Skip to content
Licensed Unlicensed Requires Authentication Published by De Gruyter September 1, 2018

Tandem DNAzyme for double digestion: a new tool for circRNA suppression

  • Junyao Ding , Wenhu Zhou , Xiaojing Li , Meng Sun , Jingsong Ding and Qubo Zhu ORCID logo EMAIL logo
From the journal Biological Chemistry

Abstract

Circular RNA (circRNA) play a crucial role in many biological processes and have been proved as potential biomarkers and therapeutic targets in many diseases. Manipulation of their expression is a critical task. In this study, we developed a new strategy for circRNA suppression with DNAzyme. Data showed single-digestion DNAzymes cleaved circRNA efficiently in vitro but not in cell culture. However, tandem DNAzymes for double digestion showed higher cleavage efficacy both in vitro and in cell culture. Functional study demonstrated that double-digestion DNAzymes suppressed the miRNA sponge function of circRNA and changed the proliferation and migration rates of HCC cells.

Keywords: circRNA; DNAzyme; siRNA

Acknowledgments

We thank Xiangya Experiment Center (Changsha, China) for providing the cell lines. We also thank Geneseed Biotech Co., Ltd. (Guangzhou, China) for constructing the circRNA OE plasmid. This research is supported by National Natural Science Foundation of China for ‘Functional studies of miR-183/-96/-182 cluster in breast cancer diagnosis and treatment’ (Grant No. C0709-31201056), Hunan Provincial Natural Science Foundation of China (Grant No. 2018JJ2493) and the Innovation Driven Project of Central South University (Grant No. 20170030010004).

  1. Conflict of interest statement:

  2. The authors declare no conflict of interest.

References

Dass, C.R., Choong, P.F.M., and Khachigian, L.M. (2008). DNAzyme technology and cancer therapy: cleave and let die. Mol. Cancer Ther. 7, 243–251.10.1158/1535-7163.MCT-07-0510Search in Google Scholar PubMed

Enuka, Y., Lauriola, M., Feldman, M.E., Sas-Chen, A., Ulitsky, I., and Yarden, Y. (2016). Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res. 44, 1370–1383.10.1093/nar/gkv1367Search in Google Scholar PubMed PubMed Central

Fan, H.H., Zhang, X.B., and Lu, Y. (2017). Recent advances in DNAzyme-based gene silencing. Sci. China Chem. 60, 591–601.10.1007/s11426-016-0472-1Search in Google Scholar

Fokina, A.A., Stetsenko, D.A., and Francois, J.C. (2015). DNA enzymes as potential therapeutics: towards clinical application of 10–23 DNAzymes. Expert Opin. Biol. Ther. 15, 689–711.10.1517/14712598.2015.1025048Search in Google Scholar PubMed

Greene, J., Baird, A.M., Brady, L., Lim, M., Gray, S.G., McDermott, R., and Finn, S.P. (2017). Circular RNAs: biogenesis, function and role in human diseases. Front. Mol. Biosci. 4, 38.10.3389/fmolb.2017.00038Search in Google Scholar PubMed PubMed Central

Han, D., Li, J.X., Wang, H.M., Su, X.P., Hou, J., Gu, Y., Qian, C., Lin, Y., Liu, X., Huang, M.Y., et al. (2017). Circular RNA circMTO1 acts as the sponge of microRNA-9 to suppress hepatocellular carcinoma progression. Hepatology 66, 1151–1164.10.1002/hep.29270Search in Google Scholar PubMed

Hansen, T.B., Jensen, T.I., Clausen, B.H., Bramsen, J.B., Finsen, B., Damgaard, C.K., and Kjems, J. (2013). Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388.10.1038/nature11993Search in Google Scholar PubMed

Jakobi, T., Czaja-Hasse, L.F., Reinhardt, R., and Dieterich, C. (2016). Profiling and validation of the circular RNA repertoire in adult murine hearts. Genom. Proteom. Bioinform. 14, 216–223.10.1016/j.gpb.2016.02.003Search in Google Scholar PubMed PubMed Central

Krug, N., Hohlfeld, J.M., Kirsten, A.M., Kornmann, O., Beeh, K.M., Kappeler, D., Korn, S., Ignatenko, S., Timmer, W., Rogon, C., et al. (2015). Allergen-induced asthmatic responses modified by a GATA3-specific DNAzyme. N. Engl. J. Med. 372, 1987–1995.10.1056/NEJMoa1411776Search in Google Scholar PubMed

Liu, J.W., Cao, Z.H., and Lu, Y. (2009). Functional nucleic acid sensors. Chem. Rev. 109, 1948–1998.10.1021/cr030183iSearch in Google Scholar PubMed PubMed Central

Meng, X., Chen, Q., Zhang, P., and Chen, M. (2017). CircPro: an integrated tool for the identification of circRNAs with protein-coding potential. Bioinformatics 33, 3314–3316.10.1093/bioinformatics/btx446Search in Google Scholar PubMed

Oka, Y., Hirabayashi, Y., Ikeda, T., Fujii, H., Ishii, T., and Harigae, H. (2011). A single-stranded DNA-cross-reactive immunogenic epitope of human homocysteine-inducible endoplasmic reticulum protein. Scand. J. Immunol. 74, 296–303.10.1111/j.1365-3083.2011.02572.xSearch in Google Scholar PubMed

Panda, A.C., Abdelmohsen, K., and Gorospe, M. (2017a). RT-qPCR detection of senescence-associated circular RNAs. Methods Mol. Biol. 1534, 79–87.10.1007/978-1-4939-6670-7_7Search in Google Scholar PubMed PubMed Central

Panda, A.C., Grammatikakis, I., Kim, K.M., De, S., Martindale, J.L., Munk, R., Yang, X., Abdelmohsen, K., and Gorospe, M. (2017b). Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1. Nucleic Acids Res. 45, 4021–4035.10.1093/nar/gkw1201Search in Google Scholar PubMed PubMed Central

Petkovic, S. and Muller, S. (2015). RNA circularization strategies in vivo and in vitro. Nucleic Acids Res. 43, 2454–2465.10.1093/nar/gkv045Search in Google Scholar PubMed PubMed Central

Rotkrua, P., Akiyama, Y., Hashimoto, Y., Otsubo, T., and Yuasa, Y. (2011). MiR-9 downregulates CDX2 expression in gastric cancer cells. Int. J. Cancer 129, 2611–2620.10.1002/ijc.25923Search in Google Scholar PubMed

Santoro, S.W. and Joyce, G.F. (1997). A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94, 4262–4266.10.1073/pnas.94.9.4262Search in Google Scholar PubMed PubMed Central

Schlosser, K., Gu, J., Sule, L., and Li, Y. (2008). Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res. 36, 1472–1481.10.1093/nar/gkm1175Search in Google Scholar PubMed PubMed Central

Scotti, M.M. and Swanson, M.S. (2016). RNA mis-splicing in disease. Nat. Rev. Genet. 17, 19–32.10.1038/nrg.2015.3Search in Google Scholar PubMed PubMed Central

Shang, X.C., Li, G.Z., Liu, H., Li, T., Liu, J., Zhao, Q., and Wang, C.X. (2016). Comprehensive circular RNA profiling reveals that hsa_circ_0005075, a new circular RNA biomarker, is involved in hepatocellular crcinoma development. Medicine 95, e3811.10.1097/MD.0000000000003811Search in Google Scholar PubMed PubMed Central

Silverman, S.K. (2016). Catalytic DNA: scope, applications, and biochemistry of deoxyribozymes. Trends Biochem. Sci. 41, 595–609.10.1016/j.tibs.2016.04.010Search in Google Scholar PubMed PubMed Central

Tan, W.L., Lim, B.T., Anene-Nzelu, C.G., Ackers-Johnson, M., Dashi, A., See, K., Tiang, Z., Lee, D.P., Chua, W.W., Luu, T.D., et al. (2017). A landscape of circular RNA expression in the human heart. Cardiovasc. Res. 113, 298–309.10.1093/cvr/cvw250Search in Google Scholar PubMed

Wang, F., Saran, R., and Liu, J. (2015). Tandem DNAzymes for mRNA cleavage: choice of enzyme, metal ions and the antisense effect. Bioorg. Med. Chem. Lett. 25, 1460–1463.10.1016/j.bmcl.2015.02.032Search in Google Scholar PubMed

Ward, W.L., Plakos, K., and DeRose, V.J. (2014). Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem. Rev. 114, 4318–4342.10.1021/cr400476kSearch in Google Scholar PubMed PubMed Central

Weinstein, S. and Peer, D. (2010). RNAi nanomedicines: challenges and opportunities within the immune system. Nanotechnology 21, 232001.10.1088/0957-4484/21/23/232001Search in Google Scholar PubMed

Wilusz, J.E. and Sharp, P.A. (2013). Molecular biology. A circuitous route to noncoding RNA. Science 340, 440–441.10.1126/science.1238522Search in Google Scholar PubMed PubMed Central

Xu, H., Guo, S., Li, W., and Yu, P. (2015). The circular RNA CDR1as, via miR-7 and its targets, regulates insulin transcription and secretion in islet cells. Sci. Rep. 5, 12453.10.1038/srep12453Search in Google Scholar PubMed PubMed Central

Yu, L., Gong, X., Sun, L., Zhou, Q., Lu, B., and Zhu, L. (2016). The circular RNA CDR1as act as an oncogene in hepatocellular carcinoma through targeting miR-7 expression. PLoS One 11, e0158347.10.1371/journal.pone.0158347Search in Google Scholar PubMed PubMed Central

Zhang, X.O., Wang, H.B., Zhang, Y., Lu, X.H., Chen, L.L., and Yang, L. (2014). Complementary sequence-mediated exon circularization. Cell 159, 134–147.10.1016/j.cell.2014.09.001Search in Google Scholar PubMed

Zheng, Q., Bao, C., Guo, W., Li, S., Chen, J., Chen, B., Luo, Y., Lyu, D., Li, Y., Shi, G., et al. (2016). Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat. Commun. 7, 11215.10.1038/ncomms11215Search in Google Scholar PubMed PubMed Central

Zhou, W.H., Ding, J.S., and Liu, J.W. (2017). Theranostic DNAzymes. Theranostics 7, 1010–1025.10.7150/thno.17736Search in Google Scholar PubMed PubMed Central


Supplementary Material

The online version of this article offers supplementary material (https://doi.org/10.1515/hsz-2018-0232).


Received: 2018-04-25
Accepted: 2018-08-29
Published Online: 2018-09-01
Published in Print: 2019-01-28

©2019 Walter de Gruyter GmbH, Berlin/Boston

Downloaded on 25.4.2024 from https://www.degruyter.com/document/doi/10.1515/hsz-2018-0232/html
Scroll to top button