vaccinia capping reaction total rna  (New England Biolabs)


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    Name:
    Vaccinia Capping System
    Description:
    Vaccinia Capping System 400 units
    Catalog Number:
    M2080S
    Price:
    140
    Category:
    Capping Reagents for DNA RNA Synthesis
    Size:
    400 units
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    Structured Review

    New England Biolabs vaccinia capping reaction total rna
    Vaccinia Capping System
    Vaccinia Capping System 400 units
    https://www.bioz.com/result/vaccinia capping reaction total rna/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    vaccinia capping reaction total rna - by Bioz Stars, 2021-06
    99/100 stars

    Images

    1) Product Images from "Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™"

    Article Title: Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0173186

    (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.
    Figure Legend Snippet: (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Techniques Used:

    (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.
    Figure Legend Snippet: (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Techniques Used:

    A. Transcript coverage (FPKM) of Wolbachia genes reveals over 88% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample. B. Transcript coverage (FPKM) of Wolbachia genes reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample.
    Figure Legend Snippet: A. Transcript coverage (FPKM) of Wolbachia genes reveals over 88% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample. B. Transcript coverage (FPKM) of Wolbachia genes reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample.

    Techniques Used:

    2) Product Images from "Structural basis of RNA cap modification by SARS-CoV-2"

    Article Title: Structural basis of RNA cap modification by SARS-CoV-2

    Journal: Nature Communications

    doi: 10.1038/s41467-020-17496-8

    Binding modes of RNA cap analogues and SAM and mechanism of methyl transfer. a Overlay of a binary (S-adenosyl methionine or SAM-bound; gray cartoons) and ternary (SAM, RNA cap-bound; light cyan cartoons) complexes shows outward motions (green arrows: 7 Å in gate loop 1, and 5.2 Å in gate loop 2) after RNA cap binding to nsp16. RNA cap, red stick; SAM in ternary complex, blue stick; SAM in binary complex, gray stick. b green sticks; nsp16 residues that interact with RNA cap. c magenta sticks; nsp16 residues that contact with SAM. d A close-up view of Cap-nsp16 interactions reveals a network of hydrogen bonding with successive phosphates, me7 G O and A 1 nucleotides of cap. Water, gray spheres, h-bonds, black dashed lines. e A water (yellow sphere) coordinates with the target 2′-O atom of A 1 , and catalytic tetrad residues and N43. The methyl group of SAM is positioned for direct in-line attack from the 2′-O. f Binding isotherms and fitting of data for nsp16 binding to RNA cap-0 ( me7 GpppA), cap-1 ( me7 GpppAm) analogues, and SAM. Each data point represents average of two independent experiments ( n = 2). g The 2′-O methyltransferase activity measured as percentage of Cap-0 to Cap-1 conversion is plotted against nsp16/nsp10 protein concentration. Higher enzymatic activity is observed on an RNA substrate with A (red circles) as the target base for 2′-O methylation (N 1 ), compared to an identical RNA but with G (black square) as N 1 or initiating nucleotide. Results are average of three independent experiments ( n = 3) with one standard deviation (s.d.) for each RNA shown as error bars. Source data are provided as a Source Data file. h Guanine base (yellow stick) is modeled at N 1 position of cognate adenine (red stick). The N2 amine of guanine intrudes into the SAM pocket and may be repelled by positively charged sulfur of SAM (blue stick).
    Figure Legend Snippet: Binding modes of RNA cap analogues and SAM and mechanism of methyl transfer. a Overlay of a binary (S-adenosyl methionine or SAM-bound; gray cartoons) and ternary (SAM, RNA cap-bound; light cyan cartoons) complexes shows outward motions (green arrows: 7 Å in gate loop 1, and 5.2 Å in gate loop 2) after RNA cap binding to nsp16. RNA cap, red stick; SAM in ternary complex, blue stick; SAM in binary complex, gray stick. b green sticks; nsp16 residues that interact with RNA cap. c magenta sticks; nsp16 residues that contact with SAM. d A close-up view of Cap-nsp16 interactions reveals a network of hydrogen bonding with successive phosphates, me7 G O and A 1 nucleotides of cap. Water, gray spheres, h-bonds, black dashed lines. e A water (yellow sphere) coordinates with the target 2′-O atom of A 1 , and catalytic tetrad residues and N43. The methyl group of SAM is positioned for direct in-line attack from the 2′-O. f Binding isotherms and fitting of data for nsp16 binding to RNA cap-0 ( me7 GpppA), cap-1 ( me7 GpppAm) analogues, and SAM. Each data point represents average of two independent experiments ( n = 2). g The 2′-O methyltransferase activity measured as percentage of Cap-0 to Cap-1 conversion is plotted against nsp16/nsp10 protein concentration. Higher enzymatic activity is observed on an RNA substrate with A (red circles) as the target base for 2′-O methylation (N 1 ), compared to an identical RNA but with G (black square) as N 1 or initiating nucleotide. Results are average of three independent experiments ( n = 3) with one standard deviation (s.d.) for each RNA shown as error bars. Source data are provided as a Source Data file. h Guanine base (yellow stick) is modeled at N 1 position of cognate adenine (red stick). The N2 amine of guanine intrudes into the SAM pocket and may be repelled by positively charged sulfur of SAM (blue stick).

    Techniques Used: Binding Assay, Activity Assay, Protein Concentration, Methylation, Standard Deviation

    Related Articles

    other:

    Article Title: Structural basis of RNA cap modification by SARS-CoV-2
    Article Snippet: S-H.C. and N.D. are employees of New England Biolabs, a manufacturer and vendor of molecular biology reagents, including vaccinia RNA capping enzyme and cap 2’O methyltransferase.

    Synthesized:

    Article Title: An in vitro single-molecule assay for eukaryotic cap-dependent translation initiation kinetics
    Article Snippet: .. The synthesized mRNAs were capped using a Vaccinia Capping System (NEB) and 3′ biotinylated using the Pierce RNA 3′ End Biotinylation Kit, performed according to the manufacturer's recommended protocol. .. After capping and biotinylation, the mRNAs were purified with phenol-chloroform extraction and the Direct-Zol RNA kit (Zymo Research), from which the RNAs were eluted in H2 O.

    Spectrophotometry:

    Article Title: Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction
    Article Snippet: Assembly PCR (30 cycles) was performed with Phusion DNA polymerase (New England Biolabs) according to the manufacturer's instructions, annealing at 65°C for 20 s and extending at 72°C for 25 s. Unpurified PCR products were transcribed with the MEGAScript T7 kit (Ambion), precipitated with an equal volume of 7.5 M LiCl/50 mM EDTA, washed with 70% ethanol and redissolved in water. .. The mRNA products were capped with the ScriptCap m7 G capping system (Epicentre Biotechnologies) or the Vaccinia Capping System (New England Biolabs), precipitated with an equal volume of 7.5 M LiCl/50 mM EDTA, washed with 70% ethanol and redissolved in RBB [50 mM Tris–HCl, pH 8.0, 50 mM KCl, 5 mM MgCl2 , 5% (v/v) glycerol, 0.05% (v/v) Tween-20]. mRNA concentrations were determined by measuring absorbance at 260 nm on a Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific). .. For cell-free translation with rabbit reticulocyte lysate (RRL), the mRNA concentration was adjusted to 133 nM in RBBD (RBB plus 1 mM dithiothreitol and 10 μg/ml bovine serum albumin, New England Biolabs) and refolded by heating at 65°C for 2 min and incubating at room temperature for 10 min. TetR(B) with N-terminal T7 and C-terminal His6 tags, and revTetR-S2 with a C-terminal His6 tag were purified from Escherichia coli as previously described ( ).

    Purification:

    Article Title: Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase
    Article Snippet: Purified RNA was then heated at 65 °C for 5 min to denature the secondary structure. .. Purified and denatured RNA was capped using Vaccinia Capping Kit (NEB) and finally purified using Monarch RNA cleanup kit. .. TLC assay for nsp14 enzymatic activity The N-7 cap guanosine methylation assay was performed according to Varshney et al. [ ].

    In Vitro:

    Article Title: A Nanostructured Lipid Carrier for Delivery of a Replicating Viral RNA Provides Single, Low-Dose Protection against Zika
    Article Snippet: Following transformation and amplification in Top10 cells (Invitrogen) and isolation using maxi-prep kits (QIAGEN), plasmids were linearized by restriction digest with NotI enzyme (New England Biolabs) and purified using phenol-chloroform. .. RNA was then transcribed in vitro using T7 megascript kit (Invitrogen) followed by lithium chloride precipitation and capping with a vaccinia capping kit (New England Biolabs). .. Capped transcripts were then precipitated in lithium chloride and resuspended in nuclease-free water to a final concentration of 1 μg/μL and analyzed by agarose-gel electrophoresis.

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    New England Biolabs vaccinia capping reaction total rna
    (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . <t>malayi</t> adult male <t>RNA</t> were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.
    Vaccinia Capping Reaction Total Rna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/vaccinia capping reaction total rna/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    vaccinia capping reaction total rna - by Bioz Stars, 2021-06
    99/100 stars
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    (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Journal: PLoS ONE

    Article Title: Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™

    doi: 10.1371/journal.pone.0173186

    Figure Lengend Snippet: (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Article Snippet: Vaccinia capping reaction Total RNA from B . malayi MF (25 μg) or adult males (1.5 μg) was capped with 3´ desthiobiotin-GTP using the Vaccinia Capping System (New England Biolabs).

    Techniques:

    (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Journal: PLoS ONE

    Article Title: Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™

    doi: 10.1371/journal.pone.0173186

    Figure Lengend Snippet: (A) Transcript abundance of all 940 annotated Wolbachia genes (listed by geneID number) reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. Each transcript is indicated by in red (the FPKM value in the total RNA) and blue (the FPKM value in capped-RNA sample)(B) A closer view (note difference in y-axis scales between panel A and B) of transcript abundance reveals an enrichment in Wolbachia transcripts in the capped RNA sample.

    Article Snippet: Vaccinia capping reaction Total RNA from B . malayi MF (25 μg) or adult males (1.5 μg) was capped with 3´ desthiobiotin-GTP using the Vaccinia Capping System (New England Biolabs).

    Techniques:

    A. Transcript coverage (FPKM) of Wolbachia genes reveals over 88% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample. B. Transcript coverage (FPKM) of Wolbachia genes reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample.

    Journal: PLoS ONE

    Article Title: Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™

    doi: 10.1371/journal.pone.0173186

    Figure Lengend Snippet: A. Transcript coverage (FPKM) of Wolbachia genes reveals over 88% of Wolbachia transcripts from B . malayi adult male RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample. B. Transcript coverage (FPKM) of Wolbachia genes reveals over 95% of Wolbachia transcripts from B . malayi MF RNA were enriched using the Cappable-seq technique. A closer view of transcript abundance (inset) reveals most Wolbachia transcripts in total RNA are present in very low abundance, whereas the Wolbachia transcripts are more abundant in the capped RNA sample. Points along the y-axis are indicative of Wolbachia transcripts that were undetectable in total RNA that were detected in the capped RNA sample.

    Article Snippet: Vaccinia capping reaction Total RNA from B . malayi MF (25 μg) or adult males (1.5 μg) was capped with 3´ desthiobiotin-GTP using the Vaccinia Capping System (New England Biolabs).

    Techniques:

    Binding modes of RNA cap analogues and SAM and mechanism of methyl transfer. a Overlay of a binary (S-adenosyl methionine or SAM-bound; gray cartoons) and ternary (SAM, RNA cap-bound; light cyan cartoons) complexes shows outward motions (green arrows: 7 Å in gate loop 1, and 5.2 Å in gate loop 2) after RNA cap binding to nsp16. RNA cap, red stick; SAM in ternary complex, blue stick; SAM in binary complex, gray stick. b green sticks; nsp16 residues that interact with RNA cap. c magenta sticks; nsp16 residues that contact with SAM. d A close-up view of Cap-nsp16 interactions reveals a network of hydrogen bonding with successive phosphates, me7 G O and A 1 nucleotides of cap. Water, gray spheres, h-bonds, black dashed lines. e A water (yellow sphere) coordinates with the target 2′-O atom of A 1 , and catalytic tetrad residues and N43. The methyl group of SAM is positioned for direct in-line attack from the 2′-O. f Binding isotherms and fitting of data for nsp16 binding to RNA cap-0 ( me7 GpppA), cap-1 ( me7 GpppAm) analogues, and SAM. Each data point represents average of two independent experiments ( n = 2). g The 2′-O methyltransferase activity measured as percentage of Cap-0 to Cap-1 conversion is plotted against nsp16/nsp10 protein concentration. Higher enzymatic activity is observed on an RNA substrate with A (red circles) as the target base for 2′-O methylation (N 1 ), compared to an identical RNA but with G (black square) as N 1 or initiating nucleotide. Results are average of three independent experiments ( n = 3) with one standard deviation (s.d.) for each RNA shown as error bars. Source data are provided as a Source Data file. h Guanine base (yellow stick) is modeled at N 1 position of cognate adenine (red stick). The N2 amine of guanine intrudes into the SAM pocket and may be repelled by positively charged sulfur of SAM (blue stick).

    Journal: Nature Communications

    Article Title: Structural basis of RNA cap modification by SARS-CoV-2

    doi: 10.1038/s41467-020-17496-8

    Figure Lengend Snippet: Binding modes of RNA cap analogues and SAM and mechanism of methyl transfer. a Overlay of a binary (S-adenosyl methionine or SAM-bound; gray cartoons) and ternary (SAM, RNA cap-bound; light cyan cartoons) complexes shows outward motions (green arrows: 7 Å in gate loop 1, and 5.2 Å in gate loop 2) after RNA cap binding to nsp16. RNA cap, red stick; SAM in ternary complex, blue stick; SAM in binary complex, gray stick. b green sticks; nsp16 residues that interact with RNA cap. c magenta sticks; nsp16 residues that contact with SAM. d A close-up view of Cap-nsp16 interactions reveals a network of hydrogen bonding with successive phosphates, me7 G O and A 1 nucleotides of cap. Water, gray spheres, h-bonds, black dashed lines. e A water (yellow sphere) coordinates with the target 2′-O atom of A 1 , and catalytic tetrad residues and N43. The methyl group of SAM is positioned for direct in-line attack from the 2′-O. f Binding isotherms and fitting of data for nsp16 binding to RNA cap-0 ( me7 GpppA), cap-1 ( me7 GpppAm) analogues, and SAM. Each data point represents average of two independent experiments ( n = 2). g The 2′-O methyltransferase activity measured as percentage of Cap-0 to Cap-1 conversion is plotted against nsp16/nsp10 protein concentration. Higher enzymatic activity is observed on an RNA substrate with A (red circles) as the target base for 2′-O methylation (N 1 ), compared to an identical RNA but with G (black square) as N 1 or initiating nucleotide. Results are average of three independent experiments ( n = 3) with one standard deviation (s.d.) for each RNA shown as error bars. Source data are provided as a Source Data file. h Guanine base (yellow stick) is modeled at N 1 position of cognate adenine (red stick). The N2 amine of guanine intrudes into the SAM pocket and may be repelled by positively charged sulfur of SAM (blue stick).

    Article Snippet: S-H.C. and N.D. are employees of New England Biolabs, a manufacturer and vendor of molecular biology reagents, including vaccinia RNA capping enzyme and cap 2’O methyltransferase.

    Techniques: Binding Assay, Activity Assay, Protein Concentration, Methylation, Standard Deviation