Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation

Abstract

The recent synthesis of pyrimidine ribonucleoside-2′,3′-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3′,5′-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2′-hydroxyl group of oligoribonucleotide-3′-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation. The 2′-O-acetyl group at the ligation junction of the product RNA strand can be removed under conditions that leave the internucleotide bonds intact. Remarkably, acetylation of mixed oligomers that possess either 2′- or 3′-terminal phosphates is selective for the 2′-hydroxyl group of the latter. This newly discovered chemistry thus suggests a prebiotic route from ribonucleoside-2′,3′-cyclic phosphates to predominantly 3′,5′-linked RNA via partially 2′-O-acetylated RNA.

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Figure 1: Chemoselective acetylation of RNA.
Figure 2: Chemoselective acetylation: mixtures and alternative electrophiles.
Figure 3: Chemoselective acetylation of 3′P-oligoribonucleotides expedites templated ligation.
Figure 4: Quantification of ligation products.
Figure 5: Chemoselective acetylation favours ligation of 3′P oligomers over 2′P oligomers.
Figure 6: Templated ligation of acetylated 3′P and 2′P oligomers affords 3′,5′- and 2′,5′-linkages, respectively.

References

  1. 1

    Joyce, G. F. The antiquity of RNA-based evolution. Nature 418, 214–221 (2002).

    CAS  Article  Google Scholar 

  2. 2

    Woese, C. The Genetic Code 179–195 (Harper & Row, 1967).

    Google Scholar 

  3. 3

    Crick, F. H. C. The origin of the genetic code. J. Mol. Biol. 38, 367–379 (1968).

    CAS  Article  Google Scholar 

  4. 4

    Orgel, L. E. Evolution of the genetic apparatus. J. Mol. Biol. 38, 381–393 (1968).

    CAS  Article  Google Scholar 

  5. 5

    Powner, M. W., Gerland, B. & Sutherland, J. D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239–242 (2009).

    CAS  Article  Google Scholar 

  6. 6

    Szostak, J. W. Systems chemistry on early Earth. Nature 459, 171–172 (2009).

    CAS  Article  Google Scholar 

  7. 7

    Renz, M., Lohrmann, R. & Orgel, L. E. Catalysts for the polymerisation of adenosine cyclic 2′,3′-phosphate on a poly (U) template. Biochim. Biophys. Acta 240, 463–471 (1971).

    CAS  Article  Google Scholar 

  8. 8

    Eftink, M. R. & Biltonen, R. L. Energetics of ribonuclease A catalysis. 2. Nonenzymatic hydrolysis of cytidine cyclic 2′,3′-phosphate. Biochemistry 22, 5134–5140 (1983).

    CAS  Article  Google Scholar 

  9. 9

    Verlander, M. S., Lohrmann, R. & Orgel, L. E. Catalysts for the self-polymerization of adenosine cyclic 2′,3′-phosphate. J. Mol. Evol. 2, 303–316 (1973).

    CAS  Article  Google Scholar 

  10. 10

    Verlander, M. S. & Orgel, L. E. Analysis of high molecular weight material from the polymerization of adenosine cyclic 2′,3′-phosphate. J. Mol. Evol. 3, 115–120 (1974).

    CAS  Article  Google Scholar 

  11. 11

    Usher, D. A. & McHale, A. H. Nonenzymic joining of oligoadenylates on a polyuridylic acid template. Science 192, 53–54 (1976).

    CAS  Article  Google Scholar 

  12. 12

    Bolli, M., Micura, R., Pitsch, S. & Eschenmoser, A. Pyranosyl-RNA: further observations on replication. Helv. Chim. Acta 80, 1901–1951 (1997).

    CAS  Article  Google Scholar 

  13. 13

    Trevino, S. G., Zhang, N., Elenko, M. P., Lupták, A. & Szostak, J. W. Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity. Proc. Natl Acad. Sci. USA 108, 13492–13497 (2011).

    CAS  Article  Google Scholar 

  14. 14

    Kierzek, R., He, L. & Turner, D. H. Association of 2′-5′ oligoribonucleotides. Nucleic Acids Res. 20, 1685–1690 (1992).

    CAS  Article  Google Scholar 

  15. 15

    Usher, D. A. Early chemical evolution of nucleic acids: a theoretical model. Science 196, 311–313 (1977).

    CAS  Article  Google Scholar 

  16. 16

    Usher, D. A. & McHale, A. H. Hydrolytic stability of helical RNA: a selective advantage for the natural 3′,5′-bond. Proc. Natl Acad. Sci. USA 73, 1149–1153 (1976).

    CAS  Article  Google Scholar 

  17. 17

    Rohatgi, R., Bartel, D. P. & Szostak, J. W. Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3′−5′ phosphodiester bonds. J. Am. Chem. Soc. 118, 3340–3344 (1996).

    CAS  Article  Google Scholar 

  18. 18

    Rammler, D. H., Lapidot, Y. & Khorana, H. G. Studies on polynucleotides. XIX. The specific synthesis of C3′-C5′ inter-ribonucleotidic linkage. A new approach and its use in the synthesis of C3′-C5′-linked uridine oligonucleotides. J. Am. Chem. Soc. 85, 1989–1997 (1963).

    Article  Google Scholar 

  19. 19

    Coutsogeorgopoulos, C. & Khorana, H. G. Studies on polynucleotides. XXXI. The specific synthesis of C3′-C5′-linked ribopolynucleotides (6). A further study of the synthesis of uridine polynucleotides. J. Am. Chem. Soc. 86, 2926–2932 (1964).

    CAS  Article  Google Scholar 

  20. 20

    Huber, C. & Wächtershäuser, G. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science 276, 245–247 (1997).

    CAS  Article  Google Scholar 

  21. 21

    Loison, A., Dubant, S., Adam, P. & Albrecht, P. Elucidation of an iterative process of carbon–carbon bond formation of prebiotic significance. Astrobiology 10, 973–988 (2010).

    CAS  Article  Google Scholar 

  22. 22

    de Duve, C. Blueprint for a Cell: the Nature and Origin of Life (Neil Patterson Publishers, 1991).

    Google Scholar 

  23. 23

    Hagan, W. J. Jr Uracil-catalyzed synthesis of acetyl phosphate: a photochemical driver for protometabolism. ChemBioChem 11, 383–387 (2010).

    CAS  Article  Google Scholar 

  24. 24

    Liu, R. & Orgel, L. E. Oxidative acylation using thioacids. Nature 389, 52–54 (1997).

    CAS  Article  Google Scholar 

  25. 25

    Biron, J-P., Parkes, A. L., Pascal, R. & Sutherland, J. D. Expeditious, potentially primordial, aminoacylation of nucleotides. Angew. Chem. Int. Ed. 44, 6731–6734 (2005).

    CAS  Article  Google Scholar 

  26. 26

    Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223–4231 (2005).

    CAS  Article  Google Scholar 

  27. 27

    McGinnis, J. L., Dunkle, J. A., Cate, J. H. D. & Weeks, K. M. The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617–6624 (2012).

    CAS  Article  Google Scholar 

  28. 28

    Gupta, S. C., Islam, N. B., Whalen, D. L., Yagi, H. & Jerina, D. M. Bifunctional catalysis in the nucleotide-catalyzed hydrolysis of (±)-7β,8α-dihydroxy-9α,10α-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. J. Org. Chem. 52, 3812–3815 (1987).

    CAS  Article  Google Scholar 

  29. 29

    Cavalieri, L. F. Studies on the structure of nucleic acids. VII. On the identification of the isomeric cytidylic and adenylic acids. J. Am. Chem. Soc. 75, 5268–5270 (1953).

    CAS  Article  Google Scholar 

  30. 30

    Rohatgi, R., Bartel, D. P. & Szostak, J. W. Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc. 118, 3332–3339 (1996).

    CAS  Article  Google Scholar 

  31. 31

    Goldsborough, A. S. Modified polynucleotides and uses thereof. US patent 6,867,290 (2005).

  32. 32

    Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B. & Steitz, T. A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA 98, 4899–4903 (2001).

    CAS  Article  Google Scholar 

  33. 33

    Altona, C. & Sundaralingam, M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94, 8205–8212 (1972).

    CAS  Article  Google Scholar 

  34. 34

    Guschlbauer, W. & Jankowski, K. Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucleic Acids Res. 8, 1421–1433 (1980).

    CAS  Article  Google Scholar 

  35. 35

    Ferris, J. P., Huang, C-H. & Hagan, W. J. Jr N-cyanoimidazole and diimidazole imine: water-soluble condensing agents for the formation of the phosphodiester bond. Nucleos. Nucleot. 8, 407–414 (1989).

    CAS  Article  Google Scholar 

  36. 36

    Kanaya, E. & Yanagawa, H. Template-directed polymerization of oligoadenylates using cyanogen bromide. Biochemistry 25, 7423–7430 (1986).

    CAS  Article  Google Scholar 

  37. 37

    Horowitz, E. D. et al. Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world. Proc. Natl Acad. Sci. USA 107, 5288–5293 (2010).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was funded by the Engineering and Physical Sciences Research Council through the provision of postdoctoral fellowships (C.D.D. and B.G.) and PhD studentships (M.W.P., S.I. and C.K.W.C.), the Medical Research Council through the provision of career development fellowships (F.R.B. and J.X., project no. MC_UP_A024_1009) and the Origin of Life Challenge, for which we thank H. Lonsdale. We thank C. Hilcenko, M. J. Churcher and V. B. Pinheiro for advice on polyacrylamide gel electrophoresis and fluorescence scanning, and D. Williams for advice on solid-phase oligonucleotide synthesis.

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F.R.B., C.K.W.C., C.D.D., B.G., S.I., M.W.P., J.D.S. and J.X. conceived and designed the experiments and analysed the data. F.R.B., C.K.W.C., C.D.D., B.G., S.I., M.W.P. and J.X. performed the experiments. F.R.B., S.I., M.W.P. and J.D.S. co-wrote the paper.

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Correspondence to John D. Sutherland.

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Bowler, F., Chan, C., Duffy, C. et al. Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation. Nature Chem 5, 383–389 (2013). https://doi.org/10.1038/nchem.1626

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