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

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Chemical Biology of Nucleic Acids

Part of the book series: RNA Technologies ((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.

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References

  • 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 126:15046–15047

    Article  CAS  PubMed  Google Scholar 

  • 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 12:47–51

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bertrand E, Chartrand P, Schaefer M et al (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437–445

    Article  CAS  PubMed  Google Scholar 

  • Brewer GJ (2010) Copper toxicity in the general population. Clin Neurophysiol 121:459–460

    Article  PubMed  Google Scholar 

  • Chang PV, Prescher JA, Sletten EM et al (2010) Copper-free click chemistry in living animals. Proc Natl Acad Sci USA 107:1821–1826

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dalhoff C, Lukinavicius G, Klimasăuskas S et al (2006) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nat Chem Biol 2:31–32

    Article  CAS  PubMed  Google Scholar 

  • Devaraj NK, Weissleder R, Hilderbrand S (2008) Tetrazine-based cycloadditions: application to pretargeted live cell imaging. Bioconjug Chem 19:2297–2299

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dojahn CM, Hesse M, Arenz C (2013) A chemo-enzymatic approach to specifically click-modified RNA. Chem Commun 9:3128–3130

    Article  Google Scholar 

  • 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 107:15329–15334

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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 10:1633–1636

    Article  CAS  PubMed  Google Scholar 

  • 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 7:581–589

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Grammel M, Hang H, Conrad NK (2012) Chemical reporters for monitoring RNA synthesis and poly(A) tail dynamics. Chembiochem 13:1112–1115

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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 127:210–216

    Article  CAS  PubMed  Google Scholar 

  • 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) 48:10835–10837

    Article  CAS  Google Scholar 

  • Islam K, Zheng W, Yu H et al (2011) Expanding cofactor repertoire of protein lysine methyltransferase. ACS Chem Biol 6:679–684

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jao CY, Salic A (2008) Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci USA 105:15779–15784

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jawalekar AM, Meeuwenoord N, Cremers JSGO et al (2008) Conjugation of nucleosides and oligonucleotides by [3 + 2] cycloaddition. J Org Chem 73:287–290

    Article  CAS  PubMed  Google Scholar 

  • Kennedy DC, McKay CS, Legault MCB et al (2011) Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions. J Am Chem Soc 133:17993–18001

    Article  CAS  PubMed  Google Scholar 

  • Kolb HC, Finn MG, Sharpless KB (2001) Click chemistry: diverse chemical function from a few good reactions. Angew Chem Int Ed Engl 40:2004–2021

    Article  CAS  PubMed  Google Scholar 

  • 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 131:174–187

    Article  PubMed  Google Scholar 

  • 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 39:1943–1952

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Paredes E, Das SR (2011) Click chemistry for rapid labeling and ligation of RNA. Chembiochem 12:125–131

    Article  CAS  PubMed  Google Scholar 

  • 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 22:5313–5316

    Article  CAS  PubMed  Google Scholar 

  • 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 49:5170–5173

    Article  CAS  PubMed  Google Scholar 

  • 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 434:128–135

    Article  CAS  PubMed  Google Scholar 

  • 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) 48:498–500

    Article  CAS  Google Scholar 

  • Rook MS, Lu M, Kosik KS (2000) CaMKII alpha 3′ untranslated region-directed mRNA translocation in living neurons: visualization by GFP linkage. J Neurosci 20:6385–6393

    CAS  PubMed  Google Scholar 

  • 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 41:2596–2599

    Article  CAS  PubMed  Google Scholar 

  • Sauer J, Mielert A, Lang D et al (1965) Umsetzung von 1.2.4.5-tetrazinen mit olefinen. Zur Struktur von dihydropyridazinen. Chem Ber 98:1435–1445

    Article  CAS  Google Scholar 

  • Saxon E, Bertozzi CR (2000) Cell surface engineering by a modified Staudinger reaction. Science 287:2007–2010

    Article  CAS  PubMed  Google Scholar 

  • Schoch J, Ameta S, Jäschke A (2011) Inverse electron-demand Diels-Alder reactions for the selective and efficient labeling of RNA. Chem Commun (Camb) 47:12536–12537

    Article  CAS  Google Scholar 

  • Schulz D, Holstein JM, Rentmeister A (2013) A chemo-enzymatic approach for site-specific modification of the RNA cap. Angew Chem Int Ed Engl 52:7874–7878

    Article  CAS  PubMed  Google Scholar 

  • 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) 48:11014–11016

    Article  CAS  Google Scholar 

  • Shukla S, Sumaria CS, Pradeepkumar PI (2010) Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 5:328–349

    Article  CAS  PubMed  Google Scholar 

  • 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 40:6765–6773

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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 67:3057–3064

    Article  PubMed  Google Scholar 

  • 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 135:1048–1056

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Willis DE, van Niekerk EA, Sasaki Y et al (2007) Extracellular stimuli specifically regulate localized levels of individual neuronal mRNAs. J Cell Biol 178:965–980

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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:e78

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, 48149, Muenster, Germany

    Daniela Schulz & Andrea Rentmeister

Authors
  1. Daniela Schulz
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  2. Andrea Rentmeister
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Correspondence to Andrea Rentmeister .

Editor information

Editors and Affiliations

  1. Institute of Chemistry/Biochemistry, Free University Berlin, Berlin, Germany

    Volker A. Erdmann

  2. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

    Wojciech T. Markiewicz

  3. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

    Jan Barciszewski

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Schulz, D., Rentmeister, A. (2014). Chemo-enzymatic Strategies to Modify RNA in vitro or in Living Cells. In: Erdmann, V., Markiewicz, W., Barciszewski, J. (eds) Chemical Biology of Nucleic Acids. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54452-1_22

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