Novel Chemically-modified DNAzyme Targeting Integrin Alpha-4 RNA Transcript As a Potential Molecule to Reduce Inflammation in Multiple Sclerosis

Overview

Journal Sci Rep

Specialty Science

Date 2017 May 11

PMID 28487530

Citations 17

Authors

Madhuri Chakravarthy

May T Aung-Htut

Bao T Le

Rakesh N Veedu

Affiliations

Soon will be listed here.

Abstract

Integrin alpha-4 (ITGA4) is a validated therapeutic target for multiple sclerosis (MS) and Natalizumab, an antibody targeting ITGA4 is currently approved for treating MS. However, there are severe side effects related to this therapy. In this study, we report the development of a novel DNAzyme that can efficiently cleave the ITGA4 transcript. We designed a range of DNAzyme candidates across various exons of ITGA4. RNV143, a 30mer arm-loop-arm type DNAzyme efficiently cleaved 84% of the ITGA4 mRNA in human primary fibroblasts. RNV143 was then systematically modified by increasing the arm lengths on both sides of the DNAzymes by one, two and three nucleotides each, and incorporating chemical modifications such as inverted-dT, phosphorothioate backbone and LNA-nucleotides. Increasing the arm length of DNAzyme RNV143 did not improve the efficiency however, an inverted-dT modification provided the most resistance to 3' → 5' exonuclease compared to other modifications tested. Our results show that RNV143A could be a potential therapeutic nucleic acid drug molecule towards the treatment for MS.

Citing Articles

Systematic bio-fabrication of aptamers and their applications in engineering biology.

Cai R, Chen X, Zhang Y, Wang X, Zhou N Syst Microbiol Biomanuf. 2023; 3(2):223-245.

PMID: 38013802 PMC: 9550155. DOI: 10.1007/s43393-022-00140-5.

A promising nucleic acid therapy drug: DNAzymes and its delivery system.

Xiao L, Zhao Y, Yang M, Luan G, Du T, Deng S Front Mol Biosci. 2023; 10:1270101.

PMID: 37753371 PMC: 10518456. DOI: 10.3389/fmolb.2023.1270101.

DNAzymes: Expanding the Potential of Nucleic Acid Therapeutics.

Larcher L, Pitout I, Keegan N, Veedu R, Fletcher S Nucleic Acid Ther. 2023; 33(3):178-192.

PMID: 37093127 PMC: 10278027. DOI: 10.1089/nat.2022.0066.

A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing.

Taylor A, Wan C, Donde M, Peak-Chew S, Holliger P Nat Chem. 2022; 14(11):1295-1305.

PMID: 36064973 PMC: 7613789. DOI: 10.1038/s41557-022-01021-z.

Site-specific functionalization with amino, guanidinium, and imidazolyl groups enabling the activation of 10-23 DNAzyme.

Du S, Li Y, Chai Z, Shi W, He J RSC Adv. 2022; 10(32):19067-19075.

PMID: 35518333 PMC: 9053948. DOI: 10.1039/d0ra02226h.

References

Cairns M, Hopkins T, Witherington C, Wang L, Sun L . Target site selection for an RNA-cleaving catalytic DNA. Nat Biotechnol. 1999; 17(5):480-6. DOI: 10.1038/8658. View

Hollenstein M . DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules. 2015; 20(11):20777-804. PMC: 6332124. DOI: 10.3390/molecules201119730. View

Ackermann J, Kanugula S, Pegg A . DNAzyme-mediated silencing of ornithine decarboxylase. Biochemistry. 2005; 44(6):2143-52. DOI: 10.1021/bi047918d. View

Cairns M, Saravolac E, Sun L . Catalytic DNA: a novel tool for gene suppression. Curr Drug Targets. 2002; 3(3):269-79. DOI: 10.2174/1389450023347722. View

Sun L, Cairns M, Gerlach W, Witherington C, Wang L, King A . Suppression of smooth muscle cell proliferation by a c-myc RNA-cleaving deoxyribozyme. J Biol Chem. 1999; 274(24):17236-41. DOI: 10.1074/jbc.274.24.17236. View

Clifford D, De Luca A, DeLuca A, Simpson D, Arendt G, Giovannoni G . Natalizumab-associated progressive multifocal leukoencephalopathy in patients with multiple sclerosis: lessons from 28 cases. Lancet Neurol. 2010; 9(4):438-46. DOI: 10.1016/S1474-4422(10)70028-4. View

Zhou W, Saran R, Huang P, Ding J, Liu J . An Exceptionally Selective DNA Cooperatively Binding Two Ca Ions. Chembiochem. 2017; 18(6):518-522. DOI: 10.1002/cbic.201600708. View

Vester B, Lundberg L, Sorensen M, Babu B, Douthwaite S, Wengel J . Improved RNA cleavage by LNAzyme derivatives of DNAzymes. Biochem Soc Trans. 2004; 32(Pt 1):37-40. DOI: 10.1042/bst0320037. View

Veedu R, Wengel J . Locked nucleic acid as a novel class of therapeutic agents. RNA Biol. 2009; 6(3):321-3. DOI: 10.4161/rna.6.3.8807. View

10.

Tsuchihashi Z, Khosla M, Herschlag D . Protein enhancement of hammerhead ribozyme catalysis. Science. 1993; 262(5130):99-102. DOI: 10.1126/science.7692597. View

11.

Santoro S, Joyce G . A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci U S A. 1997; 94(9):4262-6. PMC: 20710. DOI: 10.1073/pnas.94.9.4262. View

12.

Burnett J, Rossi J . RNA-based therapeutics: current progress and future prospects. Chem Biol. 2012; 19(1):60-71. PMC: 3269031. DOI: 10.1016/j.chembiol.2011.12.008. View

13.

Veedu R, Wengel J . Locked nucleic acids: promising nucleic acid analogs for therapeutic applications. Chem Biodivers. 2010; 7(3):536-42. DOI: 10.1002/cbdv.200900343. View

14.

Schindelin J, Rueden C, Hiner M, Eliceiri K . The ImageJ ecosystem: An open platform for biomedical image analysis. Mol Reprod Dev. 2015; 82(7-8):518-29. PMC: 5428984. DOI: 10.1002/mrd.22489. View

15.

Mendell J, Goemans N, Lowes L, Alfano L, Berry K, Shao J . Longitudinal effect of eteplirsen versus historical control on ambulation in Duchenne muscular dystrophy. Ann Neurol. 2015; 79(2):257-71. PMC: 5064753. DOI: 10.1002/ana.24555. View

16.

Crooke S, Geary R . Clinical pharmacological properties of mipomersen (Kynamro), a second generation antisense inhibitor of apolipoprotein B. Br J Clin Pharmacol. 2012; 76(2):269-76. PMC: 3731601. DOI: 10.1111/j.1365-2125.2012.04469.x. View

17.

Vester B, Hansen L, Lundberg L, Babu B, Sorensen M, Wengel J . Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets. BMC Mol Biol. 2006; 7:19. PMC: 1501032. DOI: 10.1186/1471-2199-7-19. View

18.

. A randomized controlled clinical trial of intravitreous fomivirsen for treatment of newly diagnosed peripheral cytomegalovirus retinitis in patients with AIDS. Am J Ophthalmol. 2002; 133(4):467-74. DOI: 10.1016/s0002-9394(02)01327-2. View

19.

Kurreck J, Bieber B, Jahnel R, Erdmann V . Comparative study of DNA enzymes and ribozymes against the same full-length messenger RNA of the vanilloid receptor subtype I. J Biol Chem. 2001; 277(9):7099-107. DOI: 10.1074/jbc.M107206200. View

20.

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