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Intracellular Reassociation of RNA–DNA Hybrids that Activates RNAi in HIV-Infected Cells

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

Abstract

Human immunodeficiency virus Type 1 (HIV-1) is the major cause of acquired immune deficiency syndrome (AIDS). In 2014, it was estimated that 1.2 million people died from AIDS-related illnesses. RNA interference-based therapy to block HIV replication is a field that, as of now, is without any FDA-approved drugs available for clinical use. In this chapter we describe a protocol for testing and utilizing a new approach that relies on reassociation of RNA–DNA hybrids activating RNAi and blocking HIV replication in human cells.

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References

  1. Bramsen JB, Kjems J (2012) Development of therapeutic-grade small interfering RNAs by chemical engineering. Front Genet 3:154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Fire A, Xu S, Montgomery MK et al (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811

    Article  CAS  PubMed  Google Scholar 

  3. Parrish S, Fleenor J, Xu S et al (2000) Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Mol Cell 6(5):1077–1087

    Article  CAS  PubMed  Google Scholar 

  4. Lund E, Dahlberg JE (2006) Substrate selectivity of exportin 5 and Dicer in the biogenesis of microRNAs. Cold Spring Harb Symp Quant Biol 71:59–66

    Article  CAS  PubMed  Google Scholar 

  5. Ji X (2008) The mechanism of RNase III action: how dicer dices. Curr Top Microbiol Immunol 320:99–116

    CAS  PubMed  Google Scholar 

  6. Macrae IJ, Zhou K, Li F et al (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311(5758):195–198. doi:10.1126/science.1121638

    Article  CAS  PubMed  Google Scholar 

  7. Dao BN, Viard M, Martins AN et al (2015) Triggering RNAi with multifunctional RNA nanoparticles and their delivery. DNA RNA Nanotechnol 1(1):27–38

    Google Scholar 

  8. Schwarz DS, Hutvagner G, Du T et al (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2):199–208

    Article  CAS  PubMed  Google Scholar 

  9. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2):209–216

    Article  CAS  PubMed  Google Scholar 

  10. Pratt AJ, MacRae IJ (2009) The RNA-induced silencing complex: a versatile gene-silencing machine. J Biol Chem 284(27):17897–17901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Afonin KA, Viard M, Martins AN et al (2013) Activation of different split functionalities on re-association of RNA-DNA hybrids. Nat Nanotechnol 8(4):296–304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Shekhawat SS, Ghosh I (2011) Split-protein systems: beyond binary protein-protein interactions. Curr Opin Chem Biol 15(6):789–797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Rose SD, Kim DH, Amarzguioui M et al (2005) Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res 33(13):4140–4156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Afonin KA, Viard M, Tedbury P et al (2016) The use of minimal RNA toeholds to trigger the activation of multiple functionalities. Nano Lett 16(3):1746–1753

    Article  CAS  PubMed  Google Scholar 

  15. Afonin KA, Desai R, Viard M et al (2014) Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities. Nucleic Acids Res 42(3):2085–2097

    Article  CAS  PubMed  Google Scholar 

  16. Afonin KA, Bindewald E, Kireeva M et al (2015) Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities. Methods Enzymol 553:313–334

    Article  CAS  PubMed  Google Scholar 

  17. Afonin KA, Grabow WW, Walker FM et al (2011) Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nat Protoc 6(12):2022–2034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Grabow WW, Zakrevsky P, Afonin KA et al (2011) Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett 11(2):878–887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yingling YG, Shapiro BA (2007) Computational design of an RNA hexagonal nanoring and an RNA nanotube. Nano Lett 7(8):2328–2334

    Article  CAS  PubMed  Google Scholar 

  20. Afonin KA, Bindewald E, Yaghoubian AJ et al (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat Nanotechnol 5(9):676–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Afonin KA, Kasprzak W, Bindewald E et al (2014) Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 67(2):256–265

    Article  CAS  PubMed  Google Scholar 

  22. Afonin KA, Viard M, Kagiampakis I et al (2015) Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles. ACS Nano 9(1):251–259

    Article  CAS  PubMed  Google Scholar 

  23. Afonin KA, Viard M, Koyfman AY et al (2014) Multifunctional RNA nanoparticles. Nano Lett 14(10):5662–5671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Rogers TA, Andrews GE, Jaeger L et al (2015) Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer. ACS Synth Biol 4(2):162–166

    Article  CAS  PubMed  Google Scholar 

  25. Groves B, Chen YJ, Zurla C et al (2016) Computing in mammalian cells with nucleic acid strand exchange. Nat Nanotechnol 11(3):287–294

    Article  CAS  PubMed  Google Scholar 

  26. Low JT, Knoepfel SA, Watts JM et al (2012) SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. Mol Ther 20(4):820–828

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Adachi A, Gendelman HE, Koenig S et al (1986) Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J Virol 59(2):284–291

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Waheed AA, Ono A, Freed EO (2009) Methods for the study of HIV-1 assembly. Methods Mol Biol 485:163–184

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Kirill A. Afonin .

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Martins, A.N. et al. (2017). Intracellular Reassociation of RNA–DNA Hybrids that Activates RNAi in HIV-Infected Cells. 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_18

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  • DOI: https://doi.org/10.1007/978-1-4939-7138-1_18

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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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