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shortcut rnaseiii  (New England Biolabs)


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    Structured Review

    New England Biolabs shortcut rnaseiii
    Shortcut Rnaseiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 316 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rnaseiii/ShortCut+RNase+III/pm41571440-161-3-5
    Average 96 stars, based on 316 article reviews
    shortcut rnaseiii - by Bioz Stars, 2026-09
    96/100 stars

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    Related Articles

    other:

    Article Title: Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.
    Article Snippet: Article

    In Vitro:

    Article Title: Purification/Amplification-Free RNA Detection Platform for Rapid and Multiplex Diagnosis of Plant Viral Infections.
    Article Snippet: Genetic tests are highly sensitive, and quantitative methods for diagnosing human viral infections, including COVID-19, are also being used to diagnose plant diseases in various agricultural settings.. Conventional genetic tests for plant viruses are mostly based on methods that require purification and amplification of viral genomes from plant samples, which generally take several hours in total, making it difficult to use them in rapid detection at point-of-care testing (POCT).. In this study, we developed Direct-SATORI, a rapid and robust genetic test that eliminates the purification and amplification processes of viral genomes by extending the recently developed amplification-free digital RNA detection platform called SATORI, allowing the detection of various plant viral genes in a total of less than 15 min with a limit of detection (LoD) of 98 ∼ copies/μL using tomato viruses as an example.

    Incubation:

    Article Title: Purification/Amplification-Free RNA Detection Platform for Rapid and Multiplex Diagnosis of Plant Viral Infections.
    Article Snippet: Genetic tests are highly sensitive, and quantitative methods for diagnosing human viral infections, including COVID-19, are also being used to diagnose plant diseases in various agricultural settings.. Conventional genetic tests for plant viruses are mostly based on methods that require purification and amplification of viral genomes from plant samples, which generally take several hours in total, making it difficult to use them in rapid detection at point-of-care testing (POCT).. In this study, we developed Direct-SATORI, a rapid and robust genetic test that eliminates the purification and amplification processes of viral genomes by extending the recently developed amplification-free digital RNA detection platform called SATORI, allowing the detection of various plant viral genes in a total of less than 15 min with a limit of detection (LoD) of 98 ∼ copies/μL using tomato viruses as an example.

    Article Title: Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis
    Article Snippet: .. To remove the double-stranded RNA contaminations, the transcribed RNA was incubated with RNaseIII (New England Biolabs) at 37 °C for 30 min, and then purified by 8% native polyacrylamide gel electrophoresis. .. The RNA concentration was determined from the A 260 value measured by the NanoDrop spectrophotometer.

    Purification:

    Article Title: Purification/Amplification-Free RNA Detection Platform for Rapid and Multiplex Diagnosis of Plant Viral Infections.
    Article Snippet: Genetic tests are highly sensitive, and quantitative methods for diagnosing human viral infections, including COVID-19, are also being used to diagnose plant diseases in various agricultural settings.. Conventional genetic tests for plant viruses are mostly based on methods that require purification and amplification of viral genomes from plant samples, which generally take several hours in total, making it difficult to use them in rapid detection at point-of-care testing (POCT).. In this study, we developed Direct-SATORI, a rapid and robust genetic test that eliminates the purification and amplification processes of viral genomes by extending the recently developed amplification-free digital RNA detection platform called SATORI, allowing the detection of various plant viral genes in a total of less than 15 min with a limit of detection (LoD) of 98 ∼ copies/μL using tomato viruses as an example.

    Article Title: Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape
    Article Snippet: .. The eluted chromatin was digested for one hour in RNaseIII (NEB, M0245), purified with MinElute PCR purification kit (Qiagen, 28004), and quantified using Nanodrop. .. A negative control treated for 4 hours at 37 °C with RNaseH1 (New England Biolabs) was included for each condition.

    Article Title: Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis
    Article Snippet: .. To remove the double-stranded RNA contaminations, the transcribed RNA was incubated with RNaseIII (New England Biolabs) at 37 °C for 30 min, and then purified by 8% native polyacrylamide gel electrophoresis. .. The RNA concentration was determined from the A 260 value measured by the NanoDrop spectrophotometer.

    Article Title: Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation
    Article Snippet: .. 10 μg of this genomic DNA from HEK293T cells was digested with 50 U EcoRI-HF (NEB, R3101S) and 50 U PvuII-HF (NEB, R3151S) in NEB CutSmart buffer at 37°C for 4 h. To remove RNA moieties, the products were then digested with 0.25 μg/mL RNase A (Thermo Scientific, EN0531), 25 U/ml RNase T1 (Thermo Scientific, EN0541), 25 U/ml RNaseIII (NEB, M0245S) ± RNase H (NEB, M0297S) in NEB RNase H buffer, supplemented with 0.5 mM NaCl at 37°C for 2.5 h. The DNA was subsequently purified using the Slica Bead DNA Gel extraction kit (Thermo Scientific, K0513), according to the manufacturer’s protocol. .. 3 μL of the sample was applied to glow-discharged Quantifoil R1.2/1.3 Cu 300 grids (Quantifoil) and was flash frozen in liquid ethane using Vitrobot mark IV (Thermo Scientific) set at 100% humidity and 8°C for the preparation chamber and 3∼4 s blot time.

    Article Title: Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation.
    Article Snippet: .. 10 mg of this genomic DNA from HEK293T cells was digested with 50 U EcoRI-HF (NEB, R3101S) and 50 U PvuII-HF (NEB, R3151S) in NEB CutSmart buffer at 37 C for 4 h. To remove RNA moieties, the products were then digested with 0.25 mg/mL RNase A (Thermo Scientific, EN0531), 25 U/ml RNase T1 (Thermo Scientific, EN0541), 25 U/ml RNaseIII (NEB, M0245S) ± RNase H (NEB, M0297S) in NEB RNase H buffer, supplemented with 0.5 mM NaCl at 37 C for 2.5 h. The DNA was subsequently purified using the Slica Bead DNA Gel extraction kit (Thermo Scientific, K0513), according to the manufacturer’s protocol. .. Vitrified sample preparation for Cryo-EM 3 mL of the sample was applied to glow-discharged Quantifoil R1.2/ 1.3 Cu 300 grids (Quantifoil) and was flash frozen in liquid ethane using Vitrobot mark IV (Thermo Scientific) set at 100% humidity and 8 C for the preparation chamber and 3 4 s blot time.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Purification/Amplification-Free RNA Detection Platform for Rapid and Multiplex Diagnosis of Plant Viral Infections.
    Article Snippet: Genetic tests are highly sensitive, and quantitative methods for diagnosing human viral infections, including COVID-19, are also being used to diagnose plant diseases in various agricultural settings.. Conventional genetic tests for plant viruses are mostly based on methods that require purification and amplification of viral genomes from plant samples, which generally take several hours in total, making it difficult to use them in rapid detection at point-of-care testing (POCT).. In this study, we developed Direct-SATORI, a rapid and robust genetic test that eliminates the purification and amplification processes of viral genomes by extending the recently developed amplification-free digital RNA detection platform called SATORI, allowing the detection of various plant viral genes in a total of less than 15 min with a limit of detection (LoD) of 98 ∼ copies/μL using tomato viruses as an example.

    Article Title: Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis
    Article Snippet: .. To remove the double-stranded RNA contaminations, the transcribed RNA was incubated with RNaseIII (New England Biolabs) at 37 °C for 30 min, and then purified by 8% native polyacrylamide gel electrophoresis. .. The RNA concentration was determined from the A 260 value measured by the NanoDrop spectrophotometer.

    Sterility:

    Article Title: Chronic viral mimicry induction following p53 loss promotes immune evasion
    Article Snippet: .. Double digestion reactions were prepared as follows: 1 μg cytosolic nucleic acids, 1x NEB ShortCutBuffer, 20mM MnCl 2 , RNaseIII (NEB M0245S) at 1U enzyme / 1 μg nucleic acids, RNaseI (NEB M0243L) at 1U enzyme / 0.5 μg nucleic acids and sterile H 2 O up to 10uL total volume per reaction. ..

    Polymerase Chain Reaction:

    Article Title: Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape
    Article Snippet: .. The eluted chromatin was digested for one hour in RNaseIII (NEB, M0245), purified with MinElute PCR purification kit (Qiagen, 28004), and quantified using Nanodrop. .. A negative control treated for 4 hours at 37 °C with RNaseH1 (New England Biolabs) was included for each condition.

    Gel Extraction:

    Article Title: Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation
    Article Snippet: .. 10 μg of this genomic DNA from HEK293T cells was digested with 50 U EcoRI-HF (NEB, R3101S) and 50 U PvuII-HF (NEB, R3151S) in NEB CutSmart buffer at 37°C for 4 h. To remove RNA moieties, the products were then digested with 0.25 μg/mL RNase A (Thermo Scientific, EN0531), 25 U/ml RNase T1 (Thermo Scientific, EN0541), 25 U/ml RNaseIII (NEB, M0245S) ± RNase H (NEB, M0297S) in NEB RNase H buffer, supplemented with 0.5 mM NaCl at 37°C for 2.5 h. The DNA was subsequently purified using the Slica Bead DNA Gel extraction kit (Thermo Scientific, K0513), according to the manufacturer’s protocol. .. 3 μL of the sample was applied to glow-discharged Quantifoil R1.2/1.3 Cu 300 grids (Quantifoil) and was flash frozen in liquid ethane using Vitrobot mark IV (Thermo Scientific) set at 100% humidity and 8°C for the preparation chamber and 3∼4 s blot time.

    Article Title: Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation.
    Article Snippet: .. 10 mg of this genomic DNA from HEK293T cells was digested with 50 U EcoRI-HF (NEB, R3101S) and 50 U PvuII-HF (NEB, R3151S) in NEB CutSmart buffer at 37 C for 4 h. To remove RNA moieties, the products were then digested with 0.25 mg/mL RNase A (Thermo Scientific, EN0531), 25 U/ml RNase T1 (Thermo Scientific, EN0541), 25 U/ml RNaseIII (NEB, M0245S) ± RNase H (NEB, M0297S) in NEB RNase H buffer, supplemented with 0.5 mM NaCl at 37 C for 2.5 h. The DNA was subsequently purified using the Slica Bead DNA Gel extraction kit (Thermo Scientific, K0513), according to the manufacturer’s protocol. .. Vitrified sample preparation for Cryo-EM 3 mL of the sample was applied to glow-discharged Quantifoil R1.2/ 1.3 Cu 300 grids (Quantifoil) and was flash frozen in liquid ethane using Vitrobot mark IV (Thermo Scientific) set at 100% humidity and 8 C for the preparation chamber and 3 4 s blot time.



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    Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + <t>RNaseIII</t> + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).
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    Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + <t>RNaseIII</t> + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).
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    Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + <t>RNaseIII</t> + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).
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    Image Search Results


    Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + RNaseIII + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).

    Journal: Nucleic Acids Research

    Article Title: Synergistic action of human RNaseH2 and the RNA helicase-nuclease DDX3X in processing R-loops

    doi: 10.1093/nar/gkae731

    Figure Lengend Snippet: Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + RNaseIII + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).

    Article Snippet: Enzymatic treatments were done in staining buffer supplemented with 3 mM magnesium chloride with 1:200 dilutions of RNaseT1 (EN0541; ThermoFisher Scientific), RNaseIII (AM2290; ThermoFisher Scientific) and RNaseH (M0297; NEB) and incubated for 1 h at room temperature.

    Techniques: Immunofluorescence, Transfection, Control, Two Tailed Test, Dot Blot

    Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + RNaseIII + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).

    Journal: Nucleic Acids Research

    Article Title: Synergistic action of human RNaseH2 and the RNA helicase-nuclease DDX3X in processing R-loops

    doi: 10.1093/nar/gkae731

    Figure Lengend Snippet: Silencing of DDX3X in human cells causes accumulation of genomic R-loops and phosphorylated RPA foci. ( A ) Representative immunofluorescence images obtained using antibodies against RNA:DNA hybrids (S9.6, red) and pRPA (green) after transfection of U2OS cells with control (si-control), DDX3X (siDDX3X), RNaseH2 (siRNaseH2A + siRNAseH2B) or DDX3X and RNaseH2 (siDDX3X + siRNaseH2A + siRNaseH2B) siRNAs. Treatment with RNaseH + RNaseIII + RNaseT1 was used to exclude unspecific S9.6 signals. Scale bars, 10 μm. ( B ) Quantification of mean nuclear intensity of phospho-RPA and S9.6 foci of control and DDX3X, RNaseH2A + B and DDX3x + RNaseH2A + B-depleted U2OS cells. Median with interquartile range (black lines) are indicated. P values were calculated using two-tailed unpaired Student's t test. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, not significant ( P < 0.05). At least 300 nuclei from three different experiments were analyzed. ( C ) Quantification of RNA:DNA hybrid Dot-blot of genomic DNA ± RNase H for all the siRNA conditions. S9.6 signals are normalized to dsDNA signal. P values were calculated using two-tailed unpaired Student's t test (means ± SEM; n ≥ 2).

    Article Snippet: We used 1U of RNaseIII (AM2290; ThermoFisher Scientific) per μg of genomic DNA for 2 h at 37°C and 10 U of RNaseH (M0297; NEB) per μg of DNA O/N at 37°C.

    Techniques: Immunofluorescence, Transfection, Control, Two Tailed Test, Dot Blot