agarase  (New England Biolabs)


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  • 95
    Name:
    beta Agarase I
    Description:
    beta Agarase I 500 units
    Catalog Number:
    m0392l
    Price:
    322
    Size:
    500 units
    Category:
    Agarase
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    Structured Review

    New England Biolabs agarase
    beta Agarase I
    beta Agarase I 500 units
    https://www.bioz.com/result/agarase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    agarase - by Bioz Stars, 2020-02
    95/100 stars

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    Related Articles

    Centrifugation:

    Article Title: Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
    Article Snippet: .. To prepare nucleic acid extracts for isopycnic centrifugation as previously described Buckley et al. , DNA was size selected ( > 4 kb) using 1% low melt agarose gel and β-agarase I enzyme extraction per manufacturers protocol (New England Biolab, M0392S). ..

    Article Title: Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
    Article Snippet: After centrifugation (22789 × g , 10 minutes, 4 °C), the aqueous phase was transferred to a new tube and the DNA was precipitated with one volume of isopropanol. .. In order to certify that our preparation was free of genomic DNA we isolated the band containing the plasmid and digested the agarose using ß-agarase (NEB catalog # - M0392S) according to the manufacturer’s instructions.

    Amplification:

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States). .. A single colony corresponding to approximately 108 cells was suspended in 40 μl 0.05 M NaOH and heated at 95°C for 10 min, and the resulting solution was cooled on ice for 5 min, diluted (1/15) in sterile ultrapure water, and used as the template for PCR amplification.

    Synthesized:

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: Razor blade 1.57 mm OD polyethylene tubing ( e.g ., Clay Adams® Intramedic® , BD, catalog number: 427431) Sephadex microcentrifuge columns (Illustra Microspin G-25) (GE Healthcare, catalog number: 27-5325-01) Plastic wrap ( e.g. , Fisherbrand Clear Plastic Wrap, Fisher Scientific, catalog number: 22-305654) C-fold paper towels ( e.g. , Scott paper towels, KCWW, Kimberly-Clark, catalog number: 01510) Positively charged nylon DNA blotting membrane (Hybond-N+, 30.0×50.0 cm) (GE Healthcare, catalog number: RPN3050B) Chromatography transfer paper (Whatman 3MM, 46.0×57.0 cm) (GE Healthcare, catalog number: 3030-917) Syringe tip ( e.g ., B-D 18 G 1 ½ PrecisionGlide® Needle) (BD, catalog number: 305196) phiX174 virion DNA, 1 mg/ml (New England Biolabs, catalog number: N3023L) Phi29 DNA polymerase (New England Biolabs, catalog number: M0269S) 100 mM dNTP (deoxynucleotide triphosphate) set (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0181) 1 µM CMG ( C dc45 M cm2–7 G ins) helicase (see for purification details) pUC19, 1 mg/ml (New England Biolabs, catalog number: N3041L) Bsa I-HF with CutSmart buffer (New England Biolabs, catalog number: R3535L) ‘blockLd’ oligo* ‘blockLg’ oligo* ‘Pr1B’ oligo* ‘160Ld’ oligo* ‘91Lg’ oligo* ‘Fork primer’ oligo* Nucleotide-biased template (synthesized by Biomatik, Wilmington DE)* *Note: See . .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes)

    Lambda DNA Preparation:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: Paragraph title: Lambda DNA with a single specific dye molecule at each end ... Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion.

    Cytometry:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For flow cytometry [fluorescence-activated cell sorting (FACS)], phycoerythrin (PE)-anti-mouse CD304 (NRP1; catalog no. 145203) and PE/Cy7-anti-mouse CD45 (catalog no. 103113) were obtained from BioLegend (San Diego, CA); BV421-rat anti-mouse CD140a (PDGFRα; catalog no. 562774), Alexa Fluor 647-rat anti-mouse CD71 (catalog no. 563504), and Alexa Fluor 647-rat anti-mouse CD9 (catalog no. 564233) from BD Biosciences (San Jose, CA); CD140a-FITC, mouse (clone REA637; catalog no. 130-109-735), CD140b-PE, mouse (clone REA634; catalog no. 130-109-867), anti-NES-allophycocyanin (APC), mouse and rat (clone REA575; catalog no. 130-109-058) from Miltenyi Biotech (Auburn, CA); and mouse monoclonal anti-α-SMA-A405 (clone IA4; catalog no. IC1420V) and goat polyclonal anti-DES (catalog no. AF3844) from R & D Systems (Minneapolis, MN). .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA).

    Blocking Assay:

    Article Title: Human Papillomavirus Integration: Analysis by Molecular Combing and Fiber-FISH
    Article Snippet: Agarose plug containing genomic DNA (Basic Protocol 1) 2 ml Eppendorf tubes Sterile flat spatula 0.1 M MES (2-(N-morpholino)ethanesulfonic acid), pH 6.5 β-Agarase I (New England BioLabs, M0392S) Teflon reservoir (supplied with molecular combing machine) Silane-coated 22×22 mm coverslips (MicroSurfaces) Glass microscope slides 2:10,000 YOYO-1 (ThermoFisher, Y3601) in 0.1 M MES, pH 6.5 SlowFade™ Gold Antifade Mountant (ThermoFisher, S36940) Cyanoacrylate glue Molecular combing machine (in-house, Genomic Vision) Water bath at 42°C and 70°C Epifluorescent microscope Oven at 60 °C Transfer one agarose plug to a 2 ml Eppendorf tube using a sterile flat spatula (see ) and add 1.6 ml 0.1 M MES pH 6.5 buffer. .. Place the 2 ml Eppendorf tube in a 70°C heat block for 20 minutes to melt the agarose plug.

    Microarray:

    Article Title: The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast
    Article Snippet: We prepared samples using the in gelo ssDNA labeling protocol detailed by Feng et al. [ ], and used β-agarase (NEB #M0392S) to recover the labeled ssDNA. .. We co-hybridized one G1 and one S phase sample to Agilent ChIP-on-chip 4x44 S . cerevisiae microarray.

    Incubation:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: Reaction tubes were incubated for several hours at room temperature after all ligation reagents were added. .. Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion.

    Article Title: Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
    Article Snippet: The pellets were resuspended with 25 mL of Ressuspension Buffer (50 mM Tris-HCl, 10 mM EDTA, RNAse 100 μg/mL, pH 8.0), and then 25 mL of Lysis Buffer (SDS 1%; 0.2 M NaOH) was added, with 5 minutes of room temperature incubation. .. In order to certify that our preparation was free of genomic DNA we isolated the band containing the plasmid and digested the agarose using ß-agarase (NEB catalog # - M0392S) according to the manufacturer’s instructions.

    Article Title: HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression
    Article Snippet: .. 3 units of β-agarase (New England BioLabs, M0392S) were added to cooled DNA solution and incubated overnight in a 42°C water bath. ..

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: .. 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes. .. DNA was precipitated using 2 volumes of ethanol, air dried at room temperature and resuspended in 1× TE buffer (pH 7.5) to a concentration of 100 µg/mL.

    Article Title: DNA replication is altered in Immunodeficiency Centromeric instability Facial anomalies (ICF) cells carrying DNMT3B mutations
    Article Snippet: Agarose plugs were resuspended in 10 m M Tris-HCl (pH 7.5), 50 m M EDTA (pH 8.0), 1% N -lauryl sarcosyl (Sigma), and 1 mg/ml proteinase K (no. P6556; Sigma), and were incubated at 50°C for 48 h. Next, plugs were washed four times in 10 ml TE (10 m M Tris (pH 8.0), 1 m M EDTA) and either stored in this solution at 4°C or immediately used for combing. .. Each agarose plug was melted at 65°C for 30 min in 3 ml of 50 m M 4-morpholinepropanesulfonic acid (pH 5.7), and then treated overnight at 42°C with 3 U of β -agarase no. M0392S; New England Biolabs, Ipswich, MA, USA).

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: Inactivation of proteinase K by incubation of the plugs for 30 min at 55°C in TE buffer containing phenylmethylsulfonyl fluoride (20 μg ml−1 ; Sigma) was followed by three 20-min washes in TE buffer at room temperature. .. Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States).

    Western Blot:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. For Western blotting, rabbit anti-phosphorylated (Y410) p130Cas (catalog no. ab55263) was obtained from Abcam (Cambridge, MA); rabbit monoclonal anti-NRP1 (catalog no. 3725), rabbit anti-calveolin-1 (catalog no. 3267), rabbit anti-phosphorylated (Y416) Src (catalog no. 6943), rabbit anti-Src (catalog no. 2109), and rabbit anti-p130Cas (catalog no. 13846) from Cell Signaling Technology (Danvers, MA); rabbit polyclonal anti-PDGFRα (catalog no. sc-431) from Santa Cruz Biotechnology (Dallas, TX); and mouse monoclonal β-tubulin (catalog no. T-7816) from Sigma.

    Recombinase Polymerase Amplification:

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes) .. Heating block ( e.g., VWR, catalog number: 12621-084) Fraction collector ( e.g., Gilson, model: F203B) Variable mode gel imager ( e.g., GE Typhoon) UV-vis spectrophotometer ( e.g., Thermo Fisher Scientific, Thermo Scientific™, model: NanoDrop™ 2000) Vacuum dessicator ( e.g., Thermo Fisher Scientific, Thermo Scientific™, catalog number: 5309-0250) UV light box UV blocking face shield (e.g., Sigma-Aldrich, catalog number: F8142) Note: This product has been discontinued.

    Flow Cytometry:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For flow cytometry [fluorescence-activated cell sorting (FACS)], phycoerythrin (PE)-anti-mouse CD304 (NRP1; catalog no. 145203) and PE/Cy7-anti-mouse CD45 (catalog no. 103113) were obtained from BioLegend (San Diego, CA); BV421-rat anti-mouse CD140a (PDGFRα; catalog no. 562774), Alexa Fluor 647-rat anti-mouse CD71 (catalog no. 563504), and Alexa Fluor 647-rat anti-mouse CD9 (catalog no. 564233) from BD Biosciences (San Jose, CA); CD140a-FITC, mouse (clone REA637; catalog no. 130-109-735), CD140b-PE, mouse (clone REA634; catalog no. 130-109-867), anti-NES-allophycocyanin (APC), mouse and rat (clone REA575; catalog no. 130-109-058) from Miltenyi Biotech (Auburn, CA); and mouse monoclonal anti-α-SMA-A405 (clone IA4; catalog no. IC1420V) and goat polyclonal anti-DES (catalog no. AF3844) from R & D Systems (Minneapolis, MN). .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA).

    Chromatography:

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: Razor blade 1.57 mm OD polyethylene tubing ( e.g ., Clay Adams® Intramedic® , BD, catalog number: 427431) Sephadex microcentrifuge columns (Illustra Microspin G-25) (GE Healthcare, catalog number: 27-5325-01) Plastic wrap ( e.g. , Fisherbrand Clear Plastic Wrap, Fisher Scientific, catalog number: 22-305654) C-fold paper towels ( e.g. , Scott paper towels, KCWW, Kimberly-Clark, catalog number: 01510) Positively charged nylon DNA blotting membrane (Hybond-N+, 30.0×50.0 cm) (GE Healthcare, catalog number: RPN3050B) Chromatography transfer paper (Whatman 3MM, 46.0×57.0 cm) (GE Healthcare, catalog number: 3030-917) Syringe tip ( e.g ., B-D 18 G 1 ½ PrecisionGlide® Needle) (BD, catalog number: 305196) phiX174 virion DNA, 1 mg/ml (New England Biolabs, catalog number: N3023L) Phi29 DNA polymerase (New England Biolabs, catalog number: M0269S) 100 mM dNTP (deoxynucleotide triphosphate) set (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0181) 1 µM CMG ( C dc45 M cm2–7 G ins) helicase (see for purification details) pUC19, 1 mg/ml (New England Biolabs, catalog number: N3041L) Bsa I-HF with CutSmart buffer (New England Biolabs, catalog number: R3535L) ‘blockLd’ oligo* ‘blockLg’ oligo* ‘Pr1B’ oligo* ‘160Ld’ oligo* ‘91Lg’ oligo* ‘Fork primer’ oligo* Nucleotide-biased template (synthesized by Biomatik, Wilmington DE)* *Note: See . .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes)

    Ligation:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: .. Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion. .. The packaging reaction buffer comprised 50 mM Tris-HCl pH 7.5, 6 mM MgCl2, 100 mM NaCl, 1.25 mM spermidine, 0.1 mg/ml BSA, 1.5 mm DTT, 1.5 mm ATP, 2% PEG (Fluka, 20kDa), 216 nM gp17 (monomer), 9.6 × 109 molecules 5 kbp DNA or 8.2 × 108 molecules of λ DNA substrate and 2 × 1010 purified procapsids in 16 μL volumes.

    Transferring:

    Article Title: Human Papillomavirus Integration: Analysis by Molecular Combing and Fiber-FISH
    Article Snippet: Agarose plug containing genomic DNA (Basic Protocol 1) 2 ml Eppendorf tubes Sterile flat spatula 0.1 M MES (2-(N-morpholino)ethanesulfonic acid), pH 6.5 β-Agarase I (New England BioLabs, M0392S) Teflon reservoir (supplied with molecular combing machine) Silane-coated 22×22 mm coverslips (MicroSurfaces) Glass microscope slides 2:10,000 YOYO-1 (ThermoFisher, Y3601) in 0.1 M MES, pH 6.5 SlowFade™ Gold Antifade Mountant (ThermoFisher, S36940) Cyanoacrylate glue Molecular combing machine (in-house, Genomic Vision) Water bath at 42°C and 70°C Epifluorescent microscope Oven at 60 °C Transfer one agarose plug to a 2 ml Eppendorf tube using a sterile flat spatula (see ) and add 1.6 ml 0.1 M MES pH 6.5 buffer. .. Add 3 μl (3 units) of β-agarase and tap to gently mix (do not pipette).

    Polymerase Chain Reaction:

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States). .. A single colony corresponding to approximately 108 cells was suspended in 40 μl 0.05 M NaOH and heated at 95°C for 10 min, and the resulting solution was cooled on ice for 5 min, diluted (1/15) in sterile ultrapure water, and used as the template for PCR amplification.

    Recombinant:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. Another reagent, recombinant human PDGF-AA (catalog no. 221-AA), was obtained from R & D Systems.

    Immunofluorescence:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. For Western blotting, rabbit anti-phosphorylated (Y410) p130Cas (catalog no. ab55263) was obtained from Abcam (Cambridge, MA); rabbit monoclonal anti-NRP1 (catalog no. 3725), rabbit anti-calveolin-1 (catalog no. 3267), rabbit anti-phosphorylated (Y416) Src (catalog no. 6943), rabbit anti-Src (catalog no. 2109), and rabbit anti-p130Cas (catalog no. 13846) from Cell Signaling Technology (Danvers, MA); rabbit polyclonal anti-PDGFRα (catalog no. sc-431) from Santa Cruz Biotechnology (Dallas, TX); and mouse monoclonal β-tubulin (catalog no. T-7816) from Sigma.

    Pulsed-Field Gel:

    Article Title: Using Schizosaccharomyces pombe Meiosis To Analyze DNA Recombination Intermediates
    Article Snippet: CHEF Mapper (BioRad) or other pulsed-field gel electrophoresis (PFGE) unit. .. Agarose (Sigma #A0169). β-agarase (New England Biolabs #M0392L).

    Staining:

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: To further purify the DNA and enrich for high molecular weight fragments, the sample was loaded on a 1% low melt agarose gel with 1× SYBR® Safe DNA Gel Stain (Life Technologies). .. 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes.

    DNA Extraction:

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States). .. An alternative DNA isolation protocol was also used for individual strains.

    Article Title: Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
    Article Snippet: .. DNA from each sample was extracted using a MoBio (Carlsbad, CA, USA) UltraClean Mega Soil DNA Isolation Kit (following the manufacturer's protocol, but lysis was done as previously described ( )), and then gel purified to select high molecular weight DNA ( > 4 kb) using a 1% low melt agarose gel and β -agarase I for digestion (according to the manufacturer's protocol, New England Biolabs, Ipswich, MA, USA, M0392S). .. Extracts were quantified using PicoGreen nucleic acid quantification dyes (Molecular Probes, Eugene, OR, USA).

    Nucleic Acid Electrophoresis:

    Article Title: Using Schizosaccharomyces pombe Meiosis To Analyze DNA Recombination Intermediates
    Article Snippet: Paragraph title: 2.3. Gel Electrophoresis of Recombination Intermediates ... Agarose (Sigma #A0169). β-agarase (New England Biolabs #M0392L).

    Article Title: DNA replication is altered in Immunodeficiency Centromeric instability Facial anomalies (ICF) cells carrying DNMT3B mutations
    Article Snippet: Asynchronous exponentially growing cells were subsequently labeled with 25 μ M 5-iodo-2-deoxyuridine (IdU) (no. I7125; Sigma) for 15 min and with 200 μ M 5-chloro-2-deoxyuridine (CldU) (no. 105478; MP Biomedicals, Illkirch, France) for 25 min. After washings, lymphoblasts were mixed with one volume of 1% pre-heated (42°C) low-melting point agarose and aliquoted in pulse-field gel electrophoresis molds (100 μ l per well) to obtain plugs containing ∼1 × 105 cells. .. Each agarose plug was melted at 65°C for 30 min in 3 ml of 50 m M 4-morpholinepropanesulfonic acid (pH 5.7), and then treated overnight at 42°C with 3 U of β -agarase no. M0392S; New England Biolabs, Ipswich, MA, USA).

    Fluorescence:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For flow cytometry [fluorescence-activated cell sorting (FACS)], phycoerythrin (PE)-anti-mouse CD304 (NRP1; catalog no. 145203) and PE/Cy7-anti-mouse CD45 (catalog no. 103113) were obtained from BioLegend (San Diego, CA); BV421-rat anti-mouse CD140a (PDGFRα; catalog no. 562774), Alexa Fluor 647-rat anti-mouse CD71 (catalog no. 563504), and Alexa Fluor 647-rat anti-mouse CD9 (catalog no. 564233) from BD Biosciences (San Jose, CA); CD140a-FITC, mouse (clone REA637; catalog no. 130-109-735), CD140b-PE, mouse (clone REA634; catalog no. 130-109-867), anti-NES-allophycocyanin (APC), mouse and rat (clone REA575; catalog no. 130-109-058) from Miltenyi Biotech (Auburn, CA); and mouse monoclonal anti-α-SMA-A405 (clone IA4; catalog no. IC1420V) and goat polyclonal anti-DES (catalog no. AF3844) from R & D Systems (Minneapolis, MN). .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA).

    Isolation:

    Article Title: Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
    Article Snippet: .. In order to certify that our preparation was free of genomic DNA we isolated the band containing the plasmid and digested the agarose using ß-agarase (NEB catalog # - M0392S) according to the manufacturer’s instructions. .. Optical analysis of DNA in nanochannels The optical DNA mapping of the single plasmid molecules were performed as described in ref. .

    Size-exclusion Chromatography:

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: T4 ligase, including 10× ligase buffer (New England Biolabs, catalog number: M0202M) 100 mM ATP (GE Healthcare, catalog number: 27-2056-01) 0.5 M EDTA, disodium salt (Sigma-Aldrich, catalog number: E5134) 5 M NaCl (Sigma-Aldrich, catalog number: S9888) Sepharose 4B size exclusion chromatography resin (GE Healthcare, catalog number: 17012001) 1 kb MW marker (New England Biolabs, catalog number: N3232L) Ethidium bromide (EthBr, 10 mg/ml) (Thermo Fisher Scientific, Invitrogen™, catalog number: 15585011) T4 kinase and 10× T4 kinase buffer (New England Biolabs, catalog number: M0201L) 32 P-γ-ATP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU002A) Type XI low-melt agarose (Sigma-Aldrich, catalog number: A3038) Note: This product has been discontinued . .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes)

    Labeling:

    Article Title: DNA replication is altered in Immunodeficiency Centromeric instability Facial anomalies (ICF) cells carrying DNMT3B mutations
    Article Snippet: Asynchronous exponentially growing cells were subsequently labeled with 25 μ M 5-iodo-2-deoxyuridine (IdU) (no. I7125; Sigma) for 15 min and with 200 μ M 5-chloro-2-deoxyuridine (CldU) (no. 105478; MP Biomedicals, Illkirch, France) for 25 min. After washings, lymphoblasts were mixed with one volume of 1% pre-heated (42°C) low-melting point agarose and aliquoted in pulse-field gel electrophoresis molds (100 μ l per well) to obtain plugs containing ∼1 × 105 cells. .. Each agarose plug was melted at 65°C for 30 min in 3 ml of 50 m M 4-morpholinepropanesulfonic acid (pH 5.7), and then treated overnight at 42°C with 3 U of β -agarase no. M0392S; New England Biolabs, Ipswich, MA, USA).

    Article Title: The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast
    Article Snippet: .. We prepared samples using the in gelo ssDNA labeling protocol detailed by Feng et al. [ ], and used β-agarase (NEB #M0392S) to recover the labeled ssDNA. .. We co-hybridized one G1 and one S phase sample to Agilent ChIP-on-chip 4x44 S . cerevisiae microarray.

    Purification:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: .. Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion. .. The packaging reaction buffer comprised 50 mM Tris-HCl pH 7.5, 6 mM MgCl2, 100 mM NaCl, 1.25 mM spermidine, 0.1 mg/ml BSA, 1.5 mm DTT, 1.5 mm ATP, 2% PEG (Fluka, 20kDa), 216 nM gp17 (monomer), 9.6 × 109 molecules 5 kbp DNA or 8.2 × 108 molecules of λ DNA substrate and 2 × 1010 purified procapsids in 16 μL volumes.

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: .. Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States). .. An alternative DNA isolation protocol was also used for individual strains.

    Article Title: DNA sequence homology induces cytosine-to-thymine mutation by a heterochromatin-related pathway in Neurospora
    Article Snippet: Paragraph title: I. Purification of genomic DNA ... A region of the gel containing high-molecular weight DNA was excised with a sterile razor blade under long UV light and digested with β-Agarase I (NEB, cat. no. M0392L; 3 hours at 42°C).

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes) .. Heating block ( e.g., VWR, catalog number: 12621-084) Fraction collector ( e.g., Gilson, model: F203B) Variable mode gel imager ( e.g., GE Typhoon) UV-vis spectrophotometer ( e.g., Thermo Fisher Scientific, Thermo Scientific™, model: NanoDrop™ 2000) Vacuum dessicator ( e.g., Thermo Fisher Scientific, Thermo Scientific™, catalog number: 5309-0250) UV light box UV blocking face shield (e.g., Sigma-Aldrich, catalog number: F8142) Note: This product has been discontinued.

    Article Title: Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
    Article Snippet: .. DNA from each sample was extracted using a MoBio (Carlsbad, CA, USA) UltraClean Mega Soil DNA Isolation Kit (following the manufacturer's protocol, but lysis was done as previously described ( )), and then gel purified to select high molecular weight DNA ( > 4 kb) using a 1% low melt agarose gel and β -agarase I for digestion (according to the manufacturer's protocol, New England Biolabs, Ipswich, MA, USA, M0392S). .. Extracts were quantified using PicoGreen nucleic acid quantification dyes (Molecular Probes, Eugene, OR, USA).

    Microscopy:

    Article Title: Human Papillomavirus Integration: Analysis by Molecular Combing and Fiber-FISH
    Article Snippet: .. Agarose plug containing genomic DNA (Basic Protocol 1) 2 ml Eppendorf tubes Sterile flat spatula 0.1 M MES (2-(N-morpholino)ethanesulfonic acid), pH 6.5 β-Agarase I (New England BioLabs, M0392S) Teflon reservoir (supplied with molecular combing machine) Silane-coated 22×22 mm coverslips (MicroSurfaces) Glass microscope slides 2:10,000 YOYO-1 (ThermoFisher, Y3601) in 0.1 M MES, pH 6.5 SlowFade™ Gold Antifade Mountant (ThermoFisher, S36940) Cyanoacrylate glue Molecular combing machine (in-house, Genomic Vision) Water bath at 42°C and 70°C Epifluorescent microscope Oven at 60 °C Transfer one agarose plug to a 2 ml Eppendorf tube using a sterile flat spatula (see ) and add 1.6 ml 0.1 M MES pH 6.5 buffer. .. Place the 2 ml Eppendorf tube in a 70°C heat block for 20 minutes to melt the agarose plug.

    Confocal Microscopy:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. For Western blotting, rabbit anti-phosphorylated (Y410) p130Cas (catalog no. ab55263) was obtained from Abcam (Cambridge, MA); rabbit monoclonal anti-NRP1 (catalog no. 3725), rabbit anti-calveolin-1 (catalog no. 3267), rabbit anti-phosphorylated (Y416) Src (catalog no. 6943), rabbit anti-Src (catalog no. 2109), and rabbit anti-p130Cas (catalog no. 13846) from Cell Signaling Technology (Danvers, MA); rabbit polyclonal anti-PDGFRα (catalog no. sc-431) from Santa Cruz Biotechnology (Dallas, TX); and mouse monoclonal β-tubulin (catalog no. T-7816) from Sigma.

    FACS:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For flow cytometry [fluorescence-activated cell sorting (FACS)], phycoerythrin (PE)-anti-mouse CD304 (NRP1; catalog no. 145203) and PE/Cy7-anti-mouse CD45 (catalog no. 103113) were obtained from BioLegend (San Diego, CA); BV421-rat anti-mouse CD140a (PDGFRα; catalog no. 562774), Alexa Fluor 647-rat anti-mouse CD71 (catalog no. 563504), and Alexa Fluor 647-rat anti-mouse CD9 (catalog no. 564233) from BD Biosciences (San Jose, CA); CD140a-FITC, mouse (clone REA637; catalog no. 130-109-735), CD140b-PE, mouse (clone REA634; catalog no. 130-109-867), anti-NES-allophycocyanin (APC), mouse and rat (clone REA575; catalog no. 130-109-058) from Miltenyi Biotech (Auburn, CA); and mouse monoclonal anti-α-SMA-A405 (clone IA4; catalog no. IC1420V) and goat polyclonal anti-DES (catalog no. AF3844) from R & D Systems (Minneapolis, MN). .. For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA).

    Chromatin Immunoprecipitation:

    Article Title: The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast
    Article Snippet: We prepared samples using the in gelo ssDNA labeling protocol detailed by Feng et al. [ ], and used β-agarase (NEB #M0392S) to recover the labeled ssDNA. .. We co-hybridized one G1 and one S phase sample to Agilent ChIP-on-chip 4x44 S . cerevisiae microarray.

    Plasmid Preparation:

    Article Title: Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
    Article Snippet: .. In order to certify that our preparation was free of genomic DNA we isolated the band containing the plasmid and digested the agarose using ß-agarase (NEB catalog # - M0392S) according to the manufacturer’s instructions. .. Optical analysis of DNA in nanochannels The optical DNA mapping of the single plasmid molecules were performed as described in ref. .

    Agarose Gel Electrophoresis:

    Article Title: Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
    Article Snippet: .. To prepare nucleic acid extracts for isopycnic centrifugation as previously described Buckley et al. , DNA was size selected ( > 4 kb) using 1% low melt agarose gel and β-agarase I enzyme extraction per manufacturers protocol (New England Biolab, M0392S). ..

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: To further purify the DNA and enrich for high molecular weight fragments, the sample was loaded on a 1% low melt agarose gel with 1× SYBR® Safe DNA Gel Stain (Life Technologies). .. 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes.

    Article Title: Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
    Article Snippet: .. DNA from each sample was extracted using a MoBio (Carlsbad, CA, USA) UltraClean Mega Soil DNA Isolation Kit (following the manufacturer's protocol, but lysis was done as previously described ( )), and then gel purified to select high molecular weight DNA ( > 4 kb) using a 1% low melt agarose gel and β -agarase I for digestion (according to the manufacturer's protocol, New England Biolabs, Ipswich, MA, USA, M0392S). .. Extracts were quantified using PicoGreen nucleic acid quantification dyes (Molecular Probes, Eugene, OR, USA).

    In Situ:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. For proximity ligation assay, goat polyclonal anti-NRP1 (catalog no. AF566) was obtained from R & D Systems; rabbit polyclonal anti-PDGFRα (catalog no. sc-431) from Santa Cruz Biotechnology; rabbit polyclonal anti-phosphorylated (Y410) p130Cas (BCAR-1; catalog no. ab55263) from Abcam; and Duolink in situ orange starter kit, goat/rabbit (catalog no. DUO92106-1KT) from Sigma Aldrich.

    Proximity Ligation Assay:

    Article Title: Neuropilin-1 and platelet-derived growth factor receptors cooperatively regulate intermediate filaments and mesenchymal cell migration during alveolar septation
    Article Snippet: For laser scanning confocal microscopy immunofluorescence, goat polyclonal anti-PDGFRα (catalog no. AF1062) and goat polyclonal anti-DES (catalog no. AF3844) were obtained from R & D Systems; rat IgG2a,κ-anti-PDGFRβ (catalog no. 136002) from BioLegend; mouse monoclonal anti-α-SMA-Cy3 (catalog no. C6198) and rabbit polyclonal anti-NES (catalog no. SAB4200394) from Sigma-Aldrich (St. Louis, MO); isolectin B4-AF568 (catalog no. ) and YO-PRO-1 (catalog no. Y3603) from Thermo Fisher Scientific (Waltham, MA); β-agarase (catalog no. M0392S) from New England Biolabs (Ipswich, MA); donkey anti-rat IgG-A647 (catalog no. 712-605-150) from Jackson ImmunoResearch (West Grove, PA); and Vectashield antifade mounting medium (catalog no. H-1000) from Vector Laboratories (Burlingame, CA). .. For proximity ligation assay, goat polyclonal anti-NRP1 (catalog no. AF566) was obtained from R & D Systems; rabbit polyclonal anti-PDGFRα (catalog no. sc-431) from Santa Cruz Biotechnology; rabbit polyclonal anti-phosphorylated (Y410) p130Cas (BCAR-1; catalog no. ab55263) from Abcam; and Duolink in situ orange starter kit, goat/rabbit (catalog no. DUO92106-1KT) from Sigma Aldrich.

    Concentration Assay:

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes. .. DNA was precipitated using 2 volumes of ethanol, air dried at room temperature and resuspended in 1× TE buffer (pH 7.5) to a concentration of 100 µg/mL.

    Molecular Weight:

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: To further purify the DNA and enrich for high molecular weight fragments, the sample was loaded on a 1% low melt agarose gel with 1× SYBR® Safe DNA Gel Stain (Life Technologies). .. 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes.

    Article Title: Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
    Article Snippet: .. DNA from each sample was extracted using a MoBio (Carlsbad, CA, USA) UltraClean Mega Soil DNA Isolation Kit (following the manufacturer's protocol, but lysis was done as previously described ( )), and then gel purified to select high molecular weight DNA ( > 4 kb) using a 1% low melt agarose gel and β -agarase I for digestion (according to the manufacturer's protocol, New England Biolabs, Ipswich, MA, USA, M0392S). .. Extracts were quantified using PicoGreen nucleic acid quantification dyes (Molecular Probes, Eugene, OR, USA).

    DNA Purification:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: Two dye-labeled λ DNA was prepared as follows: first, a dye-containing DNA duplex and λ DNA were heated to 65°C for 10 minutes in a single tube to melt any cohesive termini that had reannealed during DNA purification. .. Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion.

    Lysis:

    Article Title: Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
    Article Snippet: The pellets were resuspended with 25 mL of Ressuspension Buffer (50 mM Tris-HCl, 10 mM EDTA, RNAse 100 μg/mL, pH 8.0), and then 25 mL of Lysis Buffer (SDS 1%; 0.2 M NaOH) was added, with 5 minutes of room temperature incubation. .. In order to certify that our preparation was free of genomic DNA we isolated the band containing the plasmid and digested the agarose using ß-agarase (NEB catalog # - M0392S) according to the manufacturer’s instructions.

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: 500 mL of pooled human saliva (Innovative Research) was centrifuged at 14,000×g for 15 minutes at 4°C, the pellet was resuspended in 50 mL of lysis buffer, and genomic DNA was prepared as described above. .. 200 µL of 10× β Agarase I buffer and 20 units β Agarase (NEB #M0392S) were added to the sample and incubated at 42°C for 30 minutes.

    Article Title: Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization ▿Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterizati
    Article Snippet: Cell lysis was continued for another 20 h at 50°C in the same lysis solution in the presence of proteinase K (2 mg ml−1 ). .. Total DNA was recovered by digestion of the agarose with beta-agarase I (NE Biolabs, United States), using the manufacturer's recommendations, and was purified by a final dialysis step using 0.025-μm filters (VSWP type; Millipore, United States).

    Article Title: Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
    Article Snippet: .. DNA from each sample was extracted using a MoBio (Carlsbad, CA, USA) UltraClean Mega Soil DNA Isolation Kit (following the manufacturer's protocol, but lysis was done as previously described ( )), and then gel purified to select high molecular weight DNA ( > 4 kb) using a 1% low melt agarose gel and β -agarase I for digestion (according to the manufacturer's protocol, New England Biolabs, Ipswich, MA, USA, M0392S). .. Extracts were quantified using PicoGreen nucleic acid quantification dyes (Molecular Probes, Eugene, OR, USA).

    Marker:

    Article Title: In vitro Assays for Eukaryotic Leading/Lagging Strand DNA Replication
    Article Snippet: T4 ligase, including 10× ligase buffer (New England Biolabs, catalog number: M0202M) 100 mM ATP (GE Healthcare, catalog number: 27-2056-01) 0.5 M EDTA, disodium salt (Sigma-Aldrich, catalog number: E5134) 5 M NaCl (Sigma-Aldrich, catalog number: S9888) Sepharose 4B size exclusion chromatography resin (GE Healthcare, catalog number: 17012001) 1 kb MW marker (New England Biolabs, catalog number: N3232L) Ethidium bromide (EthBr, 10 mg/ml) (Thermo Fisher Scientific, Invitrogen™, catalog number: 15585011) T4 kinase and 10× T4 kinase buffer (New England Biolabs, catalog number: M0201L) 32 P-γ-ATP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU002A) Type XI low-melt agarose (Sigma-Aldrich, catalog number: A3038) Note: This product has been discontinued . .. Bts CI (New England Biolabs, catalog number: R0647L) β-Agarase I (New England Biolabs, catalog number: M0392L) 3 M sodium acetate (CH3 COONa), pH 5.2 (Sigma-Aldrich, catalog number: S2889) Isopropanol (Sigma-Aldrich, catalog number: 190764) Glycogen, molecular biology grade (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0561) Ethanol (Sigma-Aldrich, catalog number: E7023) 1 µM RFC (Replication Factor C; see for purification details) 5 µM PCNA (Proliferating Cellular Nuclear Antigen; see for purification details) 2 µM Pol ε (see for purification details) 2 µM Pol δ (see for purification details) 2 µM Pol α (see for purification details) 20 µM RPA (Replication Protein A; see for purification details) 32 P-α-dCTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU013H) 32 P-α-dGTP, 3,000 Ci/mmol, 3.3 µM (PerkinElmer, catalog number: BLU514H) LE agarose (BioExpress, GeneMate, catalog number: E-3120-500) 10 N sodium hydroxide (NaOH) (Fisher Scientific, catalog number: SS255) Glycerol Xylene cylanol Tris-HCl, pH 8.0 Tris base (RPI, catalog number: T60040-500.0) Boric acid (RPI, catalog number: B32050-5000.0) Sodium citrate 1-Butanol Tris-acetate, pH 7.5 Bovine serum albumin (BSA) (New England Biolabs, catalog number: B9000S) Tris(2-carboxyethyl)phosphine (TCEP) pH 7.5 100 mM dithiothreitol (DTT) (Thermo Fisher Scientific, Thermo Scientific™, catalog number: R0861) Potassium glutamate Magnesium acetate 1% SDS 6× gel loading dye (see Recipes) TE buffer, pH 8.0 (see Recipes) 10× TBE (Tris/Borate/EDTA; see Recipes) DNA elution buffer (see Recipes) 20× SSC (see Recipes) 1-Butanol saturated water (see Recipes) 5× TDBG (see Recipes) 10× MK (see Recipes) dA/dC mix (see Recipes) dT/dG mix (see Recipes) T/G/C mix (see Recipes) Stop solution (see Recipes) Alkaline running buffer (see Recipes)

    Gel Extraction:

    Article Title: Single Molecule- and Fluorescence Correlation Spectroscopy-FRET Analysis of Phage DNA Packaging: Co-localization of the Packaged Phage T4 DNA Ends within the Capsid
    Article Snippet: .. Finally double dye-labeled λ DNA was purified from the ligation components and unreacted short DNA fragments by gel extraction and beta-Agarase I (New England Biolabs) digestion. .. The packaging reaction buffer comprised 50 mM Tris-HCl pH 7.5, 6 mM MgCl2, 100 mM NaCl, 1.25 mM spermidine, 0.1 mg/ml BSA, 1.5 mm DTT, 1.5 mm ATP, 2% PEG (Fluka, 20kDa), 216 nM gp17 (monomer), 9.6 × 109 molecules 5 kbp DNA or 8.2 × 108 molecules of λ DNA substrate and 2 × 1010 purified procapsids in 16 μL volumes.

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    New England Biolabs β agarase
    Multiple alignment of <t>β-agarase</t> amino acid sequences of Pseudoalteromonas sp. AG52 with known agarases. The inverted triangles (▼) highlight the conserved catalytic residues, and black circles (●) represent the conserved residues involved in calcium ion binding. Identical residues in all sequences are shaded in gray and indicated by (*) under the column, conserved substitutions are indicated by (:), and semi-conserved substitutions are indicated by (.). Deletions are indicated by dashes. Sequence sources: Aeromonas sp. β-agarase (AAF03246), Pseudoalteromonas atlantica β-agarase I (AAA91888), Zobellia galactanivorans β-agarase A (AAF21820), Zobellia galactanivorans β-agarase B (AAF21821).
    β Agarase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Multiple alignment of β-agarase amino acid sequences of Pseudoalteromonas sp. AG52 with known agarases. The inverted triangles (▼) highlight the conserved catalytic residues, and black circles (●) represent the conserved residues involved in calcium ion binding. Identical residues in all sequences are shaded in gray and indicated by (*) under the column, conserved substitutions are indicated by (:), and semi-conserved substitutions are indicated by (.). Deletions are indicated by dashes. Sequence sources: Aeromonas sp. β-agarase (AAF03246), Pseudoalteromonas atlantica β-agarase I (AAA91888), Zobellia galactanivorans β-agarase A (AAF21820), Zobellia galactanivorans β-agarase B (AAF21821).

    Journal: Brazilian Journal of Microbiology

    Article Title: Molecular cloning, characterization and enzymatic properties of a novel ?eta-agarase from a marine isolate Psudoalteromonas SP. AG52

    doi: 10.1590/S1517-83822010000400006

    Figure Lengend Snippet: Multiple alignment of β-agarase amino acid sequences of Pseudoalteromonas sp. AG52 with known agarases. The inverted triangles (▼) highlight the conserved catalytic residues, and black circles (●) represent the conserved residues involved in calcium ion binding. Identical residues in all sequences are shaded in gray and indicated by (*) under the column, conserved substitutions are indicated by (:), and semi-conserved substitutions are indicated by (.). Deletions are indicated by dashes. Sequence sources: Aeromonas sp. β-agarase (AAF03246), Pseudoalteromonas atlantica β-agarase I (AAA91888), Zobellia galactanivorans β-agarase A (AAF21820), Zobellia galactanivorans β-agarase B (AAF21821).

    Article Snippet: Neoagarohexanitol (NA6) was purchased from Sigma (USA) and neoagarotetraose (NA4) and neoagarobiose (NA2) (NA4 + NA2) were prepared by digestion of neoagarohexanitol using commercial β-agarase (New England Biolab, USA).

    Techniques: Binding Assay, Sequencing

    Phylogenetic analysis of AgaA with known agarases based on amino acid sequence. Phylogenetic analysis was done by the Neighbor Joining method using MEGA3.1, based on sequence alignment using ClustalW (1.81). Numbers indicate the bootstrap confidence values of 1000 replicates. The accession numbers of the selected agarase sequences are as follows: AB178483, agarase ( Agarivorans sp. JAMB-A11); EF051475, QM38 agarase ( Agarivorans sp. QM38); EF100136, β-agarase ( Agarivorans sp. JA-1); AAA25696, β-agarase precursor ( Pseudoalteromonas atlantica ); AAP49346, AguB; AAP70390, AguH; AAP70365, AguK; AAP49316, AguD from uncultured bacterium; AAA91888, β-agarase I ( Pseudoalteromonas atlantica ); AAF03246, β-agarase ( Aeromonas sp.); AB124837, agarase ( Microbulbifer thermotolerans ); BAC99022, agarase ( Microbulbifer elongatus ); BAB79291, agarase, ( Pseudomonas sp. ND137; AAF21821, β-agarase B precursor ( Zobellia galactanivorans ); AAF21820, β-agarase A precursor ( Zobellia galactanivorans ); AAN39119, extracellular agarase precursor, ( Pseudoalteromonas sp. CY24); CAB61795, extracellular agarase precursor ( Streptomyces coelicolor A3); AAP70364, AguJ (uncultured bacterium); BAA04744, β-agarase ( Vibrio sp.); BAA03541, β-agarase ( Vibrio sp. JT0107); BAH16616, agarase ( Cellvibrio sp. OA-2007); AAT67062, β-agarase I ( Saccharophagus degradans ); AB160954, β-agarase ( Microbulbifer thermotolerans ).

    Journal: Brazilian Journal of Microbiology

    Article Title: Molecular cloning, characterization and enzymatic properties of a novel ?eta-agarase from a marine isolate Psudoalteromonas SP. AG52

    doi: 10.1590/S1517-83822010000400006

    Figure Lengend Snippet: Phylogenetic analysis of AgaA with known agarases based on amino acid sequence. Phylogenetic analysis was done by the Neighbor Joining method using MEGA3.1, based on sequence alignment using ClustalW (1.81). Numbers indicate the bootstrap confidence values of 1000 replicates. The accession numbers of the selected agarase sequences are as follows: AB178483, agarase ( Agarivorans sp. JAMB-A11); EF051475, QM38 agarase ( Agarivorans sp. QM38); EF100136, β-agarase ( Agarivorans sp. JA-1); AAA25696, β-agarase precursor ( Pseudoalteromonas atlantica ); AAP49346, AguB; AAP70390, AguH; AAP70365, AguK; AAP49316, AguD from uncultured bacterium; AAA91888, β-agarase I ( Pseudoalteromonas atlantica ); AAF03246, β-agarase ( Aeromonas sp.); AB124837, agarase ( Microbulbifer thermotolerans ); BAC99022, agarase ( Microbulbifer elongatus ); BAB79291, agarase, ( Pseudomonas sp. ND137; AAF21821, β-agarase B precursor ( Zobellia galactanivorans ); AAF21820, β-agarase A precursor ( Zobellia galactanivorans ); AAN39119, extracellular agarase precursor, ( Pseudoalteromonas sp. CY24); CAB61795, extracellular agarase precursor ( Streptomyces coelicolor A3); AAP70364, AguJ (uncultured bacterium); BAA04744, β-agarase ( Vibrio sp.); BAA03541, β-agarase ( Vibrio sp. JT0107); BAH16616, agarase ( Cellvibrio sp. OA-2007); AAT67062, β-agarase I ( Saccharophagus degradans ); AB160954, β-agarase ( Microbulbifer thermotolerans ).

    Article Snippet: Neoagarohexanitol (NA6) was purchased from Sigma (USA) and neoagarotetraose (NA4) and neoagarobiose (NA2) (NA4 + NA2) were prepared by digestion of neoagarohexanitol using commercial β-agarase (New England Biolab, USA).

    Techniques: Sequencing

    The nucleotide and deduced amino acid sequences of the β-agarase of Pseudoalteromonas sp. AG52. The predicted lipoprotein signal peptide is underlined and signal peptide sequence is in bold face. The start (ATG) and stop (TAA) codons are in bold italics and stop codon is marked with an asterisk (*). The GHF-16 β-agarase domain is in italics. Active sites and calcium binding residues are in boxes and dotted boxes, respectively.

    Journal: Brazilian Journal of Microbiology

    Article Title: Molecular cloning, characterization and enzymatic properties of a novel ?eta-agarase from a marine isolate Psudoalteromonas SP. AG52

    doi: 10.1590/S1517-83822010000400006

    Figure Lengend Snippet: The nucleotide and deduced amino acid sequences of the β-agarase of Pseudoalteromonas sp. AG52. The predicted lipoprotein signal peptide is underlined and signal peptide sequence is in bold face. The start (ATG) and stop (TAA) codons are in bold italics and stop codon is marked with an asterisk (*). The GHF-16 β-agarase domain is in italics. Active sites and calcium binding residues are in boxes and dotted boxes, respectively.

    Article Snippet: Neoagarohexanitol (NA6) was purchased from Sigma (USA) and neoagarotetraose (NA4) and neoagarobiose (NA2) (NA4 + NA2) were prepared by digestion of neoagarohexanitol using commercial β-agarase (New England Biolab, USA).

    Techniques: Sequencing, Binding Assay