neb buffer 4  (New England Biolabs)


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  • 99
    Name:
    NEBuffer 4
    Description:
    NEBuffer 4 5 0 ml
    Catalog Number:
    b7004s
    Price:
    24
    Size:
    5 0 ml
    Category:
    Buffers
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    Structured Review

    New England Biolabs neb buffer 4
    NEBuffer 4
    NEBuffer 4 5 0 ml
    https://www.bioz.com/result/neb buffer 4/product/New England Biolabs
    Average 99 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    neb buffer 4 - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579"

    Article Title: Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.06248-11

    BceSI gene organization and characterization of BceSI restriction enzyme. (A) Gene organization of the BceSI R-M system. Mod, modification subunit; Res, restriction subunit. (B) SDS-PAGE analysis of BceSI after two-column purification (nickel agarose and Hi-Trap heparin Sepharose). (C) BceSI digestion of phage λ DNA. One μg of λ DNA was digested by various amounts of BceSI endonuclease (0.5 μg/μl) in NEB buffer 4 at 37°C for 1 h. (D) BceSI digestion pattern generated by NEB cutter. The real digestion and hypothetical digestion patterns do not completely match, presumably due to BceSI requiring two sites in a head-to-head or tail-to-tail orientation for efficient cleavage. unmeth., unmethylated; CpG, CpG dinucleotide.
    Figure Legend Snippet: BceSI gene organization and characterization of BceSI restriction enzyme. (A) Gene organization of the BceSI R-M system. Mod, modification subunit; Res, restriction subunit. (B) SDS-PAGE analysis of BceSI after two-column purification (nickel agarose and Hi-Trap heparin Sepharose). (C) BceSI digestion of phage λ DNA. One μg of λ DNA was digested by various amounts of BceSI endonuclease (0.5 μg/μl) in NEB buffer 4 at 37°C for 1 h. (D) BceSI digestion pattern generated by NEB cutter. The real digestion and hypothetical digestion patterns do not completely match, presumably due to BceSI requiring two sites in a head-to-head or tail-to-tail orientation for efficient cleavage. unmeth., unmethylated; CpG, CpG dinucleotide.

    Techniques Used: Modification, SDS Page, Purification, Generated

    2) Product Images from "A quantitative understanding of lac repressor’s binding specificity and flexibility"

    Article Title: A quantitative understanding of lac repressor’s binding specificity and flexibility

    Journal: Quantitative biology (Beijing, China)

    doi: 10.1007/s40484-015-0044-z

    Specificity profiling the the whole lac operator. (A) Energy logo for the whole lac operator under 1× NEB buffer 4 condition. Energy logo was produced based on the linear regression of all the wild-type O1 operator’s single and adjacent double variants’ energy values. (B) Measured vs. predicted energy deviation for all double variant pairs. The energy value of each adjacent double variant can either be measured directly or predicted by summing up the contributions of each individual base variation. Each double variant is plotted in panel B based on its position in the operator and energy deviation value between measured and predicted numbers. (C) Distribution of measured vs. predicted energy for all double variants. All energy deviation values in panel B were re-plotted in histogram form, and it is clear that most of adjacent double variants follow “additivity assumption” reasonably well.
    Figure Legend Snippet: Specificity profiling the the whole lac operator. (A) Energy logo for the whole lac operator under 1× NEB buffer 4 condition. Energy logo was produced based on the linear regression of all the wild-type O1 operator’s single and adjacent double variants’ energy values. (B) Measured vs. predicted energy deviation for all double variant pairs. The energy value of each adjacent double variant can either be measured directly or predicted by summing up the contributions of each individual base variation. Each double variant is plotted in panel B based on its position in the operator and energy deviation value between measured and predicted numbers. (C) Distribution of measured vs. predicted energy for all double variants. All energy deviation values in panel B were re-plotted in histogram form, and it is clear that most of adjacent double variants follow “additivity assumption” reasonably well.

    Techniques Used: Produced, Variant Assay

    Related Articles

    Mutagenesis:

    Article Title: Streptococcus pneumoniae Folate Biosynthesis Responds to Environmental CO2 Levels
    Article Snippet: .. Briefly, a 200-μl solution with 2 μg S. pneumoniae mutant library genomic DNA in NEBuffer 4 (New England BioLabs) with 5 μM S -adenosylmethionine was digested with 10 U MmeI (New England BioLabs) for 4 h at 37°C and dephosphorylated with 1 U calf intestine alkaline phosphatase (Invitrogen) for 30 min at 50°C. ..

    Binding Assay:

    Article Title: A quantitative understanding of lac repressor’s binding specificity and flexibility
    Article Snippet: .. For Spec-seq runs quantifying the whole lac operator region, 3 different binding buffer conditions were used, i.e., 1×, 2×, and 4× NEB buffer 4 (50 mM Potassium Acetate, 20 mM Tris-acetate,10 mM Magnesium Acetate, 1 mM DTT, pH 7.9 @25°C) with everything else being the same (100 ng dsDNA fragments, 400 ng lac repressor protein in 15 ul reaction systems). .. For Spec-seq runs quantifying various lacI and purR mutants, 1× NEB buffer 4 was chosen as the default binding buffer.

    Article Title: Control of Cyclin G2 mRNA Expression by Forkhead Transcription Factors: Novel Mechanism for Cell Cycle Control by Phosphoinositide 3-Kinase and Forkhead
    Article Snippet: .. For binding reactions, the following components were mixed and preincubated (20 min at room temperature): 3 μl (10 to 15 μg) of nuclear extract, 7 μl of buffer D (20 mM HEPES [pH 7.9], 20% glycerol, 0.1 M KCl, 0.2 mM EDTA, 0.5 mM dithiothreitol), 2 μl (20 μg) of purified BSA (New England Biolabs), 0.4 μl (2 μg) of sheared salmon sperm DNA, and 11 μl of H2 O. Unlabeled oligonucleotide competitors (200 ng) and either 15 μg of anti-FKHRL1 antibody (Upstate Biotechology) or 5 μl of rabbit polyclonal anti-DP1 antibody ( ) were added to the initial mixture prior to the preincubation step. .. After preincubation, labeled oligonucleotides were added (2 ng), and the mixtures were incubated (20 min at room temperature).

    Purification:

    Article Title: Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579
    Article Snippet: .. DNA cleavage assays by BceSIV or Bce14579I were carried out using 1× NEB buffer 4 supplemented with ATP or GTP at 37°C for 1 h. One μg of DNA and various amounts of the indicated crude lysate or purified protein was used. ..

    Article Title: Control of Cyclin G2 mRNA Expression by Forkhead Transcription Factors: Novel Mechanism for Cell Cycle Control by Phosphoinositide 3-Kinase and Forkhead
    Article Snippet: .. For binding reactions, the following components were mixed and preincubated (20 min at room temperature): 3 μl (10 to 15 μg) of nuclear extract, 7 μl of buffer D (20 mM HEPES [pH 7.9], 20% glycerol, 0.1 M KCl, 0.2 mM EDTA, 0.5 mM dithiothreitol), 2 μl (20 μg) of purified BSA (New England Biolabs), 0.4 μl (2 μg) of sheared salmon sperm DNA, and 11 μl of H2 O. Unlabeled oligonucleotide competitors (200 ng) and either 15 μg of anti-FKHRL1 antibody (Upstate Biotechology) or 5 μl of rabbit polyclonal anti-DP1 antibody ( ) were added to the initial mixture prior to the preincubation step. .. After preincubation, labeled oligonucleotides were added (2 ng), and the mixtures were incubated (20 min at room temperature).

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    New England Biolabs hf psti high fidelity
    Adapter Design, PCR amplification of fragments. 1) The ligation product of a genomic DNA fragment (black) containing a <t>PstI</t> restriction site and a <t>MspI</t> restriction site. The forward adapter (blue) binds to a PstI generated overhang. The 4–9 bp barcode for this adapter is in bold with “X”. The MspI generated overhang corresponds to the reverse Y-adapter (green). The unpaired tail of the Y-adapter is underlined. 2) During the first round of PCR only the forward primer (red) can anneal. PCR synthesis of the complementary strand proceeds to the end of the fragment synthesizing the compliment of the Y-adapter tail. 3) During the second round of PCR the reverse primer (orange) can anneal to the newly synthesized compliment of the Y-adapter tail. This PCR reaction then proceeds to fill in the compliment of the forward adapter/primer on the other end of the same fragment.
    Hf Psti High Fidelity, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hf psti high fidelity/product/New England Biolabs
    Average 97 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
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    99
    New England Biolabs bst dna polymerase
    Single factor experiment of RealAmp. The influence of each variable on the LAMP reaction was analyzed by the amplification curve ( a ) and the melt peak ( b ). For the <t>Bst</t> <t>DNA</t> polymerase optimization, Bst polymerase quantities were adjusted to 2 U, 4 U, 6
    Bst Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bst dna polymerase/product/New England Biolabs
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    93
    New England Biolabs cas9 buffer
    Large segments of the mouse X chromosome are specifically targeted with in vitro CRISPR. ( A ) The specific products of the in vitro Otc CRISPR digestion of both YAC ADK.A6 DNA and mouse genomic DNA are resolved by PFGE and detected with Diamond stain (Promega) ( Supplementary Figure S1 ). Whereas the expected YAC digestion products are clearly detectable, digestion of the more complex mouse genomic DNA does not produce detectable products. Untreated and <t>Cas9-only</t> digestions of YAC and mouse genomic DNA serve as negative controls. ( B ) A Southern blot of the PFG shown in (A) is hybridized with a DIG-labeled Otc probe. The intact YAC chromosome (∼520 kb) and the expected 263 kb in vitro Otc CRISPR digestion product from both YAC and mouse genomic DNA are visible upon chemiluminescent detection of the probe and exposure of X-ray film. ( C ) A faint but, detectable ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is resolved by PFGE along with the multi-megabase H. wingei (Hw) chromosomes ladder (Bio-Rad) labeled on the left. ( D ) The Southern blot of the PFG shown in ( C ) is hybridized with a DIG-labeled Srsx probe. The estimated ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is visible upon chemiluminescent detection of the probe and exposure of X-ray film.
    Cas9 Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Adapter Design, PCR amplification of fragments. 1) The ligation product of a genomic DNA fragment (black) containing a PstI restriction site and a MspI restriction site. The forward adapter (blue) binds to a PstI generated overhang. The 4–9 bp barcode for this adapter is in bold with “X”. The MspI generated overhang corresponds to the reverse Y-adapter (green). The unpaired tail of the Y-adapter is underlined. 2) During the first round of PCR only the forward primer (red) can anneal. PCR synthesis of the complementary strand proceeds to the end of the fragment synthesizing the compliment of the Y-adapter tail. 3) During the second round of PCR the reverse primer (orange) can anneal to the newly synthesized compliment of the Y-adapter tail. This PCR reaction then proceeds to fill in the compliment of the forward adapter/primer on the other end of the same fragment.

    Journal: PLoS ONE

    Article Title: Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

    doi: 10.1371/journal.pone.0032253

    Figure Lengend Snippet: Adapter Design, PCR amplification of fragments. 1) The ligation product of a genomic DNA fragment (black) containing a PstI restriction site and a MspI restriction site. The forward adapter (blue) binds to a PstI generated overhang. The 4–9 bp barcode for this adapter is in bold with “X”. The MspI generated overhang corresponds to the reverse Y-adapter (green). The unpaired tail of the Y-adapter is underlined. 2) During the first round of PCR only the forward primer (red) can anneal. PCR synthesis of the complementary strand proceeds to the end of the fragment synthesizing the compliment of the Y-adapter tail. 3) During the second round of PCR the reverse primer (orange) can anneal to the newly synthesized compliment of the Y-adapter tail. This PCR reaction then proceeds to fill in the compliment of the forward adapter/primer on the other end of the same fragment.

    Article Snippet: Restriction Digest: Genomic DNA (200 ng) was digested in 20 ul reaction volume of NEB Buffer 4 with 8 U of HF-PstI (High-Fidelity) and 8 U of MspI (New England BioLabs Inc., Ipswich, MA 01938).

    Techniques: Polymerase Chain Reaction, Amplification, Ligation, Generated, Synthesized

    Single factor experiment of RealAmp. The influence of each variable on the LAMP reaction was analyzed by the amplification curve ( a ) and the melt peak ( b ). For the Bst DNA polymerase optimization, Bst polymerase quantities were adjusted to 2 U, 4 U, 6

    Journal: Scientific Reports

    Article Title: Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Ustilago maydis

    doi: 10.1038/s41598-017-13881-4

    Figure Lengend Snippet: Single factor experiment of RealAmp. The influence of each variable on the LAMP reaction was analyzed by the amplification curve ( a ) and the melt peak ( b ). For the Bst DNA polymerase optimization, Bst polymerase quantities were adjusted to 2 U, 4 U, 6

    Article Snippet: This optimized reaction mixture (total, 25 μl) contained 12.5 μl 2 × Bst DNA polymerase (NEB, Ipswich, MA, USA) reaction buffer [1 × containing 1.6 mM dNTPs, 1 M betaine, 4 mM MgSO4 , 20 mM Tris-HCl (pH 8.8), 10 mM KCl, 10 mM (NH4)2 SO4 , and 0.1% Triton X-20 (Sigma-Aldrich Inc., Saint Louis, USA), Double Helix Tech.

    Techniques: Amplification

    Large segments of the mouse X chromosome are specifically targeted with in vitro CRISPR. ( A ) The specific products of the in vitro Otc CRISPR digestion of both YAC ADK.A6 DNA and mouse genomic DNA are resolved by PFGE and detected with Diamond stain (Promega) ( Supplementary Figure S1 ). Whereas the expected YAC digestion products are clearly detectable, digestion of the more complex mouse genomic DNA does not produce detectable products. Untreated and Cas9-only digestions of YAC and mouse genomic DNA serve as negative controls. ( B ) A Southern blot of the PFG shown in (A) is hybridized with a DIG-labeled Otc probe. The intact YAC chromosome (∼520 kb) and the expected 263 kb in vitro Otc CRISPR digestion product from both YAC and mouse genomic DNA are visible upon chemiluminescent detection of the probe and exposure of X-ray film. ( C ) A faint but, detectable ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is resolved by PFGE along with the multi-megabase H. wingei (Hw) chromosomes ladder (Bio-Rad) labeled on the left. ( D ) The Southern blot of the PFG shown in ( C ) is hybridized with a DIG-labeled Srsx probe. The estimated ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is visible upon chemiluminescent detection of the probe and exposure of X-ray film.

    Journal: Nucleic Acids Research

    Article Title: CRISPR-mediated isolation of specific megabase segments of genomic DNA

    doi: 10.1093/nar/gkx749

    Figure Lengend Snippet: Large segments of the mouse X chromosome are specifically targeted with in vitro CRISPR. ( A ) The specific products of the in vitro Otc CRISPR digestion of both YAC ADK.A6 DNA and mouse genomic DNA are resolved by PFGE and detected with Diamond stain (Promega) ( Supplementary Figure S1 ). Whereas the expected YAC digestion products are clearly detectable, digestion of the more complex mouse genomic DNA does not produce detectable products. Untreated and Cas9-only digestions of YAC and mouse genomic DNA serve as negative controls. ( B ) A Southern blot of the PFG shown in (A) is hybridized with a DIG-labeled Otc probe. The intact YAC chromosome (∼520 kb) and the expected 263 kb in vitro Otc CRISPR digestion product from both YAC and mouse genomic DNA are visible upon chemiluminescent detection of the probe and exposure of X-ray film. ( C ) A faint but, detectable ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is resolved by PFGE along with the multi-megabase H. wingei (Hw) chromosomes ladder (Bio-Rad) labeled on the left. ( D ) The Southern blot of the PFG shown in ( C ) is hybridized with a DIG-labeled Srsx probe. The estimated ∼2.3 Mb in vitro Srsx CRISPR digestion product from mouse genomic DNA is visible upon chemiluminescent detection of the probe and exposure of X-ray film.

    Article Snippet: Agarose blocks are then stored long term at 4°C in TE or transferred into 1× Cas9 buffer (NEB, ) for a 2–16 h incubation with gentle shaking at 4°C prior to the CRISPR reaction.

    Techniques: In Vitro, CRISPR, Staining, Southern Blot, Labeling