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1x nebuffer 2  (New England Biolabs)


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    New England Biolabs 1x nebuffer 2
    1x Nebuffer 2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2845 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/1x+nebuffer+2/NEBuffer+2/bio_rxiv__64898__2026__02__25__708054-208-20-21
    Average 99 stars, based on 2845 article reviews
    1x nebuffer 2 - by Bioz Stars, 2026-09
    99/100 stars

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    other:

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: The retroviral plasmid expressing GFP-LC3-RFP (pMRX-IP-GFP-LC3-RFP) was a gift from Noboru Mizushima (Addgene plasmid #84573; http://n2t.net/addgene:84573 ).

    Article Title: A Plastic EMP1 + to LGR5 + Cell State Conversion as a Bypass to KRAS G12D Pharmacologic Inhibition in Metastatic Colorectal Cancer
    Article Snippet: The dissociation was quenched with 3 mL of warm Advanced DMEM/F12 (Gibco, 12634028), supplemented with 10mM HEPES (Gibco, 11560496) and Glutamax (Gibco, 11574466).

    Produced:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Mutagenesis:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Negative Control:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Positive Control:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Incubation:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: .. The lentiviral plasmid lentiCRISPRv2 (pLentiCRISPRv2), a gift from Feng Zhang (puromycin selection; Addgene plasmid # 52961; http://n2t.net/addgene:52961 ), or for targeting p53 (neomycin selection, lentiCRISPRv2-neo; Addgene; 98292), was modified by inserting the following sgRNA sequences at the BsmB1 site, with inserts prepared by annealing two primers, each containing a flanking sequence recognizing the BsmB1-digested lentiCRISPRv2 plasmid (sgRNA sequences in uppercase, Bsmb1-annealing sequences in lowercase): TSC1 5′-caccgGAGGAGCCGCCTGTTCCGGA-3’ 5′-aaacTCCGGAACAGGCGGCTCCTCc-3’ TSC2 5′-caccgGGAGAAGTCGCTCCACGCGG-3’ 5′-aaacCCGCGTGGAGCGACTTCTCCc-3’ TBC1D7 5′-caccgGCATGGGACTCGTGGTGTGG-3’ 5′-aaacCCACACCACGAGTCCCATGCc-3’ TP53 5′-caccgGAAGGGACAGAAGATGACAG-3’ 5′-aaacCTGTCATCTTCTGTCCCTTCc-3’ NPRL2 5′-caccgGGGCATCACACACGAAGCCC-3’ 5′-aaacGGGCTTCGTGTGTGATGCCCc-3’ ULK1 5′-caccgGCAGCGTCTGAGACTTGGCG-3’ 5′-aaacCGCCAAGTCTCAGACGCTGCc-3’ BECN1 5′-caccgGAAACCAGGAGAGACCCAGG-3’ 5′-aaacCCTGGGTCTCTCCTGGTTTCc-3’ ATG7 5′-caccgATAGCTGGGCAGCAACGGGC-3’ 5′-aaacGCCCGTTGCTGCCCAGCTATc-3’ TFEB 5′- caccgGCAGCAGTCGCAGCATCAGA-3’ 5′- aaacTCTGATGCTGCGACTGCTGCc-3’ To anneal primers (Integrated DNA Technologies), 100 μM of each were incubated in 1X NEBuffer 2 (New England Biolabs [NEB]; B7002S) at 94°C for 2 min, followed by 65°C for 10 min and 4°C for 1 min. .. The annealed primers (diluted 1:100) were inserted into pLentiCRISPRv2 digested by the BsmB1 enzyme (NEB; R0739S).

    Purification:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Agarose Gel Electrophoresis:

    Article Title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites
    Article Snippet: The PC was the unvaried thyroglobulin promoter sequence and the NC was a length-matched exonic sequence of the FOXA1 gene that was negative for NKX2.1 binding (for full sequences used please see Supplementary Table S1: oligos 6–7 ). .. Double-stranded DNA was produced using a Klenow enzyme with a reverse primer-only, specific to the mutant libraries ( Supplementary Table S1: oligo 8 ), the negative control ( oligo 10 ), or the positive control ( oligo 12 ). ssDNA template was incubated with 0.2 mM each of dATP, dCTP, dTTP and dGTP, 12 μM reverse primer either unlabelled or labelled with Alexa Fluor 647 dye in 1X NEBuffer 2 (New England Biolabs, Frankfurt, Germany) at 95°C for 5 minutes and slowly cooled to room temperature before adding 10 units of DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs) and incubating at 20°C for 15 minutes. dsDNA was then purified using phenol-chloroform-isoamyl precipitation and the size and purity was controlled using agarose gel electrophoresis. ..

    Polymerase Chain Reaction:

    Article Title: Gene therapy via CRISPR/Cas9-mediated Cxcr4 disease allele inactivation reverses leukopenia in WHIM mice
    Article Snippet: .. The PCR products were diluted 1:4 in 1x NEBuffer 2 and hybridized slowly in a thermal cycler. .. Twenty μl of hybridized fragments were then digested with 1.25 U of T7 endonuclease 1 (New England Biolabs) for 15 minutes at 37°C.

    Plasmid Preparation:

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: .. The lentiviral plasmid lentiCRISPRv2 (pLentiCRISPRv2), a gift from Feng Zhang (puromycin selection; Addgene plasmid # 52961; http://n2t.net/addgene:52961 ), or for targeting p53 (neomycin selection, lentiCRISPRv2-neo; Addgene; 98292), was modified by inserting the following sgRNA sequences at the BsmB1 site, with inserts prepared by annealing two primers, each containing a flanking sequence recognizing the BsmB1-digested lentiCRISPRv2 plasmid (sgRNA sequences in uppercase, Bsmb1-annealing sequences in lowercase): TSC1 5′-caccgGAGGAGCCGCCTGTTCCGGA-3’ 5′-aaacTCCGGAACAGGCGGCTCCTCc-3’ TSC2 5′-caccgGGAGAAGTCGCTCCACGCGG-3’ 5′-aaacCCGCGTGGAGCGACTTCTCCc-3’ TBC1D7 5′-caccgGCATGGGACTCGTGGTGTGG-3’ 5′-aaacCCACACCACGAGTCCCATGCc-3’ TP53 5′-caccgGAAGGGACAGAAGATGACAG-3’ 5′-aaacCTGTCATCTTCTGTCCCTTCc-3’ NPRL2 5′-caccgGGGCATCACACACGAAGCCC-3’ 5′-aaacGGGCTTCGTGTGTGATGCCCc-3’ ULK1 5′-caccgGCAGCGTCTGAGACTTGGCG-3’ 5′-aaacCGCCAAGTCTCAGACGCTGCc-3’ BECN1 5′-caccgGAAACCAGGAGAGACCCAGG-3’ 5′-aaacCCTGGGTCTCTCCTGGTTTCc-3’ ATG7 5′-caccgATAGCTGGGCAGCAACGGGC-3’ 5′-aaacGCCCGTTGCTGCCCAGCTATc-3’ TFEB 5′- caccgGCAGCAGTCGCAGCATCAGA-3’ 5′- aaacTCTGATGCTGCGACTGCTGCc-3’ To anneal primers (Integrated DNA Technologies), 100 μM of each were incubated in 1X NEBuffer 2 (New England Biolabs [NEB]; B7002S) at 94°C for 2 min, followed by 65°C for 10 min and 4°C for 1 min. .. The annealed primers (diluted 1:100) were inserted into pLentiCRISPRv2 digested by the BsmB1 enzyme (NEB; R0739S).

    Selection:

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: .. The lentiviral plasmid lentiCRISPRv2 (pLentiCRISPRv2), a gift from Feng Zhang (puromycin selection; Addgene plasmid # 52961; http://n2t.net/addgene:52961 ), or for targeting p53 (neomycin selection, lentiCRISPRv2-neo; Addgene; 98292), was modified by inserting the following sgRNA sequences at the BsmB1 site, with inserts prepared by annealing two primers, each containing a flanking sequence recognizing the BsmB1-digested lentiCRISPRv2 plasmid (sgRNA sequences in uppercase, Bsmb1-annealing sequences in lowercase): TSC1 5′-caccgGAGGAGCCGCCTGTTCCGGA-3’ 5′-aaacTCCGGAACAGGCGGCTCCTCc-3’ TSC2 5′-caccgGGAGAAGTCGCTCCACGCGG-3’ 5′-aaacCCGCGTGGAGCGACTTCTCCc-3’ TBC1D7 5′-caccgGCATGGGACTCGTGGTGTGG-3’ 5′-aaacCCACACCACGAGTCCCATGCc-3’ TP53 5′-caccgGAAGGGACAGAAGATGACAG-3’ 5′-aaacCTGTCATCTTCTGTCCCTTCc-3’ NPRL2 5′-caccgGGGCATCACACACGAAGCCC-3’ 5′-aaacGGGCTTCGTGTGTGATGCCCc-3’ ULK1 5′-caccgGCAGCGTCTGAGACTTGGCG-3’ 5′-aaacCGCCAAGTCTCAGACGCTGCc-3’ BECN1 5′-caccgGAAACCAGGAGAGACCCAGG-3’ 5′-aaacCCTGGGTCTCTCCTGGTTTCc-3’ ATG7 5′-caccgATAGCTGGGCAGCAACGGGC-3’ 5′-aaacGCCCGTTGCTGCCCAGCTATc-3’ TFEB 5′- caccgGCAGCAGTCGCAGCATCAGA-3’ 5′- aaacTCTGATGCTGCGACTGCTGCc-3’ To anneal primers (Integrated DNA Technologies), 100 μM of each were incubated in 1X NEBuffer 2 (New England Biolabs [NEB]; B7002S) at 94°C for 2 min, followed by 65°C for 10 min and 4°C for 1 min. .. The annealed primers (diluted 1:100) were inserted into pLentiCRISPRv2 digested by the BsmB1 enzyme (NEB; R0739S).

    Modification:

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: .. The lentiviral plasmid lentiCRISPRv2 (pLentiCRISPRv2), a gift from Feng Zhang (puromycin selection; Addgene plasmid # 52961; http://n2t.net/addgene:52961 ), or for targeting p53 (neomycin selection, lentiCRISPRv2-neo; Addgene; 98292), was modified by inserting the following sgRNA sequences at the BsmB1 site, with inserts prepared by annealing two primers, each containing a flanking sequence recognizing the BsmB1-digested lentiCRISPRv2 plasmid (sgRNA sequences in uppercase, Bsmb1-annealing sequences in lowercase): TSC1 5′-caccgGAGGAGCCGCCTGTTCCGGA-3’ 5′-aaacTCCGGAACAGGCGGCTCCTCc-3’ TSC2 5′-caccgGGAGAAGTCGCTCCACGCGG-3’ 5′-aaacCCGCGTGGAGCGACTTCTCCc-3’ TBC1D7 5′-caccgGCATGGGACTCGTGGTGTGG-3’ 5′-aaacCCACACCACGAGTCCCATGCc-3’ TP53 5′-caccgGAAGGGACAGAAGATGACAG-3’ 5′-aaacCTGTCATCTTCTGTCCCTTCc-3’ NPRL2 5′-caccgGGGCATCACACACGAAGCCC-3’ 5′-aaacGGGCTTCGTGTGTGATGCCCc-3’ ULK1 5′-caccgGCAGCGTCTGAGACTTGGCG-3’ 5′-aaacCGCCAAGTCTCAGACGCTGCc-3’ BECN1 5′-caccgGAAACCAGGAGAGACCCAGG-3’ 5′-aaacCCTGGGTCTCTCCTGGTTTCc-3’ ATG7 5′-caccgATAGCTGGGCAGCAACGGGC-3’ 5′-aaacGCCCGTTGCTGCCCAGCTATc-3’ TFEB 5′- caccgGCAGCAGTCGCAGCATCAGA-3’ 5′- aaacTCTGATGCTGCGACTGCTGCc-3’ To anneal primers (Integrated DNA Technologies), 100 μM of each were incubated in 1X NEBuffer 2 (New England Biolabs [NEB]; B7002S) at 94°C for 2 min, followed by 65°C for 10 min and 4°C for 1 min. .. The annealed primers (diluted 1:100) were inserted into pLentiCRISPRv2 digested by the BsmB1 enzyme (NEB; R0739S).

    Sequencing:

    Article Title: Growth factor-independent mTORC1 signaling promotes primary cilia length via suppression of autophagy
    Article Snippet: .. The lentiviral plasmid lentiCRISPRv2 (pLentiCRISPRv2), a gift from Feng Zhang (puromycin selection; Addgene plasmid # 52961; http://n2t.net/addgene:52961 ), or for targeting p53 (neomycin selection, lentiCRISPRv2-neo; Addgene; 98292), was modified by inserting the following sgRNA sequences at the BsmB1 site, with inserts prepared by annealing two primers, each containing a flanking sequence recognizing the BsmB1-digested lentiCRISPRv2 plasmid (sgRNA sequences in uppercase, Bsmb1-annealing sequences in lowercase): TSC1 5′-caccgGAGGAGCCGCCTGTTCCGGA-3’ 5′-aaacTCCGGAACAGGCGGCTCCTCc-3’ TSC2 5′-caccgGGAGAAGTCGCTCCACGCGG-3’ 5′-aaacCCGCGTGGAGCGACTTCTCCc-3’ TBC1D7 5′-caccgGCATGGGACTCGTGGTGTGG-3’ 5′-aaacCCACACCACGAGTCCCATGCc-3’ TP53 5′-caccgGAAGGGACAGAAGATGACAG-3’ 5′-aaacCTGTCATCTTCTGTCCCTTCc-3’ NPRL2 5′-caccgGGGCATCACACACGAAGCCC-3’ 5′-aaacGGGCTTCGTGTGTGATGCCCc-3’ ULK1 5′-caccgGCAGCGTCTGAGACTTGGCG-3’ 5′-aaacCGCCAAGTCTCAGACGCTGCc-3’ BECN1 5′-caccgGAAACCAGGAGAGACCCAGG-3’ 5′-aaacCCTGGGTCTCTCCTGGTTTCc-3’ ATG7 5′-caccgATAGCTGGGCAGCAACGGGC-3’ 5′-aaacGCCCGTTGCTGCCCAGCTATc-3’ TFEB 5′- caccgGCAGCAGTCGCAGCATCAGA-3’ 5′- aaacTCTGATGCTGCGACTGCTGCc-3’ To anneal primers (Integrated DNA Technologies), 100 μM of each were incubated in 1X NEBuffer 2 (New England Biolabs [NEB]; B7002S) at 94°C for 2 min, followed by 65°C for 10 min and 4°C for 1 min. .. The annealed primers (diluted 1:100) were inserted into pLentiCRISPRv2 digested by the BsmB1 enzyme (NEB; R0739S).



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