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Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice

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RNA Nanostructures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1632))

Abstract

RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape. RNA nanotechnology exemplified by the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor has provided a different prospect in nanoparticle designs. Of note, there is a robust three-way junction (3WJ) motif in pRNA which can serve as an adaptable scaffold to construct thermodynamically stable 2D planar and 3D globular RNA architectures with tunable shapes and sizes, and harboring various targeting, therapeutic, and imaging modules. This chapter focuses on the methods for constructing pRNA-3WJ based nanoparticles with controllable sizes and shapes, and assessment of their biodistribution profiles in cancer mouse models after systemic injection and ocular mouse models following subconjunctival injection.

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References

  1. Puri A, Loomis K, Smith B et al (2009) Lipid-based nanoparticles as pharmaceutical drug carriers: from concepts to clinic. Crit Rev Ther Drug Carrier Syst 26:523–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Weijun L, Francis CS (2007) Lipid-based nanoparticles for nucleic acid delivery. Pharm Res 24:438–449

    Article  Google Scholar 

  3. Vo-Dinh T (2005) Protein nanotechnology: the new frontier in biosciences. Methods Mol Biol 300:1–13

    CAS  PubMed  Google Scholar 

  4. Zhang F, Nangreave J, Liu Y et al (2014) Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 136:11198–11211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5:833–842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99:237–247

    Article  CAS  PubMed  Google Scholar 

  7. Seeman NC (2010) Nanomaterials based on DNA. Annu Rev Biochem 79:65–87

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Lin C, Liu Y, Yan H (2009) Designer DNA nanoarchitectures. Biochemistry 48:1663–1674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sugimoto N, Nakano S, Katoh M et al (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34:11211–11216

    Article  CAS  PubMed  Google Scholar 

  10. Searle MS, Williams DH (1993) On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res 21:2051–2056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lemieux S, Major F (2002) RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res 30:4250–4263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499–512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Scott WG (2007) Ribozymes. Curr Opin Struct Biol 17:280–286

    Article  CAS  PubMed  Google Scholar 

  14. Breaker RR (2012) Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 4:a003566

    Article  PubMed  PubMed Central  Google Scholar 

  15. Ryther RC, Flynt AS, Phillips JA III et al (2005) siRNA therapeutics: big potential from small RNAs. Gene Ther 12:5–11

    Article  CAS  PubMed  Google Scholar 

  16. Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524

    Article  CAS  PubMed  Google Scholar 

  17. Zhou J, Bobbin ML, Burnett JC et al (2012) Current progress of RNA aptamer-based therapeutics. Front Genet 3:234

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Shu Y, Pi F, Sharma A et al (2014) Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 66C:74–89

    Article  Google Scholar 

  19. Guo P, Haque F, Hallahan B et al (2012) Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther 22:226–245

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Li H, Lee T, Dziubla T et al (2015) RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications. Nano Today 10:631–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Guo P, Erickson S, Anderson D (1987) A small viral RNA is required for in vitro packaging of bacteriophage phi29 DNA. Science 236:690–694

    Article  CAS  PubMed  Google Scholar 

  22. Guo P, Zhang C, Chen C et al (1998) Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 2:149–155

    Article  CAS  PubMed  Google Scholar 

  23. Shu D, Shu Y, Haque F et al (2011) Thermodynamically stable RNA three-way junctions for constructing multifuntional nanoparticles for delivery of therapeutics. Nat Nanotechnol 6:658–667

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zhang H, Endrizzi JA, Shu Y et al (2013) Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA. RNA 19:1226–1237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Binzel DW, Khisamutdinov EF, Guo P (2014) Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments. Biochemistry 53:2221–2231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Binzel D, Khisamutdinov EF, Vieweger M et al (2016) Mechanism of three-component collision to produce ultra-stable pRNA three-way junction of Phi29 DNA-packaging motor by kinetic assessment. RNA 22:1710–1718

    Google Scholar 

  27. Haque F, Shu D, Shu Y et al (2012) Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. Nano Today 7:245–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Shu Y, Haque F, Shu D et al (2013) Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 19:766–777

    Article  Google Scholar 

  29. Liu J, Guo S, Cinier M et al (2011) Fabrication of stable and RNase-resistant RNA nanoparticles active in gearing the nanomotors for viral DNA packaging. ACS Nano 5:237–246

    Article  CAS  PubMed  Google Scholar 

  30. Shu D, Khisamutdinov E, Zhang L et al (2013) Programmable folding of fusion RNA complex driven by the 3WJ motif of phi29 motor pRNA. Nucleic Acids Res 42:e10

    Article  PubMed  PubMed Central  Google Scholar 

  31. Abdelmawla S, Guo S, Zhang L et al (2011) Pharmacological characterization of chemically synthesized monomeric pRNA nanoparticles for systemic delivery. Mol Ther 19:1312–1322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Cui D, Zhang C, Liu B et al (2015) Regression of gastric cancer by systemic injection of RNA nanoparticles carrying both ligand and siRNA. Sci Rep 5:10726

    Article  PubMed  PubMed Central  Google Scholar 

  33. Shu D, Li H, Shu Y et al (2015) Systemic delivery of anti-miRNA for suppression of triple negative breast cancer utilizing RNA nanotechnology. ACS Nano 9:9731–9740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Binzel D, Shu Y, Li H et al (2016) Specific delivery of MiRNA for high efficient inhibition of prostate cancer by RNA nanotechnology. Mol Ther 24(7):1267–1277

    Article  CAS  PubMed  Google Scholar 

  35. Rychahou P, Haque F, Shu Y et al (2015) Delivery of RNA nanoparticles into colorectal cancer metastases following systemic administration. ACS Nano 9:1108–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Lee TJ, Haque F, Shu D et al (2015) RNA nanoparticles as a vector for targeted siRNA delivery into glioblastoma mouse model. Oncotarget 6:14766–14776

    Article  PubMed  PubMed Central  Google Scholar 

  37. Li H, Zhang K, Pi F et al (2016) Controllable self-assembly of RNA tetrahedrons with precise shape and size for cancer targeting. Adv Mater 34:7501–7507

    Article  Google Scholar 

  38. Khisamutdinov E, Li H, Jasinski D et al (2014) Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square, and pentagon nanovehicles. Nucleic Acids Res 42:9996–10004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sharma A, Haque F, Pi F et al (2015) Controllable self-assembly of RNA dendrimers. Nanomed Nanotechnol Biol Med 12:835–844

    Article  Google Scholar 

  40. Khisamutdinov EF, Jasinski DL, Li H et al (2016) Fabrication of RNA 3D nanoprism for loading and protection of small RNAs and model drugs. Adv Mater 28(45):10079–10087

    Article  CAS  PubMed  Google Scholar 

  41. Feng L, Li SK, Liu H et al (2014) Ocular delivery of pRNA nanoparticles: distribution and clearance after subconjunctival injection. Pharm Res 31:1046–1058

    Article  CAS  PubMed  Google Scholar 

  42. Shu Y, Shu D, Haque F et al (2013) Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat Protoc 8:1635–1659

    Article  CAS  PubMed  Google Scholar 

  43. Rychahou P, Shu Y, Haque F et al (2015) Methods and assays for specific targeting and delivery of RNA nanoparticles to cancer metastases. Methods Mol Biol 1297:121–135

    Article  PubMed  Google Scholar 

  44. Lee TJ, Haque F, Vieweger M et al (2015) Functional assays for specific targeting and delivery of RNA nanoparticles to brain tumor. Methods Mol Biol 1297:137–152

    Article  PubMed  PubMed Central  Google Scholar 

  45. Jasinski D, Schwartz C, Haque F et al (2015) Large scale purification of RNA nanoparticles by preparative ultracentrifugation. Methods Mol Biol 1297:67–82

    Article  PubMed  Google Scholar 

  46. Zhang H, Pi F, Shu D et al (2015) Using RNA nanoparticles with thermostable motifs and fluorogenic modules for real-time detection of RNA folding and turnover in prokaryotic and eukaryotic cells. Methods Mol Biol 1297:95–111

    Article  PubMed  Google Scholar 

  47. Khisamutdinov EF, Bui MN, Jasinski D et al (2015) Simple method for constructing RNA triangle, square, Pentagon by tuning interior RNA 3WJ angle from 60 degrees to 90 degrees or 108 degrees. Methods Mol Biol 1316:181–193

    Article  PubMed  Google Scholar 

  48. Jasinski D, Khisamutdinov EF, Lyubchenko YL et al (2014) Physicochemically tunable poly-functionalized RNA square architecture with fluorogenic and ribozymatic properties. ACS Nano 8:7620–7629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The research was supported by NIH grants R01EB019036, U01CA151648 and U01CA207946. P.G.’s Sylvan G. Frank Endowed Chair position in Pharmaceutics and Drug Delivery is funded by the CM Chen Foundation. P.G. is the founder of P&Z Biological Technology and a consultant of Oxford Nanopore and Nanobiodelivery Pharmaceutical Co. Ltd.

Author information

Author notes

  1. Authors “Farzin Haque” and “Congcong Xu” have contributed equally to this work.

Authors and Affiliations

  1. Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA

    Farzin Haque, Congcong Xu, Daniel L. Jasinski, Hui Li & Peixuan Guo Ph.D.

  2. Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA

    Farzin Haque, Congcong Xu, Daniel L. Jasinski, Hui Li & Peixuan Guo Ph.D.

  3. Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA

    Farzin Haque, Congcong Xu, Daniel L. Jasinski, Hui Li & Peixuan Guo Ph.D.

Authors
  1. Farzin Haque
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  2. Congcong Xu
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  3. Daniel L. Jasinski
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  4. Hui Li
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  5. Peixuan Guo Ph.D.
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Corresponding author

Correspondence to Peixuan Guo Ph.D. .

Editor information

Editors and Affiliations

  1. Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland, USA

    Eckart Bindewald

  2. RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA

    Bruce A. Shapiro

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Haque, F., Xu, C., Jasinski, D.L., Li, H., Guo, P. (2017). Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice. In: Bindewald, E., Shapiro, B. (eds) RNA Nanostructures . Methods in Molecular Biology, vol 1632. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7138-1_23

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  • DOI: https://doi.org/10.1007/978-1-4939-7138-1_23

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7137-4

  • Online ISBN: 978-1-4939-7138-1

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