λ exonuclease  (New England Biolabs)


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    Structured Review

    New England Biolabs λ exonuclease
    λ Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease/product/New England Biolabs
    Average 93 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease - by Bioz Stars, 2020-04
    93/100 stars

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    Related Articles

    Selection:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The products of the digested strand were analyzed by electrophoresis in a 10% polyacrylamide/8 M urea TBE gel and the band was purified from the gel for the next round of selection.

    Labeling:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: The 5′-FAM™ labeled forward primer (5′-FAM-GCAATGGTACGGTACTTCC-3) and the 5′-phosphorylated reverse primer (5′-P-TTAGCAAAGTAGCGTGCACTTTTG-3′) were used for PCR. .. MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16).

    Purification:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: .. MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The products of the digested strand were analyzed by electrophoresis in a 10% polyacrylamide/8 M urea TBE gel and the band was purified from the gel for the next round of selection.

    Electrophoresis:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The products of the digested strand were analyzed by electrophoresis in a 10% polyacrylamide/8 M urea TBE gel and the band was purified from the gel for the next round of selection.

    Incubation:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: .. MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The products of the digested strand were analyzed by electrophoresis in a 10% polyacrylamide/8 M urea TBE gel and the band was purified from the gel for the next round of selection.

    Polymerase Chain Reaction:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: .. MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The products of the digested strand were analyzed by electrophoresis in a 10% polyacrylamide/8 M urea TBE gel and the band was purified from the gel for the next round of selection.

    Recombinant:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. MATERIALS AND METHODS SELEX procedure Selection of DNA aptamers specific to the recombinant N protein was performed as described previously (17) with slight modifications.

    Binding Assay:

    Article Title: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer.
    Article Snippet: MATERIALS AND METHODS ssDNA generation After PCR using the 5′-phosphorylated reverse primer, purified dsDNA was incubated with 25 U λ-exonuclease (NEB, Germany) in a total reaction volume of 50 μL at 37°C for 3 h (16). .. The initial ssDNA pool was heated at 90°C for 10 min, and immediately cooled on ice for 10 min, and then 5 μg of the DNA library was pre-incubated with 100 μL of Ni-NTA sepharose beads in 100 μL of binding buffer (50 mM Tris/Cl, pH 8.0, 150 mM NaCl, 1.5 mM MgCl 2 , 2 mM dithiothreitol (DTT) and 1% (w/v) BSA) for 30 min at room temperature with occasional shaking.

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    New England Biolabs lambda exonuclease
    ( A ) Fluorescence responses of Nanoprobe A (0.1 mg/ml) to APE1 at different concentrations. ( B ) Linear calibration curve for detection of the activity of APE1. The linear regression equation is F = 0.20 c (U/ml) – 2.1 × 10 −4 , and the detection limit is 0.01 U/ml. ( C ) Selectivity of Nanoprobe A toward APE1 (2.0 U/ml) over other nucleases. (DNase I: 5.0 U/ml; Exo III: 4.0 U/ml; <t>lambda</t> exo: 66.7 U/ml; Exo I: 12.5 U/ml; T5: 5.0 U/ml; T7: 50 U/ml). All experiments were repeated at least three times.
    Lambda Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda exonuclease/product/New England Biolabs
    Average 99 stars, based on 115 article reviews
    Price from $9.99 to $1999.99
    lambda exonuclease - by Bioz Stars, 2020-04
    99/100 stars
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    ( A ) Fluorescence responses of Nanoprobe A (0.1 mg/ml) to APE1 at different concentrations. ( B ) Linear calibration curve for detection of the activity of APE1. The linear regression equation is F = 0.20 c (U/ml) – 2.1 × 10 −4 , and the detection limit is 0.01 U/ml. ( C ) Selectivity of Nanoprobe A toward APE1 (2.0 U/ml) over other nucleases. (DNase I: 5.0 U/ml; Exo III: 4.0 U/ml; lambda exo: 66.7 U/ml; Exo I: 12.5 U/ml; T5: 5.0 U/ml; T7: 50 U/ml). All experiments were repeated at least three times.

    Journal: Nucleic Acids Research

    Article Title: A specific DNA-nanoprobe for tracking the activities of human apurinic/apyrimidinic endonuclease 1 in living cells

    doi: 10.1093/nar/gkw1205

    Figure Lengend Snippet: ( A ) Fluorescence responses of Nanoprobe A (0.1 mg/ml) to APE1 at different concentrations. ( B ) Linear calibration curve for detection of the activity of APE1. The linear regression equation is F = 0.20 c (U/ml) – 2.1 × 10 −4 , and the detection limit is 0.01 U/ml. ( C ) Selectivity of Nanoprobe A toward APE1 (2.0 U/ml) over other nucleases. (DNase I: 5.0 U/ml; Exo III: 4.0 U/ml; lambda exo: 66.7 U/ml; Exo I: 12.5 U/ml; T5: 5.0 U/ml; T7: 50 U/ml). All experiments were repeated at least three times.

    Article Snippet: Apurinic/apyrimidinic endonuclease I (APE1), uracil–DNA glycocasylase (UDG), deoxyribonuclease I (DNase I), exonuclease III (Exo III), exonuclease I (Exo I), lambda exonuclease (λ exo), T5 exonuclease (T5 Exo), T7 exonuclease (T7 Exo) and their corresponding buffers ( ) were all purchased from New England Biolabs (NEB, USA).

    Techniques: Fluorescence, Activity Assay

    Internal modification of DNA. DNA is first tailed with either 5- E -UTP or N 6 - P -ATP, and then elongated by primer extension. The 5′-monophosphorylated template (shown in gray) is optionally digested with λ-exonuclease (λ-Exo) and the alkyne is reacted in CuAAC, to attach biotin to the single-stranded (ss) or double-stranded (ds) DNA. 12% denaturing PAGE, visualization by SYBR Gold staining.

    Journal: Nucleic Acids Research

    Article Title: Nucleotidyl transferase assisted DNA labeling with different click chemistries

    doi: 10.1093/nar/gkv544

    Figure Lengend Snippet: Internal modification of DNA. DNA is first tailed with either 5- E -UTP or N 6 - P -ATP, and then elongated by primer extension. The 5′-monophosphorylated template (shown in gray) is optionally digested with λ-exonuclease (λ-Exo) and the alkyne is reacted in CuAAC, to attach biotin to the single-stranded (ss) or double-stranded (ds) DNA. 12% denaturing PAGE, visualization by SYBR Gold staining.

    Article Snippet: Splinted ligation was performed by first annealing tailed DNA2 with DNA5/6 and DNA7 by heating to 90°C for 30 s and cooling to room temperature for 5 min, adding all other components after this step [final concentrations: 10 μM DNA2, 22.5 μM DNA5/6, 25 μM blocked and phosphorylated DNA7, 50 μM ATP, 50 mM Tris-HCl (pH 7.4), 10 mM MgCl2 , 1.5 U/μl T4 DNA ligase] incubating at 37°C for 4 h and heating to 80°C for 10 min. DNA5/6 and DNA7 were optionally removed from reaction mixtures to obtain pure, ligated/extended ssDNA by adding λ-exonuclease (0.25 U/μl for primer extension or 0.5 U/μl for ligation; New England Biolabs) directly into the reaction mixture and incubating at 37°C for 1 h, followed by 80°C for 10 min. DNA was purified by ethanol precipitation in the presence of 0.3 M sodium acetate (pH 5.5).

    Techniques: Modification, Polyacrylamide Gel Electrophoresis, Staining

    Electrophoretic and TEM analysis of human heart mtDNA. a , one-dimensional AGE of undigested cardiac muscle mtDNA treated with the enzymes as indicated (topoisomerase ( Topo ) I, topoisomerase IV, T7 endonuclease ( endo ) I, and λ-exonuclease ( exo )). The identity of the various species is inferred by the effects of enzymatic treatments on their relative amounts and by their migration properties on two-dimensional AGE ( b ). Bands t and f are each composites of several species. λ-Exonuclease digests molecules with exposed 5′ phosphorylated ends. Because it removes or modifies the residual material running just behind open circles after topoisomerase IV treatment, i.e. 2n linear molecules plus species x ( b , panel ii ), we infer that species x has exposed ends. b , two-dimensional AGE of cardiac muscle mtDNA untreated ( panel i ), treated with topoisomerase IV ( panel ii ), treated with T7 endonuclease I ( panel iii ), and treated with topoisomerase IV + T7 endonuclease I ( panel iv ). The topology of the various forms, annotated on the gel images and inferred from the treatments and electrophoretic mobilities, is shown below the gel panels. tgl , tangled complexes (see Fig. 3 ); cat , catenanes (can also include > 2 monomeric or dimeric circles); 1n and 2n , monomeric and dimeric linear molecules, respectively; c and 2nc , monomeric and dimeric open circles, respectively; sc and 2nsc , supercoiled monomeric and dimeric circles, respectively. xc , circular molecules joined by four-way junctions; x , suggested to be circles joined to linear molecules by four-way junctions. Arrows indicate directions of first and second dimension electrophoresis. c and d , examples of forms seen by TEM following topoisomerase IV treatment of heart mtDNA alongside interpretations. Distinct circles and linear segments are indicated in different colors with inferred contour lengths in kb or (for circles) genome lengths. Scale bars , 200 nm.

    Journal: The Journal of Biological Chemistry

    Article Title: Human Heart Mitochondrial DNA Is Organized in Complex Catenated Networks Containing Abundant Four-way Junctions and Replication Forks *

    doi: 10.1074/jbc.M109.016600

    Figure Lengend Snippet: Electrophoretic and TEM analysis of human heart mtDNA. a , one-dimensional AGE of undigested cardiac muscle mtDNA treated with the enzymes as indicated (topoisomerase ( Topo ) I, topoisomerase IV, T7 endonuclease ( endo ) I, and λ-exonuclease ( exo )). The identity of the various species is inferred by the effects of enzymatic treatments on their relative amounts and by their migration properties on two-dimensional AGE ( b ). Bands t and f are each composites of several species. λ-Exonuclease digests molecules with exposed 5′ phosphorylated ends. Because it removes or modifies the residual material running just behind open circles after topoisomerase IV treatment, i.e. 2n linear molecules plus species x ( b , panel ii ), we infer that species x has exposed ends. b , two-dimensional AGE of cardiac muscle mtDNA untreated ( panel i ), treated with topoisomerase IV ( panel ii ), treated with T7 endonuclease I ( panel iii ), and treated with topoisomerase IV + T7 endonuclease I ( panel iv ). The topology of the various forms, annotated on the gel images and inferred from the treatments and electrophoretic mobilities, is shown below the gel panels. tgl , tangled complexes (see Fig. 3 ); cat , catenanes (can also include > 2 monomeric or dimeric circles); 1n and 2n , monomeric and dimeric linear molecules, respectively; c and 2nc , monomeric and dimeric open circles, respectively; sc and 2nsc , supercoiled monomeric and dimeric circles, respectively. xc , circular molecules joined by four-way junctions; x , suggested to be circles joined to linear molecules by four-way junctions. Arrows indicate directions of first and second dimension electrophoresis. c and d , examples of forms seen by TEM following topoisomerase IV treatment of heart mtDNA alongside interpretations. Distinct circles and linear segments are indicated in different colors with inferred contour lengths in kb or (for circles) genome lengths. Scale bars , 200 nm.

    Article Snippet: Subsequent treatments with topoisomerase IV (John Innes Enterprises), topoisomerase I, T7 endonuclease I, or λ-exonuclease (all New England Biolabs) used the manufacturers' recommended conditions.

    Techniques: Transmission Electron Microscopy, Migration, Electrophoresis

    hSNM1 is a single-strand-specific exonuclease. ( A ) Assay of hSNM1 IMAC fraction 3 on 20-dT substrate. Lanes: 1, RecJ f ; 2, substrate only; 3, ySNM1; Lanes 4, 116 ng protein 5, 29 ng protein; 6, 7.25 ng protein; 7, 1.8 ng protein; 8, 0.45 ng protein. ( B ) Assay of IMAC fraction 2 on internally labeled double-stranded substrate. Lanes: 1, λ exonuclease control; 2, ySNM1; 3, 140 ng protein; 4, 35 ng protein; 5, 4.4 ng protein. ( C ) Assay of FPLC fraction 16 on 20-dT substrate. Lanes: 1, substrate only; 2, RecJ f  control; 3, fraction 16 (∼10 ng); 4, ∼2.5 ng; 5, ∼0.65 ng; 6, ∼0.17 ng. ( D ) Assay of FPLC fraction 16 on internally labeled ds substrate. Lanes: 1, fraction 16 (∼10 ng); 2, ∼2.5 ng; 3, ∼0.65ng.

    Journal: Nucleic Acids Research

    Article Title: The hSNM1 protein is a DNA 5?-exonuclease

    doi: 10.1093/nar/gkm530

    Figure Lengend Snippet: hSNM1 is a single-strand-specific exonuclease. ( A ) Assay of hSNM1 IMAC fraction 3 on 20-dT substrate. Lanes: 1, RecJ f ; 2, substrate only; 3, ySNM1; Lanes 4, 116 ng protein 5, 29 ng protein; 6, 7.25 ng protein; 7, 1.8 ng protein; 8, 0.45 ng protein. ( B ) Assay of IMAC fraction 2 on internally labeled double-stranded substrate. Lanes: 1, λ exonuclease control; 2, ySNM1; 3, 140 ng protein; 4, 35 ng protein; 5, 4.4 ng protein. ( C ) Assay of FPLC fraction 16 on 20-dT substrate. Lanes: 1, substrate only; 2, RecJ f control; 3, fraction 16 (∼10 ng); 4, ∼2.5 ng; 5, ∼0.65 ng; 6, ∼0.17 ng. ( D ) Assay of FPLC fraction 16 on internally labeled ds substrate. Lanes: 1, fraction 16 (∼10 ng); 2, ∼2.5 ng; 3, ∼0.65ng.

    Article Snippet: In vitro nuclease assay The assay was similar to an assay for yeast SNM1 ( ) Briefly, 0.5 pmol of radiolabeled substrate was combined with indicated amounts of purified protein (see the figure legends) in 15 μl of 1× Buffer F (50 mM Tris-acetate pH 7.2, 10 mM Mg acetate, 75 mM Potassium acetate, 1 mM DTT) supplemented with 100 μg/ml BSA, and incubated at 37°C for 20 min. For control reactions, 10 units of Rec-Jf or λ-exonuclease (for double-stranded substrate) (New England Biolabs, Ipswich, MA, USA) were used as recommended by the supplier.

    Techniques: Labeling, Fast Protein Liquid Chromatography