RNase R
Cat. No.
E049
Unit
500 U (50 μl)
Price
$310.00
Specifications
| SKU | E049 | ||
| Name | RNase R | ||
| Unit | 500 U (50 μl) | ||
| Caution | This product is distributed for laboratory research only. Not for diagnostic use. | ||
| Reaction Buffer | 200 mM Tris-HCl, 1 M KCl, 10 mM MgCl2, pH 7.5 | ||
| Expression System | Recombinant E. coli | ||
| Reaction Definition | Use 1X RNase R Reaction Buffer and incubate at 37°C. One unit is defined as the amount of RNase R that converts 1 µg of poly(A) into acid-soluble nucleotides in 10 minutes at 37°C. | ||
| Description |
RNase R is an E. coli exoribonuclease which exhibits 3'-to-5' exonuclease activity, efficiently digesting nearly all linear RNA species. This enzyme does not digest circular, lariat, or double stranded RNA with short 3’ overhangs (less than seven nucleotides). As such, this enzyme is ideally suited to the study of lariat RNA produced by traditional splicing, as well as circRNAs which arise through back-splicing. By removing linear RNAs from cellular or RNA extracts, RNase R greatly facilitates the identification of circular species through RNA-sequencing. This enables researchers to probe the landscape of splicing events with greater depth. |
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| Applications |
• Enriching circRNAs in biological samples |
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| Concentration | 10 U/μl | ||
| Format | Enzyme supplied with 10X Reaction Buffer. | ||
| Storage Buffer | 50 mM Tris-HCl (pH 7.5), 100mM NaCl, 0.1 mM EDTA, 1 mM DTT, and 50% (v/v) Glycerol. | ||
| Storage Condition | Store all components at -20 °C. Avoid repeated freeze-thaw cycles of all components to retain maximum performance. All components are stable for 1 year from the date of shipping when stored and handled properly. | ||
| Note |
1) If degradation is inefficient, use a slightly higher incubation temperature (40-45°C) and supplement additional enzyme partway (e.g. 0.5 µl after 1 hour) through the procedure. The higher temperature is particularly useful for degrading highly structured linear RNAs, such as rRNAs. Do not exceed 45°C or incubate over 3 hours, as this may lead to non-enzymatic RNA degradation. 2) Magnesium at concentrations of 0.1-1.0 mM is required for optimal activity. If EDTA is present, compensate by adding MgCl2 to 1.0 mM final. 3) RNase R exhibits low activity on tRNA, rRNA and other highly structured RNAs, for which the 3’ end is double stranded with a short 3’ overhang. These RNA species can stall the enzyme and result in greatly reduced activity. For best results, removal of rRNA from total RNA extracts is highly recommended. |
Documents
MSDS
FAQs
| How efficiently will RNase R (when best optimized) digest linear RNA? | |
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To calculate the percentage of digested linear RNA in your experiment, perform the following steps: Step 1. Determine the Ct difference (ΔCt) between the Treated (+RNase R) and Untreated (No RNase R) Set. Step 2. Calculate the fold change using the ΔCt value: Fold Change = 2ΔCt Step 3. Calculate the percentage of RNA degraded using the fold change: % RNA Degraded = (1 - (1 / Fold Change)) × 100
For example, if your Treated Set has Ct=28.55 and Untreated Set has Ct = 18.01, the calculation will be: ΔCt = 28.55 – 18.01 = 10.54 Fold Change = 2ΔCt = 210.54 = 1488.87 % RNA Degraded = (1-(1/1488.87)) × 100 = 99.93% |
| What is the length of RNA that can be digested by RNase R? | |
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RNase R does not have a limit on the length of RNA that it can degrade. Therefore, the majority of non-circular RNA with the exception of short double-stranded RNA, 5S RNA and tRNA will be digested.
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| What inhibits RNase R? | |
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Activity of the enzyme will be abolished if EDTA is present at a concentration of 1 mM or higher. Therefore, if using EDTA compensate by adding MgCl₂ to 1.0 mM final concentration.
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| How is RNase R inactivated/removed? | |
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While the enzyme can be heat inactivated, the procedure is not recommended since high heat can lead to RNA damage. Phenol-chloroform precipitation can be used instead. For NGS, solid phase reversible immobilization (SPRI) bead cleanup is recommended.
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| Can I use higher temperatures (50°C) for my sample incubation? | |
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While some of the literature reports that RNase R enzyme is active at temperatures equal or slightly higher than 50°C, we do not recommend exceeding the suggested range of 37-45°C. For NGS applications, incubation at 37°C is recommended. This will ensure optimal activity of the enzyme and absence of non-enzymatic degradation.
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| Can RNase R be used for total RNA isolation in addition to RNA degradation? | |
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Yes, RNase R can be used for both RNA degradation and total RNA isolation. It efficiently degrades linear RNA, leaving circular RNA and genomic DNA intact.
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| Can RNase R be used for RNA integrity assessment in RNA-seq experiments? | |
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Yes, RNase R is commonly used for assessing RNA integrity before RNA-seq experiments. It helps confirm the presence of intact RNA and can be a valuable quality control step.
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| Can RNase R be used for RNA samples in difficult matrices, such as tissues or formalin-fixed paraffin-embedded (FFPE) samples? | |
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RNase R can be used for a variety of sample types, including tissues and FFPE samples. However, sample preparation methods should be optimized for challenging samples (such as incubation time and reactions conditions).
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| Is RNase R suitable for all RNA types, including eukaryotic and prokaryotic RNA? | |
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RNase R is suitable for degrading both eukaryotic and prokaryotic RNA. It is a broad-spectrum ribonuclease.
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| Does RNase R require special precautions for handling and disposal? | |
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RNase R is not hazardous. However, it is important to use appropriate lab safety practices and dispose of waste materials according to local regulations.
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| Is there any risk of contamination of RNase R with DNase or other contaminants? | |
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RNase R is rigorously tested for purity and is free from contaminants, including DNase. It is provided in a ready-to-use format.
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References
- Wesselhoeft, R. A., Kowalski, P. S., Parker-Hale, F. C., Huang, Y., Bisaria, N., & Anderson, D. G. "RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo" Molecular cell 74(3):508-520 (2019).
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Vay, K. L., Salibi, E., Ghosh, B., Dora Tang, T.-Y., & Mutschler, H. (2022). Ribozyme-phenotype coupling in peptide-based coacervate protocells. https://doi.org/10.1101/2022.10.25.513667
- Peng, L., Chen, J., Li, M., & Wang, R. (2022). Circ_MBNL3 Restrains Hepatocellular Carcinoma Progression by Sponging miR-873-5p to Release PHF2. Biochemical Genetics. https://doi.org/10.1007/s10528-022-10295-4
- Zhang, S., Shen, Z., Chao, G., Du, X., Zhang, W., Jin, D., & Liu, Y. (2022). Circ_0004712 Silencing Suppresses the Aggressive Changes of Rheumatoid Arthritis Fibroblast-Like Synoviocytes by Targeting miR-633/TRAF6 Axis. Biochemical Genetics, 1-17. https://doi.org/10.1007/s10528-022-10265-w
- Fu, C., Wang, J., Hu, M., & Zhou, W. (2022). Circ_0005615 contributes to the progression and Bortezomib resistance of multiple myeloma by sponging miR-185-5p and upregulating IRF4. Anti-Cancer Drugs, 33(9), 893-902. https://doi.org/10.1097/CAD.0000000000001378
- He, M., Jia, Z., Wen, Y., & Chen, X. (2022). Circ_0043947 contributes to interleukin 1β-induced injury in chondrocytes by sponging miR-671-5p to up-regulate RTN3 expression in osteoarthritis pathology. Journal of Orthopaedic Surgery and Research, 17(1), 1-13. https://doi.org/10.1186/s13018-022-02970-4
- Li, J., Liu, X., Dong, S., Liao, H., Huang, W., & Yuan, X. (2022). Circ_0101802 Facilitates Colorectal Cancer Progression Depending on the Regulation of miR-665/DVL3 Signaling. Biochemical Genetics, 60(6), 2250–2267. https://doi.org/10.1007/s10528-022-10207-6
- Xie, H., Yao, J., Wang, Y., & Ni, B. (2022). Exosome-transmitted circVMP1 facilitates the progression and cisplatin resistance of non-small cell lung cancer by targeting miR-524-5p-METTL3/SOX2 axis. Drug Delivery, 29(1), 1257–1271. https://doi.org/10.1080/10717544.2022.2057617
- Gao, X., Xu, N., Miao, K., Huang, G., & Huang, Y. (2022). Circ_0136666 aggravates osteosarcoma development through mediating miR-1244/CEP55 axis. Journal of Orthopaedic Surgery and Research, 17(1). https://doi.org/10.1186/s13018-022-03303-1
- Li, Z., Wang, Z., Yang, S., Shen, C., Zhang, Y., Jiang, R., Zhang, Z., Zhang, Y., & Hu, H. (2022). CircSTK39 suppresses the proliferation and invasion in Bladder Cancer via regulating miR-135a-5p/NR3C2-mediated Epithelial-Mesenchymal Transition signaling pathway. Cell Biology & Toxicology. To https://doi.org/10.21203/rs.3.rs-1867978/v1
- Zhang, M., Mou, L., Liu, S., Sun, F., & Gong, M. (2021). Circ_0001103 alleviates IL-1β-induced chondrocyte cell injuries by upregulating SIRT1 via targeting miR-375. Clinical Immunology, 227, 108718. https://doi.org/10.1016/j.clim.2021.108718
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Liu, Y., Wang, S., Pan, S., Yan, Q., Li, Y., & Zhao, Y. (2022). Circ_0000463 contributes to the progression and glutamine metabolism of non‐small‐cell lung cancer by targeting miR‐924/SLC1A5 signaling. Journal of Clinical Laboratory Analysis, 36(1), e24116. https://doi.org/10.1002/jcla.24116
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Ma, L., Liu, W., & Li, M. (2022). Circ_0061140 Contributes to Ovarian Cancer Progression by Targeting miR-761/LETM1 Signaling. Biochemical Genetics. https://doi.org/10.1007/s10528-022-10277-6
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Omata, Y., Okawa, M., Haraguchi, M., Tsuruta, A., Matsunaga, N., Koyanagi, S., & Ohdo, S. (2022). RNA editing enzyme ADAR1 controls miR-381-3p-mediated expression of multidrug resistance protein MRP4 via regulation of circRNA in human renal cells. Journal of Biological Chemistry, 298(8), 102184. https://doi.org/10.1016/j.jbc.2022.102184
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Ou, H., Li, J., Lv, Q., & Feng, D. (2022). Hsa_circ_0069094 positively regulates the expression of oncogenic ZNF217 by competitively targeting miR-758–3p to promote the development of breast cancer. Reproductive Biology, 22(4), 100708. https://doi.org/10.1016/j.repbio.2022.100708
- Wang, F., Zhong, S., Mao, C., Jin, J., & Wang, H. (2022). Circ_0000291 contributes to hepatocellular carcinoma tumorigenesis by binding to miR-1322 to up-regulate UBE2T. Annals of Hepatology, 100722. https://doi.org/10.1016/j.aohep.2022.100722
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Zhang, H., Huang, T., Yuan, S., Long, Y., Tan, S., Niu, G., ... & Yang, M. (2022). Circ_0020123 plays an oncogenic role in non‐small cell lung cancer depending on the regulation of miR‐512‐3p/CORO1C. Thoracic Cancer, 13(9), 1406-1418. https://doi.org/10.1111/1759-7714.14408
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Zhao, Y., Wang, S., Liu, S., Yan, Q., Li, Y., & Liu, Y. (2022). CircHSPG2 absence weakens hypoxia-induced dysfunction in cardiomyocytes by targeting the miR-25-3p/PAWR axis. Cardiovascular Diagnosis and Therapy, 12(5), 589-602. https://doi.org/10.21037/cdt-22-197
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Zhu, C., Jiang, X., Xiao, H., & Guan, J. (2022). Circ_0030998 Restrains Cisplatin Resistance Through Mediating miR-1323/PDCD4 Axis in Non-small Cell Lung Cancer. Biochemical Genetics, 1-21. https://doi.org/10.1007/s10528-022-10220-9
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