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Formation of Nucleosides and Nucleotides in Chemical Evolution

  • Hideo HashizumeEmail author
  • Benny K. G. Theng
  • Sjerry van der Gaast
  • Kazuko Fujii
Chapter
  • 516 Downloads

Abstract

Nucleosides and nucleotides are important biomolecules. Following Gilbert’s (Nature 319:618, 1986) proposal of an “RNA world,” various processes for the formation of nucleosides (from nucleobases and ribose) and the polymerization of nucleotides have been suggested. Problems associated with the formation of RNA have also been pointed out. The constituents of RNA are nucleobases, ribose, and phosphate. Ribose has five conformational isomers or conformers, each of which can react with a nucleobase. In life, however, only the β-furanose form of ribose is used. Curiously, when a nucleobase reacts with ribose in an aqueous solution, only a small amount of nucleoside with a β-ribofuranose component is detectable in the total products. Thus, the RNA world hypothesis has reached a deadlock. Here, we summarize the important points in the synthesis of nucleobases and ribose. We also describe the selective formation of nucleosides and touch on the one-pot synthesis of nucleotides.

References

  1. Akouche M, Jaber M, Maurel M-C, Lambert J-F, Georgelin T (2017) Phosphoribosyl pyrophosphate: a molecular vestige of the origin of life on minerals. Angew Chem Int Ed 56:7920–7923.  https://doi.org/10.1002/anie201702633CrossRefGoogle Scholar
  2. Akouche M, Jaber M, Zins E-M, Maurel M-C, Lambert J-F, Georgelin T (2016) Thermal behavior of d-ribose adsorbed on silica: effect of inorganic salt coadsorption and significance for prebiotic chemistry. Chem Eur J 22:15834–15846CrossRefGoogle Scholar
  3. Amaral AF, Marques MM, da Silva JAL, da Silva JJRF (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
  4. Becker S, Thoma I, Deutsch A, Gehrke T, Mayer P, Zipse H, Carell T (2016) A high-yielding strictly regioselective prebiotic purine nucleoside formation pathway. Science 352:833–836CrossRefGoogle Scholar
  5. Becker S, Schneider C, Okamura H, Crisp A, Amatov T, Dejmek A, Carell T (2018) Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis. Nat. Com 9:163.  https://doi.org/10.1038/s41467-017-02639-1CrossRefGoogle Scholar
  6. Benner SA, Kim H-J, Carrigan MA (2012) Asphalt, water and the prebiotic synthesis of ribose, ribonucleoside and RNA. Acc Chem Res 45:2025–2034CrossRefGoogle Scholar
  7. Cech TR (1986) A model for the RNA-catalyzed replication of RNA. Proc Natl Acad Sci USA 83:4360–4363CrossRefGoogle Scholar
  8. Chittenden GJF, Schwartz A (1976) Possible pathway for prebiotic uracil synthesis by photodehydrogenation. Nature 263:350–351CrossRefGoogle Scholar
  9. Civiš S, Szabla R, Szyja BM, Smykowski D, Ivanek O, Knížek A, Kubelik P, Šponer J, Ferus M, Šponer JE (2016) TiO2-calayzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. Sci Rep 6:23199.  https://doi.org/10.1038/srep23199CrossRefPubMedPubMedCentralGoogle Scholar
  10. Cortes SJ, Mega TL, Van Etten RL (1991) The 18O isotope shift in 13C nuclear magnetic resonance spectroscopy. 14. kinetics of oxygen exchange at the anomeric carbon of D-ribose and D-2-deoxyribose. J Org Chem 56:943–947CrossRefGoogle Scholar
  11. Ferus M, Nesvorný D, Šponer J, Kubelík P, Michalcíková R, Shestivská V, Šponer JE, Civiš S (2015) High-energy chemistry of formamide: a unified mechanism of nulcoebase formation. PNAS 112:657–662.  https://doi.org/10.1073/pnas.1412072111CrossRefPubMedGoogle Scholar
  12. Fiore M, Strazewski P (2016) Bringing prebiotic nucleosides and nucleotides down to Earth. Angew Chem Int Ed 55:13930–13933.  https://doi.org/10.1002/anie.201606232CrossRefGoogle Scholar
  13. Fuller WD, Sanchez RA, Orgel LE (1972) Studies in prebiotic synthesis VI. Synthesis of purine nucleosides. J Mol Biol 67:25–33CrossRefGoogle Scholar
  14. Furukawa Y, Kakegawa T (2017) Borate and the origin of RNA: a model for the precursors to life. Elements 13:261–265CrossRefGoogle Scholar
  15. Furukawa Y, Horiuchi M, Kakegawa T (2013) Selective stabilization of ribose by borate. Origins Life Evol Biosph 43:353–361CrossRefGoogle Scholar
  16. Furukawa Y, Kim HJ, Hutter D, Benner SA (2015) Abiotic regioselective phosphorylation of adenosine with borate in formamide. Astrobiology 15:259–267CrossRefGoogle Scholar
  17. Gabel NW, Ponnamperuma C (1967) Model of origin of monosaccharides. Nature 216:453–455CrossRefGoogle Scholar
  18. Gilbert W (1986) The RNA world. Nature 319:618CrossRefGoogle Scholar
  19. Hu H, Xue J, Wen X, Li W, Zhang C, Yang L, Xu Y, Zhao G, Bu X, Liu K, Chen J, Wu J (2013) Sugar-metal ion interactions: the complicated coordination structures of Cesium ion with D-ribose and myo-inositol. Inorg Chem 52:13132–13145CrossRefGoogle Scholar
  20. Kim H-J, Kim J (2019) A prebiotic synthesis of canonical pyrimidine and purine ribonucleotides. Astrobiology.  https://doi.org/10.1089/ast.2018.1935CrossRefPubMedPubMedCentralGoogle Scholar
  21. Lambert JB, Lu G, Singer SR, Kolb VM (2004) Silicate complexes of sugars in aqueous solution. J Am Chem Soc 126:9611–9625CrossRefGoogle Scholar
  22. Larralde R, Robertson MP, Miller SL (1995) Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc Natl Acad Sci USA 92:8158–8160CrossRefGoogle Scholar
  23. Maurel M-C, Leclerc F (2016) From foundation stones to life: Concepts and results. Elements 12:407–412CrossRefGoogle Scholar
  24. Menor-Salván C, Marín-Yaseli MR (2013) A new route for the prebiotic synthesis of nucleobases and hydantoins in water/ice solutions involving the photochemistry of acetylene. Chem Eur J 19:6488–6497CrossRefGoogle Scholar
  25. Miyawaki S, Murasawa K, Kobayashi K, Sawaoka AB (2000) Abiotic synthesis of guanine with high-temperature plasma. Origin Life Evol Biosph 30:557–566CrossRefGoogle Scholar
  26. Nam I, Nam HG, Zare RN (2018) Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets. PNAS 115:36–40.  https://doi.org/10.1073/pnas.1718559115CrossRefPubMedGoogle Scholar
  27. Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99–123CrossRefGoogle Scholar
  28. Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239–242CrossRefGoogle Scholar
  29. Quesada-Moreno MM, Azofra LM, Avilés-Moreno JR, Alkorta I, Elguero J, López-González JJ (2013) Conformational preference and chiroptical response of carbohydrates D-ribose and 2-deoxy-D-ribose in aqueous and solid phases. J Phys Chem B 117:14599–14614CrossRefGoogle Scholar
  30. Ricardo A, Carrigan MA, Olcott AN, Benner SA (2004) Borate minerals stabilize ribose. Science 303:196CrossRefGoogle Scholar
  31. 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
  32. Robertson MP, Miller SL (1995) An efficient prebiotic synthesis of cytosine and uracil. Nature 375:772–774CrossRefGoogle Scholar
  33. Robertson MP, Joyce GF (2012) The origins of the RNA world. Cold Spring Harb Perspect Biol 4:a003608.  https://doi.org/10.1101/cshperspect.a003608CrossRefPubMedPubMedCentralGoogle Scholar
  34. Saladino R, Bizzarri BM, Botta L, Šponer J, Šponer JE, Georgelin T, Jaber M, Rigaud B, Kapralov M, Timoshenko GN, Rozanov A, Krasavin E, Timperio AM, Mauro ED (2017) Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context. Sci Rep 7:14709.  https://doi.org/10.1038/s41598-017-15392-8CrossRefPubMedPubMedCentralGoogle Scholar
  35. Saladino R, Carota E, Botta G, Kapralov M, Timoshenko GN, Rozanov AY, Krasavin E, Mauro ED (2015) Meteorite-catalyzed syntheses of nucleosides and of otherprebiotic compounds from formamide under proton irradiation. PNAS 112:E2746–E2755.  https://doi.org/10.1073/pnas.1422225112CrossRefPubMedGoogle Scholar
  36. Saladino R, Neri V, Crestini C (2010) Role of clays in the preobiotic synthesis of sugar derivatives from formamide. Phil Mag 90:2329–2337CrossRefGoogle Scholar
  37. Sanchez RA, Ferris JP, Orgel LE (1966a) Conditions for purine synthesis: did prebiotic synthesis occur at low temperature? Science 153:72–73CrossRefGoogle Scholar
  38. Sanchez RA, Ferris JP, Orgel LE (1966b) Cyanoacetylene in prebiotic synthesis. Science 154:784–785CrossRefGoogle Scholar
  39. Šišak D, McCusker LB, Zandomeneghi G, Meier BH, Bläser D, Boese R, Schweizaer WB, Gilmour R, Dunitz JD (2010) The crystal structure of D-ribose- At last! Angew Chem Int Ed 49:4503–4505CrossRefGoogle Scholar
  40. Theng BKG (2018) Clay mineral catalysis of organic reactions. CRC Press, Boca Raton (FL)CrossRefGoogle Scholar
  41. Wang W, Huang F, Sun C, Liu J, Sheng X, Chen D (2017) A theoretical insight into the formation mechanisms of C/N-ribonucleosides with pyrimidine and ribose. Phys Chem Chem Phys 19:10413–10426CrossRefGoogle Scholar
  42. Xu J, Tsanakopoulou M, Magnani CJ, Szabla R, Šponer JE, Šponer J, Góra RW, Sutherland JD (2017) A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization. Nat Chem 9:303–309.  https://doi.org/10.1038/NCHEM.2664CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Hideo Hashizume
    • 1
    Email author
  • Benny K. G. Theng
    • 2
  • Sjerry van der Gaast
    • 3
  • Kazuko Fujii
    • 1
  1. 1.National Institute for Materials ScienceNamiki, TsukubaJapan
  2. 2.Manaaki Whenua–Landcare ResearchPalmerston NorthNew Zealand
  3. 3.Royal Netherlands Institute for Sea ResearchDen BurgThe Netherlands

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