:

    Article Title: Polynucleotide 3′-terminal Phosphate Modifications by RNA and DNA Ligases

    doi: 10.1074/jbc.M114.612929

    Figure Lengend Snippet: RNA 3 ′ -terminal phosphate modifications with MthRnl. A , gel shift analysis of archaeal RNA ligase (MthRnl) reaction products of either FAM-RNA17p ( column I ) or FAM-RNA17(OMe)p ( column II ) followed by phosphatase treatment with either AnP or PNK.

    Article Snippet: Antarctic phosphatase (AnP), T4 PNK, and yeast 5′Deadenylase were from New England Biolabs.

    Techniques: Electrophoretic Mobility Shift Assay, Aqueous Normal-phase Chromatography