Advertisement

Chemo-enzymatic Strategies to Modify RNA in vitro or in Living Cells

  • Daniela Schulz
  • Andrea RentmeisterEmail author
Chapter
Part of the RNA Technologies book series (RNATECHN)

Abstract

The discovery of novel RNA species and functions has generated the need for methods to selectively label different types of RNA in order to study their localization, dynamics, and structure both in vitro and in cells. Progress in the field of bioorthogonal chemistry has led to the development of a toolbox of reactions compatible with cellular components—in the best case even with living cells—that are also suitable for RNA modification. The first step, however, is the introduction of a group suitable for bioorthogonal chemistry. Besides chemical synthesis, this can be achieved by various enzymes that (1) either accept non-natural nucleotide-building blocks or (2) modify RNA with non-natural residues.

This chapter will first briefly introduce the relevant click reactions and then focus on the different state of the art approaches for modification of RNAs by chemo-enzymatic labeling. We will try to highlight the potential and limitations for broader applications, including future use in cells.

Keywords

Bioorthogonal chemistry Chemo-enzymatic modification Click chemistry Postsynthetic modification RNA labeling 

References

  1. Agard NJ, Prescher JA, Bertozzi CR (2004) A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J Am Chem Soc 126:15046–15047PubMedCrossRefGoogle Scholar
  2. Aigner M, Hartl M, Fauster K et al (2011) Chemical synthesis of site-specifically 2′-azido-modified RNA and potential applications for bioconjugation and RNA interference. Chembiochem 12:47–51PubMedCentralPubMedCrossRefGoogle Scholar
  3. Bertrand E, Chartrand P, Schaefer M et al (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437–445PubMedCrossRefGoogle Scholar
  4. Brewer GJ (2010) Copper toxicity in the general population. Clin Neurophysiol 121:459–460PubMedCrossRefGoogle Scholar
  5. Chang PV, Prescher JA, Sletten EM et al (2010) Copper-free click chemistry in living animals. Proc Natl Acad Sci USA 107:1821–1826PubMedCentralPubMedCrossRefGoogle Scholar
  6. Dalhoff C, Lukinavicius G, Klimasăuskas S et al (2006) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nat Chem Biol 2:31–32PubMedCrossRefGoogle Scholar
  7. Devaraj NK, Weissleder R, Hilderbrand S (2008) Tetrazine-based cycloadditions: application to pretargeted live cell imaging. Bioconjug Chem 19:2297–2299PubMedCentralPubMedCrossRefGoogle Scholar
  8. Dojahn CM, Hesse M, Arenz C (2013) A chemo-enzymatic approach to specifically click-modified RNA. Chem Commun 9:3128–3130CrossRefGoogle Scholar
  9. El-Sagheer AH, Brown T (2010) New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes. Proc Natl Acad Sci USA 107:15329–15334PubMedCentralPubMedCrossRefGoogle Scholar
  10. Ess DH, Jones GO, Houk KN (2008) Transition states of strain-promoted metal-free click chemistry: 1,3 dipolar cycloadditions of phenyl azide and cyclooctynes. Org Lett 10:1633–1636PubMedCrossRefGoogle Scholar
  11. Fauster K, Hartl M, Santner T et al (2012) 2′-Azido RNA, a versatile tool for chemical biology: synthesis, X-ray structure, siRNA applications, click labeling. ACS Chem Biol 7:581–589PubMedCentralPubMedCrossRefGoogle Scholar
  12. Grammel M, Hang H, Conrad NK (2012) Chemical reporters for monitoring RNA synthesis and poly(A) tail dynamics. Chembiochem 13:1112–1115PubMedCentralPubMedCrossRefGoogle Scholar
  13. Himo F, Lovell T, Hilgraf R et al (2005) Copper (I) -catalyzed synthesis of azoles. DFT study predicts unprecedented reactivity and intermediates. J Am Chem Soc 127:210–216PubMedCrossRefGoogle Scholar
  14. Ishizuka T, Kimoto M, Sato A et al (2012) Site specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry. Chem Commun (Camb) 48:10835–10837CrossRefGoogle Scholar
  15. Islam K, Zheng W, Yu H et al (2011) Expanding cofactor repertoire of protein lysine methyltransferase. ACS Chem Biol 6:679–684PubMedCentralPubMedCrossRefGoogle Scholar
  16. Jao CY, Salic A (2008) Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci USA 105:15779–15784PubMedCentralPubMedCrossRefGoogle Scholar
  17. Jawalekar AM, Meeuwenoord N, Cremers JSGO et al (2008) Conjugation of nucleosides and oligonucleotides by [3 + 2] cycloaddition. J Org Chem 73:287–290PubMedCrossRefGoogle Scholar
  18. Kennedy DC, McKay CS, Legault MCB et al (2011) Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions. J Am Chem Soc 133:17993–18001PubMedCrossRefGoogle Scholar
  19. Kolb HC, Finn MG, Sharpless KB (2001) Click chemistry: diverse chemical function from a few good reactions. Angew Chem Int Ed Engl 40:2004–2021PubMedCrossRefGoogle Scholar
  20. Lécuyer E, Yoshida H, Parthasarathy N et al (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131:174–187PubMedCrossRefGoogle Scholar
  21. Motorin Y, Burhenne J, Teimer R et al (2011) Expanding the chemical scope of RNA: methyltransferases to site-specific alkynylation of RNA for click labeling. Nucleic Acids Res 39:1943–1952PubMedCentralPubMedCrossRefGoogle Scholar
  22. Paredes E, Das SR (2011) Click chemistry for rapid labeling and ligation of RNA. Chembiochem 12:125–131PubMedCrossRefGoogle Scholar
  23. Paredes E, Das SR (2012) Optimization of acetonitrile co-solvent and copper stoichiometry for pseudo-ligandless click chemistry with nucleic acids. Bioorg Med Chem Lett 22:5313–5316PubMedCrossRefGoogle Scholar
  24. Peters W, Willnow S, Duisken M et al (2010) Enzymatic site-specific functionalization of protein methyltransferase substrates with alkynes for click labeling. Angew Chem Int Ed Engl 49:5170–5173PubMedCrossRefGoogle Scholar
  25. Qu D, Zhou L, Wang W et al (2013) 5-Ethynylcytidine as a new agent for detecting RNA synthesis in live cells by “click” chemistry. Anal Biochem 434:128–135PubMedCrossRefGoogle Scholar
  26. Rao H, Sawant A, Tanpure A, Srivatsan SG (2012) Posttranscriptional chemical functionalization of azide-modified oligoribonucleotides by bioorthogonal click and Staudinger reactions. Chem Commun (Camb) 48:498–500CrossRefGoogle Scholar
  27. Rook MS, Lu M, Kosik KS (2000) CaMKII alpha 3′ untranslated region-directed mRNA translocation in living neurons: visualization by GFP linkage. J Neurosci 20:6385–6393PubMedGoogle Scholar
  28. Rostovtsev VV, Green LG, Fokin VV et al (2002) A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew Chem Int Ed Engl 41:2596–2599PubMedCrossRefGoogle Scholar
  29. Sauer J, Mielert A, Lang D et al (1965) Umsetzung von 1.2.4.5-tetrazinen mit olefinen. Zur Struktur von dihydropyridazinen. Chem Ber 98:1435–1445CrossRefGoogle Scholar
  30. Saxon E, Bertozzi CR (2000) Cell surface engineering by a modified Staudinger reaction. Science 287:2007–2010PubMedCrossRefGoogle Scholar
  31. Schoch J, Ameta S, Jäschke A (2011) Inverse electron-demand Diels-Alder reactions for the selective and efficient labeling of RNA. Chem Commun (Camb) 47:12536–12537CrossRefGoogle Scholar
  32. Schulz D, Holstein JM, Rentmeister A (2013) A chemo-enzymatic approach for site-specific modification of the RNA cap. Angew Chem Int Ed Engl 52:7874–7878PubMedCrossRefGoogle Scholar
  33. Seidu-Larry S, Krieg B, Hirsch M et al (2012) A modified guanosine phosphoramidite for click functionalization of RNA on the sugar edge. Chem Commun (Camb) 48:11014–11016CrossRefGoogle Scholar
  34. Shukla S, Sumaria CS, Pradeepkumar PI (2010) Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 5:328–349PubMedCrossRefGoogle Scholar
  35. Tomkuviene M, Clouet-d’Orval B, Cerniauskas I et al (2012) Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases. Nucleic Acids Res 40:6765–6773PubMedCentralPubMedCrossRefGoogle Scholar
  36. Tornøe CW, Christensen C, Meldal M (2002) Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J Org Chem 67:3057–3064PubMedCrossRefGoogle Scholar
  37. Wang R, Islam K, Liu Y et al (2013) Profiling genome-wide chromatin methylation with engineered posttranslation apparatus within living cells. J Am Chem Soc 135:1048–1056PubMedCentralPubMedCrossRefGoogle Scholar
  38. Willis DE, van Niekerk EA, Sasaki Y et al (2007) Extracellular stimuli specifically regulate localized levels of individual neuronal mRNAs. J Cell Biol 178:965–980PubMedCentralPubMedCrossRefGoogle Scholar
  39. Winz M-L, Samanta A, Benzinger D et al (2012) Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry. Nucleic Acids Res 40:e78PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Department of Chemistry, Institute of BiochemistryUniversity of MuensterMuensterGermany

Personalised recommendations