Effects of Silicate, Phosphate, and Calcium on the Stability of Aldopentoses

  • Sakiko Nitta
  • Yoshihiro Furukawa
  • Takeshi Kakegawa
Prebiotic Chemistry


Ribose is an important constituent of RNA: ribose connects RNA bases and forms a strand of sugar phosphates. Accumulation of ribose on prebiotic Earth was difficult because of its low stability. Improvement in the yield of ribose by the introduction of borate or silicate in a formose-like reaction has been proposed. The effects of borates have been further analyzed and confirmed in subsequent studies. Nonetheless, the effects of silicates and phosphates remain unclear. In the present study, we incubated aldopentoses in a highly alkaline aqueous solution at a moderate temperature to determine the effects of silicate or phosphate on the degradation rates of ribose and its isomeric aldopentoses. The formation of a complex of silicate (or phosphate) with ribose was also analyzed in experiments with 29Si and 31P nuclear magnetic resonance (NMR). We found that silicate or phosphate complexes of ribose were not detectable under our experimental conditions. The stability of ribose and lyxose improved after addition of 40-fold molar excess (relative to a pentose) of sodium silicate or sodium phosphate to the alkaline solution. The stability was not improved further when an 80-fold molar excess of sodium silicate or sodium phosphate was added. Calcium was removed from these solutions by precipitation of calcium salts. The drop in Ca2+ concentration might have improved the stability of ribose and lyxose, which are susceptible to aldol addition. The improvement of ribose stability by the removal of Ca2+ and by addition of silicate or phosphate was far smaller than the improvement by borate. Furthermore, all aldopentoses showed similar stability in silicate- and phosphate-containing solutions. These results clearly show that selective stabilization of ribose by borate cannot be replaced by the effects of silicate or phosphate; this finding points to the importance of borate in prebiotic RNA formation.


Ribose RNA Silicate Phosphate Borate 



This work was supported by JSPS KAKENHI, grant numbers 23740402, 15H02144, and 24244084. The authors acknowledge S. A. Benner and H. J. Kim for the discussion on carbohydrate chemistry, F. W. Nara for ICP-AES analysis, and the staff of Tohoku University Research and Analytical Center for Giant Molecules for NMR analysis. We also appreciate an anonymous reviewer for helpful comments to improve the manuscript.


  1. Amaral AF, Marques MM, da Silva JAL, da Silva J (2008) Interactions of D-ribose with polyatomic anions, and alkaline and alkaline-earth cations: possible clues to environmental synthesis conditions in the pre-RNA world. New J Chem 32:2043–2049CrossRefGoogle Scholar
  2. Angyal SJ (1984) The composition of reducing sugars in solution. Adv Carbohydr Chem Biochem 42:15–68CrossRefGoogle Scholar
  3. Angyal SJ (2001) The lobrt de bruyn-alberda van ekenstein transformation and related reactions. In: Sututz AE (ed) Glycoscience: epimerization, isomerization and rearrangement reactions of carbohydrates. Springer-Verlag, Berlin, pp. 1–14CrossRefGoogle Scholar
  4. Benner SA, Ellington AD, Tauer A (1989) Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci U S A 86:7054–7058PubMedCentralCrossRefPubMedGoogle Scholar
  5. Breslow R (1959) On the mechanism of the formose reaction. Tetrahedron Lett 1:22–26CrossRefGoogle Scholar
  6. Butlerow A (1860) Ueber ein neues methylenderivat. Justus Liebigs Annalen der Chemie 115:322–327CrossRefGoogle Scholar
  7. Chapelle S, Verchere JF (1988) A 11B and 13C NMR determination of the structures of borate complexes of pentoses and related sugars. Tetrahedron 44:4469–4482CrossRefGoogle Scholar
  8. Cleaves HJ (2008) The prebiotic geochemistry of formaldehyde. Precambrian Res 164:111–118CrossRefGoogle Scholar
  9. Crick FHC (1968) Origin of genetic code. J Mol Biol 38:367–379CrossRefPubMedGoogle Scholar
  10. El Khadem HS, Ennifar S, Isbell HS (1987) Contribution of the reaction pathways involved in the isomerization of monosaccharides by alkali. Carbohydr Res 169:13–21CrossRefGoogle Scholar
  11. Furukawa Y, Horiuchi M, Kakegawa T (2013) Selective stabilization of ribose by borate. Orig Life Evol Biosph 43:353–361CrossRefPubMedGoogle Scholar
  12. Georgelin T, Jaber M, Fournier F, Laurent G, Costa-Torro F, Maurel MC, Lambert JF (2015) Stabilization of ribofuranose by a mineral surface. Carbohydr Res 402:241–244CrossRefPubMedGoogle Scholar
  13. Joyce GF (1989) RNA evolution and the origins of life. Nature 338:217–224CrossRefPubMedGoogle Scholar
  14. Kim HJ, Benner SA (2010) Comment on "the silicate-mediated formose reaction: bottom-up synthesis of sugar silicates". Science 329:902CrossRefPubMedGoogle Scholar
  15. Kim H, Ricardo A, Illangkoon HI, Kim MJ, Carrigan MA, Frye F, Benner SA (2011) Synthesis of carbohydrates in mineral-guided prebiotic cycles. J Am Chem Soc 133:9457–9468CrossRefPubMedGoogle Scholar
  16. Lambert JB, Lu G, Singer SR, Kolb VM (2004) Silicate complexes of sugars in aqueous solution. J Am Chem Soc 126:9611–9625CrossRefPubMedGoogle Scholar
  17. Lambert JB, Gurusamy-Thangavelu SA, Ma KBA (2010) The silicate-mediated formose reaction: bottom-up synthesis of sugar silicates. Science 327:984–986CrossRefPubMedGoogle Scholar
  18. Larralde R, Robertson MP, Miller SL (1995) Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc Natl Acad Sci U S A 92:8158–8160PubMedCentralCrossRefPubMedGoogle Scholar
  19. Lenkinski RE, Reuben J (1976) Studies of the binding of calcium and lanthanum ions to D-lyxose and D-ribose in aqueous solutions using proton magnetic resonance. J Am Chem Soc 98:3089–3094CrossRefGoogle Scholar
  20. Li Q, Ricardo A, Benner SA, Winefordner JD, Powell DH (2005) Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes. Anal Chem 77:4503–4508CrossRefPubMedGoogle Scholar
  21. Mizuno T, Weiss AH (1974) Synthesis and utilization of formose sugars. Adv Carbohydr Chem Biochem 29:173–229CrossRefGoogle Scholar
  22. Pepi F, Garzoli S, Tata A, Giacomello P (2010) Low-energy collisionally activated dissociation of pentose-borate complexes. Int J Mass Spectrom 289:76–83CrossRefGoogle Scholar
  23. Petrus P, Petrusova M, Hricoviniva Z (2001) The bílik reaction. In: Stutz AE (ed) Glycoscience: epimerization, isomerization and rearrangement reactions of carbohydrates. Springer-Verlag, Berlin, pp. 15–42CrossRefGoogle Scholar
  24. Pinto JP, Gladstone GR, Yung YL (1980) Photochemical production of formaldehyde in earths primitive atmosphere. Science 210:183–184CrossRefPubMedGoogle Scholar
  25. Prieur BE (2001) Étude de l’activité prébiotique potentielle de l’acide borique. C. R. Acad. Sci. Paris, Chimie/Chemistry 4:667–670Google Scholar
  26. Ricardo A, Carrigan MA, Olcott AN, Benner SA (2004) Borate minerals stabilize ribose. Science 303:196–196CrossRefPubMedGoogle Scholar
  27. Rich A (1962) On the problems of evolution and biochemical information transfer. In: Kasha M, Pullman B (eds) Horizons in biochemistry. Academic Press, New York, pp. 103–126Google Scholar
  28. Schwartz AW, Degraaf RM (1993) The prebiotic synthesis of carbohydrates: a reassessment. J Mol Evol 36:101–106CrossRefGoogle Scholar
  29. Scorei R, Cimpoiasu VM (2006) Boron enhances the thermostability of carbohydrates. Orig Life Evol Biosph 36:1–11CrossRefPubMedGoogle Scholar
  30. Shapiro R (1988) Prebiotic ribose synthesis: a critical analysis. Orig Life Evol Biosph 18:71–85CrossRefPubMedGoogle Scholar
  31. Šponer JE, Sumpter BG, Leszczynski J, Šponer J, Fuentes-Cabrera M (2008) Theoretical study on the factors controlling the stability of the borate complexes of ribose, arabinose, lyxose, and xylose. Chem Eur J 14:9990–9998CrossRefPubMedGoogle Scholar
  32. Symons MCR, Benbow JA, Pelmore H (1982) Study of calcium ion binding to D-ribose in aqueous solutions using hydroxy-proton resonance shifts. J Chem Soc Faraday Trans 1(78):3671–3677CrossRefGoogle Scholar
  33. Vazquez-Mayagoitia A, Horton SR, Sumpter BG, Sponer J, Sponer JE, Fuentes-Cabrera M (2011) On the stabilization of ribose by silicate minerals. Astrobiology 11:115–121CrossRefPubMedGoogle Scholar
  34. Yanagihara R, Soeda K, Shiina S, Osanai S, Yoshikawa S (1993) C-2 epimerization of aldoses by calcium ion in basic solutions: a simple system to transform D-glucose and D-xylose into D-mannose and D-lyxose. Bull Chem Soc Jpn 66:2268–2272CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Sakiko Nitta
    • 1
  • Yoshihiro Furukawa
    • 1
  • Takeshi Kakegawa
    • 1
  1. 1.Department of Earth SciencesTohoku UniversitySendaiJapan

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