RNase R with RNaseOFF Bundle
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Cat. No.
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E049-G138S
Print
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Name
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RNase R with RNaseOFF Bundle
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Unit
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Bundle
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Category
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Molecular Biology Enzymes and Kits
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Description
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Pair one of abm's best-selling products with our high performance RNaseOFF Ribonuclease Inhibitor!
RNase R (Cat. No. E049) is an E. coli exoribonuclease that 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. To further the protection and enhancement of circRNAs, this bundle includes our high performance RNaseOFF Ribonuclease Inhibitor (Cat. No. G138S) for one special price!
This bundle includes:
- RNase R (500 U,10 U/µl)
- 10X RNase R Reaction Buffer
- RNaseOFF Ribonuclease Inhibitor (800 U, 40 U/µl)
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Application
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- Enriching circRNAs in biological samples
- Identification of intronic lariat sequences
- Identification of exonic circRNAs
- Studying alternative splicing
- Production of artificial circular RNAs
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Material Citation
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If use of this material results in a scientific publication, please cite the material in the following manner: Applied Biological Materials Inc, Cat. No. E049-G138S
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How many reactions can be performed?
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The appropriate number of units per reaction will vary depending on the amount of RNase contamination that is present in the reaction mixture for any given experiment. One unit of RNaseOFF Ribonuclease Inhibitor will inhibit the activity of 5 ng of RNase by 50%; thus, the more RNase contamination present in the specific reaction, the larger number of units of RNaseOFF that will be required for the inhibition. As a general guideline, a typical amount of RNaseOFF used would be around 25-50 U per 50 µl reaction; note that this is a general guideline only and the number of units required will vary from case to case.
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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%
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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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Is RNaseOFF suitable for PCR, RT-PCR, RNA isolation, and other RNA-based applications?
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Yes, RNaseOFF is ideal for PCR, RT-PCR, RNA isolation, cDNA synthesis, qPCR, and other RNA-based applications. It effectively prevents RNA degradation without inhibiting polymerase activity, ensuring RNA integrity and high-quality results in all these experiments.
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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).
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
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
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
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
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
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
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
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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Alfonso-Gonzalez, C., Holec, S., Gorey, S., Shi, M., Rauer, M., Carrasco, J., ... & Hilgers, V. (2024). ELAV mediates circular RNA biogenesis in neurons. bioRxiv, 2024-06. https://doi.org/10.1101/2024.06.22.600180
De Tomi E, Orlandi E, Belpinati F, Patuzzo C, Trabetti E, Gomez-Lira M, Malerba G. New Axes of Interaction in Circ_0079593/miR-516b-5p Network in Melanoma Metastasis Cell Lines. Genes (Basel). 2024 Dec 21;15(12):1647. https://doi.org/10.3390/genes15121647. PMID: 39766913; PMCID: PMC11675925.
Drula, R., Braicu, C., Chira, S., & Berindan-Neagoe, I. (2023). Investigating circular RNAs using qRT-PCR; roundup of optimization and processing steps. International Journal of Molecular Sciences, 24(6), 5721. https://doi.org/10.3390/ijms24065721
Frei, J., Jarzebska, N.T., Mellett, M., Kündig, T.M., Pascolo, S., Reichmuth, A.M. (2024). Design and Synthesis of Circular RNA Expression Vectors. In: Kramps, T. (eds) RNA Vaccines. Methods in Molecular Biology, vol 2786. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3770-8_9
Hu, Q., Zhao, H., Zhou, K., Hua, X., & Zhang, X. (2024). Scarless circular mRNA-based CAR-T cell therapy elicits superior anti-tumor efficacy. bioRxiv, 2024-08. https://doi.org/10.1101/2024.08.05.606578
Liu, W., Yin, C., & Liu, Y. (2021). Circular RNA circ_0091579 promotes hepatocellular carcinoma proliferation, migration, invasion, and glycolysis through miR-490-5p/CASC3 axis. Cancer Biotherapy & Radiopharmaceuticals, 36(10), 863-878. https://doi.org/10.1089/cbr.2019.3472
Massu A, Mahanil K, Limkul S, Phiwthong T, Boonanuntanasarn S, Teaumroong N, Somboonwiwat K, Boonchuen P. Identification of immune-responsive circular RNAs in shrimp (Litopenaeus vannamei) upon yellow head virus infection. Fish Shellfish Immunol. 2024 Jan;144:109246. https://doi.org/10.1016/j.fsi.2023.109246. Epub 2023 Nov 25. PMID: 38013134.
Nanishi, K., Konishi, H., Shoda, K., Arita, T., Kosuga, T., Komatsu, S., ... & Otsuji, E. (2020). Circulating circERBB2 as a potential prognostic biomarker for gastric cancer: an investigative study. Cancer Science, 111(11), 4177-4186. https://doi.org/10.1111/cas.14645
Ron, M., Ulitsky, I. Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs. Nat Commun 13, 2481 (2022). https://doi.org/10.1038/s41467-022-30183-0
Takaki, W., Konishi, H., Shoda, K. et al. Significance of Circular FAT1 as a Prognostic Factor and Tumor Suppressor for Esophageal Squamous Cell Carcinoma. Ann Surg Oncol 28, 8508–8518 (2021). https://doi.org/10.1245/s10434-021-10089-9
Ungerleider, N., Concha, M., Lin, Z., Roberts, C., Wang, X., Cao, S., ... & Flemington, E. K. (2018). The epstein barr virus circRNAome. PLoS pathogens, 14(8), e1007206. https://doi.org/10.1371/journal.ppat.1007206
Wesselhoeft, R. A., Kowalski, P. S., Parker-Hale, F. C., Huang, Y., Bisaria, N., & Anderson, D. G. (2019). RNA circularization diminishes immunogenicity and can extend translation duration in vivo. Molecular cell, 74(3), 508-520. https://doi.org/10.1016/j.molcel.2019.02.015
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