Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides


The nature of the first genetic polymer is the subject of major debate1. Although the ‘RNA world’ theory suggests that RNA was the first replicable information carrier of the prebiotic era—that is, prior to the dawn of life2,3—other evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA4. Such a theory streamlines the eventual ‘genetic takeover’ of homogeneous DNA from RNA as the principal information-storage molecule, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario. Here we demonstrate a high-yielding, completely stereo-, regio- and furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides: deoxyadenosine and deoxyinosine. Our synthesis uses key intermediates in the prebiotic synthesis of the canonical pyrimidine ribonucleosides (cytidine and uridine), and we show that, once generated, the pyrimidines persist throughout the synthesis of the purine deoxyribonucleosides, leading to a mixture of deoxyadenosine, deoxyinosine, cytidine and uridine. These results support the notion that purine deoxyribonucleosides and pyrimidine ribonucleosides may have coexisted before the emergence of life5.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Previous synthesis of RNA pyrimidine nucleosides C (1), U (2) and a deoxypyrimidine nucleoside (5), and the present work.
Fig. 2: Prebiotic route to purine deoxyribonucleosides, 7 (dA) and 9 (dI).
Fig. 3: Proposed mechanism of photoreduction of N7-8,2′-anhydro-thioadenosine (18) and N9-8,2′-anhydro-thioadenosine (19) nucleosides.
Fig. 4: A systems-level approach to a potential primordial genetic alphabet composed of 1 (C), 2 (U), 7 (dA) and 9 (dI).

Data and materials availability

The Supplementary Information available for this Article contains all procedures, characterization data, NMR spectra, HPLC traces, X-ray data and Cambridge Crystallographic Data Centre (CCDC) numbers, plus theoretical methods and data. Any additional data are available from the corresponding author upon reasonable request.

Code availability

All custom code used to generate the data in this study is available upon reasonable request.


  1. 1.

    Samanta, B. & Joyce, G. F. A reverse transcriptase ribozyme. eLife 6, e31153 (2017).

    PubMed  PubMed Central  Google Scholar 

  2. 2.

    Gilbert, W. Origin of life: the RNA world. Nature 319, 618 (1986).

    ADS  Google Scholar 

  3. 3.

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

    ADS  CAS  PubMed  Google Scholar 

  4. 4.

    Bhowmik, S. & Krishnamurthy, R. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nat. Chem. 11, 1009–1018 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Xu, J., Green, N. J., Gibard, C., Krishnamurthy, R. & Sutherland, J. D. Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction. Nat. Chem. 11, 457–462 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

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

    ADS  CAS  PubMed  Google Scholar 

  7. 7.

    Xu, J. et al. A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization. Nat. Chem. 9, 303–309 (2017).

    CAS  PubMed  Google Scholar 

  8. 8.

    Heuberger, B. D., Pal, A., Del Frate, F., Topkar, V. V. & Szostak, J. W. Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension. J. Am. Chem. Soc. 137, 2769–2775 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Walton, T. & Szostak, J. W. A highly reactive imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension. J. Am. Chem. Soc. 138, 11996–12002 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Li, L. et al. Enhanced nonenzymatic RNA copying with 2-aminoimidazole activated nucleotides. J. Am. Chem. Soc. 139, 1810–1813 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Fuller, W. D., Orgel, L. E. & Sanchez, R. A. Studies in prebiotic synthesis: VI. Solid-state synthesis of purine nucleosides. J. Mol. Evol. 1, 249–257 (1972).

    ADS  CAS  PubMed  Google Scholar 

  12. 12.

    Becker, S. et al. A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway. Science 352, 833–836 (2016).

    ADS  CAS  PubMed  Google Scholar 

  13. 13.

    Kim, H. & Benner, S. A. Prebiotic stereoselective synthesis of purine and noncanonical pyrimidine nucleotides from nucleobases and phosphorylated carbohydrates. Proc. Natl Acad. Sci. USA 114, 11315–11320 (2017).

    CAS  PubMed  Google Scholar 

  14. 14.

    Becker, S. et al. Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science 366, 76–82 (2019).

    ADS  CAS  PubMed  Google Scholar 

  15. 15.

    Teichert, J. S., Kruse, F. M. & Trapp, O. Direct prebiotic pathway to DNA nucleosides. Angew. Chem. Int. Ed. 58, 9944–9947 (2019).

    CAS  Google Scholar 

  16. 16.

    Reichard, P. From RNA to DNA, why so many ribonucleotide reductases? Science 260, 1773–1777 (1993).

    ADS  CAS  PubMed  Google Scholar 

  17. 17.

    Leu, K., Obermayer, B., Rajamani, S., Gerland, U. & Chen, I. A. The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res. 39, 8135–8147 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Sutherland, J. D. & Whitfield, J. N. Prebiotic chemistry: a bioorganic perspective. Tetrahedron 53, 11493–11527 (1997).

    CAS  Google Scholar 

  19. 19.

    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).

    ADS  CAS  PubMed  Google Scholar 

  20. 20.

    Gavette, J. V., Stoop, M., Hud, N. V. & Krishnamurthy, R. RNA–DNA chimeras in the context of an RNA world transition to an RNA/DNA world. Angew. Chem. Int. Ed. 55, 13204–13209 (2016).

    CAS  Google Scholar 

  21. 21.

    Schoffstall, A. M. Prebiotic phosphorylation of nucleosides in formamide. Orig. Life 7, 399–412 (1976).

    ADS  CAS  PubMed  Google Scholar 

  22. 22.

    Lohrmann, R. & Orgel, L. E. Urea-inorganic phosphate mixtures as prebiotic phosphorylating agents. Science 171, 490–494 (1971).

    ADS  CAS  PubMed  Google Scholar 

  23. 23.

    Patel, B. H., Percivalle, C., Ritson, D. J., Duffy, C. D. & Sutherland, J. D. Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism. Nat. Chem. 7, 301–307 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Ishiwata, A., Lee, Y. J. & Ito, Y. Recent advances in stereoselective glycosylation through intramolecular aglycon delivery. Org. Biomol. Chem. 8, 3596–3608 (2010).

    CAS  PubMed  Google Scholar 

  25. 25.

    Springsteen, G. & Joyce, G. F. Selective derivatization and sequestration of ribose from a prebiotic mix. J. Am. Chem. Soc. 126, 9578–9583 (2004).

    CAS  PubMed  Google Scholar 

  26. 26.

    Anastasi, C., Crowe, M. A., Powner, M. W. & Sutherland, J. D. Direct assembly of nucleoside precursors from two- and three-carbon units. Angew. Chem. Int. Ed. 45, 6176–6179 (2006).

    CAS  Google Scholar 

  27. 27.

    Vorbrüggen, H. & Ruh-Pohlenz, C. Handbook of Nucleoside Synthesis (Wiley, 2001).

  28. 28.

    Holm, N. G., Oze, C., Mousis, O., Waite, J. H. & Guilbert-Lepoutre, A. Serpentinization and the formation of H2 and CH4 on celestial bodies (planets, moons, comets). Astrobiology 15, 587–600 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Sanchez, R. A., Ferris, J. P. & Orgel, L. E. Studies in prebiotic synthesis. II: Synthesis of purine precursors and amino acids from aqueous hydrogen cyanide. J. Mol. Biol. 80, 223–253 (1967).

    Google Scholar 

  30. 30.

    Hudson, J. S. et al. A unified mechanism for abiotic adenine and purine synthesis in formamide. Angew. Chem. Int. Ed. 51, 5134–5137 (2012).

    CAS  Google Scholar 

  31. 31.

    Giner-Sorolla, A., Thom, E. & Bendich, A. Studies on the thiation of purines. J. Org. Chem. 29, 3209–3212 (1964).

    CAS  Google Scholar 

  32. 32.

    Levy, M. & Miller, S. L. The stability of the RNA bases: implications for the origin of life. Proc. Natl Acad. Sci. USA 95, 7933–7938 (1998).

    ADS  CAS  PubMed  Google Scholar 

  33. 33.

    Ritson, D. J. & Sutherland, J. D. Synthesis of aldehydic ribonucleotide and amino acid precursors by photoredox chemistry. Angew. Chem. Int. Ed. 52, 5845–5847 (2013).

    CAS  Google Scholar 

  34. 34.

    Robertson, M. P., Levy, M. & Miller, S. L. Prebiotic synthesis of diaminopyrimidine and thiocytosine. J. Mol. Evol. 43, 543–550 (1996).

    ADS  CAS  PubMed  Google Scholar 

  35. 35.

    Roberts, S. J. et al. Selective prebiotic conversion of pyrimidine and purine anhydronucleosides into Watson–Crick base-pairing arabino-furanosyl nucleosides in water. Nat. Commun. 9, 4073–4082 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Ranjan, S., Todd, Z. R., Rimmer, P. B., Sasselov, D. D. & Babbin, A. R. Nitrogen oxide concentrations in natural waters on early Earth. Geochem. Geophys. Geosyst. 20, 2021–2039 (2019).

    ADS  CAS  Google Scholar 

  37. 37.

    Xu, J. et al. Photochemical reductive homologation of hydrogen cyanide using sulfite and ferrocyanide. Chem. Commun. 54, 5566–5569 (2018).

    CAS  Google Scholar 

  38. 38.

    Marion, G. M., Kargel, J. S., Crowley, J. K. & Catling, D. C. Sulfite–sulfide–sulfate–carbonate equilibria with applications to Mars. Icarus 225, 342–351 (2013).

    ADS  CAS  Google Scholar 

  39. 39.

    Rios, A. C. & Tor, Y. On the origin of the canonical nucleobases: an assessment of selection pressures across chemical and early biological evolution. Isr. J. Chem. 53, 469–483 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Rios, A. C., Yu, H. T. & Tor, Y. Hydrolytic fitness of N-glycosyl bonds: comparing the deglycosylation kinetics of modified, alternative, and native nucleosides. J. Phys. Org. Chem. 28, 173–180 (2014).

    PubMed Central  Google Scholar 

  41. 41.

    Panzica, R. P., Rousseau, R. J., Robins, R. K. & Townsend, L. B. Relative stability and a quantitative approach to the reaction mechanism of the acid-catalyzed hydrolysis of certain 7-and 9-β-d-ribofuranosylpurines. J. Am. Chem. Soc. 94, 4708–4714 (1972).

    CAS  PubMed  Google Scholar 

  42. 42.

    Lindahl, T. & Nyberg, B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610–3618 (1972).

    CAS  PubMed  Google Scholar 

  43. 43.

    Hättig, C. Structure optimizations for excited states with correlated second-order methods: CC2 and ADC(2). Adv. Quantum Chem. 50, 37–60 (2005).

    ADS  Google Scholar 

  44. 44.

    Dreuw, A. & Wormit, M. The algebraic diagrammatic construction scheme for the polarization propagator for the calculation of excited states. Wiley Interdiscip. Rev. Comput. Mol. Sci. 5, 82–95 (2015).

    CAS  Google Scholar 

  45. 45.

    Sauer, M. C., Crowell, R. A. & Shkrob, I. A. Electron photodetachment from aqueous anions. 1. Quantum yields for generation of hydrated electron by 193 and 248 nm laser photoexcitation of miscellaneous inorganic anions. J. Phys. Chem. A 108, 5490–5502 (2004).

    CAS  Google Scholar 

  46. 46.

    Pascoe, D. J., Ling, K. B. & Cockroft, S. L. The origin of chalcogen-bonding interactions. J. Am. Chem. Soc. 139, 15160–15167 (2017).

    CAS  PubMed  Google Scholar 

  47. 47.

    Kim, S. C., O’Flaherty, D. K., Zhou, L., Lelyveld, V. S. & Szostak, J. W. Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA. Proc. Natl Acad. Sci. USA 115, 13318–13323 (2018).

    CAS  PubMed  Google Scholar 

  48. 48.

    Karran, P. & Lindahl, T. Hypoxanthine in deoxyribonucleic acid: generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus. Biochemistry 19, 6005–6011 (1980).

    CAS  PubMed  Google Scholar 

  49. 49.

    Shapiro, R. & Pohl, S. H. Reaction of ribonucleosides with nitrous acid. Side products and kinetics. Biochemistry 7, 448–455 (1968).

    CAS  PubMed  Google Scholar 

  50. 50.

    Mariani, A. D., Russell, A., Javelle, T. & Sutherland, J. D. A light-releasable potentially prebiotic nucleotide activating agent. J. Am. Chem. Soc. 140, 8657–8661 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references


The authors thank all JDS group members for discussions. This research was supported by the Medical Research Council (MC_UP_A024_1009), the Simons Foundation (290362 to J.D.S., 494188 to R.S.), and a grant from the National Science Centre Poland (2016/23/B/ST4/01048 to R.W.G.). M.J.J. acknowledges the support of the ‘Diamond Grant’ (0144/DIA/2017/46) from the Polish Ministry of Science and Higher Education and a computational grant from Wrocław Centre of Networking and Supercomputing (WCSS). R.S. thanks the Foundation for Polish Science for support from the START Fellowship.

Author information




Experimental contributions by J.X., V.C., N.J.G., D.A.R. and A.D.B. Theoretical contributions by M.J.J., R.W.G. and R.S. Crystallography by A.D.B. This work was supervised by J.D.S. All authors co-wrote the manuscript.

Corresponding author

Correspondence to John D. Sutherland.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Hannes Mutschler and Yitzhak Tor for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 A summary of the main findings of the work.

Previously, a prebiotically plausible synthesis of β-ribopyrimdines C and U has been identified using α-thiocytidine. Herein, we demonstrate that the same intermediate can undergo a distinct prebiotically plausible process that could have happened in a similar—or the same—environment. This process furnishes β-D-N9-deoxyribopurine nucleosides dA and dI alongside the pyrimidines. Remarkable selectivity enforced by UV irradiation and hydrolysis operates throughout the reported ribosylpyrimidine synthesis and the discovered deoxyribosylpurine synthesis, resulting in a set of nucleosides with only the canonical regio- and stereochemistry. The coexistence in one location of a set of nucleosides similar to this is thought to be a precondition for the spontaneous emergence of life on Earth6,47.

Extended Data Fig. 2 1H NMR spectra of conversion of α-anhydrouridine (15) from α-thiouridine (14).

a, 1H NMR spectrum of 15. b, 1H NMR spectrum of the reaction mixture after heating 14 in H2O. c, 1H NMR spectrum of the reaction mixture after heating 14 in formamide. f1, chemical shift (δ).

Extended Data Fig. 3 1H NMR spectra of photoreduction of N7-8,2′-anhydro-thioadenosine (18) and N9-8,2′-anhydro-thioadenosine (19) mixture with bisulfite.

a, 1H NMR spectrum of the crude mixture before irradiation; the ratio of N7:N9 isomer was 4:5. b, 1H NMR spectrum of the mixture after irradiation for 7 h; the N9 isomers dA (7) and 26 are the only detectable products. f1, chemical shift (δ).

Extended Data Fig. 4 Potential energy surfaces and S1/S0 state crossings of the key photochemical steps in deoxyadenosine synthesis calculated using ADC(2) and the ma-def2-TZVP basis set.

See Supplementary Information for details. a, Potential energy profile of UV-induced C–S bond scission of 18. C–S bond opening may spontaneously occur in 18, leading to a peaked S1/S0 state crossing; however, a reducing agent is necessary to maintain that geometry after reaching the S0 state. b, Potential energy profile of UV-induced N7–C8 bond scission of 19 . N7–C8 bond rupture is the lowest-energy photochemical process in 19 and results in destruction of the purine ring. c, d, Potential energy profiles of the UV-induced C–S bond scission of encounter complexes 18 (c) and 19 (d) with HS. Photochemical C–S bond rupture induced by charge transfer from HS to a chromophore and is a barrierless process.

Extended Data Fig. 5 Equilibrium geometries of C2, S8 radical anion (31) and C8, N9 radical anion (32).

Radical anions may be formed after accepting a hydrated electron from the environment. The adiabatic electron affinities are calculated using ωB97X-D/IEFPCM and the ma-def2-TZVP basis set.

Extended Data Fig. 6 1H NMR spectra for the reactions of deoxyadenosine (dA, 7) and cytidine (C, 1) with nitrous acid.

a, 1H NMR spectrum of the mixture of dA (7) and C (1). b, 1H NMR spectrum of the reaction mixture after 4 d, showing that the ratio of the four (deoxy)nucleosides dA (7), deoxyinosine (dI, 9), C (1), and uridine (U, 2) is 30:17:42:11. f1, chemical shift (δ).

Extended Data Fig. 7 1H NMR spectra for stability study of cytidine (C; 1) and uridine (U; 2) at 254 nm irradiation with bisulfite.

a, 1H NMR spectrum of the mixture of C (1), bisulfite and K4Fe(CN)6 in the dark. b, As in a, after 10 h of irradiation. c, 1H NMR spectrum of the mixture of U (2), bisulfite and K4Fe(CN)6 in the dark. d, As in c, after 10 h of irradiation. e, 1H NMR spectrum of the mixture of C (1), U (2), N9-thioanhydroadenosine (18), bisulfite and K4Fe(CN)6 in the dark. f, As in e, after 10 h of irradiation. f1, chemical shift (δ).

Extended Data Fig. 8 1H NMR spectra for sequential reactions with the mixture of α-anhydrouridine (15), C (1) and U (2).

a, 1H NMR spectrum of the mixture after heating with 8-mercaptoadenine (16) and magnesium chloride at 150 °C for 1.5 d. b, As in a, after irradiation with hydrogen sulfide at 254 nm. c, As in a, after reacting with nitrous acid for 2 d; dA (7):dI (9):C (1):U (2) = 14:14:44:28). f1, chemical shift (δ).

Supplementary information

Supplementary Information

This file contains Supplementary Materials and Methods, Supplementary Figures 1-56, Supplementary Tables 1-9 and Supplementary References.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Xu, J., Chmela, V., Green, N. et al. Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides. Nature 582, 60–66 (2020).

Download citation


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.