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rnase v1  (Thermo Fisher)


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    Structured Review

    Thermo Fisher rnase v1
    Rnase V1, supplied by Thermo Fisher, 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/product/rnase+v1/Ribonuclease+A/pm41406077-234-40-46
    Average 99 stars, based on 1 article reviews
    rnase v1 - by Bioz Stars, 2026-09
    99/100 stars

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    Related Articles

    Concentration Assay:

    Article Title: The FsrA-Mediated Iron-Sparing Response Regulates the Biosynthesis of the Epipeptide EPE in Bacillus subtilis.
    Article Snippet: .. The samples were subjected to enzymatic or chemical cleavage using either RNase T1 (0.1 U; Ambion, AM2283, Thermo Fisher, Waltham, USA) for 3 min, lead(II) acetate (final concentration: 6.25 mM; SigmaAldrich, 316512- 5G) for 1 min and 45 s, or RNase V1 (2 × 10−5 U; Ambion, AM2275, Thermo Fisher, Waltham, USA) for 1 min. ..

    Article Title: ProQ-associated small RNAs control motility in Vibrio cholerae
    Article Snippet: .. The samples were then treated with either RNase T1 (0.1 U; Ambion, AM2283) for 3 min, lead (II) acetate (final concentration: 6.25 mM; Sigma-Aldrich, 316512–5G) for 1 min and 45 s or RNase V1 (2 × 10 −5 U; Ambion, AM2275) for 1 min. ..

    Saline:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Lysis:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Protease Inhibitor:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Plasmid Preparation:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Transfection:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Immunoprecipitation:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Negative Control:

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells/well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFNα1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4°C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U/ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4°C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Article Title: Caspase-mediated processing of TRBP regulates apoptosis during viral infection.
    Article Snippet: A HeLa cell suspension (7 × 10 5 cells / well) was plated into a 6-well plate 1 day before plasmid transfection with human type-I IFN (IFN α1; Cell Signaling). .. Cells were washed with phosphate-buffered saline and lysed in cold lysis buffer (10 mM Hepes–NaOH [pH 7.9], 1.5 mM MgCl 2 , 10 mM KCl, 0.5 mM DTT, 140 mM NaCl, 1 mM EDTA, 1 mM Na 3 VO 4 , 10 mM NaF, 0.5% NP-40, and complete protease inhibitor) 24 h following the plasmid transfection, then the cell lysates were centrifuged at 14 000 rpm for 10 min. For immunoprecipitation, 30 μl of Dynabeads Protein G (Thermo Fisher Scientific) was mixed with 2.5 μg of mouse anti-FLAG antibody (Sigma), or 2.5 μg of mouse IgG (Santa Cruz Biotechnology) as a negative control and rotated at 4 ◦C for 2 h. The cell lysates in the presence or absence of RNase V1 (0.3 U / ml; Ambion) were then mixed with the antibody-bound Dynabeads Protein G and rotated at 4 ◦C for 2 h. The beads were washed twice with wash buffer containing 300 mM NaCl and once with lysis buffer. ..

    Labeling:

    Article Title: Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR
    Article Snippet: .. S7 Conditions that gave single-hit digestion were 0.001 U μL-1 RNase T1 (Ambion), 37 ̊C, 15 min; 0.005 ng μL-1 RNase A (Ambion), room temperature, 15 min; and 0.001 U μL-1 RNase V1 (Ambion), room temperature, 15 min. To generate a hydrolysis ladder, labeled RNA was incubated in 100 mM Na2CO3/NaHCO3, pH 9 and 2 mM EDTA for 8 min at 90 ̊C. ..

    Incubation:

    Article Title: Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR
    Article Snippet: .. S7 Conditions that gave single-hit digestion were 0.001 U μL-1 RNase T1 (Ambion), 37 ̊C, 15 min; 0.005 ng μL-1 RNase A (Ambion), room temperature, 15 min; and 0.001 U μL-1 RNase V1 (Ambion), room temperature, 15 min. To generate a hydrolysis ladder, labeled RNA was incubated in 100 mM Na2CO3/NaHCO3, pH 9 and 2 mM EDTA for 8 min at 90 ̊C. ..



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    Sequentially processed MIRNAs generate several small RNA duplexes with different structural requirements. ( A ) Scheme of a sequential MIRNA . The first DCL1 cut is highlighted with a black arrow. Small RNAs derived from sequential precursors. MiRNA is shown in red, distal miRNA duplex (miRNA.2) is depicted in light blue and proximal miRNA duplex (miRNA.1) is indicated in dark grey (right). ( B ) Top panel: logarithm in base 10 of number of reads of small RNA duplex (n.d.: not detected). See for the number of reads detected for each duplex. Bottom panel: dot plot representing |Δ G | calculated for each small RNA duplex from evolutionary conserved sequentially processed MIRNAs . The colour code of the small RNA duplexes is shown in (A). ( C ) Structural analysis of MIR319a . Denaturing 8% (w/v) polyacrylamide gels shown: OH−: alkaline hydrolysis; <t>V1:</t> <t>RNAse</t> V1 in decreasing concentrations; H2O: incubation with water (control). Blue lines indicate the double-stranded bases obtained after V1 digestion as determined from polyacrylamide gels. The arrows correlate the position of DCL1 cuts in the precursor (right) with the experimental determination of the secondary structure (left). See for the original image of the polyacrylamide gel. ( D, F and H ) Small RNA blots of transgenic lines expressing different precursors from the 35S promoter. Each sample corresponds to 15 pooled inflorescences from independent primary transgenic plants. Numbers above small RNA blots correspond to miRNA levels quantified relative to the wt precursor. The EB staining of each gel is shown below. Top panels show a schematic representation of MIR319a including the wt and modified sequences of (D) miR319.2 (miR319a.2GU and miR319a.2AU) (F) MIR319a-MIL where a black arrow indicates how the central internal loop in miRNA.1 duplex was moved closer to DCL1 second cut (F); and MIR319a-3MM wt and MIR319a-5MM (H). These depictions represent the mfold secondary structure prediction for each precursor (see Appendix II). Black letters specify the closed mismatches, and the numbers indicate their position counting from the 5′end of the miRNA or miRNA.2. MiRNA is shown in red and miRNA* in grey, miRNA.2 is shown in light blue, and miRNA.2* is shown in grey. |Δ G | is shown above each small RNA sequence. ( E , G and I ) RT-qPCR of pri-miRNA determined in three biological replicates are shown as triangles in different shades of grey. Lines represent the mean value for each MIRNA . No statistically significant differences in E, G and I. See for the statistical analysis conducted in all the samples.
    V1 Rnase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Sequentially processed MIRNAs generate several small RNA duplexes with different structural requirements. ( A ) Scheme of a sequential MIRNA . The first DCL1 cut is highlighted with a black arrow. Small RNAs derived from sequential precursors. MiRNA is shown in red, distal miRNA duplex (miRNA.2) is depicted in light blue and proximal miRNA duplex (miRNA.1) is indicated in dark grey (right). ( B ) Top panel: logarithm in base 10 of number of reads of small RNA duplex (n.d.: not detected). See for the number of reads detected for each duplex. Bottom panel: dot plot representing |Δ G | calculated for each small RNA duplex from evolutionary conserved sequentially processed MIRNAs . The colour code of the small RNA duplexes is shown in (A). ( C ) Structural analysis of MIR319a . Denaturing 8% (w/v) polyacrylamide gels shown: OH−: alkaline hydrolysis; V1: RNAse V1 in decreasing concentrations; H2O: incubation with water (control). Blue lines indicate the double-stranded bases obtained after V1 digestion as determined from polyacrylamide gels. The arrows correlate the position of DCL1 cuts in the precursor (right) with the experimental determination of the secondary structure (left). See for the original image of the polyacrylamide gel. ( D, F and H ) Small RNA blots of transgenic lines expressing different precursors from the 35S promoter. Each sample corresponds to 15 pooled inflorescences from independent primary transgenic plants. Numbers above small RNA blots correspond to miRNA levels quantified relative to the wt precursor. The EB staining of each gel is shown below. Top panels show a schematic representation of MIR319a including the wt and modified sequences of (D) miR319.2 (miR319a.2GU and miR319a.2AU) (F) MIR319a-MIL where a black arrow indicates how the central internal loop in miRNA.1 duplex was moved closer to DCL1 second cut (F); and MIR319a-3MM wt and MIR319a-5MM (H). These depictions represent the mfold secondary structure prediction for each precursor (see Appendix II). Black letters specify the closed mismatches, and the numbers indicate their position counting from the 5′end of the miRNA or miRNA.2. MiRNA is shown in red and miRNA* in grey, miRNA.2 is shown in light blue, and miRNA.2* is shown in grey. |Δ G | is shown above each small RNA sequence. ( E , G and I ) RT-qPCR of pri-miRNA determined in three biological replicates are shown as triangles in different shades of grey. Lines represent the mean value for each MIRNA . No statistically significant differences in E, G and I. See for the statistical analysis conducted in all the samples.

    Journal: Nucleic Acids Research

    Article Title: Principles of miRNA/miRNA* function in plant MIRNA processing

    doi: 10.1093/nar/gkae458

    Figure Lengend Snippet: Sequentially processed MIRNAs generate several small RNA duplexes with different structural requirements. ( A ) Scheme of a sequential MIRNA . The first DCL1 cut is highlighted with a black arrow. Small RNAs derived from sequential precursors. MiRNA is shown in red, distal miRNA duplex (miRNA.2) is depicted in light blue and proximal miRNA duplex (miRNA.1) is indicated in dark grey (right). ( B ) Top panel: logarithm in base 10 of number of reads of small RNA duplex (n.d.: not detected). See for the number of reads detected for each duplex. Bottom panel: dot plot representing |Δ G | calculated for each small RNA duplex from evolutionary conserved sequentially processed MIRNAs . The colour code of the small RNA duplexes is shown in (A). ( C ) Structural analysis of MIR319a . Denaturing 8% (w/v) polyacrylamide gels shown: OH−: alkaline hydrolysis; V1: RNAse V1 in decreasing concentrations; H2O: incubation with water (control). Blue lines indicate the double-stranded bases obtained after V1 digestion as determined from polyacrylamide gels. The arrows correlate the position of DCL1 cuts in the precursor (right) with the experimental determination of the secondary structure (left). See for the original image of the polyacrylamide gel. ( D, F and H ) Small RNA blots of transgenic lines expressing different precursors from the 35S promoter. Each sample corresponds to 15 pooled inflorescences from independent primary transgenic plants. Numbers above small RNA blots correspond to miRNA levels quantified relative to the wt precursor. The EB staining of each gel is shown below. Top panels show a schematic representation of MIR319a including the wt and modified sequences of (D) miR319.2 (miR319a.2GU and miR319a.2AU) (F) MIR319a-MIL where a black arrow indicates how the central internal loop in miRNA.1 duplex was moved closer to DCL1 second cut (F); and MIR319a-3MM wt and MIR319a-5MM (H). These depictions represent the mfold secondary structure prediction for each precursor (see Appendix II). Black letters specify the closed mismatches, and the numbers indicate their position counting from the 5′end of the miRNA or miRNA.2. MiRNA is shown in red and miRNA* in grey, miRNA.2 is shown in light blue, and miRNA.2* is shown in grey. |Δ G | is shown above each small RNA sequence. ( E , G and I ) RT-qPCR of pri-miRNA determined in three biological replicates are shown as triangles in different shades of grey. Lines represent the mean value for each MIRNA . No statistically significant differences in E, G and I. See for the statistical analysis conducted in all the samples.

    Article Snippet: Radioactively labelled products of in vitro transcription were partially digested using T1 RNAse (Fermentas, denaturing conditions), V1 RNase (Ambion, native conditions) and S1 nuclease (Fermentas, native conditions) as described before ( ).

    Techniques: Derivative Assay, Incubation, Control, Transgenic Assay, Expressing, Staining, Modification, Sequencing, Quantitative RT-PCR