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Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°

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RNA Scaffolds

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1316))

Abstract

Precise shape control of architectures at the nanometer scale is an intriguing but extremely challenging facet. RNA has recently emerged as a unique material and thermostable building block for use in nanoparticle construction. Here, we describe a simple method from design to synthesis of RNA triangle, square, and pentagon by stretching RNA 3WJ native angle from 60° to 90° and 108°, using the three-way junction (3WJ) of the pRNA from bacteriophage phi29 dsDNA packaging motor. These methods for the construction of elegant polygons can be applied to other RNA building blocks including the utilization and application of RNA 4-way, 5-way, and other multi-way junctions.

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References

  1. Guo P, Zhang C, Chen C, Trottier M, Garver K (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 

  2. Soni GV, Singer A, Yu Z, Sun Y, McNally B, Meller A (2010) Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores. Rev Sci Instrum 81:014301

    Article  PubMed Central  PubMed  Google Scholar 

  3. Tombelli S, Mascini M (2009) Aptamers as molecular tools for bioanalytical methods. Curr Opin Mol Ther 11:179–188

    CAS  PubMed  Google Scholar 

  4. Haes AJ, Van Duyne RP (2002) A nanoscale optical biosensor: sensitivity and selectivity of an approach based on the localized surface plasmon resonance spectroscopy of triangular silver nanoparticles. J Am Chem Soc 124:10596–10604

    Article  CAS  PubMed  Google Scholar 

  5. Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA (2012) Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs. Nano Lett 12:5192–5195

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Afonin KA, Grabow WW, Walker FM, Bindewald E, Dobrovolskaia MA, Shapiro BA, Jaeger L (2011) Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nat Protoc 6:2022–2034

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L et al (2014) Multifunctional RNA nanoparticles. Nano Lett 14:5662–5671

    Article  CAS  PubMed  Google Scholar 

  8. Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers BM, Guo P (2014) Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 66C:74–89

    Article  Google Scholar 

  9. Shu Y, Haque F, Shu D, Li W, Zhu Z, Kotb M, Lyubchenko Y, Guo P (2013) Fabrication of 14 different RNA nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 19:766–777

    Article  Google Scholar 

  10. Shu Y, Shu D, Haque F, Guo P (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 

  11. Shu D, Shu Y, Haque F, Abdelmawla S, Guo P (2011) Thermodynamically stable RNA three-way junctions for constructing multifunctional nanoparticles for delivery of therapeutics. Nat Nanotechnol 6:658–667

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Haque F, Shu D, Shu Y, Shlyakhtenko L, Rychahou P, Evers M, Guo P (2012) Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. Nano Today 7:245–257

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi J, Leontis N, Guo P (2013) RNA nanotechnology for computer design and in vivo computation. Philos Trans R Soc A 371(2000):201203120

    Article  Google Scholar 

  14. Amir Y, Ben-Ishay E, Levner D, Ittah S, Bu-Horowitz A, Bachelet I (2014) Universal computing by DNA origami robots in a living animal. Nat Nanotechnol 9:353–357

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Reif R, Haque F, Guo P (2013) Fluorogenic RNA nanoparticles for monitoring RNA folding and degradation in real time in living cells. Nucleic Acid Ther 22(6):428–437

    Google Scholar 

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

    Article  PubMed Central  PubMed  Google Scholar 

  17. Muller MC, Gattermann N, Lahaye T, Deininger MW, Berndt A, Fruehauf S, Neubauer A, Fischer T, Hossfeld DK, Schneller F et al (2003) Dynamics of BCR-ABL mRNA expression in first-line therapy of chronic myelogenous leukemia patients with imatinib or interferon alpha/ara-C. Leukemia 17:2392–2400

    Article  CAS  PubMed  Google Scholar 

  18. Novoa EM, Pavon-Eternod M, Pan T, de Ribas PL (2012) A role for tRNA modifications in genome structure and codon usage. Cell 149:202–213

    Article  CAS  PubMed  Google Scholar 

  19. Motorin Y, Helm M (2010) tRNA stabilization by modified nucleotides. Biochemistry 49:4934–4944

    Article  CAS  PubMed  Google Scholar 

  20. Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD (2010) Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 464:1012–1017

    Article  CAS  PubMed  Google Scholar 

  21. Liao J, Yu L, Mei Y, Guarnera M, Shen J, Li R, Liu Z, Jiang F (2010) Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol Cancer 9:198

    Article  PubMed Central  PubMed  Google Scholar 

  22. Hertel J, Hofacker IL, Stadler PF (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24:158–164

    Article  CAS  PubMed  Google Scholar 

  23. Bachellerie JP, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84:775–790

    Article  CAS  PubMed  Google Scholar 

  24. Westhof E (2012) Ribozymes, catalytically active RNA molecules. Introduction. Methods Mol Biol 848:1–4

    Article  CAS  PubMed  Google Scholar 

  25. Mulhbacher J, St-Pierre P, Lafontaine DA (2010) Therapeutic applications of ribozymes and riboswitches. Curr Opin Pharmacol 10:551–556

    Article  CAS  PubMed  Google Scholar 

  26. Steiner M, Karunatilaka KS, Sigel RK, Rueda D (2008) Single-molecule studies of group II intron ribozymes. Proc Natl Acad Sci U S A 105:13853–13858

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  28. Wacker A, Buck J, Mathieu D, Richter C, Wohnert J, Schwalbe H (2011) Structure and dynamics of the deoxyguanosine-sensing riboswitch studied by NMR-spectroscopy. Nucleic Acids Res 39:6802–6812

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Schroeder A, Goldberg MS, Kastrup C, Wang Y, Jiang S, Joseph BJ, Levins CG, Kannan ST, Langer R, Anderson DG (2012) Remotely activated protein-producing nanoparticles. Nano Lett 12:2685–2689

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Sternberg SH, Fei J, Prywes N, McGrath KA, Gonzalez RL Jr (2009) Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol 16:861–868

    Article  CAS  PubMed  Google Scholar 

  32. Shoji S, Walker SE, Fredrick K (2009) Ribosomal translocation: one step closer to the molecular mechanism. ACS Chem Biol 4:93–107

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Schroeder KT, McPhee SA, Ouellet J, Lilley DM (2010) A structural database for k-turn motifs in RNA. RNA 16:1463–1468

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H (2011) Synthetic RNA-protein complex shaped like an equilateral triangle. Nat Nanotechnol 6:116–120

    Article  CAS  PubMed  Google Scholar 

  35. 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 

  36. Zhao Z, Khisamutdinov E, Schwartz C, Guo P (2013) Mechanism of one-way traffic of hexameric phi29 DNA packaging motor with four electropositive relaying layers facilitating anti-parallel revolution. ACS Nano 7:4082–4092

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Guo P, Zhao Z, Haak J, Wang S, Wu D, Meng B, Weitao T (2014) Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation. Biotechnol Adv 32:853–872

    Article  CAS  PubMed  Google Scholar 

  38. 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  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  40. Khisamutdinov EF, Jasinski DL, Guo P (2014) RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano 8:4771–4781

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Khisamutdinov E, Li H, Jasinski D, Chen J, Fu J, Guo P (2014) Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square, and pentagon nanovehicles. Nucleic Acids Res 42:9996–10004

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Lescoute A, Westhof E (2006) Topology of three-way junctions in folded RNAs. RNA 12:83–93

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA (2011) NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 32:170–173

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The work was supported by NIH grants CA151648 and EB003730, and funding to Peixuan Guo’s Endowed Chair in Nanobiotechnology position from the William Fairish Endowment Fund. The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH. We would like to acknowledge the core facilities of the Markey Cancer Center at the University of Kentucky.

Conflicts of interest: P.G. is a co-founder of Kylin Therapeutics, Inc.; RNA Nano LLC; and Biomotor and RNA Nanotech Development Co., Ltd.

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Authors and Affiliations

  1. Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA

    Emil F. Khisamutdinov, Daniel Jasinski, Zhengyi Zhao, Zheng Cui & Peixuan Guo

  2. Nanobiotechnology Center, Markey Cancer Center, University of Kentucky, Lexington, KY, 40536, USA

    Emil F. Khisamutdinov, Daniel Jasinski, Zhengyi Zhao, Zheng Cui & Peixuan Guo

  3. Department of Chemistry, Ball State University, Muncie, IN, 47306, USA

    Emil F. Khisamutdinov & My Nguyen Hoan Bui

Authors
  1. Emil F. Khisamutdinov
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  2. My Nguyen Hoan Bui
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  3. Daniel Jasinski
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  4. Zhengyi Zhao
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  5. Zheng Cui
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  6. Peixuan Guo
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Corresponding authors

Correspondence to Emil F. Khisamutdinov or Peixuan Guo .

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Editors and Affiliations

  1. University of Paris Descartes, Paris, France

    Luc Ponchon

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Khisamutdinov, E.F., Bui, M.N.H., Jasinski, D., Zhao, Z., Cui, Z., Guo, P. (2015). Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°. In: Ponchon, L. (eds) RNA Scaffolds. Methods in Molecular Biology, vol 1316. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2730-2_15

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  • DOI: https://doi.org/10.1007/978-1-4939-2730-2_15

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2729-6

  • Online ISBN: 978-1-4939-2730-2

  • eBook Packages: Springer Protocols

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