bal 31 nuclease  (New England Biolabs)


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    Name:
    Nuclease BAL 31
    Description:
    Nuclease BAL 31 50 units
    Catalog Number:
    m0213s
    Price:
    67
    Size:
    50 units
    Category:
    Exonucleases
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    Structured Review

    New England Biolabs bal 31 nuclease
    Nuclease BAL 31
    Nuclease BAL 31 50 units
    https://www.bioz.com/result/bal 31 nuclease/product/New England Biolabs
    Average 90 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    bal 31 nuclease - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR"

    Article Title: T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of Covalently Closed Circular DNA by PCR

    Journal: Journal of Virology

    doi: 10.1128/JVI.01117-18

    Identification of exonucleases selectively digesting rcDNA. (A) Properties of exonucleases tested in this study. +, strong activity; -, no significant activity; +/-, reduced activity; ss, single stranded; ds, double stranded; endo, endonuclease activity; dNMP, deoxyribonucleoside monophosphate; oligos, oligonucleotides. (B) Copies (3 × 10 8 ) of cell culture-derived viral DNA containing rcDNA and dslDNA were incubated for 1 h at 37°C with PSD (5 U), BAL-31 (5 U), Exo I (5 U), Exo V (5 U), and T5 Exo (5 U). Mung bean nuclease (5 U), EcoRI (5 U), and DNase I (5 U) were included as controls. After heat inactivation, the products were subjected to Southern blotting. The plasmid pUCX3.2 served as a marker for indicating the expected sizes of rcDNA and cccDNA.
    Figure Legend Snippet: Identification of exonucleases selectively digesting rcDNA. (A) Properties of exonucleases tested in this study. +, strong activity; -, no significant activity; +/-, reduced activity; ss, single stranded; ds, double stranded; endo, endonuclease activity; dNMP, deoxyribonucleoside monophosphate; oligos, oligonucleotides. (B) Copies (3 × 10 8 ) of cell culture-derived viral DNA containing rcDNA and dslDNA were incubated for 1 h at 37°C with PSD (5 U), BAL-31 (5 U), Exo I (5 U), Exo V (5 U), and T5 Exo (5 U). Mung bean nuclease (5 U), EcoRI (5 U), and DNase I (5 U) were included as controls. After heat inactivation, the products were subjected to Southern blotting. The plasmid pUCX3.2 served as a marker for indicating the expected sizes of rcDNA and cccDNA.

    Techniques Used: Activity Assay, Cell Culture, Derivative Assay, Incubation, Southern Blot, Plasmid Preparation, Marker

    Related Articles

    Neutralization:

    Article Title: Telomerase-dependent and independent chromosome healing in mouse embryonic stem cells
    Article Snippet: Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs). .. Southern blot analysis involved depurination of DNA by treatment with 0.25 M HCl for 20 minutes, denaturation in 0.5 M NaOH / 1.5 M NaCl for 30 minutes, neutralization in 1 M Tris/1.5 M NaCl pH 7.5 for 30 minutes, and transfer onto a charged nylon Hybond-N+ membrane (Amersham) in 10 X SSC (1.5 M NaCl / 0.15 M Na Citrate, pH 7.0) using a vacuum transfer apparatus (Pharmacia).

    Article Title: PIF1 disruption or NBS1 hypomorphism does not affect chromosome healing or fusion resulting from double-strand breaks near telomeres in murine embryonic stem cells
    Article Snippet: Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs). .. Southern blot analysis involved depurination of DNA by treatment with 0.25 M HCl for 20 minutes, denaturation in 0.5 M NaOH/1.5 M NaCl for 30 minutes, neutralization in 1 M Tris/1.5 M NaCl pH 7.5 for 30 minutes, and transfer onto a charged nylon Hybond-N+ membrane (Amersham) in 10 × SSC (1.5 M NaCl/0.15 M Na Citrate, pH 7.0) using a vacuum transfer apparatus (Pharmacia).

    Incubation:

    Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
    Article Snippet: .. Bal31 assay 1.4 μg gDNA was incubated with 0.3U of Bal31 nuclease (NEB) for increasing time at 30°. ..

    Mass Spectrometry:

    Article Title: MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
    Article Snippet: Modified protease trypsin (Gold, mass spectrometry grade) was purchased from Promega (Madison, WI, USA). .. Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA).

    Modification:

    Article Title: MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
    Article Snippet: Modified protease trypsin (Gold, mass spectrometry grade) was purchased from Promega (Madison, WI, USA). .. Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA).

    Transformation Assay:

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends. .. Ligation mixtures were transformed into E. coli JM109 by electroporation, and transformants were selected on LB plates supplemented with Cb.

    Derivative Assay:

    Article Title: Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA
    Article Snippet: .. Single strands of 5′-CGCGCAATTGCGCG-3′ (Integrated DNA Technologies; Coralville, IA) were annealed by slow cooling of the solution from 95°C to 10°C over 48 h. The concentration of the single stranded DNA was measured spectrophotometrically using extinction coefficient derived from the nearest neighbor approximation (125, 800 M−1 cm−1 at 260 nm) or after the complete digestion using nuclease BAL-31 (New England Biolabs; Ipswich, MA) ( ). ..

    Electroporation:

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends. .. Ligation mixtures were transformed into E. coli JM109 by electroporation, and transformants were selected on LB plates supplemented with Cb.

    Transfection:

    Article Title: Inter-telomeric recombination is present in telomerase-positive human cells
    Article Snippet: .. Restriction enzymes (New England Biolabs): HindIII (R0104S), ClaI (R0197S), XbaI (R0145S), KpnI (R0142S), AflII (R0520S), SacI (R0156S), AluI (R0137S), CfoI (R6241), HaeI (R0107S), HinfI (R0155S), MspI (R0106S), RsaI (R0167S) Plasmids (Invitrogen): pSV-Zeo V860-20 pCDNA3.1 Hygro (−) V870-20 Reagents and consumables: Fugene Transfection reagent (Roche) 05061377001 Zeocin (Invitrogen) ant-zn-1 Hygromycin (Invitrogen) 10687-010 Aphidicolin (Sigma) A0781-1MG Puromycin (Invitrogen) A11138-02 TmpY4 (Calbiochem) 613560-25MG Bal31 (New England Biolabs) M0213S streptavidin-coated magnetic beads (New England Biolabs) S1420S Hybond N membrane (Amersham) RPN82N DNA random prime labeling kit (Roche) 11004760001 T4 DNA ligase (Roche) 10481220001 DH5a competent cells (Invitrogen) 18258-012 Blasticidin (Invitrogen) R210-01 Purgene DNA extraction kit (Gentra Systems) 158422 Trapeze kit (Intergen) S7700 Failsafe PCR kit (epicenter) FS99060 ..

    Southern Blot:

    Article Title: Telomerase-dependent and independent chromosome healing in mouse embryonic stem cells
    Article Snippet: Paragraph title: 2.7. Southern blot analysis ... Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

    Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
    Article Snippet: Bal31 assay 1.4 μg gDNA was incubated with 0.3U of Bal31 nuclease (NEB) for increasing time at 30°. .. DNA was phenol-chloroform-extracted, ethanol-precipitated, and treated by either Hind III or Dde I. Digested DNA was separated on a 0.8% agarose gel (140 ng DNA per well) and subjected to Southern blot analysis as described above.

    Article Title: PIF1 disruption or NBS1 hypomorphism does not affect chromosome healing or fusion resulting from double-strand breaks near telomeres in murine embryonic stem cells
    Article Snippet: Paragraph title: 2.7 Southern blot analysis ... Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

    Ligation:

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends. .. Ligation mixtures were transformed into E. coli JM109 by electroporation, and transformants were selected on LB plates supplemented with Cb.

    Article Title: Selective DNA amplification from complex genomes using universal double-sided adapters
    Article Snippet: .. The ligation reaction was then treated with 1 U of Bal31 nuclease (NEB) in the presence of 1× Bal31 nuclease buffer (NEB) for 30 min at 30°C and then heat inactivated at 75°C for 10 min. .. The sample was diluted 10-fold with TE and 8 µl were digested with 2.5 U of NotI enzyme (NEB) in a 10 µl volume before 1 µl was used in a 30 µl PCR.

    SDS Page:

    Article Title: MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
    Article Snippet: Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA). .. Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA).

    other:

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
    Article Snippet: Du et al . showed earlier that 63-bp DNA minicircles are so strongly bent that they form kinks and become sensitive to Bal31 nuclease, while 85-bp DNA minicircles can accommodate their bending stress without kinks and without becoming sensitive to Bal31 nuclease ( ).

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
    Article Snippet: However, torsionally relaxed extremely small DNA minicircles having only 63 base pairs were digested by Bal31 nuclease.

    Article Title: Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity
    Article Snippet: We next used Bal31 nuclease to detect the presence of DNA distortions within our constrained minicircles.

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA
    Article Snippet: This result indicates that the negative torsional stress sustained within MC100, previously shown to result in sensitivity to Bal31 nuclease, also leads to the creation of easily bendable sites that permit the molecules to minimize their bending energy by adopting elongated, elliptical shapes.

    Sequencing:

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
    Article Snippet: .. However, the 94-bp-long minicircles with the sequence selected for their very efficient cyclization by C & W were not previously tested for their sensitivity to Bal31 nuclease. ..

    Molecular Weight:

    Article Title: Structural diversity of supercoiled DNA
    Article Snippet: .. BbvCI, EcoRV, Nb.BbvCI, NdeI, Nuclease Bal-31, T4 DNA Ligase, low molecular weight DNA ladder and 100 bp DNA ladder were purchased from New England Biolabs (Ipswich, MA). .. Proteinase K was purchased from Roche Molecular Biochemicals (Mannheim, Germany).

    DNA Extraction:

    Article Title: Inter-telomeric recombination is present in telomerase-positive human cells
    Article Snippet: .. Restriction enzymes (New England Biolabs): HindIII (R0104S), ClaI (R0197S), XbaI (R0145S), KpnI (R0142S), AflII (R0520S), SacI (R0156S), AluI (R0137S), CfoI (R6241), HaeI (R0107S), HinfI (R0155S), MspI (R0106S), RsaI (R0167S) Plasmids (Invitrogen): pSV-Zeo V860-20 pCDNA3.1 Hygro (−) V870-20 Reagents and consumables: Fugene Transfection reagent (Roche) 05061377001 Zeocin (Invitrogen) ant-zn-1 Hygromycin (Invitrogen) 10687-010 Aphidicolin (Sigma) A0781-1MG Puromycin (Invitrogen) A11138-02 TmpY4 (Calbiochem) 613560-25MG Bal31 (New England Biolabs) M0213S streptavidin-coated magnetic beads (New England Biolabs) S1420S Hybond N membrane (Amersham) RPN82N DNA random prime labeling kit (Roche) 11004760001 T4 DNA ligase (Roche) 10481220001 DH5a competent cells (Invitrogen) 18258-012 Blasticidin (Invitrogen) R210-01 Purgene DNA extraction kit (Gentra Systems) 158422 Trapeze kit (Intergen) S7700 Failsafe PCR kit (epicenter) FS99060 ..

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: Construction and screening of PAO1 shotgun antisense libraries Genomic DNA was isolated from P. aeruginosa PAO1 using an illustra GenomicPrep Cells and Tissue DNA Isolation Kit (GE Healthcare). .. Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends.

    Magnetic Beads:

    Article Title: Inter-telomeric recombination is present in telomerase-positive human cells
    Article Snippet: .. Restriction enzymes (New England Biolabs): HindIII (R0104S), ClaI (R0197S), XbaI (R0145S), KpnI (R0142S), AflII (R0520S), SacI (R0156S), AluI (R0137S), CfoI (R6241), HaeI (R0107S), HinfI (R0155S), MspI (R0106S), RsaI (R0167S) Plasmids (Invitrogen): pSV-Zeo V860-20 pCDNA3.1 Hygro (−) V870-20 Reagents and consumables: Fugene Transfection reagent (Roche) 05061377001 Zeocin (Invitrogen) ant-zn-1 Hygromycin (Invitrogen) 10687-010 Aphidicolin (Sigma) A0781-1MG Puromycin (Invitrogen) A11138-02 TmpY4 (Calbiochem) 613560-25MG Bal31 (New England Biolabs) M0213S streptavidin-coated magnetic beads (New England Biolabs) S1420S Hybond N membrane (Amersham) RPN82N DNA random prime labeling kit (Roche) 11004760001 T4 DNA ligase (Roche) 10481220001 DH5a competent cells (Invitrogen) 18258-012 Blasticidin (Invitrogen) R210-01 Purgene DNA extraction kit (Gentra Systems) 158422 Trapeze kit (Intergen) S7700 Failsafe PCR kit (epicenter) FS99060 ..

    Isolation:

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: Construction and screening of PAO1 shotgun antisense libraries Genomic DNA was isolated from P. aeruginosa PAO1 using an illustra GenomicPrep Cells and Tissue DNA Isolation Kit (GE Healthcare). .. Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends.

    Labeling:

    Article Title: Inter-telomeric recombination is present in telomerase-positive human cells
    Article Snippet: .. Restriction enzymes (New England Biolabs): HindIII (R0104S), ClaI (R0197S), XbaI (R0145S), KpnI (R0142S), AflII (R0520S), SacI (R0156S), AluI (R0137S), CfoI (R6241), HaeI (R0107S), HinfI (R0155S), MspI (R0106S), RsaI (R0167S) Plasmids (Invitrogen): pSV-Zeo V860-20 pCDNA3.1 Hygro (−) V870-20 Reagents and consumables: Fugene Transfection reagent (Roche) 05061377001 Zeocin (Invitrogen) ant-zn-1 Hygromycin (Invitrogen) 10687-010 Aphidicolin (Sigma) A0781-1MG Puromycin (Invitrogen) A11138-02 TmpY4 (Calbiochem) 613560-25MG Bal31 (New England Biolabs) M0213S streptavidin-coated magnetic beads (New England Biolabs) S1420S Hybond N membrane (Amersham) RPN82N DNA random prime labeling kit (Roche) 11004760001 T4 DNA ligase (Roche) 10481220001 DH5a competent cells (Invitrogen) 18258-012 Blasticidin (Invitrogen) R210-01 Purgene DNA extraction kit (Gentra Systems) 158422 Trapeze kit (Intergen) S7700 Failsafe PCR kit (epicenter) FS99060 ..

    Purification:

    Article Title: Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA
    Article Snippet: Single strands of 5′-CGCGCAATTGCGCG-3′ (Integrated DNA Technologies; Coralville, IA) were annealed by slow cooling of the solution from 95°C to 10°C over 48 h. The concentration of the single stranded DNA was measured spectrophotometrically using extinction coefficient derived from the nearest neighbor approximation (125, 800 M−1 cm−1 at 260 nm) or after the complete digestion using nuclease BAL-31 (New England Biolabs; Ipswich, MA) ( ). .. The buffer components, netropsin, pentamidine (Sigma-Aldrich; St. Louis, MO), and DAPI (Molecular Probes; Carlsbad, CA) were used without purification.

    Polymerase Chain Reaction:

    Article Title: Inter-telomeric recombination is present in telomerase-positive human cells
    Article Snippet: .. Restriction enzymes (New England Biolabs): HindIII (R0104S), ClaI (R0197S), XbaI (R0145S), KpnI (R0142S), AflII (R0520S), SacI (R0156S), AluI (R0137S), CfoI (R6241), HaeI (R0107S), HinfI (R0155S), MspI (R0106S), RsaI (R0167S) Plasmids (Invitrogen): pSV-Zeo V860-20 pCDNA3.1 Hygro (−) V870-20 Reagents and consumables: Fugene Transfection reagent (Roche) 05061377001 Zeocin (Invitrogen) ant-zn-1 Hygromycin (Invitrogen) 10687-010 Aphidicolin (Sigma) A0781-1MG Puromycin (Invitrogen) A11138-02 TmpY4 (Calbiochem) 613560-25MG Bal31 (New England Biolabs) M0213S streptavidin-coated magnetic beads (New England Biolabs) S1420S Hybond N membrane (Amersham) RPN82N DNA random prime labeling kit (Roche) 11004760001 T4 DNA ligase (Roche) 10481220001 DH5a competent cells (Invitrogen) 18258-012 Blasticidin (Invitrogen) R210-01 Purgene DNA extraction kit (Gentra Systems) 158422 Trapeze kit (Intergen) S7700 Failsafe PCR kit (epicenter) FS99060 ..

    Article Title: Selective DNA amplification from complex genomes using universal double-sided adapters
    Article Snippet: The ligation reaction was then treated with 1 U of Bal31 nuclease (NEB) in the presence of 1× Bal31 nuclease buffer (NEB) for 30 min at 30°C and then heat inactivated at 75°C for 10 min. .. The sample was diluted 10-fold with TE and 8 µl were digested with 2.5 U of NotI enzyme (NEB) in a 10 µl volume before 1 µl was used in a 30 µl PCR.

    IA:

    Article Title: Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA
    Article Snippet: .. Single strands of 5′-CGCGCAATTGCGCG-3′ (Integrated DNA Technologies; Coralville, IA) were annealed by slow cooling of the solution from 95°C to 10°C over 48 h. The concentration of the single stranded DNA was measured spectrophotometrically using extinction coefficient derived from the nearest neighbor approximation (125, 800 M−1 cm−1 at 260 nm) or after the complete digestion using nuclease BAL-31 (New England Biolabs; Ipswich, MA) ( ). ..

    Liquid Chromatography:

    Article Title: MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
    Article Snippet: Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA). .. Liquid chromatography solvents of LC/MS grade were purchased from Thermo Fisher Scientific (Waltham, MA, USA).

    Plasmid Preparation:

    Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
    Article Snippet: Bal31 assay 1.4 μg gDNA was incubated with 0.3U of Bal31 nuclease (NEB) for increasing time at 30°. .. As a control, linear plasmid DNA was incubated with Bal31 and digestion was assessed by a decrease in size of the linear plasmid DNA on an agarose gel (data not shown).

    Selection:

    Article Title: Selective DNA amplification from complex genomes using universal double-sided adapters
    Article Snippet: Paragraph title: First-round selection ... The ligation reaction was then treated with 1 U of Bal31 nuclease (NEB) in the presence of 1× Bal31 nuclease buffer (NEB) for 30 min at 30°C and then heat inactivated at 75°C for 10 min.

    Agarose Gel Electrophoresis:

    Article Title: Telomerase-dependent and independent chromosome healing in mouse embryonic stem cells
    Article Snippet: Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs). .. Standard agarose gel electrophoresis was performed as previously described [ ].

    Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
    Article Snippet: Bal31 assay 1.4 μg gDNA was incubated with 0.3U of Bal31 nuclease (NEB) for increasing time at 30°. .. DNA was phenol-chloroform-extracted, ethanol-precipitated, and treated by either Hind III or Dde I. Digested DNA was separated on a 0.8% agarose gel (140 ng DNA per well) and subjected to Southern blot analysis as described above.

    Article Title: PIF1 disruption or NBS1 hypomorphism does not affect chromosome healing or fusion resulting from double-strand breaks near telomeres in murine embryonic stem cells
    Article Snippet: Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs). .. Standard agarose gel electrophoresis was performed as described previously [ ].

    Ethanol Precipitation:

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa
    Article Snippet: .. Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends. .. After enzyme inactivation with 1 mM EDTA, DNA was dialyzed against 20 mM Tris–HCl (pH 8.0). pVI533EH and pHERD20T were digested with Sma I (New England Biolabs) and dephosphorylated using shrimp alkaline phosphatase (Roche).

    Concentration Assay:

    Article Title: Telomerase-dependent and independent chromosome healing in mouse embryonic stem cells
    Article Snippet: 5M NaCl was then added to a final concentration of 1.4 M, and the samples chilled on ice for 30 minutes. .. Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

    Article Title: PIF1 disruption or NBS1 hypomorphism does not affect chromosome healing or fusion resulting from double-strand breaks near telomeres in murine embryonic stem cells
    Article Snippet: 5M NaCl was then added to a final concentration of 1.4 M, and the samples chilled on ice for 30 minutes. .. Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

    Article Title: Hydration Changes Accompanying the Binding of Minor Groove Ligands with DNA
    Article Snippet: .. Single strands of 5′-CGCGCAATTGCGCG-3′ (Integrated DNA Technologies; Coralville, IA) were annealed by slow cooling of the solution from 95°C to 10°C over 48 h. The concentration of the single stranded DNA was measured spectrophotometrically using extinction coefficient derived from the nearest neighbor approximation (125, 800 M−1 cm−1 at 260 nm) or after the complete digestion using nuclease BAL-31 (New England Biolabs; Ipswich, MA) ( ). ..

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
    Article Snippet: Nuclease Bal-31 was obtained from New England BioLabs (Ipswich, MA, USA). .. Liquid chromatography solvents of LC/MS grade were purchased from Thermo Fisher Scientific (Waltham, MA, USA).

    Lysis:

    Article Title: Telomerase-dependent and independent chromosome healing in mouse embryonic stem cells
    Article Snippet: The lysis solution was then centrifuged at 3,000 g, and the clear DNA solution removed using a wide-bore pipet. .. Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

    Article Title: PIF1 disruption or NBS1 hypomorphism does not affect chromosome healing or fusion resulting from double-strand breaks near telomeres in murine embryonic stem cells
    Article Snippet: The lysis solution was then centrifuged at 3,000 g, and the clear DNA solution removed using a wide-bore pipet. .. Digestion of DNA with restriction enzymes and BAL31 nuclease was performed following the manufacturer’s recommendations (New England Biolabs).

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  • 90
    New England Biolabs nuclease bal 31
    Construction and screening of PAO1 SALs. (A) Genomic DNA was isolated from P. aeruginosa PAO1 and nebulized to obtain sheared fragments of 200–800 bp. After treatment with exonuclease <t>BAL-31</t> and Klenow polymerase, the genomic DNA fragments were cloned into the E. coli strain JM109, downstream of the arabinose-inducible promoter P BAD of the pHERD20T vector. (B) E. coli transformants, representing the PAO1 shotgun antisense library (SAL), were arrayed in 96-well microplates and (C) mated with P. aeruginosa PAO1 in the presence of a helper strain (triparental mating). (D) SAL recipient PAO1 exconjugants were selected by spotting on PIA plates supplemented with Cb both in the absence and in the presence of the P BAD inducer arabinose. Recipient PAO1 exconjugant spots were inspected for growth defects following 24 h of incubation at 37°C. (E) The identity of the genomic fragments eliciting growth defects (lethal effects, indicated by a lack of a spot: only with inducer, e.g. clones A4, A8, B5, and E4, and with and without an inducer, e.g. clones A2 and E6; growth impairment, indicated as gray spots: only with an inducer, e.g. clones C2, A6, and B6, and with and without an inducer, e.g. C3 and B8) was determined by sequencing the inserts in the corresponding clones of E. coli SAL.
    Nuclease Bal 31, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nuclease bal 31/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nuclease bal 31 - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

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    Construction and screening of PAO1 SALs. (A) Genomic DNA was isolated from P. aeruginosa PAO1 and nebulized to obtain sheared fragments of 200–800 bp. After treatment with exonuclease BAL-31 and Klenow polymerase, the genomic DNA fragments were cloned into the E. coli strain JM109, downstream of the arabinose-inducible promoter P BAD of the pHERD20T vector. (B) E. coli transformants, representing the PAO1 shotgun antisense library (SAL), were arrayed in 96-well microplates and (C) mated with P. aeruginosa PAO1 in the presence of a helper strain (triparental mating). (D) SAL recipient PAO1 exconjugants were selected by spotting on PIA plates supplemented with Cb both in the absence and in the presence of the P BAD inducer arabinose. Recipient PAO1 exconjugant spots were inspected for growth defects following 24 h of incubation at 37°C. (E) The identity of the genomic fragments eliciting growth defects (lethal effects, indicated by a lack of a spot: only with inducer, e.g. clones A4, A8, B5, and E4, and with and without an inducer, e.g. clones A2 and E6; growth impairment, indicated as gray spots: only with an inducer, e.g. clones C2, A6, and B6, and with and without an inducer, e.g. C3 and B8) was determined by sequencing the inserts in the corresponding clones of E. coli SAL.

    Journal: BMC Microbiology

    Article Title: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa

    doi: 10.1186/1471-2180-14-24

    Figure Lengend Snippet: Construction and screening of PAO1 SALs. (A) Genomic DNA was isolated from P. aeruginosa PAO1 and nebulized to obtain sheared fragments of 200–800 bp. After treatment with exonuclease BAL-31 and Klenow polymerase, the genomic DNA fragments were cloned into the E. coli strain JM109, downstream of the arabinose-inducible promoter P BAD of the pHERD20T vector. (B) E. coli transformants, representing the PAO1 shotgun antisense library (SAL), were arrayed in 96-well microplates and (C) mated with P. aeruginosa PAO1 in the presence of a helper strain (triparental mating). (D) SAL recipient PAO1 exconjugants were selected by spotting on PIA plates supplemented with Cb both in the absence and in the presence of the P BAD inducer arabinose. Recipient PAO1 exconjugant spots were inspected for growth defects following 24 h of incubation at 37°C. (E) The identity of the genomic fragments eliciting growth defects (lethal effects, indicated by a lack of a spot: only with inducer, e.g. clones A4, A8, B5, and E4, and with and without an inducer, e.g. clones A2 and E6; growth impairment, indicated as gray spots: only with an inducer, e.g. clones C2, A6, and B6, and with and without an inducer, e.g. C3 and B8) was determined by sequencing the inserts in the corresponding clones of E. coli SAL.

    Article Snippet: Following ethanol precipitation, fragmented DNA was treated with nuclease BAL-31 and Klenow (New England Biolabs) for 10 min at 30°C to obtain blunt ends.

    Techniques: Isolation, Clone Assay, Plasmid Preparation, Incubation, Sequencing

    Mapping Bal-31 cleavage. To determine whether Bal-31 cleavage occurs at multiple sites or at a preferred site, the Δ Lk =−6 topoisomer was cleaved with Bal-31 and various restriction enzymes. ( a ) Products were separated by agarose gel electrophoresis. Left, (lanes 1–5), control reactions, mc336 (approximately equal mixture of Δ Lk =−2 and Δ Lk =−3 topoisomers) with combinations of the various restriction enzymes (as indicated) to generate fragments of known DNA lengths. Right, (lanes 6–9), Δ Lk =−6 topoisomer cleaved first with Bal-31, followed by a restriction enzyme (as indicated). Mr 1 : 100 bp DNA ladder, Mr 2 : Low molecular weight DNA ladder. ( b ) Map of the minicircle sequence showing the positions of the restriction enzymes used, the estimated location of Bal-31 cleavage (with parentheses indicating the range), and the location of the observed base-pair breaking in MD simulation of the Δ Lk =−3 topoisomer.

    Journal: Nature Communications

    Article Title: Structural diversity of supercoiled DNA

    doi: 10.1038/ncomms9440

    Figure Lengend Snippet: Mapping Bal-31 cleavage. To determine whether Bal-31 cleavage occurs at multiple sites or at a preferred site, the Δ Lk =−6 topoisomer was cleaved with Bal-31 and various restriction enzymes. ( a ) Products were separated by agarose gel electrophoresis. Left, (lanes 1–5), control reactions, mc336 (approximately equal mixture of Δ Lk =−2 and Δ Lk =−3 topoisomers) with combinations of the various restriction enzymes (as indicated) to generate fragments of known DNA lengths. Right, (lanes 6–9), Δ Lk =−6 topoisomer cleaved first with Bal-31, followed by a restriction enzyme (as indicated). Mr 1 : 100 bp DNA ladder, Mr 2 : Low molecular weight DNA ladder. ( b ) Map of the minicircle sequence showing the positions of the restriction enzymes used, the estimated location of Bal-31 cleavage (with parentheses indicating the range), and the location of the observed base-pair breaking in MD simulation of the Δ Lk =−3 topoisomer.

    Article Snippet: BbvCI, EcoRV, Nb.BbvCI, NdeI, Nuclease Bal-31, T4 DNA Ligase, low molecular weight DNA ladder and 100 bp DNA ladder were purchased from New England Biolabs (Ipswich, MA).

    Techniques: Agarose Gel Electrophoresis, Molecular Weight, Sequencing

    Effect of supercoiling on DNA base accessibility. ( a ) Minicircle DNA incubated with nuclease Bal-31. Over time, samples were removed, quenched by the addition of stop buffer and the products analysed by polyacrylamide gel electrophoresis. Mr: 100 bp DNA ladder, L: linearized 336 bp DNA, N: nicked 336 bp minicircle. ( b ) Graphic representation of the data shown in ( a ) Fitted lines are for visualization purposes only. ( c ) MD simulation of the Δ Lk =−3 topoisomer in explicit solvent. Splayed bases were found at a sharp bend of a needle conformation. This may be a potential atomistic explanation for Bal-31 susceptibility of negatively supercoiled topoisomers.

    Journal: Nature Communications

    Article Title: Structural diversity of supercoiled DNA

    doi: 10.1038/ncomms9440

    Figure Lengend Snippet: Effect of supercoiling on DNA base accessibility. ( a ) Minicircle DNA incubated with nuclease Bal-31. Over time, samples were removed, quenched by the addition of stop buffer and the products analysed by polyacrylamide gel electrophoresis. Mr: 100 bp DNA ladder, L: linearized 336 bp DNA, N: nicked 336 bp minicircle. ( b ) Graphic representation of the data shown in ( a ) Fitted lines are for visualization purposes only. ( c ) MD simulation of the Δ Lk =−3 topoisomer in explicit solvent. Splayed bases were found at a sharp bend of a needle conformation. This may be a potential atomistic explanation for Bal-31 susceptibility of negatively supercoiled topoisomers.

    Article Snippet: BbvCI, EcoRV, Nb.BbvCI, NdeI, Nuclease Bal-31, T4 DNA Ligase, low molecular weight DNA ladder and 100 bp DNA ladder were purchased from New England Biolabs (Ipswich, MA).

    Techniques: Incubation, Polyacrylamide Gel Electrophoresis