rnase v1 structure mapping  (Thermo Fisher)


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    Name:
    Propidium Iodide
    Description:
    Propidium iodide PI is a popular red fluorescent nuclear and chromosome counterstain Since propidium iodide is not permeant to live cells it is also commonly used to detect dead cells in a population PI binds to DNA by intercalating between the bases with little or no sequence preference In aqueous solution the dye has excitation emission maxima of 493 636 nm Once the dye is bound its fluorescence is enhanced 20 to 30 fold the fluorescence excitation maximum is shifted 30 40 nm to the red and the fluorescence emission maximum is shifted 15 nm to the blue resulting in an excitation maximum at 535 nm and fluorescence emission maximum at 617 nm PI is widely used in fluorescence microscopy confocal laser scanning microscopy flow cytometry and fluorometry Learn more about propidium iodide and propidium iodide containing products
    Catalog Number:
    p1304mp
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    None
    Applications:
    Cell Analysis|Cell Viability & Cytotoxicity|Cellular Imaging|Chromatin-Related Products|Flow Cytometry Controls, Standards & General Reagents|Flow Cytometry Staining by Cell Structure|Flow Cytometry Viability & Cytotoxicity Assays|Flow Cytometry of Cellular Processes|Immunofluorescence (IF)|Immunofluorescence Counterstaining, Mounting & Fade Prevention|Immunofluorescence Staining & Detection|Nuclear Stains|Nucleus, Nucleoli & Nuclear Envelope|Organelle Tracing|RNAi, Epigenetics & Non-Coding RNA Research|Chromatin Biology|Flow Cytometry|Cell Tracing & Tracking|Cell Structure|Cell Viability, Proliferation & Function
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    Labeling Detection Products
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    Structured Review

    Thermo Fisher rnase v1 structure mapping
    Propidium iodide PI is a popular red fluorescent nuclear and chromosome counterstain Since propidium iodide is not permeant to live cells it is also commonly used to detect dead cells in a population PI binds to DNA by intercalating between the bases with little or no sequence preference In aqueous solution the dye has excitation emission maxima of 493 636 nm Once the dye is bound its fluorescence is enhanced 20 to 30 fold the fluorescence excitation maximum is shifted 30 40 nm to the red and the fluorescence emission maximum is shifted 15 nm to the blue resulting in an excitation maximum at 535 nm and fluorescence emission maximum at 617 nm PI is widely used in fluorescence microscopy confocal laser scanning microscopy flow cytometry and fluorometry Learn more about propidium iodide and propidium iodide containing products
    https://www.bioz.com/result/rnase v1 structure mapping/product/Thermo Fisher
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rnase v1 structure mapping - by Bioz Stars, 2020-07
    99/100 stars

    Related Products / Commonly Used Together

    rnase v1
    rnase
    target rna
    structure buffer

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    Related Articles

    Labeling:

    Article Title: Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge ▿
    Article Snippet: .. Samples labeled with primary and secondary antibodies were stained with propidium iodide by mixing equal volumes of sludge sample with a stock solution of propidium iodide (60 μM) (Molecular Probes, The Netherlands), followed by a 15-min incubation in the dark. .. Staining with propidium iodide was performed only on prefixed samples to ensure penetration of propidium iodide.

    Acid Assay:

    Article Title: Polyacrylic acid-coated iron oxide nanoparticles could be a useful tool for tracking inflammatory monocytes
    Article Snippet: .. Carboxyfluorescein diacetate succinimidyl ester (CFSE), DIOC6 , 7-AAD and propidium iodide (PI) were purchased from Thermo Invitrogen (MA, USA), and Bicinchoninic Acid Assay from Merck KGaA (Darmstadt, Germany). ..

    Incubation:

    Article Title: Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge ▿
    Article Snippet: .. Samples labeled with primary and secondary antibodies were stained with propidium iodide by mixing equal volumes of sludge sample with a stock solution of propidium iodide (60 μM) (Molecular Probes, The Netherlands), followed by a 15-min incubation in the dark. .. Staining with propidium iodide was performed only on prefixed samples to ensure penetration of propidium iodide.

    other:

    Article Title: Aspartic Acid Residue 51 of SaeR Is Essential for Staphylococcus aureus Virulence
    Article Snippet: The following formula was used to determine % propidium iodide+ : %Propidium Iodide+ = (Mean PI signalExperimental – Mean PI signal untreated )/(Mean PI signalTriton-X – Mean PI signal untreated ).

    Modification:

    Article Title: Effect of silica and gold nanoparticles on macrophage proliferation, activation markers, cytokine production, and phagocytosis in vitro
    Article Snippet: .. Reagents RAW 264.7 cells and Dulbecco’s Modified Eagle’s Medium culture media were purchased from American Type Culture Collection (ATCC); fetal bovine serum (FBS), penicillin/streptomycin, phosphate-buffered saline (PBS), propidium iodide (PI), calcein AM, 4′,6-diamidino-2-phenylindole (DAPI), SYTO® Green, Fluorescein isothiocyanate (FITC)-Escherichia coli , and the opsonization reagent were purchased from Invitrogen. .. SiO2 NPs (10 nm; Ludox, SM-30 colloidal silica, hydroxyl surface with Na+ stabilizing counterion) were purchased from Sigma Aldrich.

    Staining:

    Article Title: Exosomes miR-126a released from MDSC induced by DOX treatment promotes lung metastasis
    Article Snippet: .. Viability and cell number were determined by propidium iodide exclusion or with Calcein Dyes (eBioscience) for staining live cells. .. Exosomes isolation For preparation of tumor exosomes, 4T1 cells was cultured in vitro at 37°C in a humidified 5% CO2 atmosphere in air in complete medium (DMEM with 5% FCS that had been ultracentrifuged for 16 h at 100,000 g to exclude bovine exosomes).

    Article Title: Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water
    Article Snippet: .. To increase the robustness of counting viable P . aeruginosa cells in water, we assessed the LIVE/DEAD staining patterns of cells in water using the DNA binding dyes SYTO 9 and propidium iodide (PI). .. While the majority of cells in water were a homogenous SYTO 9 population, there was also a subpopulation of PI stained cells ( ).

    Article Title: Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge ▿
    Article Snippet: .. Samples labeled with primary and secondary antibodies were stained with propidium iodide by mixing equal volumes of sludge sample with a stock solution of propidium iodide (60 μM) (Molecular Probes, The Netherlands), followed by a 15-min incubation in the dark. .. Staining with propidium iodide was performed only on prefixed samples to ensure penetration of propidium iodide.

    Binding Assay:

    Article Title: Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water
    Article Snippet: .. To increase the robustness of counting viable P . aeruginosa cells in water, we assessed the LIVE/DEAD staining patterns of cells in water using the DNA binding dyes SYTO 9 and propidium iodide (PI). .. While the majority of cells in water were a homogenous SYTO 9 population, there was also a subpopulation of PI stained cells ( ).

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  • 92
    Thermo Fisher rnase v1
    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific <t>RNase</t> V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.
    Rnase V1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 123 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnase v1/product/Thermo Fisher
    Average 92 stars, based on 123 article reviews
    Price from $9.99 to $1999.99
    rnase v1 - by Bioz Stars, 2020-07
    92/100 stars
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    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Journal: Nucleic Acids Research

    Article Title: Unstructured 5′-tails act through ribosome standby to override inhibitory structure at ribosome binding sites

    doi: 10.1093/nar/gky073

    Figure Lengend Snippet: Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Article Snippet: RNase V1 probing used a final concentration of 0.01 U/μl (ThermoFisher Scientific, #AM2275) for 5 min at 37°C.

    Techniques: Sequencing

    Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Journal: Nucleic Acids Research

    Article Title: Unstructured 5′-tails act through ribosome standby to override inhibitory structure at ribosome binding sites

    doi: 10.1093/nar/gky073

    Figure Lengend Snippet: Addition of CA-repeats does not change the secondary structure of the coat RBS stem–loop. ( A ) Enzymatic and chemical structure probing was conducted on control mRNA (00) or mRNAs with tails of 4, 6 or 8 (CA)-repeats, (see Materials and Methods), as indicated. The mRNAs were mock-treated (lanes ‘–’), partially digested with double-strand-specific RNase V1 (V1), or treated with lead(II) acetate (Pb 2+ ). UCGA: sequencing reactions on (CA)8 mRNA. The position of the SD and AUG start codon are indicated by red boxes. Regions of reactivity toward RNase V1 (red solid line) and lead(II) acetate (red dashed line) are indicated on the autoradiogram. ( B ) The localization of RNase V1 (filled triangles) and lead(II) acetate (black dots) cuts are shown on the secondary structure of the 5′-segment of (CA)8 mRNA. Black boxes: SD and AUG.

    Article Snippet: RNase V1 probing used a final concentration of 0.01 U/μl (ThermoFisher Scientific, #AM2275) for 5 min at 37°C.

    Techniques: Sequencing

    Enzymatic degradation of RNA causes protein aggregation. a Diagram showing the experimental design. b SDS-PAGE analysis of soluble (Supernatant) and insoluble proteins (Pellet) from human neurons after treatment with a mixture of RNase A and RNase T1 (A/T1), or vehicle (Ve-). c Protein aggregation (Pellet) after incubation with different ribonucleases or DNase I in the presence of either EDTA or Mg 2+ . Ribonucleases used were RNase A (A), RNase T1 (T1), a mixture of RNase A and RNase T1 (A/T1), RNase 1f (1f), and RNase V1 (V1),

    Journal: bioRxiv

    Article Title: Enzymatic degradation of RNA causes widespread protein aggregation in cell and tissue lysates

    doi: 10.1101/841577

    Figure Lengend Snippet: Enzymatic degradation of RNA causes protein aggregation. a Diagram showing the experimental design. b SDS-PAGE analysis of soluble (Supernatant) and insoluble proteins (Pellet) from human neurons after treatment with a mixture of RNase A and RNase T1 (A/T1), or vehicle (Ve-). c Protein aggregation (Pellet) after incubation with different ribonucleases or DNase I in the presence of either EDTA or Mg 2+ . Ribonucleases used were RNase A (A), RNase T1 (T1), a mixture of RNase A and RNase T1 (A/T1), RNase 1f (1f), and RNase V1 (V1),

    Article Snippet: Enzymes and reagents RNase T1 (AM2280), RNase V1 (AM2275), RNase A/T1 cocktail (EN0551), DNase I (2222), and Yeast t-RNA (15401-011) were from Thermo Fisher Scientific.

    Techniques: SDS Page, Incubation

    Representative probing experiments using 5′-endlabeled aptamer A011 RNA and analyzed by ( A ) 20% or ( B ) 10% denaturing PAGE. Lanes 1 and 13, undigested RNA control (con.); lanes 2 and 14, limited alkaline hydrolysis; lanes 3, 12, 15 and 24, partial digestion with RNase T1 under denaturing (denat.) conditions; lanes 4, 5, 16 and 17, with two concentrations of RNase T1 under native conditions; lanes 6, 7, 18 and 19, with two concentrations of RNase V1; lanes 8, 9, 20 and 21, with two concentrations of nuclease P1; lane 10 and 22, with nuclease S1; lanes 11 and 23, Pb2+-induced hydrolysis. For experimental details, see Materials and Methods. Alkaline hydrolysis bands and the corresponding structure elements are indicated at the left and right margins, respectively, according to the numbering system presented in Figure 2 (A011, center). ( C , D ) Illustration of prominent cleavage sites in the context of the secondary structure of A011, derived from probing experiments such as those shown in panels A and B . Symbol sizes suggests the relative intensity of cleavage bands based on visual inspection.

    Journal: International Journal of Molecular Sciences

    Article Title: 2′-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP)

    doi: 10.3390/ijms19123883

    Figure Lengend Snippet: Representative probing experiments using 5′-endlabeled aptamer A011 RNA and analyzed by ( A ) 20% or ( B ) 10% denaturing PAGE. Lanes 1 and 13, undigested RNA control (con.); lanes 2 and 14, limited alkaline hydrolysis; lanes 3, 12, 15 and 24, partial digestion with RNase T1 under denaturing (denat.) conditions; lanes 4, 5, 16 and 17, with two concentrations of RNase T1 under native conditions; lanes 6, 7, 18 and 19, with two concentrations of RNase V1; lanes 8, 9, 20 and 21, with two concentrations of nuclease P1; lane 10 and 22, with nuclease S1; lanes 11 and 23, Pb2+-induced hydrolysis. For experimental details, see Materials and Methods. Alkaline hydrolysis bands and the corresponding structure elements are indicated at the left and right margins, respectively, according to the numbering system presented in Figure 2 (A011, center). ( C , D ) Illustration of prominent cleavage sites in the context of the secondary structure of A011, derived from probing experiments such as those shown in panels A and B . Symbol sizes suggests the relative intensity of cleavage bands based on visual inspection.

    Article Snippet: Enzymatic digestions were performed as follows: RNase T1 (Thermo Fisher Scientific, Waltham, MA, USA) either in 20 mM sodium citrat (pH 5.0), 7 mM urea, 1 mM EDTA and 1 unit RNase T1 for 30 min at 55 °C (denaturing conditions) or in binding buffer (see above) with 0.5 or 0.05 units for 20 min at room temperature (RT); 0.01 or 0.05 units RNase V1 (Thermo Fisher Scientific Pierce) in binding buffer for 20 min at RT; 1 unit RNase S1 (Thermo Fisher Scientific, Waltham, MA, USA) in binding buffer containing 4.5 mM ZnSO4 for 20 min at RT; 0.01 or 0.05 units nuclease P1 (Sigma-Aldrich, St. Louis, MO, USA) in binding buffer containing 0.4 mM ZnSO4 for 20 min at RT.

    Techniques: Polyacrylamide Gel Electrophoresis, Derivative Assay