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Annual Review of Biophysics

Volume 44, 2015

Structure and Mechanism of RNA Mimics of Green Fluorescent Protein

Abstract

RNAs have highly complex and dynamic cellular localization patterns. Technologies for imaging RNA in living cells are important for uncovering their function and regulatory pathways. One approach for imaging RNA involves genetically encoding fluorescent RNAs using RNA mimics of green fluorescent protein (GFP). These mimics are RNA aptamers that bind fluorophores resembling those naturally found in GFP and activate their fluorescence. These RNA–fluorophore complexes, including Spinach, Spinach2, and Broccoli, can be used to tag RNAs and to image their localization in living cells. In this article, we describe the generation and optimization of these aptamers, along with strategies for expanding the spectral properties of their associated RNA–fluorophore complexes. We also discuss the structural basis for the fluorescence and photophysical properties of Spinach, and we describe future prospects for designing enhanced RNA–fluorophore complexes with enhanced photostability and increased sensitivity.

Keyword(s): aptamers, fluorescence, imaging, microscopy, RNA
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2015-06-22
2024-04-25
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Literature Cited

  1. Anderson P, Kedersha N. 1.  2002. Visibly stressed: the role of eIF2, TIA-1, and stress granules in protein translation. Cell Stress Chaperones 7:213–21 [Google Scholar]
  2. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P. 2.  et al. 2006. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203–7 [Google Scholar]
  3. Babendure JR, Adams SR, Tsien RY. 3.  2003. Aptamers switch on fluorescence of triphenylmethane dyes. J. Am. Chem. Soc. 125:14716–17 [Google Scholar]
  4. Baffour-Awuah NA, Zimmer M. 4.  2004. Hula-twisting in green fluorescent protein. Chem. Phys. 303:7–11 [Google Scholar]
  5. Bagni C, Greenough WT. 5.  2005. From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome. Nat. Rev. Neurosci. 6:376–87 [Google Scholar]
  6. Batista PJ, Chang HY. 6.  2013. Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–307 [Google Scholar]
  7. Beermann AE, Jay DG. 7.  1994. Chromophore-assisted laser inactivation of cellular proteins. Methods Cell Biol 44:715–32 [Google Scholar]
  8. Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM. 8.  1998. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2:437–45 [Google Scholar]
  9. Bokman SH, Ward WW. 9.  1981. Renaturation of Aequorea green-fluorescent protein. Biochem. Biophys. Res. Commun 101:1372–80 [Google Scholar]
  10. Brion P, Westhof E. 10.  1997. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26:113–37 [Google Scholar]
  11. Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. 11.  2014. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143–46 [Google Scholar]
  12. Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. 12.  2010. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90:1103–63 [Google Scholar]
  13. Clore GM, Gronenborn AM. 13.  1985. Probing the three-dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements. FEBS Lett 179:187–98 [Google Scholar]
  14. Cody CW, Prasher DC, Westler WM, Prendergast FG, Ward WW. 14.  1993. Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. Biochemistry 32:1212–18 [Google Scholar]
  15. De S, Girigoswami A, Mandal S. 15.  2002. Enhanced fluorescence of triphenylmethane dyes in aqueous surfactant solutions at supramicellar concentrations—effect of added electrolyte. Spectrochim. Acta A 58:2547–55 [Google Scholar]
  16. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S. 16.  et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–89 [Google Scholar]
  17. Dolgosheina EV, Jeng SCY, Panchapakesan SSS, Cojocaru R, Chen PSK. 17.  et al. 2014. RNA Mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem. Biol. 9:2412–20 [Google Scholar]
  18. Famulok M, Mayer G, Blind M. 18.  2000. Nucleic acid aptamers—from selection in vitro to applications in vivo. Acc. Chem. Res. 33:591–99 [Google Scholar]
  19. Filonov GS, Moon JD, Svensen N, Jaffrey SR. 19.  2014. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136:16299–308Describes directed evolution of RNA–fluorophore complexes and the generation of Broccoli. [Google Scholar]
  20. Gold L, Polisky B, Uhlenbeck O, Yarus M. 20.  1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64:763–97 [Google Scholar]
  21. Grate D, Wilson C. 21.  1999. Laser-mediated, site-specific inactivation of RNA transcripts. PNAS 96:6131–36 [Google Scholar]
  22. Green R, Ellington AD, Szostak JW. 22.  1990. In vitro genetic analysis of the Tetrahymena self-splicing intron. Nature 347:406–8 [Google Scholar]
  23. Guidry G. 23.  1999. A method for counterstaining tissues in conjunction with the glyoxylic acid condensation reaction for detection of biogenic amines. J. Histochem. Cytochem. 47:261–64 [Google Scholar]
  24. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J. 24.  et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129–41 [Google Scholar]
  25. Haidekker MA, Theodorakis EA. 25.  2010. Environment-sensitive behavior of fluorescent molecular rotors. J. Biol. Eng. 4:11 [Google Scholar]
  26. Han J, Kim D, Morris KV. 26.  2007. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. PNAS 104:12422–27 [Google Scholar]
  27. Han KY, Leslie BJ, Fei J, Zhang J, Ha T. 27.  2013. Understanding the photophysics of the Spinach–DFHBI RNA aptamer–fluorogen complex to improve live-cell RNA imaging. J. Am. Chem. Soc. 135:19033–38Describes a photophysical study of the photobleaching and photoconversion of the Spinach–DFHBI complex. [Google Scholar]
  28. Hell SW. 28.  2009. Microscopy and its focal switch. Nat. Methods 6:24–32 [Google Scholar]
  29. Hesselberth JR, Miller D, Robertus J, Ellington AD. 29.  2000. In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J. Biol. Chem. 275:4937–42 [Google Scholar]
  30. Hocine S, Raymond P, Zenklusen D, Chao JA, Singer RH. 30.  2013. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods 10:119–21 [Google Scholar]
  31. Hofmann M, Eggeling C, Jakobs S, Hell SW. 31.  2005. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. PNAS 102:17565–69 [Google Scholar]
  32. Holeman LA, Robinson SL, Szostak JW, Wilson C. 32.  1998. Isolation and characterization of fluorophore-binding RNA aptamers. Fold. Des. 3:423–31 [Google Scholar]
  33. Huang B, Bates M, Zhuang X. 33.  2009. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78:993–1016 [Google Scholar]
  34. Huang H, Suslov NB, Li NS, Shelke SA, Evans ME. 34.  et al. 2014. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat. Chem. Biol. 10:686–91Describes the crystal structure of the Spinach–DFHBI complex and provides insights into the mechanism of fluorescence activation (see also Reference 65). [Google Scholar]
  35. Kiebler MA, Bassell GJ. 35.  2006. Neuronal RNA granules: movers and makers. Neuron 51:685–90 [Google Scholar]
  36. Kojima S, Ohkawa H, Hirano T, Maki S, Niwa H. 36.  et al. 1998. Fluorescent properties of model chromophores of tyrosine-66 substituted mutants of Aequorea green fluorescent protein (GFP). Tetrahedron Lett. 39:5239–42 [Google Scholar]
  37. Kummer AD, Kompa C, Lossau H, Pollinger-Dammer F, Michel-Beyerle ME. 37.  et al. 1998. Dramatic reduction in fluorescence quantum yield in mutants of Green Fluorescent Protein due to fast internal conversion. Chem. Phys. 237:183–93 [Google Scholar]
  38. Likhtenshtein GI, Bishara R, Papper V, Uzan B, Fishov I. 38.  et al. 1996. Novel fluorescence-photochrome labeling method in the study of biomembrane dynamics. J. Biochem. Biophys. Methods 33:117–33 [Google Scholar]
  39. Martell RE, Nevins JR, Sullenger BA. 39.  2002. Optimizing aptamer activity for gene therapy applications using expression cassette SELEX. Mol. Ther. 6:30–34 [Google Scholar]
  40. Meech SR. 40.  2009. Excited state reactions in fluorescent proteins. Chem. Soc. Rev. 38:2922–34 [Google Scholar]
  41. Merzlyak EM, Goedhart J, Shcherbo D, Bulina ME, Shcheglov AS. 41.  et al. 2007. Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat. Methods 4:555–57 [Google Scholar]
  42. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. 42.  2012. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149:1635–46 [Google Scholar]
  43. Mhlanga MM, Tyagi S. 43.  2006. Using tRNA-linked molecular beacons to image cytoplasmic mRNAs in live cells. Nat. Protoc. 1:1392–98 [Google Scholar]
  44. Niwa H, Inouye S, Hirano T, Matsuno T, Kojima S. 44.  et al. 1996. Chemical nature of the light emitter of the Aequorea green fluorescent protein. PNAS 93:13617–22 [Google Scholar]
  45. Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. 45.  1996. Crystal structure of the Aequorea victoria green fluorescent protein. Science 273:1392–95 [Google Scholar]
  46. Paige JS, Wu KY, Jaffrey SR. 46.  2011. RNA mimics of green fluorescent protein. Science 333:642–46Describes the initial generation of Spinach for RNA imaging. [Google Scholar]
  47. Parker R, Song H. 47.  2004. The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11:121–27 [Google Scholar]
  48. Paul CP, Good PD, Li SXL, Kleihauer A, Rossi JJ, Engelke DR. 48.  2003. Localized expression of small RNA inhibitors in human cells. Mol. Ther. 7:237–47 [Google Scholar]
  49. Ponchon L, Dardel F. 49.  2007. Recombinant RNA technology: the tRNA scaffold. Nat. Methods 4:571–76 [Google Scholar]
  50. Pothoulakis G, Ceroni F, Reeve B, Ellis T. 50.  2013. The Spinach RNA aptamer as a characterization tool for synthetic biology. ACS Synth. Biol. 3:182–87 [Google Scholar]
  51. Remington SJ. 51.  2011. Green fluorescent protein: a perspective. Protein Sci 20:1509–19 [Google Scholar]
  52. Sando S, Narita A, Hayami M, Aoyama Y. 52.  2008. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem. Commun. 33:3858–60 [Google Scholar]
  53. Shank NI, Pham HH, Waggoner AS, Armitage BA. 53.  2013. Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. J. Am. Chem. Soc. 135:242–51 [Google Scholar]
  54. Shu D, Khisamutdinov EF, Zhang L, Guo P. 54.  2014. Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor. Nucleic Acids Res 42:e10 [Google Scholar]
  55. Song W, Strack RL, Svensen N, Jaffrey SR. 55.  2014. Plug-and-play fluorophores extend the spectral properties of Spinach. J. Am. Chem. Soc. 136:1198–201 [Google Scholar]
  56. Spector DL, Lamond AI. 56.  2011. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 3:a000646 [Google Scholar]
  57. Strack RL, Disney MD, Jaffrey SR. 57.  2013. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat RNA. Nat. Methods 10:1219–24Describes the generation of Spinach2, a Spinach variant with improved folding and imaging properties. [Google Scholar]
  58. Stsiapura VI, Maskevich AA, Kuzmitsky VA, Uversky VN, Kuznetsova IM, Turoverov KK. 58.  2008. Thioflavin T as a molecular rotor: fluorescent properties of thioflavin T in solvents with different viscosity. J. Phys. Chem. B 112:15893–902 [Google Scholar]
  59. Tsien RY. 59.  1998. The green fluorescent protein. Annu. Rev. Biochem. 67:509–44 [Google Scholar]
  60. Tyagi S. 60.  2009. Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods 6:331–38 [Google Scholar]
  61. Tyagi S, Alsmadi O. 61.  2004. Imaging native β-actin mRNA in motile fibroblasts. Biophys. J 87:4153–62 [Google Scholar]
  62. Valencia-Burton M, McCullough RM, Cantor CR, Broude NE. 62.  2007. RNA visualization in live bacterial cells using fluorescent protein complementation. Nat. Methods 4:421–27 [Google Scholar]
  63. van Nies P, Nourian Z, Kok M, van Wijk R, Moeskops J. 63.  et al. 2013. Unbiased tracking of the progression of mRNA and protein synthesis in bulk and in liposome-confined reactions. ChemBioChem 14:1963–66 [Google Scholar]
  64. Wang P, Querard J, Maurin S, Nath SS, Le Saux T. 64.  et al. 2013. Photochemical properties of Spinach and its use in selective imaging. Chem. Sci. 4:2865–73 [Google Scholar]
  65. Warner KD, Chen MC, Song W, Strack RL, Thorn A. 65.  et al. 2014. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat. Struct. Mol. Biol. 21:658–63 [Google Scholar]
  66. Yang F, Moss LG, Phillips GN Jr. 66.  1996. The molecular structure of green fluorescent protein. Nat. Biotechnol. 14:1246–51 [Google Scholar]
  67. Zhang X, Potty AS, Jackson GW, Stepanov V, Tang A. 67.  et al. 2009. Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green. J. Mol. Recognit. 22:154–61 [Google Scholar]
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Structure and Mechanism of RNA Mimics of Green Fluorescent Protein
Annual Review of Biophysics 44, 187 (2015); https://doi.org/10.1146/annurev-biophys-060414-033954
/content/journals/10.1146/annurev-biophys-060414-033954
/content/journals/10.1146/annurev-biophys-060414-033954
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