substrate  (New England Biolabs)


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    New England Biolabs substrate
    Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dna substrate  (New England Biolabs)


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    New England Biolabs dna substrate
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Dna Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Engineering of a high-fidelity Cas12a nuclease variant capable of allele-specific editing"

    Article Title: Engineering of a high-fidelity Cas12a nuclease variant capable of allele-specific editing

    Journal: PLOS Biology

    doi: 10.1371/journal.pbio.3002680

    ( A ) DNA cleavage of Mb4Cas12a at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Figure Legend Snippet: ( A ) DNA cleavage of Mb4Cas12a at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.

    Techniques Used: Incubation, Sequencing

    plasmid substrate  (New England Biolabs)


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    New England Biolabs plasmid substrate
    Plasmid Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    snap substrate dye solution  (New England Biolabs)


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    New England Biolabs snap substrate dye solution
    Snap Substrate Dye Solution, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    vf2468 substrates  (New England Biolabs)


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    New England Biolabs vf2468 substrates
    Vf2468 Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ccr5 224 substrates  (New England Biolabs)


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    New England Biolabs ccr5 224 substrates
    Ccr5 224 Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dna substrates  (New England Biolabs)


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    New England Biolabs dna substrates
    Dna Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tmr star substrate  (New England Biolabs)


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    New England Biolabs tmr star substrate
    A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the <t>SNAP</t> <t>substrate</t> <t>TMR-Star</t> and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).
    Tmr Star Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "The impact of YabG mutations on C. difficile spore germination and processing of spore substrates"

    Article Title: The impact of YabG mutations on C. difficile spore germination and processing of spore substrates

    Journal: bioRxiv

    doi: 10.1101/2024.06.10.598338

    A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the SNAP substrate TMR-Star and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).
    Figure Legend Snippet: A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the SNAP substrate TMR-Star and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).

    Techniques Used: Staining, Fluorescence, Microscopy

    substrates  (New England Biolabs)


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    New England Biolabs substrates
    Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide <t>substrates</t> tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .
    Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes"

    Article Title: Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkae353

    Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide substrates tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .
    Figure Legend Snippet: Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide substrates tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .

    Techniques Used: Staining, Generated, Ligation

    snap surface alexa fluor 647 substrate  (New England Biolabs)


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    New England Biolabs snap surface alexa fluor 647 substrate
    (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of <t>AF647-MAVS-CARD</t> (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.
    Snap Surface Alexa Fluor 647 Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Observation of Higher-Order Assemblies Controlled by Protein One-dimensional Movement"

    Article Title: Observation of Higher-Order Assemblies Controlled by Protein One-dimensional Movement

    Journal: bioRxiv

    doi: 10.1101/2024.06.06.597732

    (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.
    Figure Legend Snippet: (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.

    Techniques Used: Functional Assay

    (A) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of images. (B) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of images.
    Figure Legend Snippet: (A) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of images. (B) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of images.

    Techniques Used:

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    New England Biolabs substrate
    Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dna substrate
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Dna Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs plasmid substrate
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Plasmid Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs snap substrate dye solution
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Snap Substrate Dye Solution, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs vf2468 substrates
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
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    86
    New England Biolabs ccr5 224 substrates
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Ccr5 224 Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs dna substrates
    ( A ) <t>DNA</t> cleavage <t>of</t> <t>Mb4Cas12a</t> at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.
    Dna Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs tmr star substrate
    A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the <t>SNAP</t> <t>substrate</t> <t>TMR-Star</t> and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).
    Tmr Star Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs substrates
    Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide <t>substrates</t> tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .
    Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs snap surface alexa fluor 647 substrate
    (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of <t>AF647-MAVS-CARD</t> (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.
    Snap Surface Alexa Fluor 647 Substrate, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ( A ) DNA cleavage of Mb4Cas12a at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.

    Journal: PLOS Biology

    Article Title: Engineering of a high-fidelity Cas12a nuclease variant capable of allele-specific editing

    doi: 10.1371/journal.pbio.3002680

    Figure Lengend Snippet: ( A ) DNA cleavage of Mb4Cas12a at 37°C for 8 hours. The PAMs are shown on the top; the cleaved bands are indicated by green asterisks; the cleavage efficiency is shown below. ( B ) DNA cleavage of Mb4Cas12a at different temperatures for 1 hour. Temperatures are shown on the top; the cleavage efficiency is shown below. Ctr, control, the DNA fragment without incubation with Mb4Cas12a and crRNA. ( C ) Sanger sequencing traces from Mb4Cas12a-cleaved target show staggered 5-nt 5’ overhang. NTS, nontarget site; TS, target site. The cleaved target sites are indicated by red triangles.

    Article Snippet: Approximately 200 ng DNA substrate was incubated with 250 nM Mb4Cas12a protein, 500 ng crRNA, and 0.3 μL RNase inhibitor in 1x NEB Buffer 3.1 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl 2 , and 100 μg/mL BSA).

    Techniques: Incubation, Sequencing

    A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the SNAP substrate TMR-Star and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).

    Journal: bioRxiv

    Article Title: The impact of YabG mutations on C. difficile spore germination and processing of spore substrates

    doi: 10.1101/2024.06.10.598338

    Figure Lengend Snippet: A) C. difficile sporulating cells carrying fusions of the WT yabG promoter or alleles with the G-8A or C-41T mutations fused to the SNAP Cd reporter in an otherwise WT background (630Δ erm ) were collected after 20 hours of growth on 70:30 agar plates. The cells were stained with the SNAP substrate TMR-Star and examined by phase contrast (top panels) and fluorescence microscopy (middle panel, SNAP Cd signal; bottom panels, autofluorescence). The black arrowheads show cells at early stages of sporulation, with no visible signs of a forespore; the grey arrowheads show sporangia of phase dark forespores and the white arrowheads indicate sporangia of phase grey or phase bright forespores. Scale bar, 1 μm. B) Intensity of the fluorescence signal per cell for the P yabG - SNAP Cd fusions described in A) in cells at early stages of sporulation or in sporangia of phase dark or phase grey/phase bright forespores. Fluorescence intensity is shown in arbitrary units (AU). The data from three independent experiments was represented using SuperPlots, with each color corresponding to a replicate ( Lord et al ., 2020 ). Statistical analysis was carried out using the ordinary one-way ANOVA and Tukey’s test. Asterisks correspond to p-values of p<0.05 (*) or p<0.01 (**).

    Article Snippet: For SNAP labelling, cells were withdrawn from sporulating cultures after 20 hours of growth on 70:30 medium ( Putnam et al ., 2013 ); the samples were mixed for 30 min in the dark with the TMR-Star substrate (New England Biolabs) at a final concentration of 250 nM ( Pereira et al ., 2013 ).

    Techniques: Staining, Fluorescence, Microscopy

    Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide substrates tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .

    Journal: Nucleic Acids Research

    Article Title: Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes

    doi: 10.1093/nar/gkae353

    Figure Lengend Snippet: Cleavage of UDP-sugars, sugar-capped dinucleotides and sugar-capped RNA by the Nudix hydrolases hNudt5 and NudF. ( A ) The Nudix enzyme hNudt5 was found to decap UDP-GlcNAc- and UDP-GlcNAz-RNA, leading to 5′-monophosphate-RNA by hydrolyzing the pyrophosphate bridge of the sugar cap. ( B ) Mononucleotide and dinucleotide substrates tested and the ability of hNudt5 and NudF to hydrolyze them. ( C ) Conversion of UDP-GlcNAc, GlcNAcppUpG 4 and GlcNAzppUpG 5 by hNudt5 ( n = 3, data points show mean ± S.D.). Hydrolysis was analyzed by RP-HPLC. ( D ) 10% PAGE analysis of a PABLO assay conducted with hNudt5-treated sugar-capped 11mer RNA (SYBR Gold stain). If the enzyme hydrolyzes the cap, generated 5′-monophosphate-RNA can be ligated to a 39mer DNA leading to a chimeric 50mer. A 50-nucleotide long ligation product can only be detected for hNudt5-treated GlcNAc-11mer and GlcNAz-11mer RNA as well as for 5′-monophosphate-11mer RNA positive controls. The experiment was repeated in triplicate using GlcNAc-11mer RNA and GlcNAz-11mer RNA .

    Article Snippet: Filtrates were analyzed by RP-HPLC and ESI-MS. For NudC reactions, substrates (0.625 mM), DTT (5 mM), NEBuffer r3.1 (1×) and NudC (0.5 μM) (NEB) in a total volume of 20 μl were incubated for 4 h at 37°C.

    Techniques: Staining, Generated, Ligation

    (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.

    Journal: bioRxiv

    Article Title: Observation of Higher-Order Assemblies Controlled by Protein One-dimensional Movement

    doi: 10.1101/2024.06.06.597732

    Figure Lengend Snippet: (A) A schematic illustration of the MAVS-CARD recruitment experiment. (B) The frequency of MAVS-CARD foci recruited by MDA5 under various conditions (mean ± s.d.; n = number of dsRNA molecules). (C) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of kymographs. (D) A schematic illustration showing the CARDs from mobile MDA5 molecules are unable to form tetramers, whereas the CARDs from immobile MDA5-LGP2 complexes can assemble into functional tetramers. (E) The frequency of MAVS-CARD foci recruited by MDA5 or MDA5ΔN under various conditions (mean ± s.d.; n = number of dsRNA molecules). (F) Representative kymographs showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of kymographs.

    Article Snippet: Cell pellets were freeze-thawed three times, sonicated twice, and centrifuged at 50,000 × g for 1 h. The supernatants were then loaded onto a Ni-NTA column, washed with Buffer A, Buffer D (25 mM Tris-HCl pH 7.5, 500 mM NaCl, 20 % glycerol and 60 mM imidazole), and eluted with Buffer B. Fractions containing MAVS-CARD were pooled, and incubated with SNAP-Surface Alexa Fluor 647 substrate (New England Biolabs) in 1 mM DTT at 4 °C for overnight.

    Techniques: Functional Assay

    (A) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of images. (B) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of images.

    Journal: bioRxiv

    Article Title: Observation of Higher-Order Assemblies Controlled by Protein One-dimensional Movement

    doi: 10.1101/2024.06.06.597732

    Figure Lengend Snippet: (A) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (20 nM) under various conditions. The absence or presence of LGP2/LGP2(E116A) (20 nM) is indicated above each set of images. (B) Representative images showing the recruitments of AF647-MAVS-CARD (100 nM) by Cy3-MDA5 or Cy3-MDA5ΔN (100 nM) under various conditions. The presence of ATP or ADPCP is indicated above each set of images.

    Article Snippet: Cell pellets were freeze-thawed three times, sonicated twice, and centrifuged at 50,000 × g for 1 h. The supernatants were then loaded onto a Ni-NTA column, washed with Buffer A, Buffer D (25 mM Tris-HCl pH 7.5, 500 mM NaCl, 20 % glycerol and 60 mM imidazole), and eluted with Buffer B. Fractions containing MAVS-CARD were pooled, and incubated with SNAP-Surface Alexa Fluor 647 substrate (New England Biolabs) in 1 mM DTT at 4 °C for overnight.

    Techniques: