mung bean nuclease  (New England Biolabs)


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    Name:
    Mung Bean Nuclease
    Description:
    Mung Bean Nuclease 7 500 units
    Catalog Number:
    m0250l
    Price:
    260
    Size:
    7 500 units
    Category:
    Other Endonucleases
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    Structured Review

    New England Biolabs mung bean nuclease
    Mung Bean Nuclease
    Mung Bean Nuclease 7 500 units
    https://www.bioz.com/result/mung bean nuclease/product/New England Biolabs
    Average 90 stars, based on 98 article reviews
    Price from $9.99 to $1999.99
    mung bean nuclease - by Bioz Stars, 2020-01
    90/100 stars

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    Related Articles

    Clone Assay:

    Article Title: RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs ▿
    Article Snippet: The 3′ mutations were created by digesting the cloned S segment with a variety of different restriction enzymes, creating unique 3′ ends. .. After digestion with AlwNI, which produces a 3′ overhang not compatible with transcription reactions, the vector was again digested with mung bean nuclease (New England Biolabs), which removed the 3′ overhang and created a blunt end.

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: .. After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. The obtained fragment (588 bp) (Fig. ) was cloned into the Pseudomonas suicide vector pMP5285 (digested with KpnI treated with mung bean nuclease), resulting in pMP5564 (Fig. ).

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: .. Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen). .. One microgram of linearized DNA template was used for RNA transcription using T7 RNA polymerase (MEGAscript; Ambion) for 1 h at 37°C.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: To ensure that the DNA produced during EXPAR was double-stranded and blunt-ended for cloning, 5′-overhangs were filled using Klenow exo- and 3′-overhangs were removed using mung bean nuclease. .. The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C.

    Amplification:

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB). .. The library was PCR amplified through 15 cycles, and final library was size-selected at 150–210 bp.

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: Paragraph title: Plasmid extraction, digest and PCR amplification ... In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: Paragraph title: Sequencing of EXPAR Amplification Products ... The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C.

    Expressing:

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA 16S rRNA was isolated from 30S particles previously in vitro methylated (as described above), or from E. coli BL21(DE3) cells expressing recombinant Sgm protein (i.e. in vivo methylated). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Construct:

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: .. After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. The obtained fragment (588 bp) (Fig. ) was cloned into the Pseudomonas suicide vector pMP5285 (digested with KpnI treated with mung bean nuclease), resulting in pMP5564 (Fig. ).

    Electrophoresis:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: The resulting RNAs were purified by electrophoresis through 6% denaturing polyacrylamide (19:1 acrylamide:bisacrylamide) gels containing 7.5 M urea, followed by UV shadowing over thin layer chromatography plates containing fluorescent indicator, excision of RNA bands, elution overnight at 37°C into a buffer containing SDS, phenol:chloroform extraction and ethanol precipitation. .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice.

    Incubation:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice. .. RNAs were analyzed by electrophoresis on 6% denaturing polyacrylamide sequencing gels followed by storage phosphorimaging.

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations. .. After incubation at 30°C for ≥6 h, 2.5 units RQ1 DNase was added and the reaction mixture was left at 37°C for a further 30 min. RNAs were recovered using RNA Clean & Concentrator-25 spin columns (Zymo Research), and transcript integrity was assessed by gel electrophoresis.

    Article Title: Unusual Structures Are Present in DNA Fragments Containing Super-Long Huntingtin CAG Repeats
    Article Snippet: Mung bean nuclease (New England BioLabs) digestion was carried out for 30 min at 30°C in buffer containing 50 mM sodium acetate, pH 5.0, 30 mM NaCl and 1 mM ZnSO4 . .. Where appropriate, nuclease-treated DNA was melted by incubation at 94°C for 5 min.

    Article Title: A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
    Article Snippet: .. The mixture was incubated for 5 min at 90°C and then allowed to hybridize during slow cooling to 45°C over 3.5 h. Mung bean nuclease buffer was added to a final concentration of 50 mM NaOAc (pH 5) at 25°C, 30 mM NaCl, and 1 mM ZnCl2 together with 30 units of mung bean nuclease (New England Biolabs) and 0.5 μg of RNase A (Sigma-Aldrich), followed by a 50-min incubation at 35°C. ..

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C. .. The resulting DNA–RNA hybrid was recovered by phenol–chloroform extraction and ethanol precipitation.

    Article Title: AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W]AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W] [OPEN]
    Article Snippet: In a second step, the previously annealed splayed arm structures were combined and incubated at 37°C for 30 min followed by another 30 min at . .. To create pIR9, pAT153 (MoBiTec) was linearized by Eco RI digestion, and the single-strand overhangs were converted to blunt ends using mung bean nuclease (NEB).

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: .. The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. ..

    Mass Spectrometry:

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Paragraph title: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA ... 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Transformation Assay:

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. .. The blunt-ended DNA was cloned into a Sma I-linerarized, 2× calf intestinal phosphatase, pUC19 plasmid using T4 DNA ligase: 25 fmol of linearized pUC19, 5 μ L of blunted DNA, and 400 ceU/ μ L T4 DNA ligase (NEB) were combined in T4 DNA ligase buffer [NEB (1× final concentration), 50 mM Tris-HCl, 10 mM MgCl2 , 1 mM ATP, and 10 mM dithiothreitol (pH 7.5) at 25 °C] in a total volume of 40 μ L. The reaction was allowed to proceed at 16 °C for 12 h prior to the mixture being transformed into DH5α chemically competent cells (Invitrogen), plated on 25 μ g/mL ampicillin plates, and incubated at 37 °C for 16 h. Single colonies were selected for colony PCR and inserts verified using M13 forward (−20) and M13 reverse (−27).

    Hybridization:

    Article Title: A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
    Article Snippet: Paragraph title: Isolation of a defined rRNA sequence by specific hybridization and single-strand digestion ... The mixture was incubated for 5 min at 90°C and then allowed to hybridize during slow cooling to 45°C over 3.5 h. Mung bean nuclease buffer was added to a final concentration of 50 mM NaOAc (pH 5) at 25°C, 30 mM NaCl, and 1 mM ZnCl2 together with 30 units of mung bean nuclease (New England Biolabs) and 0.5 μg of RNase A (Sigma-Aldrich), followed by a 50-min incubation at 35°C.

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C. .. The resulting DNA–RNA hybrid was recovered by phenol–chloroform extraction and ethanol precipitation.

    Electroporation:

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: Paragraph title: RNA transcription and electroporation of cells. ... Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations.

    Article Title: Differential regulation of the Wnt/β-catenin pathway by hepatitis C virus recombinants expressing core from various genotypes
    Article Snippet: Genome-length Jad and intergenotypic Jad/C recombinant cDNAs were linearized with Xba I and treated with mung bean nuclease (New England BioLabs, Evry, France) prior to in vitro transcription using T7 RiboMAX Express Large Scale RNA production system (Promega) and purification of resulting synthetic RNAs, as described previously . .. Huh-7.5 cells (2 × 106 cells) were transfected by electroporation with 5 µg of synthetic, genome-length RNAs, in 4-mm-gap-width cuvettes by applying one pulse at 240 V at 900 F using EasyjecT Plus instrument (Equibio, Lancashire, United Kingdom).

    Transfection:

    Article Title: Differential regulation of the Wnt/β-catenin pathway by hepatitis C virus recombinants expressing core from various genotypes
    Article Snippet: Paragraph title: In vitro transcription and RNA transfection ... Genome-length Jad and intergenotypic Jad/C recombinant cDNAs were linearized with Xba I and treated with mung bean nuclease (New England BioLabs, Evry, France) prior to in vitro transcription using T7 RiboMAX Express Large Scale RNA production system (Promega) and purification of resulting synthetic RNAs, as described previously .

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: Plasmid extraction, digest and PCR amplification 40 hours after transfection plasmids were extracted using a simplified Hirt protocol and subjected to Dpn I digestion as described . .. In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C.

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: .. Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ). .. The amount of RNA transcripts was estimated by standard agarose gel electrophoresis.

    Generated:

    Article Title: RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs ▿
    Article Snippet: One nonviral RNA was generated from pGem7zf(+) (Promega) linearized with DraI. .. After digestion with AlwNI, which produces a 3′ overhang not compatible with transcription reactions, the vector was again digested with mung bean nuclease (New England Biolabs), which removed the 3′ overhang and created a blunt end.

    Sequencing:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice. .. RNAs were analyzed by electrophoresis on 6% denaturing polyacrylamide sequencing gels followed by storage phosphorimaging.

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: A sequencing library was created using a previously described method ( ) with modifications. .. DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB).

    Article Title: A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
    Article Snippet: Paragraph title: Isolation of a defined rRNA sequence by specific hybridization and single-strand digestion ... The mixture was incubated for 5 min at 90°C and then allowed to hybridize during slow cooling to 45°C over 3.5 h. Mung bean nuclease buffer was added to a final concentration of 50 mM NaOAc (pH 5) at 25°C, 30 mM NaCl, and 1 mM ZnCl2 together with 30 units of mung bean nuclease (New England Biolabs) and 0.5 μg of RNase A (Sigma-Aldrich), followed by a 50-min incubation at 35°C.

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: A defined 16S rRNA sequence, C1378-G1432, was isolated by hybridization to a complementary deoxyoligonucleotide ( ). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: Paragraph title: Sequencing of EXPAR Amplification Products ... The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C.

    Recombinant:

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations. .. The DNA was used in a 50-μl reaction mixture containing 40 units T7 polymerase plus associated buffer (Fermentas), 50 units RiboLock RNase inhibitor (Fermentas), and 8 mM recombinant nucleoside triphosphates (Promega).

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: Paragraph title: Construction of a single homologous recombinant and of a mutY construct for complementation. ... After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands).

    Article Title: Differential regulation of the Wnt/β-catenin pathway by hepatitis C virus recombinants expressing core from various genotypes
    Article Snippet: .. Genome-length Jad and intergenotypic Jad/C recombinant cDNAs were linearized with Xba I and treated with mung bean nuclease (New England BioLabs, Evry, France) prior to in vitro transcription using T7 RiboMAX Express Large Scale RNA production system (Promega) and purification of resulting synthetic RNAs, as described previously . .. Huh-7.5 cells (2 × 106 cells) were transfected by electroporation with 5 µg of synthetic, genome-length RNAs, in 4-mm-gap-width cuvettes by applying one pulse at 240 V at 900 F using EasyjecT Plus instrument (Equibio, Lancashire, United Kingdom).

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA 16S rRNA was isolated from 30S particles previously in vitro methylated (as described above), or from E. coli BL21(DE3) cells expressing recombinant Sgm protein (i.e. in vivo methylated). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Molecular Weight:

    Article Title: BAC CLONES GENERATED FROM SHEARED DNA
    Article Snippet: The agarose-embedded DNA is treated with Mung Bean nuclease (40 units, New England Biolabs) in the commercially supplied buffer [50 mM sodium acetate (pH5.0), 30 mM NaCl, 1 mM ZnSO4 ] in 1.5 ml reaction mixture at 30°C for 2 hrs. .. The agarose blocks are transferred into dialysis tubing (3/4 in. diameter, molecular weight exclusion limit of 12,000–14,000 daltons; Invitrogen).

    Nucleic Acid Electrophoresis:

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations. .. After incubation at 30°C for ≥6 h, 2.5 units RQ1 DNase was added and the reaction mixture was left at 37°C for a further 30 min. RNAs were recovered using RNA Clean & Concentrator-25 spin columns (Zymo Research), and transcript integrity was assessed by gel electrophoresis.

    In Vivo:

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA 16S rRNA was isolated from 30S particles previously in vitro methylated (as described above), or from E. coli BL21(DE3) cells expressing recombinant Sgm protein (i.e. in vivo methylated). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ). .. After 12 to 24 h, lipofection complexes (2.5 μg of RNA transcripts and 5 μl of Lipofectamine 2000 [Invitrogen] in 500 μl of Opti-MEM [Invitrogen]) were added to cells for approximately 16 h. For in vivo transfections, chimpanzees were housed in compliance with relevant guidelines and requirements ( ) in a facility fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International.

    RNA Sequencing Assay:

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: Paragraph title: 3’ RNA-seq to detect global 3’ ends of genes in the embryo ... DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB).

    Methylation:

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Paragraph title: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA ... 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Isolation:

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. After growth in KB and selection on KB with kanamycin a single homologous mutY recombinant , referred to as PCL1805, was isolated.

    Article Title: A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
    Article Snippet: Paragraph title: Isolation of a defined rRNA sequence by specific hybridization and single-strand digestion ... The mixture was incubated for 5 min at 90°C and then allowed to hybridize during slow cooling to 45°C over 3.5 h. Mung bean nuclease buffer was added to a final concentration of 50 mM NaOAc (pH 5) at 25°C, 30 mM NaCl, and 1 mM ZnCl2 together with 30 units of mung bean nuclease (New England Biolabs) and 0.5 μg of RNase A (Sigma-Aldrich), followed by a 50-min incubation at 35°C.

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: A defined 16S rRNA sequence, C1378-G1432, was isolated by hybridization to a complementary deoxyoligonucleotide ( ). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Purification:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: Radiolabeled RNA was then again purified by denaturing PAGE prior to enzymatic analysis. .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice.

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB). .. The concentration of ligated sequencing adapters was lowered two-fold to decrease unincorporated adapters sequenced, and final library was size-selected from a 2% Ultra Pure LMP Agarose (Invitrogen), extracted from gel slices using β-Agarase I (NEB), and purified with a phenol:chloroform extraction as described above.

    Article Title: RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs ▿
    Article Snippet: After digestion with AlwNI, which produces a 3′ overhang not compatible with transcription reactions, the vector was again digested with mung bean nuclease (New England Biolabs), which removed the 3′ overhang and created a blunt end. .. Following DNA removal by digestion with RQ1 DNase (Promega), the transcripts were purified over Bio-Rad spin columns to remove unincorporated nucleotides (Hercules, CA).

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: .. Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations. .. The DNA was used in a 50-μl reaction mixture containing 40 units T7 polymerase plus associated buffer (Fermentas), 50 units RiboLock RNase inhibitor (Fermentas), and 8 mM recombinant nucleoside triphosphates (Promega).

    Article Title: Differential regulation of the Wnt/β-catenin pathway by hepatitis C virus recombinants expressing core from various genotypes
    Article Snippet: .. Genome-length Jad and intergenotypic Jad/C recombinant cDNAs were linearized with Xba I and treated with mung bean nuclease (New England BioLabs, Evry, France) prior to in vitro transcription using T7 RiboMAX Express Large Scale RNA production system (Promega) and purification of resulting synthetic RNAs, as described previously . .. Huh-7.5 cells (2 × 106 cells) were transfected by electroporation with 5 µg of synthetic, genome-length RNAs, in 4-mm-gap-width cuvettes by applying one pulse at 240 V at 900 F using EasyjecT Plus instrument (Equibio, Lancashire, United Kingdom).

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C. .. The target RNA sequence was excised from a 13% polyacrylamide gel containing 7 M urea, after visualization with ethidium bromide, and purified using an RNaid Spin Kit (MP Biochemicals).

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: .. Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen). .. One microgram of linearized DNA template was used for RNA transcription using T7 RNA polymerase (MEGAscript; Ambion) for 1 h at 37°C.

    Article Title: AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W]AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W] [OPEN]
    Article Snippet: All substrates (except the X26-S) were purified by 10% [w/v] native Tris-borate/EDTA ( ) -PAGE and electroelution into Tris-borate/MgCl2 buffer (44.5 m m Tris-Base, 44.5 m m boric acid, and 5 m m MgCl2 ) using D -Tube Dialyzers (Merck). .. To create pIR9, pAT153 (MoBiTec) was linearized by Eco RI digestion, and the single-strand overhangs were converted to blunt ends using mung bean nuclease (NEB).

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C. .. The reactions were stopped by adding 0.01% SDS, the products were purified by ethanol precipitation, and used as template for one PCR reaction.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: .. The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. ..

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: Plasmid DNA was linearized with XbaI (New England BioLabs), purified (Wizard SV gel and PCR clean-up system; Promega), and in vitro transcribed with T7 RNA polymerase (Promega) ( ). .. Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ).

    Polymerase Chain Reaction:

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB). .. The library was PCR amplified through 15 cycles, and final library was size-selected at 150–210 bp.

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: .. After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. The obtained fragment (588 bp) (Fig. ) was cloned into the Pseudomonas suicide vector pMP5285 (digested with KpnI treated with mung bean nuclease), resulting in pMP5564 (Fig. ).

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: .. Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen). .. One microgram of linearized DNA template was used for RNA transcription using T7 RNA polymerase (MEGAscript; Ambion) for 1 h at 37°C.

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: Paragraph title: Plasmid extraction, digest and PCR amplification ... In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. .. The blunt-ended DNA was cloned into a Sma I-linerarized, 2× calf intestinal phosphatase, pUC19 plasmid using T4 DNA ligase: 25 fmol of linearized pUC19, 5 μ L of blunted DNA, and 400 ceU/ μ L T4 DNA ligase (NEB) were combined in T4 DNA ligase buffer [NEB (1× final concentration), 50 mM Tris-HCl, 10 mM MgCl2 , 1 mM ATP, and 10 mM dithiothreitol (pH 7.5) at 25 °C] in a total volume of 40 μ L. The reaction was allowed to proceed at 16 °C for 12 h prior to the mixture being transformed into DH5α chemically competent cells (Invitrogen), plated on 25 μ g/mL ampicillin plates, and incubated at 37 °C for 16 h. Single colonies were selected for colony PCR and inserts verified using M13 forward (−20) and M13 reverse (−27).

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: Plasmid DNA was linearized with XbaI (New England BioLabs), purified (Wizard SV gel and PCR clean-up system; Promega), and in vitro transcribed with T7 RNA polymerase (Promega) ( ). .. Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ).

    Polyacrylamide Gel Electrophoresis:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: Radiolabeled RNA was then again purified by denaturing PAGE prior to enzymatic analysis. .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice.

    Article Title: AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W]AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity 1 [W] [OPEN]
    Article Snippet: All substrates (except the X26-S) were purified by 10% [w/v] native Tris-borate/EDTA ( ) -PAGE and electroelution into Tris-borate/MgCl2 buffer (44.5 m m Tris-Base, 44.5 m m boric acid, and 5 m m MgCl2 ) using D -Tube Dialyzers (Merck). .. To create pIR9, pAT153 (MoBiTec) was linearized by Eco RI digestion, and the single-strand overhangs were converted to blunt ends using mung bean nuclease (NEB).

    Plasmid Preparation:

    Article Title: RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs ▿
    Article Snippet: .. After digestion with AlwNI, which produces a 3′ overhang not compatible with transcription reactions, the vector was again digested with mung bean nuclease (New England Biolabs), which removed the 3′ overhang and created a blunt end. .. This allowed for a 912-nucleotide transcript to be produced.

    Article Title: Genetic Complementation of Hepatitis C Virus Nonstructural Protein Functions Associated with Replication Exhibits Requirements That Differ from Those for Virion Assembly
    Article Snippet: .. Five micrograms of plasmid DNA was linearized with XbaI (Fermentas), polished with mung bean nuclease (NEB), purified by phenol-chloroform extraction, ethanol precipitated, and treated with the RNAsecure reagent (Ambion) according to the manufacturer's recommendations. .. The DNA was used in a 50-μl reaction mixture containing 40 units T7 polymerase plus associated buffer (Fermentas), 50 units RiboLock RNase inhibitor (Fermentas), and 8 mM recombinant nucleoside triphosphates (Promega).

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. The obtained fragment (588 bp) (Fig. ) was cloned into the Pseudomonas suicide vector pMP5285 (digested with KpnI treated with mung bean nuclease), resulting in pMP5564 (Fig. ).

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: .. In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C. ..

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. .. The blunt-ended DNA was cloned into a Sma I-linerarized, 2× calf intestinal phosphatase, pUC19 plasmid using T4 DNA ligase: 25 fmol of linearized pUC19, 5 μ L of blunted DNA, and 400 ceU/ μ L T4 DNA ligase (NEB) were combined in T4 DNA ligase buffer [NEB (1× final concentration), 50 mM Tris-HCl, 10 mM MgCl2 , 1 mM ATP, and 10 mM dithiothreitol (pH 7.5) at 25 °C] in a total volume of 40 μ L. The reaction was allowed to proceed at 16 °C for 12 h prior to the mixture being transformed into DH5α chemically competent cells (Invitrogen), plated on 25 μ g/mL ampicillin plates, and incubated at 37 °C for 16 h. Single colonies were selected for colony PCR and inserts verified using M13 forward (−20) and M13 reverse (−27).

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: Plasmid DNA was linearized with XbaI (New England BioLabs), purified (Wizard SV gel and PCR clean-up system; Promega), and in vitro transcribed with T7 RNA polymerase (Promega) ( ). .. Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ).

    Selection:

    Article Title: Generation of Enhanced Competitive Root-Tip-Colonizing Pseudomonas Bacteria through Accelerated Evolution
    Article Snippet: After the 1,187-bp PCR fragment was cloned into pGEM-T Easy (Promega, Leiden, The Netherlands) (pMP5465) the construct was digested with SmaI and EcoRI made blunt by treatment with mung bean nuclease (New England Biolabs, Westburg, Leusden, The Netherlands). .. After growth in KB and selection on KB with kanamycin a single homologous mutY recombinant , referred to as PCL1805, was isolated.

    Agarose Gel Electrophoresis:

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen). .. RNA was cleaned up using the RNeasy kit (Qiagen), and the integrity of the RNA was analyzed by nondenaturing agarose gel electrophoresis.

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ). .. The amount of RNA transcripts was estimated by standard agarose gel electrophoresis.

    In Vitro:

    Article Title: Differential regulation of the Wnt/β-catenin pathway by hepatitis C virus recombinants expressing core from various genotypes
    Article Snippet: .. Genome-length Jad and intergenotypic Jad/C recombinant cDNAs were linearized with Xba I and treated with mung bean nuclease (New England BioLabs, Evry, France) prior to in vitro transcription using T7 RiboMAX Express Large Scale RNA production system (Promega) and purification of resulting synthetic RNAs, as described previously . .. Huh-7.5 cells (2 × 106 cells) were transfected by electroporation with 5 µg of synthetic, genome-length RNAs, in 4-mm-gap-width cuvettes by applying one pulse at 240 V at 900 F using EasyjecT Plus instrument (Equibio, Lancashire, United Kingdom).

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) MS analysis of methylated 16S rRNA 16S rRNA was isolated from 30S particles previously in vitro methylated (as described above), or from E. coli BL21(DE3) cells expressing recombinant Sgm protein (i.e. in vivo methylated). .. 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C.

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: Paragraph title: (iii) In vitro RNA transcripts. ... Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen).

    Article Title: Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies ▿ Pathogenesis Studies ▿ †
    Article Snippet: .. Before generation of RNA transcripts for in vitro transfection, XbaI-digested pED43 with and without adaptive mutations was treated with mung bean nuclease (New England BioLabs) ( ). .. The amount of RNA transcripts was estimated by standard agarose gel electrophoresis.

    Ethanol Precipitation:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: Radiolabeled RNA was purified by ethanol precipitation from NH4 OAC solution in the presence of carrier tRNA. .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice.

    Article Title: Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
    Article Snippet: 16S rRNA (100 pmol) was incubated with deoxyoligonucleotide (1000 pmol) at 95°C for 5 min in 200 μl hybridization buffer (250 mM HEPES pH 7.5, 500 mM KCl), followed by slow cooling to 30°C over 3 h. Unhybridized regions of the 16S rRNA were digested with 40 U mung bean nuclease (NEB) and 0.5 μg RNase A (Sigma), for 60 min at 37°C. .. The resulting DNA–RNA hybrid was recovered by phenol–chloroform extraction and ethanol precipitation.

    Article Title: Analysis of CPD Ultraviolet Lesion Bypass in Chicken DT40 Cells: Polymerase ? and PCNA Ubiquitylation Play Identical Roles
    Article Snippet: In case of the single strand specific nuclease digest, the same amount of recovered plasmid mixture was treated with 0.1 unit of mung bean nuclease (New England Biolabs) in 10 μl for 15 minutes at 25°C. .. The reactions were stopped by adding 0.01% SDS, the products were purified by ethanol precipitation, and used as template for one PCR reaction.

    Spectrophotometry:

    Article Title: Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes
    Article Snippet: Full-length cDNA clones of the HCV strains H77 and JFH-1 were linearized with XbaI, treated with mung bean nuclease (New England BioLabs) to remove 5′-end overhangs and purified (PureLink PCR purification kit; Invitrogen). .. RNA concentrations were determined using spectrophotometry.

    Produced:

    Article Title: RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs ▿
    Article Snippet: After digestion with AlwNI, which produces a 3′ overhang not compatible with transcription reactions, the vector was again digested with mung bean nuclease (New England Biolabs), which removed the 3′ overhang and created a blunt end. .. This allowed for a 912-nucleotide transcript to be produced.

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: To ensure that the DNA produced during EXPAR was double-stranded and blunt-ended for cloning, 5′-overhangs were filled using Klenow exo- and 3′-overhangs were removed using mung bean nuclease. .. The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C.

    Concentration Assay:

    Article Title: A developmental program truncates long transcripts to temporally regulate cell signaling
    Article Snippet: DNA fragments were cleaved and blunted at the site of the translated nick with T7 Exonuclease (NEB), Mung Bean Nuclease (NEB), and Klenow DNA Pol I (NEB). .. Illumina TruSeq adapters were ligated onto the DNA fragments at two-fold lower concentration than the original protocol in order to reduce unincorporated adapters.

    Article Title: A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA
    Article Snippet: .. The mixture was incubated for 5 min at 90°C and then allowed to hybridize during slow cooling to 45°C over 3.5 h. Mung bean nuclease buffer was added to a final concentration of 50 mM NaOAc (pH 5) at 25°C, 30 mM NaCl, and 1 mM ZnCl2 together with 30 units of mung bean nuclease (New England Biolabs) and 0.5 μg of RNase A (Sigma-Aldrich), followed by a 50-min incubation at 35°C. ..

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: .. The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. ..

    Thin Layer Chromatography:

    Article Title: In vivo selection of spectinomycin-binding RNAs
    Article Snippet: The resulting RNAs were purified by electrophoresis through 6% denaturing polyacrylamide (19:1 acrylamide:bisacrylamide) gels containing 7.5 M urea, followed by UV shadowing over thin layer chromatography plates containing fluorescent indicator, excision of RNA bands, elution overnight at 37°C into a buffer containing SDS, phenol:chloroform extraction and ethanol precipitation. .. For studies of spectinomycin effects on mung bean nuclease reactivity, radiolabeled RNAs (600 000 c.p.m., 1 µM final, achieved by mixing radiolabeled and unlabeled RNA) were incubated at 22°C in 10 mM Tris–HCl buffer with the indicated concentrations of spectinomycin for 15 min. Mung bean nuclease (1 U; New England Biolabs, Beverly, MA) was then added and reactions were allowed to proceed for 2 min prior to addition of urea loading buffer and freezing on dry ice.

    Gel Extraction:

    Article Title: Specific versus Nonspecific Isothermal DNA Amplification through Thermophilic Polymerase and Nicking Enzyme Activities
    Article Snippet: The remaining 3′-overhangs were removed using the following protocol: 40 μ L of purified EXPAR/Klenow reaction products was combined with mung bean nuclease buffer [NEB (1× final concentration), 50 mM sodium acetate, 30 mM NaCl, and 1 mM ZnSO4 (pH 5.0) at 25 °C] and 5 units/ μ L mung bean nuclease (NEB), in a total volume of 50 μ L, and incubated for 30 min at 30 °C. .. The excised agarose sections were purified using the QIAquick gel extraction kit (Qiagen) following the manufacturer’s protocol.

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    New England Biolabs mung bean nuclease
    Mung Bean Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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