Abstract
RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149–155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833–842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860–921, 2001) that used to be called “junk DNA” actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.
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References
Sugimoto N, Nakano S, Katoh M et al (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34:11211–11216
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
Ikawa Y, Tsuda K, Matsumura S et al (2004) De novo synthesis and development of an RNA enzyme. Proc Natl Acad Sci U S A 101:13750–13755
Matsumura S, Ohmori R, Saito H et al (2009) Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction. FEBS Lett 583:2819–2826
Leontis NB, Lescoute A, Westhof E (2006) The building blocks and motifs of RNA architecture. Curr Opin Struct Biol 16:279–287
Schroeder KT, McPhee SA, Ouellet J et al (2010) A structural database for k-turn motifs in RNA. RNA 16:1463–1468
Li X, Horiya S, Harada K (2006) An efficient thermally induced RNA conformational switch as a framework for the functionalization of RNA nanostructures. J Am Chem Soc 128:4035–4040
Laurenti E, Barde I, Verp S et al (2010) Inducible gene and shRNA expression in resident hematopoietic stem cells in vivo. Stem Cells 28:1390–1398
Hoeprich S, Zhou Q, Guo S et al (2003) Bacterial virus phi29 pRNA as a hammerhead ribozyme escort to destroy hepatitis B virus. Gene Ther 10:1258–1267
Chang KY, Tinoco I Jr (1994) Characterization of a “kissing” hairpin complex derived from the human immunodeficiency virus genome. Proc Natl Acad Sci U S A 91(18):8705–8709
Bindewald E, Hayes R, Yingling YG et al (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res 36:D392–D397
Wagner C, Ehresmann C, Ehresmann B et al (2004) Mechanism of dimerization of bicoid mRNA: initiation and stabilization. J Biol Chem 279:4560–4569
Chen C, Sheng S, Shao Z et al (2000) A dimer as a building block in assembling RNA: A hexamer that gears bacterial virus phi29 DNA-translocating machinery. J Biol Chem 275(23):17510–17516
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
Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5:833–842
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
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
Freier SM, Kierzek R, Jaeger JA et al (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A 83:9373–9377
Ehresmann C, Baudin F, Mougel M et al (1987) Probing the structure of RNAs in solution. Nucleic Acids Res 15:9109–9128
Privalov PL, Filiminov VV (1978) Thermodynamic analysis of transfer RNA unfolding. J Mol Biol 122:447–464
Pleij CWA, Rietveld K, Bosch L (1985) A new principle of RNA folding based on pseudonotting. Nucleic Acids Res 13(5):1717–1731
Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244:48–52
Studnicka GM, Rahn GM, Cummings IW et al (1978) Computer method for predicting the secondary structure of single-stranded RNA. Nucleic Acids Res 5:3365–3387
Reid BR (1981) NMR studies on RNA structure and dynamics. Annu Rev Biochem 50:969–96
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
Haque F, Shu D, Shu Y et al (2012) Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. Nano Today 7:245–257
Liu J, Guo S, Cinier M et al (2010) Fabrication of stable and RNase-resistant RNA nanoparticles active in gearing the nanomotors for viral DNA packaging. ACS Nano 5:237–246
de Fougerolles A, Vornlocher HP, Maraganore J et al (2007) Interfering with disease: a progress report on siRNA-based therapeutics. Nat Rev Drug Discov 6:443–453
Kim DH, Rossi JJ (2007) Strategies for silencing human disease using RNA interference. Nat Rev Genet 8:173–184
Rozema DB, Lewis DL, Wakefield DH et al (2007) Dynamic polyconjugates for targeted in vivo delivery of siRNA to hepatocytes. Proc Natl Acad Sci U S A 104:12982–12987
Seth S, Johns R, Templin MV (2012) Delivery and biodistribution of siRNA for cancer therapy: challenges and future prospects. Ther Deliv 3:245–261
Bae YH, Park K (2011) Targeted drug delivery to tumors: myths, reality and possibility. J Control Release 153:198–205
Shu D, Moll WD, Deng Z et al (2004) Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology. Nano Lett 4:1717–1723
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
Li W, Szoka F (2007) Lipid-based Nanoparticles for Nucleic Acid Delivery. Pharm Res 24:438–449
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
Guo P, Haque F (eds) (2013) RNA Nanotechnology and Therapeutics. CRC Press, Boca Raton, FL
Shukla GC, Haque F, Tor Y et al (2011) A Boost for the Emerging Field of RNA Nanotechnology. ACS Nano 5:3405–3418
Leontis N, Sweeney B, Haque F et al (2013) Conference Scene: Advances in RNA nanotechnology promise to transform medicine. Nanomedicine 8:1051–1054
Guo P (ed) (2011) Methods: RNA nanotechnology. Elsevier, Amsterdam
Guo P (2005) RNA Nanotechnology: Engineering, assembly and applications in detection, gene delivery and therapy. J Nano Nanotechnol 5(12):1964–1982
Guo P, Coban O, Snead NM et al (2010) Engineering RNA for targeted siRNA delivery and medical application. Advan Drug Delivery Rev 62:650–666
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Andronescu M, Fejes AP, Hutter F et al (2004) A new algorithm for RNA secondary structure design. J Mol Biol 336:607–624
Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32:W135–W141
Zadeh JN, Steenberg CD, Bois JS et al (2011) NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 32:170–173
Delebecque CJ, Silver PA, Lindner AB (2012) Designing and using RNA scaffolds to assemble proteins in vivo. Nat Protoc 7:1797–1807
Watts JK, Deleavey GF, Damha MJ (2008) Chemically modified siRNA: tools and applications. Drug Discov Today 13:842–855
Shaw BR, Moussa L, Sharaf M et al (2008) Boranophosphate siRNA-aptamer chimeras for tumor-specific downregulation of cancer receptors and modulators. Nucleic Acids Symp Ser (Oxf) 52:655–656
Helmling S, Moyroud E, Schroeder W et al (2003) A new class of Spiegelmers containing 2′-fluoro-nucleotides. Nucleosides Nucleotides Nucleic Acids 22:1035–1038
Luy B, Marino JP (2001) Measurement and application of 1H-19F dipolar couplings in the structure determination of 2′-fluorolabeled RNA. J Biomol NMR 20:39–47
Reif B, Wittmann V, Schwalbe H et al (1997) Structural comparison of oligoribonucleotides and their 2′-deoxy-2′-fluoro analogs by heteronuclear NMR spectroscopy. Helv Chim Acta 80:1952–1971
Binzel DW, Khisamutdinov EF, Guo P (2014) Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments. Biochemistry 53:2221–2231
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
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
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
Khisamutdinov E, Li H, Jasinski D et al (2014) Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square, and pentagon nanovehicles. Nucelic Acids Research 42:9996–10004
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
Martinez HM, Maizel JV, Shapiro BA (2008) RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA. J Biomol Str Dyn 25:669–683
Bindewald E, Grunewald C, Boyle B et al (2008) Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler. J Mol Graph Model 27:299–308
Grabow WW, Zakrevsky P, Afonin KA et al (2011) Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett 11:878–887
Afonin KA, Bindewald E, Yaghoubian AJ et al (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat Nanotechnol 5:676–682
Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453:3–31
Ohno H, Kobayashi T, Kabata R et al (2011) Synthetic RNA-protein complex shaped like an equilateral triangle. Nat Nanotechnol 6:116–120
Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA ploymerase. Science 249:505–510
Mi J, Liu Y, Rabbani ZN et al (2010) In vivo selection of tumor-targeting RNA motifs. Nat Chem Biol 6:22–24
Lupold SE, Hicke BJ, Lin Y et al (2002) Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res 62:4029–4033
Sharma AK, Kent AD, Heemstra JM (2012) Enzyme-linked small-molecule detection using split aptamer ligation. Anal Chem 84:6104–6109
Sharma AK, Heemstra JM (2011) Small-molecule-dependent split aptamer ligation. J Am Chem Soc 133:12426–12429
Low PS, Henne WA, Doorneweerd DD (2008) Discovery and development of folic-acid-based receptor targeting for imaging and therapy of cancer and inflammatory diseases. Acc Chem Res 41:120–129
Toffoli G, Cernigoi C, Russo A et al (1997) Overexpression of folate binding protein in ovarian cancers. Int J Cancer 74:193–198
Gosselin MA, Guo W, Lee RJ (2002) Incorporation of reversibly cross-linked polyplexes into LPDII vectors for gene delivery. Bioconjug Chem 13:1044–1053
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
Li H, Li WX, Ding SW (2002) Induction and suppression of RNA silencing by an animal virus. Science 296:1319–1321
Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553
Jacque JM, Triques K, Stevenson M (2002) Modulation of HIV-1 replication by RNA interference. Nature 418:435–438
Varambally S, Dhanasekaran SM, Zhou M et al (2002) The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419:624–629
Carmichael GG (2002) Medicine: silencing viruses with RNA. Nature 418:379–380
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233
Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866
Ye X, Liu Z, Hemida MG et al (2011) Targeted delivery of mutant tolerant anti-coxsackievirus artificial microRNAs using folate conjugated bacteriophage Phi29 pRNA. PLoS One 6:e21215
Hanagata N (2012) Structure-dependent immunostimulatory effect of CpG oligodeoxynucleotides and their delivery system. Int J Nanomedicine 7:2181–2195
Klinman DM (2004) Immunotherapeutic uses of CpG oligodeoxynucleotides. Nat Rev Immunol 4:248–257
Paredes E, Evans M, Das SR (2011) RNA labeling, conjugation and ligation. Methods 54(2):251–259
Grate D, Wilson C (1999) Laser-mediated, site-specific inactivation of RNA transcripts. Proc Natl Acad Sci U S A 96:6131–6136
Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642–646
Shu D, Zhang L, Khisamutdinov E et al (2013) Programmable folding of fusion RNA complex driven by the 3WJ motif of phi29 motor pRNA. Nucleic Acids Res 42:e10
Shlyakhtenko LS, Gall AA, Filonov A et al (2003) Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials. Ultramicroscopy 97:279–287
Acknowledgements
The research was supported by NIH grants R01-EB003730 and U01-CA151648 to P.G. The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH. Funding to Peixuan Guo’s Endowed Chair in Nanobiotechnology position is from the William Fairish Endowment Fund. P.G. is a cofounder of Kylin Therapeutics, Inc., RNA Nano, LLC., and Biomotor and Nucleic Acid Nanotechnology Development Corp., Ltd.
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Haque, F., Guo, P. (2015). Overview of Methods in RNA Nanotechnology: Synthesis, Purification, and Characterization of RNA Nanoparticles. In: Guo, P., Haque, F. (eds) RNA Nanotechnology and Therapeutics. Methods in Molecular Biology, vol 1297. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2562-9_1
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