Abstract
Nucleic acids (DNA and RNA) have been recognized as promising building blocks to fabricate a variety of well-defined two- and three-dimensional architectures through the programmable molecular self-assembly of multiple oligomeric strands. Y-shaped oligonucleotides are currently among the most widely employed nanostructures in the field of nucleic acid nanotechnology due to their unique features, including high structural stability, excellent biocompatibility, simplicity and ease of synthesis, and precisely controlled sizes. To functionalize biological activity, Y-shaped oligonucleotides can be incorporated with therapeutic genes such as small interfering RNA (siRNA) for target gene-specific silencing and CpG oligonucleotides (CpG ODN) for the activation of innate immune responses. Compared to the linear structures of siRNA and CpG ODN, Y-shaped siRNA and CpG ODN structures have demonstrated significant potential in the treatment of various diseases due to improved serum stability and intracellular uptake. Here, we review a broad spectrum of related topics, including the design, construction, and characteristics of Y-shaped oligonucleotides with a specific focus on their potential as a promising platform for enhancing the therapeutic efficacy of siRNA and CpG ODN.
Similar content being viewed by others
References
Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99:237–247. https://doi.org/10.1016/0022-5193(82)90002-9
Chidchob P, Sleiman HF (2018) Recent advances in DNA nanotechnology. Curr Opin Chem Biol 46:63–70. https://doi.org/10.1016/j.cbpa.2018.04.012
Seeman NC, Belcher AM (2002) Emulating biology: building nanostructures from the bottom up. Proc Natl Acad Sci U S A 99(Suppl 2):6451–6455. https://doi.org/10.1073/pnas.221458298
Egli M, Manoharan M (2023) Chemistry, structure and function of approved oligonucleotide therapeutics. Nucleic Acids Res 51:2529–2573. https://doi.org/10.1093/nar/gkad067
Bujold KE, Lacroix A, Sleiman HF (2018) DNA nanostructures at the interface with biology. Chem 4:495–521. https://doi.org/10.1016/j.chempr.2018.02.005
Dong Y, Yao C, Zhu Y et al (2020) DNA functional materials assembled from branched DNA: design, synthesis, and applications. Chem Rev 120:9420–9481. https://doi.org/10.1021/acs.chemrev.0c00294
Seeman NC (2005) Structural DNA nanotechnology: an overview. Methods Mol Biol 303:143–166. https://doi.org/10.1385/1-59259-901-X:143
Seeman N, Sleiman H (2018) DNA nanotechnology. Nat Rev Mater 3:17068. https://doi.org/10.1038/natrevmats.2017.68
Wang W, Lin M, Wang W et al (2023) DNA tetrahedral nanostructures for the biomedical application and spatial orientation of biomolecules. Bioact Mater 33:279–310. https://doi.org/10.1016/j.bioactmat.2023.10.025
Ma W, Zhan Y, Zhang Y et al (2021) The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 6:351. https://doi.org/10.1038/s41392-021-00727-9
Zhou J, Wang W, Li S et al (2020) Dual-mode amplified detection of rabies virus oligonucleotide via Y-shaped DNA assembly. Sens Actuators B Chem 304:127267. https://doi.org/10.1016/j.snb.2019.127267
Ram Kumar Pandian S, Yuan CJ, Lin CC et al (2017) DNA-based nanowires and nanodevices. Adv Phys-X 2:22–34. https://doi.org/10.1080/23746149.2016.1254065
Zhao M, Wang R, Yang K et al (2023) Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 13:916–941. https://doi.org/10.1016/j.apsb.2022.10.019
Zhu G, Song P, Wu J et al (2022) Application of nucleic acid frameworks in the construction of nanostructures and cascade biocatalysts: recent progress and perspective. Front Bioeng Biotechnol 9:792489. https://doi.org/10.3389/fbioe.2021.792489
Gubu A, Zhang X, Lu A et al (2023) Nucleic acid amphiphiles: synthesis, properties, and applications. Mol Ther Nucleic Acids 33:144–163. https://doi.org/10.1016/j.omtn.2023.05.022
Meng HM, Zhang X, Lv Y et al (2014) DNA dendrimer: an efficient nanocarrier of functional nucleic acids for intracellular molecular sensing. ACS Nano 8:6171–6181. https://doi.org/10.1021/nn5015962
Yan J, Zhan X, Zhang Z et al (2021) Tetrahedral DNA nanostructures for effective treatment of cancer: advances and prospects. J Nanobiotechnol 19:412. https://doi.org/10.1186/s12951-021-01164-0
Wang DX, Wang J, Wang YX et al (2021) DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem Sci 12:7602–7622. https://doi.org/10.1039/d1sc00587a
Kong D, Wang X, Gu C et al (2021) Direct SARS-CoV-2 nucleic acid detection by Y-shaped DNA dual-probe transistor assay. J Am Chem Soc 143:17004–17014. https://doi.org/10.1021/jacs.1c06325
Mei-Ling L, Yi L, Mei-Ling Z et al (2022) Y-shaped DNA nanostructures assembled-spherical nucleic acids as target converters to activate CRISPR-Cas12a enabling sensitive ECL biosensing. Biosens Bioelectron 214:114512. https://doi.org/10.1016/j.bios.2022.114512
Yu X, Hu L, He H et al (2019) Y-shaped DNA-Mediated hybrid nanoflowers as efficient gene carriers for fluorescence imaging of tumor-related mRNA in living cells. Anal Chim Acta 1057:114–122. https://doi.org/10.1016/j.aca.2018.12.062
Chatterjee S, Lee JB, Valappil NV et al (2012) Probing Y-shaped DNA structure with time-resolved FRET. Nanoscale 4:1568–1571. https://doi.org/10.1039/c2nr12039a
Zhong W, Zheng Y, Huang L et al (2023) Construction of an ATP-activated Y-shape DNA probe for smart miRNA imaging in living cells. Chemistry 5:1634–1644. https://doi.org/10.3390/chemistry5030112
Zhang K, Li Y, Liu J et al (2020) Y-shaped circular aptamer-DNAzyme conjugates for highly efficient in vivo gene silencing. CCS Chem 2:631–641. https://doi.org/10.31635/ccschem.020.202000170
Komiyama M, Sumaoka J (2023) Nanoarchitectures to deliver nucleic acid drugs to disease sites. ChemNanoMat 9:e202300069. https://doi.org/10.1002/cnma.202300069
Nishikawa M, Tan M, Liao W et al (2019) Nanostructured DNA for the delivery of therapeutic agents. Adv Drug Deliv Rev 147:29–36. https://doi.org/10.1016/j.addr.2019.09.004
Lv Z, Zhu Y, Li F (2021) DNA functional nanomaterials for controlled delivery of nucleic acid-based drugs. Front Bioeng Biotechnol 9:720291. https://doi.org/10.3389/fbioe.2021.720291
Um SH, Lee JB, Park N et al (2006) Enzyme-catalysed assembly of DNA hydrogel. Nat Mater 5:797–801. https://doi.org/10.1038/nmat1741
Fire A, Xu S, Montgomery MK et al (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811. https://doi.org/10.1038/35888
Elbashir SM, Harborth J, Lendeckel W et al (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494–498. https://doi.org/10.1038/35078107
Levanova A, Poranen MM (2018) RNA interference as a prospective tool for the control of human viral infections. Front Microbiol 9:2151. https://doi.org/10.3389/fmicb.2018.02151
Hu B, Zhong L, Weng Y et al (2020) Therapeutic siRNA: state of the art. Signal Transduct Target Ther 5:101. https://doi.org/10.1038/s41392-020-0207-x
Svoboda P (2020) Key mechanistic principles and considerations concerning RNA interference. Front Plant Sci 11:1237. https://doi.org/10.3389/fpls.2020.01237
Wang J, Li Y (2024) Current advances in antiviral RNA interference in mammals. FEBS J 291:208–216. https://doi.org/10.1111/febs.16728
Kanasty RL, Whitehead KA, Vegas AJ et al (2012) Action and reaction: the biological response to siRNA and its delivery vehicles. Mol Ther 20:513–524. https://doi.org/10.1038/mt.2011.294
Dominska M, Dykxhoorn DM (2010) Breaking down the barriers: siRNA delivery and endosome escape. J Cell Sci 123:1183–1189. https://doi.org/10.1242/jcs.066399
Kang H, Ga YJ, Kim SH et al (2023) Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges. J Biomed Sci 30:88. https://doi.org/10.1186/s12929-023-00981-9
Draz MS, Fang BA, Zhang P et al (2014) Nanoparticle-mediated systemic delivery of siRNA for treatment of cancers and viral infections. Theranostics 4:872–892. https://doi.org/10.7150/thno.9404
Tsui NB, Ng EK, Lo YM (2002) Stability of endogenous and added RNA in blood specimens, serum, and plasma. Clin Chem 48:1647–1653
Nakashima Y, Abe H, Abe N et al (2011) Branched RNA nanostructures for RNA interference. Chem Commun (Camb) 47:8367–8369. https://doi.org/10.1039/c1cc11780g
Nair BG, Zhou Y, Hagiwara K et al (2017) Enhancement of synergistic gene silencing by RNA interference using branched “3-in-1” trimer siRNA. J Mater Chem B 5:4044–4051. https://doi.org/10.1039/c7tb00846e
Hong CA, Eltoukhy AA, Lee H et al (2015) Dendrimeric siRNA for efficient gene silencing. Angew Chem Int Ed Engl 54:6740–6744. https://doi.org/10.1002/anie.201412493
Hong CA, Lee SH, Kim JS et al (2011) Gene silencing by siRNA microhydrogels via polymeric nanoscale condensation. J Am Chem Soc 133:13914–13917. https://doi.org/10.1021/ja2056984
Jang B, Kim B, Kim H et al (2018) Enzymatic synthesis of self-assembled dicer substrate RNA nanostructures for programmable gene silencing. Nano Lett 18:4279–4284. https://doi.org/10.1021/acs.nanolett.8b01267
Krieg AM (2002) CpG motifs in bacterial DNA and their immune effects. Annu Rev Immunol 20:709–760. https://doi.org/10.1146/annurev.immunol.20.100301.064842
Lai CY, Yu GY, Luo Y et al (2019) Immunostimulatory activities of CpG-oligodeoxynucleotides in teleosts: toll-like receptors 9 and 21. Front Immunol 10:179. https://doi.org/10.3389/fimmu.2019.00179
Otsuka T, Nishida S, Shibahara T et al (2022) CpG ODN (K3)-toll-like receptor 9 agonist-induces Th1-type immune response and enhances cytotoxic activity in advanced lung cancer patients: a phase I study. BMC Cancer 22:744. https://doi.org/10.1186/s12885-022-09818-4
Jin Y, Zhuang Y, Dong X et al (2021) Development of CpG oligodeoxynucleotide TLR9 agonists in anti-cancer therapy. Expert Rev Anticancer Ther 21:841–851. https://doi.org/10.1080/14737140.2021.1915136
Gunawardana T, Ahmed KA, Goonewardene K et al (2019) Synthetic CpG-ODN rapidly enriches immune compartments in neonatal chicks to induce protective immunity against bacterial infections. Sci Rep 9:341. https://doi.org/10.1038/s41598-018-36588-6
Chen X, Wu Y, Qiu Y et al (2023) CpG ODN 2102 promotes antibacterial immune responses and enhances vaccine-induced protection in golden pompano (Trachinotusovatus). Fish Shellfish Immunol 137:108783. https://doi.org/10.1016/j.fsi.2023.108783
Hemmi H, Takeuchi O, Kawai T et al (2000) A Toll-like receptor recognizes bacterial DNA. Nature 408:740–745. https://doi.org/10.1038/35047123
Wagner H (2001) Toll meets bacterial CpG-DNA. Immunity 14:499–502. https://doi.org/10.1016/s1074-7613(01)00144-3
Klinman DM, Yi AK, Beaucage SL et al (1996) CpG motifs present in bacteria DNA rapidly induce lymphocytes to secrete interleukin 6, interleukin 12, and interferon gamma. Proc Natl Acad Sci U S A 93:2879–2883. https://doi.org/10.1073/pnas.93.7.2879
Sparwasser T, Miethke T, Lipford G et al (1997) Macrophages sense pathogens via DNA motifs: induction of tumor necrosis factor-alpha-mediated shock. Eur J Immunol 27:1671–1679. https://doi.org/10.1002/eji.1830270712
Sun S, Zhang X, Tough DF et al (1998) Type I interferon-mediated stimulation of T cells by CpG DNA. J Exp Med 188:2335–2342. https://doi.org/10.1084/jem.188.12.2335
Lin SY, Yao BY, Hu CJ et al (2020) Induction of robust immune responses by CpG-ODN-loaded hollow polymeric nanoparticles for antiviral and vaccine applications in chickens. Int J Nanomedicine 15:3303–3318. https://doi.org/10.2147/IJN.S241492
Dalpke A, Zimmermann S, Heeg K (2002) Immunopharmacology of CpG DNA. Biol Chem 383:1491–1500. https://doi.org/10.1515/BC.2002.171
Klinman DM (2004) Immunotherapeutic uses of CpG oligodeoxynucleotides. Nat Rev Immunol 4:249–258. https://doi.org/10.1038/nri1329
Krieg AM (2006) Therapeutic potential of Toll-like receptor 9 activation. Nat Rev Drug Discov 5:471–484. https://doi.org/10.1038/nrd2059
Li T, Wu J, Zhu S et al (2020) A novel C type CpG oligodeoxynucleotide exhibits immunostimulatory activity in vitro and enhances antitumor effect in vivo. Front Pharmacol 11:8. https://doi.org/10.3389/fphar.2020.00008
Kandimalla ER, Yu D, Agrawal S (2002) Towards optimal design of second-generation immunomodulatory oligonucleotides. Curr Opin Mol Ther 4:122–129
Vollmer J, Krieg AM (2009) Immunotherapeutic applications of CpG oligodeoxynucleotide TLR9 agonists. Adv Drug Deliv Rev 61:195–204. https://doi.org/10.1016/j.addr.2008.12.008
Adamus T, Kortylewski M (2018) The revival of CpG oligonucleotide-based cancer immunotherapies. Contemp Oncol (Pozn) 22:56–60. https://doi.org/10.5114/wo.2018.73887
Ruan M, Thorn K, Liu S et al (2014) The secretion of IL-6 by CpG-ODN-treated cancer cells promotes T-cell immune responses partly through the TLR-9/AP-1 pathway in oral squamous cell carcinoma. Int J Oncol 44:2103–2110. https://doi.org/10.3892/ijo.2014.2356
Yuan S, Qiao T, Li X et al (2018) Toll-like receptor 9 activation by CpG oligodeoxynucleotide 7909 enhances the radiosensitivity of A549 lung cancer cells via the p53 signaling pathway. Oncol Lett 15:5271–5279. https://doi.org/10.3892/ol.2018.7916
Huang L, Wang Z, Liu C et al (2017) CpG-based immunotherapy impairs antitumor activity of BRAF inhibitors in a B-cell-dependent manner. Oncogene 36:4081–4086. https://doi.org/10.1038/onc.2017.35
Givens BE, Geary SM, Salem AK (2018) Nanoparticle-based CpG-oligonucleotide therapy for treating allergic asthma. Immunotherapy 10:595–604. https://doi.org/10.2217/imt-2017-0142
Mutwiri GK, Nichani AK, Babiuk S et al (2004) Strategies for enhancing the immunostimulatory effects of CpG oligodeoxynucleotides. J Control Release 97:1–17. https://doi.org/10.1016/j.jconrel.2004.02.022
Chiodetti AL, Sánchez Vallecillo MF, Dolina JS et al (2018) Class-B CpG-ODN formulated with a nanostructure induces type I interferons-dependent and CD4+ T cell-independent CD8+ T-cell response against unconjugated protein antigen. Front Immunol 9:2319. https://doi.org/10.3389/fimmu.2018.02319
Nagaoka M, Liao W, Kusamori K et al (2022) Targeted delivery of immunostimulatory CpG oligodeoxynucleotides to antigen-presenting cells in draining lymph nodes by stearic acid modification and nanostructurization. Int J Mol Sci 23:1350. https://doi.org/10.3390/ijms23031350
Takano S, Miyashima Y, Fujii S et al (2023) Molecular bottlebrushes for immunostimulatory CpG ODN delivery: relationship among cation density, complex formation ability, and cytotoxicity. Biomacromol 24:1299–1309. https://doi.org/10.1021/acs.biomac.2c01348
Cheng T, Miao J, Kai D et al (2018) Polyethylenimine-mediated CpG oligodeoxynucleotide delivery stimulates bifurcated cytokine induction. ACS Biomater Sci Eng 4:1013–1018. https://doi.org/10.1021/acsbiomaterials.8b00049
Chi Q, Yang Z, Xu K et al (2020) DNA nanostructure as an efficient drug delivery platform for immunotherapy. Front Pharmacol 10:1585. https://doi.org/10.3389/fphar.2019.01585
Nishikawa M, Matono M, Rattanakiat S et al (2008) Enhanced immunostimulatory activity of oligodeoxynucleotides by Y-shape formation. Immunology 124:247–255. https://doi.org/10.1111/j.1365-2567.2007.02762.x
Rattanakiat S, Nishikawa M, Funabashi H et al (2009) The assembly of a short linear natural cytosine-phosphate-guanine DNA into dendritic structures and its effect on immunostimulatory activity. Biomaterials 30:5701–5706. https://doi.org/10.1016/j.biomaterials.2009.06.053
Sands H, Gorey-Feret LJ, Cocuzza AJ et al (1994) Biodistribution and metabolism of internally 3H-labeled oligonucleotides. I. Comparison of a phosphodiester and a phosphorothioate. Mol Pharmacol 45:932–943
Matsuoka N, Nishikawa M, Mohri K et al (2010) Structural and immunostimulatory properties of Y-shaped DNA consisting of phosphodiester and phosphorothioate oligodeoxynucleotides. J Control Release 148:311–316. https://doi.org/10.1016/j.jconrel.2010.09.019
Jung H, Kim D, Kang YY et al (2018) CpG incorporated DNA microparticles for elevated immune stimulation for antigen presenting cells. RSC Adv 8:6608–6615. https://doi.org/10.1039/c7ra13293j
Qu Y, Ju Y, Cortez-Jugo C et al (2020) Template-mediated assembly of DNA into microcapsules for immunological modulation. Small 16:e2002750. https://doi.org/10.1002/smll.202002750
Acknowledgements
This work was supported by a Yeungnam University Research Grant (220A580028).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Ethical approval
Neither ethical approval nor informed consent was required for this study.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Yoon, I.S., Nam, H.J. & Hong, C.A. Y-shaped oligonucleotides: a promising platform for enhanced therapy with siRNA and CpG Oligodeoxyribonucleotides. Biotechnol Bioproc E (2024). https://doi.org/10.1007/s12257-024-00109-2
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12257-024-00109-2