Metabolic Incorporation of Azide Functionality into Cellular RNA

Overview

Journal Chembiochem

Specialty Biochemistry

Date 2016 Sep 6

PMID 27595557

Citations 29

Authors

Sarah Nainar

Samantha Beasley

Michael Fazio

Miles Kubota

Nan Dai

Ivan R Correa Jr

Robert C Spitale

Affiliations

Soon will be listed here.

Abstract

Real-time tracking of RNA expression can provide insight into the mechanisms used to generate cellular diversity, as well as help determine the underlying causes of disease. Here we present the exploration of azide-modified nucleoside analogues and their ability to be metabolically incorporated into cellular RNA. We report robust incorporation of adenosine analogues bearing azide handles at both the 2'- and N6-positions; 5-methylazidouridine was not incorporated into cellular RNA. We further demonstrate selectivity of our adenosine analogues for transcription and polyadenylation. We predict that azidonucleosides will find widespread utility in examining RNA functions inside living cells, as well as in more complex systems such as tissues and living animals.

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References

Rao H, Tanpure A, Sawant A, Srivatsan S . Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization. Nat Protoc. 2012; 7(6):1097-112. DOI: 10.1038/nprot.2012.046. View

Jao C, Salic A . Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci U S A. 2008; 105(41):15779-84. PMC: 2572917. DOI: 10.1073/pnas.0808480105. View

Martin G, Keller W, Doublie S . Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 2000; 19(16):4193-203. PMC: 302044. DOI: 10.1093/emboj/19.16.4193. View

Zheng Y, Beal P . Synthesis and evaluation of an alkyne-modified ATP analog for enzymatic incorporation into RNA. Bioorg Med Chem Lett. 2016; 26(7):1799-802. PMC: 4785081. DOI: 10.1016/j.bmcl.2016.02.038. View

Agard N, Prescher J, Bertozzi C . A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J Am Chem Soc. 2004; 126(46):15046-7. DOI: 10.1021/ja044996f. View

Dieterich D, Link A, Graumann J, Tirrell D, Schuman E . Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci U S A. 2006; 103(25):9482-7. PMC: 1480433. DOI: 10.1073/pnas.0601637103. View

Santner T, Hartl M, Bister K, Micura R . Efficient access to 3'-terminal azide-modified RNA for inverse click-labeling patterns. Bioconjug Chem. 2013; 25(1):188-95. PMC: 3898571. DOI: 10.1021/bc400513z. View

Samanta A, Krause A, Jaschke A . A modified dinucleotide for site-specific RNA-labelling by transcription priming and click chemistry. Chem Commun (Camb). 2013; 50(11):1313-6. DOI: 10.1039/c3cc46132g. View

Golitsina N, Danehy Jr F, Fellows R, Cretton-Scott E, Standring D . Evaluation of the role of three candidate human kinases in the conversion of the hepatitis C virus inhibitor 2'-C-methyl-cytidine to its 5'-monophosphate metabolite. Antiviral Res. 2009; 85(3):470-81. DOI: 10.1016/j.antiviral.2009.10.020. View

10.

Grammel M, Hang H, Conrad N . Chemical reporters for monitoring RNA synthesis and poly(A) tail dynamics. Chembiochem. 2012; 13(8):1112-5. PMC: 3359407. DOI: 10.1002/cbic.201200091. View

11.

Sun H, Jiang S, Caton-Williams J, Liu H, Huang Z . 2-Selenouridine triphosphate synthesis and Se-RNA transcription. RNA. 2013; 19(9):1309-14. PMC: 3753936. DOI: 10.1261/rna.038075.112. View

12.

Curanovic D, Cohen M, Singh I, Slagle C, Leslie C, Jaffrey S . Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap. Nat Chem Biol. 2013; 9(11):671-3. PMC: 3805764. DOI: 10.1038/nchembio.1334. View

13.

Neef A, Pernot L, Schreier V, Scapozza L, Luedtke N . A Bioorthogonal Chemical Reporter of Viral Infection. Angew Chem Weinheim Bergstr Ger. 2020; 127(27):8022-8025. PMC: 7159771. DOI: 10.1002/ange.201500250. View

14.

Paredes E, Das S . Click chemistry for rapid labeling and ligation of RNA. Chembiochem. 2010; 12(1):125-31. DOI: 10.1002/cbic.201000466. View

15.

Neef A, Pernot L, Schreier V, Scapozza L, Luedtke N . A Bioorthogonal Chemical Reporter of Viral Infection. Angew Chem Int Ed Engl. 2015; 54(27):7911-4. PMC: 7159598. DOI: 10.1002/anie.201500250. View

16.

Rabani M, Levin J, Fan L, Adiconis X, Raychowdhury R, Garber M . Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol. 2011; 29(5):436-42. PMC: 3114636. DOI: 10.1038/nbt.1861. View

17.

SAXON E, Bertozzi C . Cell surface engineering by a modified Staudinger reaction. Science. 2000; 287(5460):2007-10. DOI: 10.1126/science.287.5460.2007. View

18.

Quinn J, Chang H . Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2015; 17(1):47-62. DOI: 10.1038/nrg.2015.10. View

19.

Feng H, Zhang X, Zhang C . mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. Nat Commun. 2015; 6:7816. PMC: 4523900. DOI: 10.1038/ncomms8816. View

20.

Morris K, Mattick J . The rise of regulatory RNA. Nat Rev Genet. 2014; 15(6):423-37. PMC: 4314111. DOI: 10.1038/nrg3722. View