Development of 8-17 XNAzymes That Are Functional in Cells

Overview

Journal Chem Sci

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2023 Jul 21

PMID 37476720

Authors

Kosuke Chiba

Takao Yamaguchi

Satoshi Obika

Affiliations

Soon will be listed here.

Abstract

DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8-17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides, rationally designed 8-17 XNAzyme ("X8-17") that achieved high potency in terms of RNA cleavage and biostability against nucleases. X8-17, modified with 2'--methyl RNA, locked nucleic acid and phosphorothioate, successfully induced endogenous and RNA knockdown in cells. This approach may help in developing XNAzyme-based novel therapeutic agents.

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References

Lennox K, Owczarzy R, Thomas D, Walder J, Behlke M . Improved Performance of Anti-miRNA Oligonucleotides Using a Novel Non-Nucleotide Modifier. Mol Ther Nucleic Acids. 2013; 2:e117. PMC: 3759741. DOI: 10.1038/mtna.2013.46. View

Inoue H, Hayase Y, Imura A, Iwai S, Miura K, Ohtsuka E . Synthesis and hybridization studies on two complementary nona(2'-O-methyl)ribonucleotides. Nucleic Acids Res. 1987; 15(15):6131-48. PMC: 306073. DOI: 10.1093/nar/15.15.6131. View

Braasch D, Corey D . Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol. 2001; 8(1):1-7. DOI: 10.1016/s1074-5521(00)00058-2. View

McGhee C, Yang Z, Guo W, Wu Y, Lyu M, DeLong C . DNAzyme-Based Lithium-Selective Imaging Reveals Higher Lithium Accumulation in Bipolar Disorder Patient-Derived Neurons. ACS Cent Sci. 2021; 7(11):1809-1820. PMC: 8614110. DOI: 10.1021/acscentsci.1c00843. View

Takahashi H, Hamazaki H, Habu Y, Hayashi M, Abe T, Miyano-Kurosaki N . A new modified DNA enzyme that targets influenza virus A mRNA inhibits viral infection in cultured cells. FEBS Lett. 2004; 560(1-3):69-74. DOI: 10.1016/S0014-5793(04)00073-0. View

Purtha W, Coppins R, Smalley M, Silverman S . General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages. J Am Chem Soc. 2005; 127(38):13124-5. DOI: 10.1021/ja0533702. View

Crooke S, Baker B, Crooke R, Liang X . Antisense technology: an overview and prospectus. Nat Rev Drug Discov. 2021; 20(6):427-453. DOI: 10.1038/s41573-021-00162-z. View

Appaiahgari M, Vrati S . DNAzyme-mediated inhibition of Japanese encephalitis virus replication in mouse brain. Mol Ther. 2007; 15(9):1593-9. DOI: 10.1038/sj.mt.6300231. View

Micura R, Hobartner C . Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev. 2020; 49(20):7331-7353. DOI: 10.1039/d0cs00617c. View

10.

Taylor A, Holliger P . On gene silencing by the X10-23 DNAzyme. Nat Chem. 2022; 14(8):855-858. DOI: 10.1038/s41557-022-00990-5. View

11.

Schubert S, Gul D, Grunert H, Zeichhardt H, Erdmann V, Kurreck J . RNA cleaving '10-23' DNAzymes with enhanced stability and activity. Nucleic Acids Res. 2003; 31(20):5982-92. PMC: 219472. DOI: 10.1093/nar/gkg791. View

12.

Kim H, Rasnik I, Liu J, Ha T, Lu Y . Dissecting metal ion-dependent folding and catalysis of a single DNAzyme. Nat Chem Biol. 2007; 3(12):763-8. PMC: 4376948. DOI: 10.1038/nchembio.2007.45. View

13.

Hu B, Zhong L, Weng Y, Peng L, Huang Y, Zhao Y . Therapeutic siRNA: state of the art. Signal Transduct Target Ther. 2020; 5(1):101. PMC: 7305320. DOI: 10.1038/s41392-020-0207-x. View

14.

Fokina A, Meschaninova M, Durfort T, Venyaminova A, Francois J . Targeting insulin-like growth factor I with 10-23 DNAzymes: 2'-O-methyl modifications in the catalytic core enhance mRNA cleavage. Biochemistry. 2012; 51(11):2181-91. DOI: 10.1021/bi201532q. View

15.

Spitale R, Chaput J . Reply to: On gene silencing by the X10-23 DNAzyme. Nat Chem. 2022; 14(8):859-861. DOI: 10.1038/s41557-022-00983-4. View

16.

Krug N, Hohlfeld J, Kirsten A, Kornmann O, Beeh K, Kappeler D . Allergen-induced asthmatic responses modified by a GATA3-specific DNAzyme. N Engl J Med. 2015; 372(21):1987-95. DOI: 10.1056/NEJMoa1411776. View

17.

Cho E, Moloney F, Cai H, Au-Yeung A, China C, Scolyer R . Safety and tolerability of an intratumorally injected DNAzyme, Dz13, in patients with nodular basal-cell carcinoma: a phase 1 first-in-human trial (DISCOVER). Lancet. 2013; 381(9880):1835-43. PMC: 3951714. DOI: 10.1016/S0140-6736(12)62166-7. View

18.

Borggrafe J, Victor J, Rosenbach H, Viegas A, Gertzen C, Wuebben C . Time-resolved structural analysis of an RNA-cleaving DNA catalyst. Nature. 2021; 601(7891):144-149. DOI: 10.1038/s41586-021-04225-4. View

19.

Pereyra Gerber P, Donde M, Matheson N, Taylor A . XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun. 2022; 13(1):6716. PMC: 9668987. DOI: 10.1038/s41467-022-34339-w. View

20.

Peracchi A, Bonaccio M, Clerici M . A mutational analysis of the 8-17 deoxyribozyme core. J Mol Biol. 2005; 352(4):783-94. DOI: 10.1016/j.jmb.2005.07.059. View