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Thermo Fisher rnase h
Rnase H, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/rnase h/product/Thermo Fisher
Average 99 stars, based on 116 article reviews
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rnase h - by Bioz Stars, 2020-01
99/100 stars

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Amplification:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: Paragraph title: qRT-PCR amplification analyses. ... RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
Article Snippet: The reverse transcription (RT) reaction mixture was incubated at 50°C for 1 h, then 55°C for 1 h, and then 70°C for 15 min, after which 4 units of RNase H (Invitrogen) was added and samples were incubated at 37°C for 20 min. .. Samples were stored at −80°C prior to amplicon generation.

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: .. Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min. .. The resulting cDNA products were diluted in a final volume of 200 μl and a 2-μl aliquot was used as template for subsequent quantification by real-time PCR amplification.

Article Title: Inhibition of Ongoing Influenza A Virus Replication Reveals Different Mechanisms of RIG-I Activation
Article Snippet: .. The cDNA was treated with RNase H (Invitrogen), followed by PCR amplification with segment-specific primers for PB2, PB1, PA, and NA using Q5 high-fidelity DNA polymerase (NEB). ..

Article Title: T-Cell Growth Transformation by Herpesvirus Saimiri Is Independent of STAT3 Activation
Article Snippet: Paragraph title: RNA isolation, cDNA synthesis, and amplification. ... RNA complementary to the cDNA was removed by addition of 1 U of RNase H (MBI Fermentas) and incubation for 20 min at 37°C.

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA). .. After end repair, adaptor ligation, and the addition of index codes for each sample, PCR amplification was conducted.

Expressing:

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Sequencing libraries were constructed following the protocol of the Gene Expression Sample Prep Kit (Illumina, San Diego, CA, USA). .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Article Title: Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6
Article Snippet: Paragraph title: Gene expression analysis ... RNA complimentary to cDNA was removed using 1 μL of RNase H (Invitrogen).

Synthesized:

Article Title: Loss of Leukemia Inhibitory Factor Receptor β or Cardiotrophin-1 Causes Similar Deficits in Preganglionic Sympathetic Neurons and Adrenal Medulla
Article Snippet: First-strand cDNA was synthesized in a final volume of 40 μl. .. The reaction mixture was incubated at 37°C for 2 h, heated for 5 min at 90°C, cooled to 4°C for 5 min, and supplemented with 2 U of RNase H (Invitrogen).

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: Total RNA was extracted using NucleoSpin RNA II columns (Macherey-Nagel) according to the manufacturer’s instructions. cDNA was synthesized by reverse transcription of 1 μg total RNA in a total volume of 20 μl containing 1X reverse transcriptase buffer (Invitrogen), 25 μg/ml oligo (dT)12–18 (Invitrogen), 0.5 mM dNTP mix (GeneChoice), 10 mM dithiothreitol (Invitrogen), 20 U of RNase inhibitor (RNasin®, Promega), and 100 U of SuperScript™ II reverse transcriptase (Invitrogen). .. Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min.

Article Title: Genome Organization Drives Chromosome Fragility
Article Snippet: .. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), following AMPure XP purification (1.8X) and elution in 20 µl second-strand cDNA was synthesized with 0.6 mM dNTPs in the presence of 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 µl for 2.5 hours at 16°C. ..

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA). .. After end repair, adaptor ligation, and the addition of index codes for each sample, PCR amplification was conducted.

Quantitative RT-PCR:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: Paragraph title: qRT-PCR amplification analyses. ... RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: Paragraph title: RNA isolation and real-time RT-PCR ... Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min.

Real-time Polymerase Chain Reaction:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C. .. Quantitative real-time PCR (qRT-PCR) amplification was performed separately with two sets of primers for each cDNA sample.

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min. .. The resulting cDNA products were diluted in a final volume of 200 μl and a 2-μl aliquot was used as template for subsequent quantification by real-time PCR amplification.

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter). .. Relative concentrations of cDNA were then determined by qPCR.).

Article Title: Chorionic Somatomammotropin Impacts Early Fetal Growth and Placental Gene Expression
Article Snippet: Paragraph title: cDNA synthesis and quantitative real-time PCR ... All cDNA samples were treated with 5 units of RNase H (Thermo Fisher Scientific, Waltham, MA) at 37°C for 20 minutes.

Random Hexamer Labeling:

Article Title: Loss of Leukemia Inhibitory Factor Receptor β or Cardiotrophin-1 Causes Similar Deficits in Preganglionic Sympathetic Neurons and Adrenal Medulla
Article Snippet: Reactions consisted of 3 μg of total RNA and final concentrations of 1× first-strand buffer [5× first-strand buffer (in m m ): 250 Tris-HCl, pH 8.3, 375 KCl, and 15 MgCl2 ; Invitrogen, Karlsruhe, Germany], 10 m m dithiothreitol (DTT), 1 m m each of deoxynucleotide triphosphates (dNTPs; Amersham Biosciences, Freiburg, Germany), 25 ng/μl random hexamer primers (Roche Diagnostics, Mannheim, Germany) or oligo-dT primers (Promega, Madison, WI), 1 U/μl RNase inhibitor (Fermentas), and 20 U/μl Moloney murine leukemia virus (M-MLV) reverse transcriptase (Invitrogen). .. The reaction mixture was incubated at 37°C for 2 h, heated for 5 min at 90°C, cooled to 4°C for 5 min, and supplemented with 2 U of RNase H (Invitrogen).

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA). .. After end repair, adaptor ligation, and the addition of index codes for each sample, PCR amplification was conducted.

Mass Spectrometry:

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ). .. High performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) was performed for quantitative assessment of the 2’-O-methylation status of the target nucleotide as described earlier ( ).

Gel Purification:

Article Title: Visualizing the splicing of single pre-mRNA molecules in whole cell extract
Article Snippet: Oligo 6 , representing the first 26 nt of the capped 5′-exon, was prepared by first transcribing (trace [α-32 P]UTP-labeled) full-length RP51A pre-mRNA with T7 RNA polymerase, followed by gel purification on a 5% 1× TBE denaturing gel. .. The 26-nt fragment was then generated by RNase H (Invitrogen) cleavage with a chimeric 2′- O -methyl RNA/DNA oligonucleotide (oligo 7 ) ( ; ; ) and purification on a 5% × TBE denaturing gel.

High Performance Liquid Chromatography:

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: Paragraph title: RNase H- and HPLC-MS/MS-Based Method ... The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ).

Sequencing:

Article Title: Acetylation of cytidine in messenger RNA promotes translation efficiency
Article Snippet: For this purpose, primer complementary to the probe sequence (5 pmol, 5’-CACATTCTACC-3’) was radiolabeled with 20 U T4 Polynucleotide kinase (NEB) and 10 μCi 32 P-γATP (3000 Ci/mmol, PerkinElmer) in a 10 μl reaction. .. Reactions were stopped by heating at 95 °C for 5 min. Template RNA was digested with 2U RNase H (ThermoFisher Scientific) for 30 min at 37 °C and reactions were stopped by adding one volume of 2× loading dye (95% formamide, 0.025% bromophenol blue, 0.025% xylene cyanol, 0.5 mM EDTA) and heating at 95 °C for 5 min. RT products were resolved in 8M Urea/8% PAGE gels and examined through phosphorimager analysis.

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: Paragraph title: Preparation of RNA for high-throughput sequencing ... The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter).

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Paragraph title: 4.3. Transcriptome Sequencing and Data Analysis ... The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Article Title: Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6
Article Snippet: RNA complimentary to cDNA was removed using 1 μL of RNase H (Invitrogen). .. Gene expression was assessed by Sanger sequencing of PCR-amplified cDNA.

Ligation:

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA). .. After end repair, adaptor ligation, and the addition of index codes for each sample, PCR amplification was conducted.

Biomarker Assay:

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Transcriptome Sequencing and Data Analysis RNA extraction, transcriptome library preparation, sequencing, and bioinformatics analysis were conducted at the Biomarker Technologies (Beijing, China, www.biomarker.com.cn ) following their standard procedures and previously described by Zhu et al. [ ]. .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Northern Blot:

Article Title: The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA
Article Snippet: After incubation of the mixtures for 10 min at room temperature, 2 units of RNase H (Invitrogen, catalog no. 18021071) were added, and the reactions were incubated at the same temperature for 1 h. TRIzol reagent (Invitrogen, catalog no. 15596026) was used to isolate the RNA from the reactions according to the manufacturer's instructions. .. RNA was fractionated on denaturing polyacrylamide gels containing 8 m urea, transferred to Hybond-N+ nylon membrane (Amersham Biosciences), and subjected to Northern blotting with 5′-end 32 P-labeled probe against the T. brucei vtRNA (5′-CTTTGCTGTTTGCTATGCAGAAGTATC-3′) using standard procedures.

Cell Culture:

Article Title: Inhibition of Ongoing Influenza A Virus Replication Reveals Different Mechanisms of RIG-I Activation
Article Snippet: Viral genomic/subgenomic RNA was extracted from chicken egg allantoic fluids or MDCK cell culture supernatants using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. .. The cDNA was treated with RNase H (Invitrogen), followed by PCR amplification with segment-specific primers for PB2, PB1, PA, and NA using Q5 high-fidelity DNA polymerase (NEB).

Generated:

Article Title: Visualizing the splicing of single pre-mRNA molecules in whole cell extract
Article Snippet: .. The 26-nt fragment was then generated by RNase H (Invitrogen) cleavage with a chimeric 2′- O -methyl RNA/DNA oligonucleotide (oligo 7 ) ( ; ; ) and purification on a 5% × TBE denaturing gel. .. Oligo 8 , a 308-nt fragment representing most of the intron and the 3′-exon, was prepared by transcription of a trace [α-32 P]UTP-labeled RP51A RNA generated from a PCR template initiated 17 nt downstream from the 5′-splice site, followed by gel purification and RNase H cleavage (with oligo 9 ) as above.

Article Title: Chorionic Somatomammotropin Impacts Early Fetal Growth and Placental Gene Expression
Article Snippet: cDNA was generated from 1 μg of total cellular RNA using iScript Reverse Transcription Supermix (Bio-Rad, Hercules, CA) according to the manufacturer’s protocol. .. All cDNA samples were treated with 5 units of RNase H (Thermo Fisher Scientific, Waltham, MA) at 37°C for 20 minutes.

Reverse Transcription Polymerase Chain Reaction:

Article Title: T-Cell Growth Transformation by Herpesvirus Saimiri Is Independent of STAT3 Activation
Article Snippet: The samples were then divided into two parallel reaction mixtures and processed with the ThermoScript reverse transcription PCR (RT-PCR) system (Invitrogen) in 20-μl reaction mixtures with or without reverse transcriptase according to the supplier's protocol. .. RNA complementary to the cDNA was removed by addition of 1 U of RNase H (MBI Fermentas) and incubation for 20 min at 37°C.

Cleavage Assay:

Article Title: The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA
Article Snippet: Paragraph title: RNase H cleavage assay ... After incubation of the mixtures for 10 min at room temperature, 2 units of RNase H (Invitrogen, catalog no. 18021071) were added, and the reactions were incubated at the same temperature for 1 h. TRIzol reagent (Invitrogen, catalog no. 15596026) was used to isolate the RNA from the reactions according to the manufacturer's instructions.

Marker:

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min. .. Quantitative real-time PCR was performed in a 25 μl reaction mixture containing 1X BD QTaq polymerase reaction mix (BD Biosciences), 1X SybrGreen (Invitrogen) as a marker of DNA amplification, and 0.1 μM of each primer.

RNA Sequencing Assay:

Article Title: Genome Organization Drives Chromosome Fragility
Article Snippet: For Nascent RNA-seq, B cell cultures stimulated for 12 hours and 4 million were labeled with 0.5 mM 5-ethynyl uridine (EU) for 30 minutes. .. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), following AMPure XP purification (1.8X) and elution in 20 µl second-strand cDNA was synthesized with 0.6 mM dNTPs in the presence of 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 µl for 2.5 hours at 16°C.

Magnetic Beads:

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: .. The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter). .. Relative concentrations of cDNA were then determined by qPCR.).

Isolation:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: RNA was isolated from wild-type cells grown in RL and GL as described previously ( ). .. RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: Paragraph title: RNA isolation and real-time RT-PCR ... Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min.

Article Title: T-Cell Growth Transformation by Herpesvirus Saimiri Is Independent of STAT3 Activation
Article Snippet: Paragraph title: RNA isolation, cDNA synthesis, and amplification. ... RNA complementary to the cDNA was removed by addition of 1 U of RNase H (MBI Fermentas) and incubation for 20 min at 37°C.

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: RNase H- and HPLC-MS/MS-Based Method For analysis of the 2’-O-methylation status by HPLC-MS/MS, rRNA was separated from short RNA forms using miRNA isolation kit LRU-100-50 (BIOLABMIX Ltd., Novosibirsk, Russia). .. The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ).

Size-exclusion Chromatography:

Article Title: Acetylation of cytidine in messenger RNA promotes translation efficiency
Article Snippet: RT reactions were initiated by adding one volume of a mixture containing 0.5 mM dNTPs, 50 U SuperScript III (ThermoFisher Scientific), 40 U RNase Out (ThermoFisher Scientific), 1× SuperScript buffer (ThermoFisher Scientific), 5 mM MgCl2 and 0.05 mM DTT in a 20 μl reaction for 15, 30, 60 or 120 sec at 50 °C. .. Reactions were stopped by heating at 95 °C for 5 min. Template RNA was digested with 2U RNase H (ThermoFisher Scientific) for 30 min at 37 °C and reactions were stopped by adding one volume of 2× loading dye (95% formamide, 0.025% bromophenol blue, 0.025% xylene cyanol, 0.5 mM EDTA) and heating at 95 °C for 5 min. RT products were resolved in 8M Urea/8% PAGE gels and examined through phosphorimager analysis.

Labeling:

Article Title: Genome Organization Drives Chromosome Fragility
Article Snippet: For Nascent RNA-seq, B cell cultures stimulated for 12 hours and 4 million were labeled with 0.5 mM 5-ethynyl uridine (EU) for 30 minutes. .. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), following AMPure XP purification (1.8X) and elution in 20 µl second-strand cDNA was synthesized with 0.6 mM dNTPs in the presence of 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 µl for 2.5 hours at 16°C.

Article Title: Visualizing the splicing of single pre-mRNA molecules in whole cell extract
Article Snippet: Paragraph title: Preparation of fluorescently labeled RP51A-biotin pre-mRNAs ... The 26-nt fragment was then generated by RNase H (Invitrogen) cleavage with a chimeric 2′- O -methyl RNA/DNA oligonucleotide (oligo 7 ) ( ; ; ) and purification on a 5% × TBE denaturing gel.

Purification:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: Purified RNA was treated with a Turbo DNA-free kit (Ambion, Austin, TX) to remove genomic DNA according to the manufacturer's instructions. .. RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: .. The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter). .. Relative concentrations of cDNA were then determined by qPCR.).

Article Title: Genome Organization Drives Chromosome Fragility
Article Snippet: .. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), following AMPure XP purification (1.8X) and elution in 20 µl second-strand cDNA was synthesized with 0.6 mM dNTPs in the presence of 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 µl for 2.5 hours at 16°C. ..

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Briefly, total RNA was extracted from the leaf samples using a Spin Column Plant total RNA Purification Kit (Sangon Biotech, Shanghai, China) according to the manufacturer’s instructions. .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Article Title: Visualizing the splicing of single pre-mRNA molecules in whole cell extract
Article Snippet: .. The 26-nt fragment was then generated by RNase H (Invitrogen) cleavage with a chimeric 2′- O -methyl RNA/DNA oligonucleotide (oligo 7 ) ( ; ; ) and purification on a 5% × TBE denaturing gel. .. Oligo 8 , a 308-nt fragment representing most of the intron and the 3′-exon, was prepared by transcription of a trace [α-32 P]UTP-labeled RP51A RNA generated from a PCR template initiated 17 nt downstream from the 5′-splice site, followed by gel purification and RNase H cleavage (with oligo 9 ) as above.

Polymerase Chain Reaction:

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter). .. Five cycles were used in the first round of PCR and 4–6 cycles were used in the second round (based on cDNA qPCR results).

Article Title: Inhibition of Ongoing Influenza A Virus Replication Reveals Different Mechanisms of RIG-I Activation
Article Snippet: .. The cDNA was treated with RNase H (Invitrogen), followed by PCR amplification with segment-specific primers for PB2, PB1, PA, and NA using Q5 high-fidelity DNA polymerase (NEB). ..

Article Title: T-Cell Growth Transformation by Herpesvirus Saimiri Is Independent of STAT3 Activation
Article Snippet: The samples were then divided into two parallel reaction mixtures and processed with the ThermoScript reverse transcription PCR (RT-PCR) system (Invitrogen) in 20-μl reaction mixtures with or without reverse transcriptase according to the supplier's protocol. .. RNA complementary to the cDNA was removed by addition of 1 U of RNase H (MBI Fermentas) and incubation for 20 min at 37°C.

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA). .. After end repair, adaptor ligation, and the addition of index codes for each sample, PCR amplification was conducted.

Article Title: Visualizing the splicing of single pre-mRNA molecules in whole cell extract
Article Snippet: The 26-nt fragment was then generated by RNase H (Invitrogen) cleavage with a chimeric 2′- O -methyl RNA/DNA oligonucleotide (oligo 7 ) ( ; ; ) and purification on a 5% × TBE denaturing gel. .. Oligo 8 , a 308-nt fragment representing most of the intron and the 3′-exon, was prepared by transcription of a trace [α-32 P]UTP-labeled RP51A RNA generated from a PCR template initiated 17 nt downstream from the 5′-splice site, followed by gel purification and RNase H cleavage (with oligo 9 ) as above.

Article Title: Identification and targeted management of a neurodegenerative disorder caused by biallelic mutations in SLC5A6
Article Snippet: RNA complimentary to cDNA was removed using 1 μL of RNase H (Invitrogen). .. Gene expression was assessed by Sanger sequencing of PCR-amplified cDNA.

Construct:

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Sequencing libraries were constructed following the protocol of the Gene Expression Sample Prep Kit (Illumina, San Diego, CA, USA). .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Polyacrylamide Gel Electrophoresis:

Article Title: Acetylation of cytidine in messenger RNA promotes translation efficiency
Article Snippet: .. Reactions were stopped by heating at 95 °C for 5 min. Template RNA was digested with 2U RNase H (ThermoFisher Scientific) for 30 min at 37 °C and reactions were stopped by adding one volume of 2× loading dye (95% formamide, 0.025% bromophenol blue, 0.025% xylene cyanol, 0.5 mM EDTA) and heating at 95 °C for 5 min. RT products were resolved in 8M Urea/8% PAGE gels and examined through phosphorimager analysis. .. To confirm anti-ac4C antibody enrichment potential, RNA immunoprecipitation was performed on the in vitro transcribed probes.

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: .. The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ). ..

Software:

Article Title: Chorionic Somatomammotropin Impacts Early Fetal Growth and Placental Gene Expression
Article Snippet: All cDNA samples were treated with 5 units of RNase H (Thermo Fisher Scientific, Waltham, MA) at 37°C for 20 minutes. .. Forward and reverse primers for qPCR were designed using Oligo software (Molecular Biology Insights, Cascade, CO) to amplify an intron-spanning product.

RNA Extraction:

Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
Article Snippet: Paragraph title: Viral RNA extraction and cDNA synthesis. ... The reverse transcription (RT) reaction mixture was incubated at 50°C for 1 h, then 55°C for 1 h, and then 70°C for 15 min, after which 4 units of RNase H (Invitrogen) was added and samples were incubated at 37°C for 20 min.

Article Title: Genome Organization Drives Chromosome Fragility
Article Snippet: Total RNA extraction was performed using TRIzol (Ambion) and 1 µg was rRNA depleted using the NEBNext rRNA Depletion kit (human/mouse/rat) (New England Biosciences), prior to biotinylation by the Click-it reaction (Click-iT Nascent RNA Capture Kit, ThermoFisher ) using manofacture’s specification. .. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), following AMPure XP purification (1.8X) and elution in 20 µl second-strand cDNA was synthesized with 0.6 mM dNTPs in the presence of 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 µl for 2.5 hours at 16°C.

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Transcriptome Sequencing and Data Analysis RNA extraction, transcriptome library preparation, sequencing, and bioinformatics analysis were conducted at the Biomarker Technologies (Beijing, China, www.biomarker.com.cn ) following their standard procedures and previously described by Zhu et al. [ ]. .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

Sample Prep:

Article Title: Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers
Article Snippet: Sequencing libraries were constructed following the protocol of the Gene Expression Sample Prep Kit (Illumina, San Diego, CA, USA). .. The first-strand cDNAs were synthesized from the total RNA with random hexamer primers, followed by second-strand cDNAs synthesis using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) and RNase H (Invitrogen, Waltham, MA, USA).

In Vitro:

Article Title: Acetylation of cytidine in messenger RNA promotes translation efficiency
Article Snippet: To evaluate whether ac4C affects reverse transcription, first strand cDNA synthesis was performed on the C- or ac4C-RNA probes (see in vitro transcription). .. Reactions were stopped by heating at 95 °C for 5 min. Template RNA was digested with 2U RNase H (ThermoFisher Scientific) for 30 min at 37 °C and reactions were stopped by adding one volume of 2× loading dye (95% formamide, 0.025% bromophenol blue, 0.025% xylene cyanol, 0.5 mM EDTA) and heating at 95 °C for 5 min. RT products were resolved in 8M Urea/8% PAGE gels and examined through phosphorimager analysis.

Incubation:

Article Title: Loss of Leukemia Inhibitory Factor Receptor β or Cardiotrophin-1 Causes Similar Deficits in Preganglionic Sympathetic Neurons and Adrenal Medulla
Article Snippet: .. The reaction mixture was incubated at 37°C for 2 h, heated for 5 min at 90°C, cooled to 4°C for 5 min, and supplemented with 2 U of RNase H (Invitrogen). .. Total RNA (1 μg per reaction) was denatured for 5 min at 70°C and then reverse transcribed for 60 min at 42°C in 1× first-strand buffer (Invitrogen) containing 20 U of RNase inhibitor (Fermentas), 10 m m DTT, 1.5 μ m oligo-dT, 0.3 m m dNTPs (Amersham Biosciences), and 200 U of M-MLV reverse transcriptase (Invitrogen).

Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
Article Snippet: .. The reverse transcription (RT) reaction mixture was incubated at 50°C for 1 h, then 55°C for 1 h, and then 70°C for 15 min, after which 4 units of RNase H (Invitrogen) was added and samples were incubated at 37°C for 20 min. .. Samples were stored at −80°C prior to amplicon generation.

Article Title: Long term low-dose arsenic exposure induces loss of DNA methylation
Article Snippet: .. Before amplification, the reverse transcriptase was inactivated by heating to 70ºC for 15 min, and RNA was hydrolyzed by incubation with 2 U RNase H (Invitrogen) at 37°C for 20 min. .. The resulting cDNA products were diluted in a final volume of 200 μl and a 2-μl aliquot was used as template for subsequent quantification by real-time PCR amplification.

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: .. The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter). .. Relative concentrations of cDNA were then determined by qPCR.).

Article Title: The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA
Article Snippet: .. After incubation of the mixtures for 10 min at room temperature, 2 units of RNase H (Invitrogen, catalog no. 18021071) were added, and the reactions were incubated at the same temperature for 1 h. TRIzol reagent (Invitrogen, catalog no. 15596026) was used to isolate the RNA from the reactions according to the manufacturer's instructions. .. RNA was fractionated on denaturing polyacrylamide gels containing 8 m urea, transferred to Hybond-N+ nylon membrane (Amersham Biosciences), and subjected to Northern blotting with 5′-end 32 P-labeled probe against the T. brucei vtRNA (5′-CTTTGCTGTTTGCTATGCAGAAGTATC-3′) using standard procedures.

Article Title: T-Cell Growth Transformation by Herpesvirus Saimiri Is Independent of STAT3 Activation
Article Snippet: .. RNA complementary to the cDNA was removed by addition of 1 U of RNase H (MBI Fermentas) and incubation for 20 min at 37°C. ..

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: .. The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ). ..

Spectrophotometry:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: The concentration and purity of the RNA were determined spectrophotometrically using a Beckman DU640B spectrophotometer. .. RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Concentration Assay:

Article Title: Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness ▿
Article Snippet: The concentration and purity of the RNA were determined spectrophotometrically using a Beckman DU640B spectrophotometer. .. RNA was removed by RNase H (Invitrogen, Carlsbad, CA) treatment for 20 min at 37°C.

Article Title: Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells
Article Snippet: .. The following pair of oligonucleotides was used: 5’-CACTTATTCTACACACCTC-3’ and 5’-CTCCCCCCACGGCACTGTC-3’ Next, RNase H (Thermo Scientific, USA) was added to the reaction mixture to a final concentration of 80 U/ml and incubated at 37 °C for 2 h. The RNase H cleavage products were precipitated in 2% LiClO4/acetone and then separated on a denaturing Page gel ( ). ..

High Throughput Screening Assay:

Article Title: Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching
Article Snippet: Paragraph title: Preparation of RNA for high-throughput sequencing ... The RNA was then degraded by incubation with RNase A (0.5 µg/µL; Thermo Fisher Scientific) and RNase H (0.1 U/µL; Invitrogen) at 37°C for 1 h. The resulting cDNA was purified using Agencourt Ampure XP magnetic beads (Beckman Coulter).

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    Thermo Fisher rnase h
    Determination of the cleavage site by site-specific disconnection (SSD) . ( a ) Sequences of the fluorescein isothiocyanate (FITC)-labelled DNA/RNA chimeric oligomer. The red text indicates the DNA sequence, and the other text indicates the RNA portion that is complementary to the Aid-DNA (purple, italicized, underlined characters indicate the sequence of 2′-O-methyl-modified nucleotides). The expected cleavage site “UG” was shown by the green arrow. ( b ) Analysis of the cleavage product. Compared to the standard samples, the length of cleavage product was determined to be 17 nt. Other conditions used were 1.0 μmol/l substrate and Aid-DNA-16-1, 125 U/ml RNase H, 37 °C, 40 minutes, 20% denaturing urea polyacrylamide gel electrophoresis (PAGE).
    Rnase H, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Determination of the cleavage site by site-specific disconnection (SSD) . ( a ) Sequences of the fluorescein isothiocyanate (FITC)-labelled DNA/RNA chimeric oligomer. The red text indicates the DNA sequence, and the other text indicates the RNA portion that is complementary to the Aid-DNA (purple, italicized, underlined characters indicate the sequence of 2′-O-methyl-modified nucleotides). The expected cleavage site “UG” was shown by the green arrow. ( b ) Analysis of the cleavage product. Compared to the standard samples, the length of cleavage product was determined to be 17 nt. Other conditions used were 1.0 μmol/l substrate and Aid-DNA-16-1, 125 U/ml RNase H, 37 °C, 40 minutes, 20% denaturing urea polyacrylamide gel electrophoresis (PAGE).

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Preparation of Small RNAs Using Rolling Circle Transcription and Site-Specific RNA Disconnection

    doi: 10.1038/mtna.2014.66

    Figure Lengend Snippet: Determination of the cleavage site by site-specific disconnection (SSD) . ( a ) Sequences of the fluorescein isothiocyanate (FITC)-labelled DNA/RNA chimeric oligomer. The red text indicates the DNA sequence, and the other text indicates the RNA portion that is complementary to the Aid-DNA (purple, italicized, underlined characters indicate the sequence of 2′-O-methyl-modified nucleotides). The expected cleavage site “UG” was shown by the green arrow. ( b ) Analysis of the cleavage product. Compared to the standard samples, the length of cleavage product was determined to be 17 nt. Other conditions used were 1.0 μmol/l substrate and Aid-DNA-16-1, 125 U/ml RNase H, 37 °C, 40 minutes, 20% denaturing urea polyacrylamide gel electrophoresis (PAGE).

    Article Snippet: Then, the mixture with RNase H was kept at 37 °C for 40 minutes, followed by inactivation of the RNase H at 65 °C for 10 minutes.

    Techniques: Sequencing, Modification, Polyacrylamide Gel Electrophoresis

    Synthesis of the mir-16 oligomer using rolling circle transcription (RCT) site-specific disconnection (SSD) . ( a ) Ligation products of the cDNA and transcript of the RCT reaction on circular cDNA. C72, C66, and C60 are synthesized circular ssDNA oligomers used as markers; Lane L, RNA ladder. Samples were separated by 14% denaturing PAGE (8 mol/l urea). ( b ) Analysis of synthesized mir-16. Lane 1, chemically synthesized mir-16; lane 2, RNase H was absent during RCT; lane 3, RNase-H (2.5 U/ml) was present during RCT. Samples were separated by 20% denaturing PAGE (8 mol/l urea). Other conditions used for RCT were: 0.5 μmol/l cDNA, 2.5 U/ml RNA polymerase, 37 °C, 2 hours; other conditions used for SSD were, 125 U/ml RNase H, 1.0 μmol/l Aid-DNA, 37 °C, 2 hours.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Preparation of Small RNAs Using Rolling Circle Transcription and Site-Specific RNA Disconnection

    doi: 10.1038/mtna.2014.66

    Figure Lengend Snippet: Synthesis of the mir-16 oligomer using rolling circle transcription (RCT) site-specific disconnection (SSD) . ( a ) Ligation products of the cDNA and transcript of the RCT reaction on circular cDNA. C72, C66, and C60 are synthesized circular ssDNA oligomers used as markers; Lane L, RNA ladder. Samples were separated by 14% denaturing PAGE (8 mol/l urea). ( b ) Analysis of synthesized mir-16. Lane 1, chemically synthesized mir-16; lane 2, RNase H was absent during RCT; lane 3, RNase-H (2.5 U/ml) was present during RCT. Samples were separated by 20% denaturing PAGE (8 mol/l urea). Other conditions used for RCT were: 0.5 μmol/l cDNA, 2.5 U/ml RNA polymerase, 37 °C, 2 hours; other conditions used for SSD were, 125 U/ml RNase H, 1.0 μmol/l Aid-DNA, 37 °C, 2 hours.

    Article Snippet: Then, the mixture with RNase H was kept at 37 °C for 40 minutes, followed by inactivation of the RNase H at 65 °C for 10 minutes.

    Techniques: Ligation, Synthesized, Polyacrylamide Gel Electrophoresis

    Strategy for rolling circle transcription (RCT) site-specific disconnection (SSD) synthesis . cDNA is circularized to form a circular DNA template, and long RNA strands are generated by RCT consisting of tandem repeats of desired RNA. With the help of Aid-DNA, RNase H disconnects the transcript to generate thousands of copies of the desired RNA.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Preparation of Small RNAs Using Rolling Circle Transcription and Site-Specific RNA Disconnection

    doi: 10.1038/mtna.2014.66

    Figure Lengend Snippet: Strategy for rolling circle transcription (RCT) site-specific disconnection (SSD) synthesis . cDNA is circularized to form a circular DNA template, and long RNA strands are generated by RCT consisting of tandem repeats of desired RNA. With the help of Aid-DNA, RNase H disconnects the transcript to generate thousands of copies of the desired RNA.

    Article Snippet: Then, the mixture with RNase H was kept at 37 °C for 40 minutes, followed by inactivation of the RNase H at 65 °C for 10 minutes.

    Techniques: Generated