inorganic e coli pyrophosphatase  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic e coli pyrophosphatase
    Inorganic E Coli Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic e coli pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic e coli pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    inorganic e coli pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic e coli pyrophosphatase
    Inorganic E Coli Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic e coli pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic e coli pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    inorganic pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic pyrophosphatase
    Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    e coli inorganic ppase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs e coli inorganic ppase
    E Coli Inorganic Ppase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli inorganic ppase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e coli inorganic ppase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    inorganic pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic pyrophosphatase
    Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    inorganic pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic pyrophosphatase
    Master Mix
    Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    1) Product Images from "CRISPR-Based Multiplex Detection of Human Papillomaviruses for One-Pot Point-of-Care Diagnostics"

    Article Title: CRISPR-Based Multiplex Detection of Human Papillomaviruses for One-Pot Point-of-Care Diagnostics

    Journal: ACS Synthetic Biology

    doi: 10.1021/acssynbio.3c00655

    Master Mix
    Figure Legend Snippet: Master Mix

    Techniques Used: Concentration Assay

    e coli inorganic pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs e coli inorganic pyrophosphatase
    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the <t>E.</t> <t>coli</t> 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    E Coli Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e coli inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    1) Product Images from "Minimization of the E. coli ribosome, aided and optimized by community science"

    Article Title: Minimization of the E. coli ribosome, aided and optimized by community science

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkad1254

    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the E. coli 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    Figure Legend Snippet: Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the E. coli 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.

    Techniques Used: Cryo-EM Sample Prep, Residue, Construct

    WT mini-PTC recapitulates several structural elements of the ribosomal PTC. ( A ) Structure of 1M7 alongside the SHAPE reactivity of WT mini-PTC plotted as a heatmap on the predicted secondary structure of the E. coli 50S ribosomal subunit. Nucleotide positions were indicated using conventional E. coli 23S rRNA numbering. ( B ) Heatmap showing the difference between predicted and experimental SHAPE reactivity. SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-pairing residues and loop regions described in Results were marked with a black line and a gray line, respectively, over the heatmap.
    Figure Legend Snippet: WT mini-PTC recapitulates several structural elements of the ribosomal PTC. ( A ) Structure of 1M7 alongside the SHAPE reactivity of WT mini-PTC plotted as a heatmap on the predicted secondary structure of the E. coli 50S ribosomal subunit. Nucleotide positions were indicated using conventional E. coli 23S rRNA numbering. ( B ) Heatmap showing the difference between predicted and experimental SHAPE reactivity. SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-pairing residues and loop regions described in Results were marked with a black line and a gray line, respectively, over the heatmap.

    Techniques Used:

    Eterna challenge allows selection of mini-PTC designs 1.1–1.7 that show diverse secondary structures. ( A ) Process in Eterna challenges for designing RNA molecules. Eterna players design new RNA constructs by making mutations within the provided sequence. Hundreds of designs were submitted by players at this stage. Arbitrary sequences are shown here for simplicity. Selected number of designs were evaluated by players voting and synthesized. Chemical probing methods were used to analyze the secondary structure between each design. ( B ) A bar graph summarizes the number of mutations of seven Eterna Mini-PTC. ( C ) A bar graph shows the noise-adjusted Pearson correlation between predicted SHAPE reactivity profile and experimental reactivity profile of WT mini-PTC and seven Eterna mini-PTC designs. ( D ) Heatmap showing the predicted and experimental SHAPE reactivity of the WT mini-PTC and seven Eterna mini-PTC designs from the first challenge (mini-PTC 1.1–1.7). SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-paired residues and loops described in Results were marked with a black or gray line, respectively, over the heatmap. Residues were identified on the bottom using WT E. coli 23S rRNA numbering. Mutations in mini-PTC 1.1–1.7 were highlighted using a black square box. Residues in mini-PTC 1.1 that exhibited folding patterns closer to the predicted pattern were indicated using a blue box, whereas residues of mini-PTC 1.1 that exhibited differences from the prediction were indicated using a green box. Residues in H80 (G2246-C2248 and G2256-C2258), A2453, U2068 and U2609 were indicated using asterisks, triangle, circle, and diamond, respectively.
    Figure Legend Snippet: Eterna challenge allows selection of mini-PTC designs 1.1–1.7 that show diverse secondary structures. ( A ) Process in Eterna challenges for designing RNA molecules. Eterna players design new RNA constructs by making mutations within the provided sequence. Hundreds of designs were submitted by players at this stage. Arbitrary sequences are shown here for simplicity. Selected number of designs were evaluated by players voting and synthesized. Chemical probing methods were used to analyze the secondary structure between each design. ( B ) A bar graph summarizes the number of mutations of seven Eterna Mini-PTC. ( C ) A bar graph shows the noise-adjusted Pearson correlation between predicted SHAPE reactivity profile and experimental reactivity profile of WT mini-PTC and seven Eterna mini-PTC designs. ( D ) Heatmap showing the predicted and experimental SHAPE reactivity of the WT mini-PTC and seven Eterna mini-PTC designs from the first challenge (mini-PTC 1.1–1.7). SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-paired residues and loops described in Results were marked with a black or gray line, respectively, over the heatmap. Residues were identified on the bottom using WT E. coli 23S rRNA numbering. Mutations in mini-PTC 1.1–1.7 were highlighted using a black square box. Residues in mini-PTC 1.1 that exhibited folding patterns closer to the predicted pattern were indicated using a blue box, whereas residues of mini-PTC 1.1 that exhibited differences from the prediction were indicated using a green box. Residues in H80 (G2246-C2248 and G2256-C2258), A2453, U2068 and U2609 were indicated using asterisks, triangle, circle, and diamond, respectively.

    Techniques Used: Selection, Construct, Sequencing, Synthesized

    Mini-PTC 1.1 inhibits the peptidyl transferase activity as evaluated by the fragment reaction. ( A ) Schematic representation of fragment reaction, followed by RNase A/LC-MS assay. CCA-pcb and C-pmn were used as a P-site and an A-site analog, respectively. The reaction was incubated with varied time (2 or 24 h) and temperature (–20, 4 or 50ºC). The product from this reaction (C-pmn-pcb) was subsequently digested by RNase A that cleaves off terminal puromycin-pcb (pmn-pcb), which can be quantified by LC–MS analysis. Leu-enkephalin was used as an internal standard. Reactions were run with water (mock), 20 μM mini-PTC 1.1, and 0.1 μM E. coli 50S ribosomal subunit at –20, 4 or 50ºC for 2 h ( B ) or 24 h ( C ). Reactions were run as triplicates ( n = 3). The yield of the fragment reaction between water (mock), mini-PTC 1.1 and E. coli 50S ribosomal subunit was compared by using two-way ANOVA with Tukey's multiple comparison test. **** P ≤ 0.0001, *** P ≤ 0.002, ** P ≤ 0.021, * P ≤ 0.032, ns ≤ 0.1234.
    Figure Legend Snippet: Mini-PTC 1.1 inhibits the peptidyl transferase activity as evaluated by the fragment reaction. ( A ) Schematic representation of fragment reaction, followed by RNase A/LC-MS assay. CCA-pcb and C-pmn were used as a P-site and an A-site analog, respectively. The reaction was incubated with varied time (2 or 24 h) and temperature (–20, 4 or 50ºC). The product from this reaction (C-pmn-pcb) was subsequently digested by RNase A that cleaves off terminal puromycin-pcb (pmn-pcb), which can be quantified by LC–MS analysis. Leu-enkephalin was used as an internal standard. Reactions were run with water (mock), 20 μM mini-PTC 1.1, and 0.1 μM E. coli 50S ribosomal subunit at –20, 4 or 50ºC for 2 h ( B ) or 24 h ( C ). Reactions were run as triplicates ( n = 3). The yield of the fragment reaction between water (mock), mini-PTC 1.1 and E. coli 50S ribosomal subunit was compared by using two-way ANOVA with Tukey's multiple comparison test. **** P ≤ 0.0001, *** P ≤ 0.002, ** P ≤ 0.021, * P ≤ 0.032, ns ≤ 0.1234.

    Techniques Used: Activity Assay, Liquid Chromatography with Mass Spectroscopy, Incubation, Comparison

    pyrophosphates inorganic  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs pyrophosphates inorganic
    Pyrophosphates Inorganic, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pyrophosphates inorganic/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pyrophosphates inorganic - by Bioz Stars, 2024-05
    95/100 stars

    Images

    inorganic ipp  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs inorganic ipp
    Inorganic Ipp, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic ipp/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic ipp - by Bioz Stars, 2024-05
    95/100 stars

    Images

    ipp  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs ipp
    Ipp, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ipp/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ipp - by Bioz Stars, 2024-05
    95/100 stars

    Images

    e coli inorganic pyrophosphatase  (New England Biolabs)


    Bioz Verified Symbol New England Biolabs is a verified supplier
    Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    New England Biolabs e coli inorganic pyrophosphatase
    E Coli Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e coli inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars

    Images

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95
    New England Biolabs inorganic e coli pyrophosphatase
    Inorganic E Coli Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic e coli pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic e coli pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs inorganic pyrophosphatase
    Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs e coli inorganic ppase
    E Coli Inorganic Ppase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli inorganic ppase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e coli inorganic ppase - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs e coli inorganic pyrophosphatase
    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the <t>E.</t> <t>coli</t> 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    E Coli Inorganic Pyrophosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e coli inorganic pyrophosphatase/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e coli inorganic pyrophosphatase - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs pyrophosphates inorganic
    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the <t>E.</t> <t>coli</t> 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    Pyrophosphates Inorganic, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pyrophosphates inorganic/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pyrophosphates inorganic - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs inorganic ipp
    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the <t>E.</t> <t>coli</t> 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    Inorganic Ipp, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/inorganic ipp/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    inorganic ipp - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    95
    New England Biolabs ipp
    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the <t>E.</t> <t>coli</t> 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.
    Ipp, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ipp/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ipp - by Bioz Stars, 2024-05
    95/100 stars
      Buy from Supplier

    Image Search Results


    Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the E. coli 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.

    Journal: Nucleic Acids Research

    Article Title: Minimization of the E. coli ribosome, aided and optimized by community science

    doi: 10.1093/nar/gkad1254

    Figure Lengend Snippet: Design of a first generation mini-PTC (WT mini-PTC). ( A ) Cartoon illustrating the cryo-EM structure of the E. coli 50S ribosomal subunit (PDB: 7K00) visualized using Chimera X 1.5, viewed from the subunit interface . The 23S rRNA and 5S rRNA are shown as blue ribbons, and ribosomal proteins are shown in gray. The PTC is shown in green, purple, and pink to highlight three noncontiguous segments of the PTC, respectively. ( B ) Secondary structure of domain V of the E. coli 23S rRNA, showing the central loop and nearby helices and stems. Residue numbers and helices are provided in gray and black, respectively. Bases shown in green, purple, and pink correspond to the PTC region shown in (C). P-loop and A-loop shown in (C) are highlighted in red and yellow, respectively. Highly conserved PTC residues mentioned in the text are highlighted within the black open circles. ( C ) Ribbon structure of the PTC viewed from the same orientation as in (A). ( D ) Secondary structure diagram of the first-generation mini-PTC design. Additional E. coli 23S RNA residues that were extended to the construct are shown in black. Arbitrary A4 tetraloop is highlighted within the black open circles. Residue numbers and helices are provided in gray and black, respectively.

    Article Snippet: Transcription reactions (200 μl) contained the following components: 50 mM Tris–HCl (pH 8.1), 0.01% Triton X-100, 100 mM DTT, 2 mM spermidine, 10 mM ATP, 10 mM CTP, 10 mM GTP, 10 mM UTP, 50 mM MgCl 2 , 10 ng μl −1 DNA template, 1 unit ml −1 E. coli inorganic pyrophosphatase (New England Biolabs) and 0.2 mg ml −1 in-house T7 RNA polymerase.

    Techniques: Cryo-EM Sample Prep, Residue, Construct

    WT mini-PTC recapitulates several structural elements of the ribosomal PTC. ( A ) Structure of 1M7 alongside the SHAPE reactivity of WT mini-PTC plotted as a heatmap on the predicted secondary structure of the E. coli 50S ribosomal subunit. Nucleotide positions were indicated using conventional E. coli 23S rRNA numbering. ( B ) Heatmap showing the difference between predicted and experimental SHAPE reactivity. SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-pairing residues and loop regions described in Results were marked with a black line and a gray line, respectively, over the heatmap.

    Journal: Nucleic Acids Research

    Article Title: Minimization of the E. coli ribosome, aided and optimized by community science

    doi: 10.1093/nar/gkad1254

    Figure Lengend Snippet: WT mini-PTC recapitulates several structural elements of the ribosomal PTC. ( A ) Structure of 1M7 alongside the SHAPE reactivity of WT mini-PTC plotted as a heatmap on the predicted secondary structure of the E. coli 50S ribosomal subunit. Nucleotide positions were indicated using conventional E. coli 23S rRNA numbering. ( B ) Heatmap showing the difference between predicted and experimental SHAPE reactivity. SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-pairing residues and loop regions described in Results were marked with a black line and a gray line, respectively, over the heatmap.

    Article Snippet: Transcription reactions (200 μl) contained the following components: 50 mM Tris–HCl (pH 8.1), 0.01% Triton X-100, 100 mM DTT, 2 mM spermidine, 10 mM ATP, 10 mM CTP, 10 mM GTP, 10 mM UTP, 50 mM MgCl 2 , 10 ng μl −1 DNA template, 1 unit ml −1 E. coli inorganic pyrophosphatase (New England Biolabs) and 0.2 mg ml −1 in-house T7 RNA polymerase.

    Techniques:

    Eterna challenge allows selection of mini-PTC designs 1.1–1.7 that show diverse secondary structures. ( A ) Process in Eterna challenges for designing RNA molecules. Eterna players design new RNA constructs by making mutations within the provided sequence. Hundreds of designs were submitted by players at this stage. Arbitrary sequences are shown here for simplicity. Selected number of designs were evaluated by players voting and synthesized. Chemical probing methods were used to analyze the secondary structure between each design. ( B ) A bar graph summarizes the number of mutations of seven Eterna Mini-PTC. ( C ) A bar graph shows the noise-adjusted Pearson correlation between predicted SHAPE reactivity profile and experimental reactivity profile of WT mini-PTC and seven Eterna mini-PTC designs. ( D ) Heatmap showing the predicted and experimental SHAPE reactivity of the WT mini-PTC and seven Eterna mini-PTC designs from the first challenge (mini-PTC 1.1–1.7). SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-paired residues and loops described in Results were marked with a black or gray line, respectively, over the heatmap. Residues were identified on the bottom using WT E. coli 23S rRNA numbering. Mutations in mini-PTC 1.1–1.7 were highlighted using a black square box. Residues in mini-PTC 1.1 that exhibited folding patterns closer to the predicted pattern were indicated using a blue box, whereas residues of mini-PTC 1.1 that exhibited differences from the prediction were indicated using a green box. Residues in H80 (G2246-C2248 and G2256-C2258), A2453, U2068 and U2609 were indicated using asterisks, triangle, circle, and diamond, respectively.

    Journal: Nucleic Acids Research

    Article Title: Minimization of the E. coli ribosome, aided and optimized by community science

    doi: 10.1093/nar/gkad1254

    Figure Lengend Snippet: Eterna challenge allows selection of mini-PTC designs 1.1–1.7 that show diverse secondary structures. ( A ) Process in Eterna challenges for designing RNA molecules. Eterna players design new RNA constructs by making mutations within the provided sequence. Hundreds of designs were submitted by players at this stage. Arbitrary sequences are shown here for simplicity. Selected number of designs were evaluated by players voting and synthesized. Chemical probing methods were used to analyze the secondary structure between each design. ( B ) A bar graph summarizes the number of mutations of seven Eterna Mini-PTC. ( C ) A bar graph shows the noise-adjusted Pearson correlation between predicted SHAPE reactivity profile and experimental reactivity profile of WT mini-PTC and seven Eterna mini-PTC designs. ( D ) Heatmap showing the predicted and experimental SHAPE reactivity of the WT mini-PTC and seven Eterna mini-PTC designs from the first challenge (mini-PTC 1.1–1.7). SHAPE reactivity was plotted on a red-yellow-white spectrum where red represents high SHAPE reactivity (>0.5 predicted; >1.5 experimental) and white represents low SHAPE reactivity (<0.25 predicted; <0.5 experimental). Variations between experimental and predicted SHAPE reactivity were attributed to higher background in the experimental data. Base-paired residues and loops described in Results were marked with a black or gray line, respectively, over the heatmap. Residues were identified on the bottom using WT E. coli 23S rRNA numbering. Mutations in mini-PTC 1.1–1.7 were highlighted using a black square box. Residues in mini-PTC 1.1 that exhibited folding patterns closer to the predicted pattern were indicated using a blue box, whereas residues of mini-PTC 1.1 that exhibited differences from the prediction were indicated using a green box. Residues in H80 (G2246-C2248 and G2256-C2258), A2453, U2068 and U2609 were indicated using asterisks, triangle, circle, and diamond, respectively.

    Article Snippet: Transcription reactions (200 μl) contained the following components: 50 mM Tris–HCl (pH 8.1), 0.01% Triton X-100, 100 mM DTT, 2 mM spermidine, 10 mM ATP, 10 mM CTP, 10 mM GTP, 10 mM UTP, 50 mM MgCl 2 , 10 ng μl −1 DNA template, 1 unit ml −1 E. coli inorganic pyrophosphatase (New England Biolabs) and 0.2 mg ml −1 in-house T7 RNA polymerase.

    Techniques: Selection, Construct, Sequencing, Synthesized

    Mini-PTC 1.1 inhibits the peptidyl transferase activity as evaluated by the fragment reaction. ( A ) Schematic representation of fragment reaction, followed by RNase A/LC-MS assay. CCA-pcb and C-pmn were used as a P-site and an A-site analog, respectively. The reaction was incubated with varied time (2 or 24 h) and temperature (–20, 4 or 50ºC). The product from this reaction (C-pmn-pcb) was subsequently digested by RNase A that cleaves off terminal puromycin-pcb (pmn-pcb), which can be quantified by LC–MS analysis. Leu-enkephalin was used as an internal standard. Reactions were run with water (mock), 20 μM mini-PTC 1.1, and 0.1 μM E. coli 50S ribosomal subunit at –20, 4 or 50ºC for 2 h ( B ) or 24 h ( C ). Reactions were run as triplicates ( n = 3). The yield of the fragment reaction between water (mock), mini-PTC 1.1 and E. coli 50S ribosomal subunit was compared by using two-way ANOVA with Tukey's multiple comparison test. **** P ≤ 0.0001, *** P ≤ 0.002, ** P ≤ 0.021, * P ≤ 0.032, ns ≤ 0.1234.

    Journal: Nucleic Acids Research

    Article Title: Minimization of the E. coli ribosome, aided and optimized by community science

    doi: 10.1093/nar/gkad1254

    Figure Lengend Snippet: Mini-PTC 1.1 inhibits the peptidyl transferase activity as evaluated by the fragment reaction. ( A ) Schematic representation of fragment reaction, followed by RNase A/LC-MS assay. CCA-pcb and C-pmn were used as a P-site and an A-site analog, respectively. The reaction was incubated with varied time (2 or 24 h) and temperature (–20, 4 or 50ºC). The product from this reaction (C-pmn-pcb) was subsequently digested by RNase A that cleaves off terminal puromycin-pcb (pmn-pcb), which can be quantified by LC–MS analysis. Leu-enkephalin was used as an internal standard. Reactions were run with water (mock), 20 μM mini-PTC 1.1, and 0.1 μM E. coli 50S ribosomal subunit at –20, 4 or 50ºC for 2 h ( B ) or 24 h ( C ). Reactions were run as triplicates ( n = 3). The yield of the fragment reaction between water (mock), mini-PTC 1.1 and E. coli 50S ribosomal subunit was compared by using two-way ANOVA with Tukey's multiple comparison test. **** P ≤ 0.0001, *** P ≤ 0.002, ** P ≤ 0.021, * P ≤ 0.032, ns ≤ 0.1234.

    Article Snippet: Transcription reactions (200 μl) contained the following components: 50 mM Tris–HCl (pH 8.1), 0.01% Triton X-100, 100 mM DTT, 2 mM spermidine, 10 mM ATP, 10 mM CTP, 10 mM GTP, 10 mM UTP, 50 mM MgCl 2 , 10 ng μl −1 DNA template, 1 unit ml −1 E. coli inorganic pyrophosphatase (New England Biolabs) and 0.2 mg ml −1 in-house T7 RNA polymerase.

    Techniques: Activity Assay, Liquid Chromatography with Mass Spectroscopy, Incubation, Comparison