Sequence-Controlled Spherical Nucleic Acids: Gene Silencing, Encapsulation, and Cellular Uptake
Publication: nucleic acid therapeutics
Volume 33, Issue Number 4
Abstract
Antisense oligonucleotides (ASOs) can predictably alter RNA processing and control protein expression; however, challenges in the delivery of these therapeutics to specific tissues, poor cellular uptake, and endosomal escape have impeded progress in translating these agents into the clinic. Spherical nucleic acids (SNAs) are nanoparticles with a DNA external shell and a hydrophobic core that arise from the self-assembly of ASO strands conjugated to hydrophobic polymers. SNAs have recently shown significant promise as vehicles for improving the efficacy of ASO cellular uptake and gene silencing. However, to date, no studies have investigated the effect of the hydrophobic polymer sequence on the biological properties of SNAs. In this study, we created a library of ASO conjugates by covalently attaching polymers with linear or branched [dodecanediol phosphate] units and systematically varying polymer sequence and composition. We show that these parameters can significantly impact encapsulation efficiency, gene silencing activity, SNA stability, and cellular uptake, thus outlining optimized polymer architectures for gene silencing.
Get full access to this article
View all available purchase options and get full access to this article.
References
1. Crooke ST, X-H Liang, BF Baker and RM Crooke. (2021). Antisense technology: a review. J Biol Chem 296:100416.
2. Khvorova A and JK Watts. (2017). The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol 35:238–248.
3. Flor PJ and Neumann I. (2010). In: Encyclopedia of Psychopharmacology. Stolerman IP, ed. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 277–278.
4. Prakash TP and B Bhat. (2007). 2′-Modified oligonucleotides for antisense therapeutics. Curr Top Med Chem 7:641–649.
5. Shen X and DR Corey. (2018). Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucl Acids Res 46:1584–1600.
6. Aoki Y and MJ Wood. (2021). Emerging oligonucleotide therapeutics for rare neuromuscular diseases. J Neuromusc Dis 8:869–884.
7. Fakih HH, A Katolik, E Malek-Adamian, JJ Fakhoury, S Kaviani, MJ Damha and HF Sleiman. (2021). Design and enhanced gene silencing activity of spherical 2′-fluoroarabinose nucleic acids (FANA-SNAs). Chem Sci 12:2993–3003.
8. Kuijper EC, AJ Bergsma, WP Pijnappel and A Aartsma-Rus. (2021). Opportunities and challenges for antisense oligonucleotide therapies. J Inherit Metab Dis 44:72–87.
9. Dowler T, D Bergeron, A-L Tedeschi, L Paquet, N Ferrari and MJ Damha. (2006). Improvements in siRNA properties mediated by 2′-deoxy-2′-fluoro-β-D-arabinonucleic acid (FANA). Nucl Acids Res 34:1669–1675.
10. Istrate A, A Katolik, A Istrate and CJ Leumann. (2017). 2′ β-fluoro-tricyclo nucleic acids (2′ F-tc-ANA): thermal duplex stability, structural studies, and RNase H activation. Chem A Eur J 23:10310–10318.
11. Kalota A, L Karabon, C Swider, E Viazovkina, M Elzagheid, M Damha and A Gewirtz. (2006). 2′-deoxy-2′-fluoro-β-D-arabinonucleic acid (2′ F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing. Nucl Acids Res 34:451–461.
12. Lok C-N, E Viazovkina, K-L Min, E Nagy, CJ Wilds, MJ Damha and MA Parniak. (2002). Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2′-deoxy-2′-fluoro-d-arabinose and 2′-deoxyribose nucleotides. Biochemistry 41:3457–3467.
13. Souleimanian N, GF Deleavey, H Soifer, S Wang, K Tiemann, MJ Damha and CA Stein. (2012). Antisense 2′-deoxy, 2′-fluoroarabino nucleic acid (2′F-ANA) oligonucleotides: In vitro gymnotic silencers of gene expression whose potency is enhanced by fatty acids. Mol Ther Nucl Acids 1:e43.
14. Peer D, JM Karp, S Hong, OC Farokhzad, R Margalit and R Langer. (2020). Nanocarriers as an emerging platform for cancer therapy. Nano Enabl Med Appl 61–91.
15. Weng Y, Q Huang, C Li, Y Yang, X Wang, J Yu, Y Huang and X-J Liang. (2020). Improved nucleic acid therapy with advanced nanoscale biotechnology. Mol Ther Nucl Acids 19:581–601.
16. Banga RJ, N Chernyak, SP Narayan, ST Nguyen and CA Mirkin. (2014). Liposomal spherical nucleic acids. J Am Chem Soc 136:9866–9869.
17. Cutler JI, E Auyeung and CA Mirkin. (2012). Spherical nucleic acids. J Am Chem Soc 134:1376–1391.
18. Gulumkar V, A Aarela, O Moisio, J Rahkila, V Tahtinen, L Leimu, N Korsoff, H Korhonen, P Poijarvi-Virta and S Mikkola. (2021). Controlled monofunctionalization of molecular spherical nucleic acids on a Buckminster fullerene core. Bioconjug Chem 32:1130–1138.
19. Samanta D, SB Ebrahimi, CD Kusmierz, HF Cheng and CA Mirkin. (2020). Protein spherical nucleic acids for live-cell chemical analysis. J Am Chem Soc 142:13350–13355.
20. Zhu S, H Xing, P Gordiichuk, J Park and CA Mirkin. (2018). PLGA spherical nucleic acids. Adv Mater 30:1707113.
21. Kapadia CH, JR Melamed and ES Day. (2018). Spherical nucleic acid nanoparticles: therapeutic potential. BioDrugs 32:297–309.
22. Lewandowski KT, R Thiede, N Guido, WL Daniel, R Kang, M-IGuerrero-Zayas, MA Seeger, X-Q Wang, DA Giljohann and AS Paller. (2017). Topically delivered tumor necrosis factor-α–targeted gene regulation for psoriasis. J Invest Dermatol 137:2027.
23. Li H, B Zhang, X Lu, X Tan, F Jia, Y Xiao, Z Cheng, Y Li, DO Silva and HS Schrekker. (2018). Molecular spherical nucleic acids. Proc Natl Acad Sci U S A 115:4340–4344.
24. Altintas O and C Barner-Kowollik. (2012). Single chain folding of synthetic polymers by covalent and non-covalent interactions: current status and future perspectives. Macromol Rapid Commun 33:958–971.
25. Edwardson TG, KM Carneiro, CJ Serpell and HF Sleiman. (2014). An efficient and modular route to sequence-defined polymers appended to DNA. Angew Chem 126:4655–4659.
26. Bousmail D, L Amrein, JJ Fakhoury, HH Fakih, JC Hsu, L Panasci and HF Sleiman. (2017). Precision spherical nucleic acids for delivery of anticancer drugs. Chem Sci 8:6218–6229.
27. Bousmail D, P Chidchob and HF Sleiman. (2018). Cyanine-mediated DNA nanofiber growth with controlled dimensionality. J Am Chem Soc 140:9518–9530.
28. Dore MD, T Trinh, M Zorman, D de Rochambeau, CM Platnich, P Xu, X Luo, JM Remington, V Toader and G Cosa. (2021). Thermosetting supramolecular polymerization of compartmentalized DNA fibers with stereo sequence and length control. Chem 7:2395–2414.
29. Deleavey GF and Damha MJ. (2012). Designing chemically modified oligonucleotides for targeted gene silencing. Chem Biol 19:937–954.
30. Zimmermann J, M Kwak, AJ Musser and A Herrmann. (2011). Bioconjugation Protocols. Springer, New York, Dordrecht, Heidelberg, London, pp. 239–266.
31. Astakhova K and SA Bukhari. (2020). Nucleic Acid Detection and Structural Investigations. Springer, New York, United States.
32. Chidchob P, TG Edwardson, CJ Serpell and HF Sleiman. (2016). Synergy of two assembly languages in DNA nanostructures: self-assembly of sequence-defined polymers on DNA cages. J Am Chem Soc 138:4416–4425.
33. de Rochambeau D, Y Sun, M Barlog, HS Bazzi and Sleiman HF. (2018). Modular strategy to expand the chemical diversity of DNA and sequence-controlled polymers. J Organ Chem 83:9774–9786.
34. Dore MD, JJ Fakhoury, A Lacroix and HF Sleiman. (2018). Templated synthesis of spherical RNA nanoparticles with gene silencing activity. Chem Commun 54:11296–11299.
35. Fakih HH, JJ Fakhoury, D Bousmail and HF Sleiman. (2019). Minimalist design of a stimuli-responsive spherical nucleic acid for conditional delivery of oligonucleotide therapeutics. ACS Appl Mater Interface 11:13912–13920.
36. Hu Y, G Bebb, S Tan, R Ng, H Yan, JR Sartor, LD Mayer and MB Bally. (2004). Antitumor efficacy of oblimersen Bcl-2 antisense oligonucleotide alone and in combination with vinorelbine in xenograft models of human non–small cell lung cancer. Clin Cancer Res 10:7662–7670.
37. Patel S and MR Player. (2008). Small-molecule inhibitors of the p53-HDM2 interaction for the treatment of cancer. Exp Opin Invest Drugs 17:1865–1882.
38. Tsui P, M Rubenstein and P Guinan. (2004). Synergistic effects of combination therapy employing antisense oligonucleotides with traditional chemotherapeutics in the PC-3 prostate cancer model. Med Oncol 21:339–348.
39. Ke W, N Lu, AA-WMM Japir, Q Zhou, L Xi, Y Wang, D Dutta, M Zhou, Y Pan and Z Ge. (2020). Length effect of stimuli-responsive block copolymer prodrug filomicelles on drug delivery efficiency. J Control Release 318:67–77.
40. Zhang Z, C Liu, C Li, W Wu and X Jiang. (2019). Shape effects of cylindrical versus spherical unimolecular polymer nanomaterials on in vitro and in vivo behaviors. Research 2019:2391486.
41. Zhang Z, J Zhao, C Li, W Wu and X Jiang. (2019). Length effects of cylindrical polymer brushes on their in vitro and in vivo properties. Biomater Sci 7:5124–5131.
42. Lacroix Al, E Vengut-Climent, D de Rochambeau and HF Sleiman. (2019). Uptake and fate of fluorescently labeled DNA nanostructures in cellular environments: a cautionary tale. ACS Central Sci 5:882–891.
43. Malmo J, H Sørgård, KM Vårum and SP Strand. (2012). siRNA delivery with chitosan nanoparticles: molecular properties favoring efficient gene silencing. J Control Release 158:261–268.
44. Choi K-m, IC Kwon and HJ Ahn. (2013). Self-assembled amphiphilic DNA-cholesterol/DNA-peptide hybrid duplexes with liposome-like structure for doxorubicin delivery. Biomaterials 34:4183–4190.
45. Kolishetti N, S Dhar, PM Valencia, LQ Lin, R Karnik, SJ Lippard, R Langer and OC Farokhzad. (2010). Engineering of self-assembled nanoparticle platform for precisely controlled combination drug therapy. Proc Natl Acad Sci U S A 107:17939–17944.
46. Pokholenko O, A Gissot, B Vialet, K Bathany, A Thiéry and P Barthélémy. (2013). Lipid oligonucleotide conjugates as responsive nanomaterials for drug delivery. J Mater Chem B 1:5329–5334.
47. Rosi NL, DA Giljohann, CS Thaxton, AK Lytton-Jean, MS Han and CA Mirkin. (2006). Oligonucleotide-modified gold nanoparticles for intracellular gene regulation. Science 312:1027–1030.
48. Zhu G, J Zheng, E Song, M Donovan, K Zhang, C Liu and W Tan. (2013). Self-assembled, aptamer-tethered DNA nanotrains for targeted transport of molecular drugs in cancer theranostics. Proc Natl Acad Sci U S A 110:7998–8003.
49. Song Y, W Song, X Lan, W Cai and D Jiang. (2022). Spherical nucleic acids: organized nucleotide aggregates as versatile nanomedicine. Aggregate 3:e120.
50. Meckes B, RJ Banga, ST Nguyen and CA Mirkin. (2018). Enhancing the stability and immunomodulatory activity of liposomal spherical nucleic acids through lipid-tail DNA modifications. Small 14:1702909.
51. Ferrer JR, AJ Sinegra, D Ivancic, XY Yeap, L Qiu, J-J Wang, ZJ Zhang, JA Wertheim and CA Mirkin. (2020). Structure-dependent biodistribution of liposomal spherical nucleic acids. ACS Nano 14:1682–1693.
52. Kim C-J, G-H Kim, Jeong EH, H Lee and S-J Park. (2021). The core composition of DNA block copolymer micelles dictates DNA hybridization properties, nuclease stabilities, and cellular uptake efficiencies. Nanoscale 13:13758–13763.
53. Barbon SM, NP Truong, AG Elliott, MA Cooper, TP Davis, MR Whittaker, CJ Hawker and A Anastasaki. (2020). Elucidating the effect of sequence and degree of polymerization on antimicrobial properties for block copolymers. Polymer Chem 11:84–90.
54. Fröhlich T, D Edinger, R Kläger, C Troiber, E Salcher, N Badgujar, I Martin, D Schaffert, A Cengizeroglu and P Hadwiger. (2012). Structure–activity relationships of siRNA carriers based on sequence-defined oligo (ethane amino) amides. J Control Release 160:532–541.
55. Crooke ST, TA Vickers and X-h Liang. (2020). Phosphorothioate modified oligonucleotide–protein interactions. Nucl Acids Res 48:5235–5253.
56. Miyake H, KN Chi and ME Gleave. (2000). Antisense TRPM-2 oligodeoxynucleotides chemosensitize human androgen-independent PC-3 prostate cancer cells both in vitro and in vivo. Clin Cancer Res 6:1655–1663.
57. Miyake H, I Hara, S Kamidono and ME Gleave. (2001). Synergistic chemsensitization and inhibition of tumor growth and metastasis by the antisense oligodeoxynucleotide targeting clusterin gene in a human bladder cancer model. Clin Cancer Res 7:4245–4252.
58. Zellweger T, H Miyake, LV July, M Akbari, S Kiyama and ME Gleave. (2001). Chemosensitization of human renal cell cancer using antisense oligonucleotides targeting the antiapoptotic gene clusterin. Neoplasia 3:360–367.
59. Deleavey GF and MJ Damha. (2012). Designing chemically modified oligonucleotides for targeted gene silencing. Chem Biol 19:937–954.
60. Min K-L, E Viazovkina, A Galarneau, MA Parniak and MJ Damha. (2002). Oligonucleotides comprised of alternating 2′-Deoxy-2′-fluoro-β-d-arabinonucleosides and d-2′-deoxyribonucleosides (2′ F-ANA/DNA ‘Altimers’) induce efficient RNA cleavage mediated by RNase H. Bioorgan Med Chem Letters 12:2651–2654.
Information & Authors
Information
Published In
Copyright
Copyright 2023, Mary Ann Liebert, Inc., publishers.
History
Published online: 9 August 2023
Published in print: August 2023
Published ahead of print: 17 May 2023
Received: 2 October 2022
Accepted: 17 March 2022
Topics
Authors
Author Disclosure Statement
No competing financial interests exist.
Funding Information
We have received funding from Natural Sciences and Engineering Research Council; RGPIN-2018-06861.
Canada Foundation for Innovation; 23690.
Canada Research Chairs Program; 950-232579.
SK and HF would like to thank Fonds de Recherche du Quebec—Nature et Technologies and NSERC CREATE PROMOTE for fellowships.
Metrics & Citations
Metrics
Citations
Export Citation
Export citation
Select the format you want to export the citations of this publication.
View Options
Get Access
Access content
To read the fulltext, please use one of the options below to sign in or purchase access.⚠ Society Access
If you are a member of a society that has access to this content please log in via your society website and then return to this publication.