From formamide to RNA: the roles of formamide and water in the evolution of chemical information

Research in Microbiology

Volumn 160, Issue 7, 2009, Pages 441-448

  Saladino, Raffaele ^a   Crestini, Claudia ^b   Ciciriello, Fabiana ^c   Pino, Samanta ^c   Costanzo, Giovanna ^d   Di Mauro, Ernesto ^c  

^a UNIVERSITY OF TUSCIA   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c SAPIENZA UNIVERSITY OF ROME   (Italy)

^d CNR   (Italy)

Author keywords

Formamide; Molecular evolution; Nucleic bases; Nucleotides; RNA origin; Water

Indexed keywords

FORMAMIDE; INORGANIC COMPOUND; MONOMER; NUCLEIC ACID BASE; NUCLEOTIDE DERIVATIVE; POLYMER; RNA; WATER;

ARTICLE; BIOCHEMISTRY; CARBON FIXATION; CATALYSIS; CHEMICAL REACTION; CHEMICAL REACTION KINETICS; CHEMICAL STRUCTURE; CROSS LINKING; CYTOLOGY; DNA DETERMINATION; DNA SYNTHESIS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE METABOLISM; OLIGOMERIZATION; PHYSICAL CHEMISTRY; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; RNA ANALYSIS; RNA SYNTHESIS; SYNTHESIS; THERMODYNAMICS;

BIOGENESIS; CATALYSIS; EVOLUTION, CHEMICAL; FORMAMIDES; RNA; WATER;

EID: 70350047058     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2009.06.001     Document Type: Article

References (47)

1. Alberty R.A. Thermodynamic properties of enzyme-catalyzed reactions involving guanine, xanthine, and their nucleosides and nucleotides. Biophys. Chem. 121 (2006) 157-162
2. Bean H.D., Anet F.A.L., Gould I.R., and Hud N.V. Glyoxylate as a backbone linkage for a prebiotic ancestor of RNA. Orig. Life Evol. Biosph. 36 (2006) 39-63
3. Bean H.D., Sheng Y., Collins J.P., Anet F.A., Leszczynski J., and Hud N.V. Formation of a beta-pyrimidine nucleoside by a free pyrimidine base and ribose in a plausible prebiotic reaction. J. Am. Chem. Soc. 129 (2007) 9556-9557
4. Berkessel A. Biomimetic and organocatalytic approaches to oxidation catalysis. Pure Appl. Chem. 77 (2005) 1277-1284
5. Butlerow A. Bildung einer zuckerartigen Substanz durch Synthese. Annalen 120 (1861) 295-298
6. Ciciriello F., Costanzo G., Pino S., Crestini C., Saladino R., and Di Mauro E. Molecular complexity favors the evolution of ribopolymers. Biochemistry 47 (2008) 2732-2742
7. Costanzo G., Saladino R., Crestini C., Ciciriello F., and Di Mauro E. Nucleoside phosphorylation by phosphate minerals. J. Biol. Chem. 282 (2007) 16729-16735
8. Costanzo G., Saladino R., Crestini C., Ciciriello F., and Di Mauro E. Formamide as main building block in the origin of life. BMC Evol. Biol. 7 (2007) 1-8
9. Egholm M., Buchardt O., Nielsen P.E., and Berg R.H. Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone. J. Am. Chem. Soc. 114 (1992) 1895-1897
10. Eschenmoser A., and Loewenthal E. Chemistry of potentially prebiological natural products. Chem. Soc. Rev. 21 (1992) 1-16
11. Eschenmoser A. Towards a chemical etiology of nucleic acid structure. Orig. Life Evol. Biosph. 27 (1997) 535-553
12. Ferris J.P., and Ertem G. Montmorillonite catalysis of RNA oligomer formation in aqueous solution. A model for the prebiotic formation of RNA. J. Am. Chem. Soc. 115 (1993) 12270-12275
13. Ferris J.P., Joshi P.C., Wang K.J., Miyakawa S., and Huang W. Catalysis in prebiotic chemistry: application to the synthesis of RNA oligomers. Adv. Space Res. 33 (2004) 100-105
14. Huang W., and Ferris J.P. Synthesis of 35-40 mers of RNA oligomers from unblocked monomers A simple approach to the RNA world. Chem. Commun. (Camb.) 21 (2003) 1458-1459
15. Huber C., and Wächtershäuser G. Activated acetic acid by carbon fixation on (Fe, Ni)S under primordial conditions. Science 276 (1997) 245-247
16. Hutter D., Blaettler M.O., and Benner S.A. From phosphate to Bis(methylene) sulfone: non-ionic backbone linkers in DNA. Helv. Chim. Acta 85 (2002) 2777-2806
17. Joyce G.F. Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73 (2004) 791-836
18. Kanavarioti A., Monnard P.A., and Deamer D.W. Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis. Astrobiology 1 (2001) 271-281
19. Kozlov I.A., De Bouvere B., Van Aerschot A., Herdewijn P., and Orgel L.E. Efficient transfer of information from hexitol nucleic acids to RNA during nonenzymatic oligomerization. J. Am. Chem. Soc. 121 (1999) 5856-5859
20. Lohrmann R. Formation of nucleoside 5′-phosphoramidates under potentially prebiological conditions. J. Mol. Evol. 10 (1977) 137-154
21. Monnard P.A., Kanavarioti A., and Deamer D.W. Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases. J. Am. Chem. Soc. 125 (2003) 13734-13740
22. Orgel L.E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 39 (2004) 99-123
23. Pino S., Ciciriello F., Costanzo G., and Di Mauro E. Nonenzymatic RNA ligation in water. J. Biol. Chem. 283 (2008) 36494-36503
24. Renz M., Lohrmann R., and Orgel L.E. Catalysts for the polymerization of adenosine cyclic 2′,3′-phosphate on a poly (U) template. Biochim. Biophys. Acta 240 (1971) 463-471
25. Saladino R., Mincione E., Crestini C., Negri R., Costanzo G., and Di Mauro E. Mechanism of degradation of purine nucleosides by formamide. Implications for chemical DNA sequencing procedure. J. Am. Chem. Soc. 118 (1996) 5615-5619
26. Saladino R., Crestini C., Mincione E., Costanzo G., Di Mauro E., and Negri R. Mechanism of degradation of 2′-deoxycytidine by formamide. Implications for chemical DNA sequencing procedures. Bioorg. Med. Chem. 5 (1997) 2041-2048
27. Saladino R., Crestini C., Costanzo G., Negri R., and Di Mauro E. A possible prebiotic synthesis of purine, adenine, cytosine, and 4(3H)-pyrimidinone from formamide: implications for the origin of life. Bioorg. Med. Chem. 9 (2001) 1249-1253
28. 2-catalyzed synthesis of nucleic bases and acyclonucleosides from formamide: implications for the origin of life. Chembiochem 4 (2003) 514-521
29. Saladino R., Ciambecchini U., Crestini C., Ciciriello F., Costanzo G., and Di Mauro E. Synthesis and degradation of nucleobases and nucleic acids by formamide in the presence of montmorillonites. Chembiochem 5 (2004) 1558-1566
30. Saladino R., Crestini C., Costanzo G., and Di Mauro E. On the prebiotic synthesis of nucleobases, nucleotides, oligonucleotides, pre-RNA and pre-DNA molecules. In: Walde P. (Ed). Topics in Current Chemistry "Prebiotic Chemistry" vol. 259 (2005), Springer Verlag 29-68
31. Saladino R., Crestini C., Busiello V., Ciciriello F., Costanzo G., and Di Mauro E. Origin of informational polymers: differential stability of 3′- and 5′-phosphoester bonds in deoxy monomers and oligomers. J. Biol. Chem. 280 (2005) 35658-35669
32. Saladino R., Crestini C., Neri V., Brucato J.R., Colangeli L., Ciciriello F., Costanzo G., and Di Mauro E. Synthesis and degradation of nucleic acid components by formamide and cosmic dust analogues. Chembiochem 6 (2005) 1368-1374
33. Saladino R., Crestini C., Neri V., Ciciriello F., Costanzo G., and Di Mauro E. Origin of informational polymers: the concurrent roles of formamide and phosphates. Chembiochem 7 (2006) 1707-1714
34. Saladino R., Crestini C., Ciciriello F., Di Mauro E., and Costanzo G. Origin of informational polymers: differential stability of phosphoester bonds in ribo monomers and oligomers. J. Biol. Chem. 281 (2006) 5790-5796
35. Saladino R., Crestini C., Ciciriello F., Costanzo G., and Di Mauro E. Formamide chemistry and the origin of informational polymers. Chemistry & biodiversity. Helv. Chim. Acta 4 (2007) 694-720
36. Saladino R., Neri V., Crestini C., Costanzo G., Graciotti M., and Di Mauro E. Synthesis and degradation of nucleic acid components by formamide and iron sulphur minerals. J. Am. Chem. Soc. 130 (2008) 15512-15518
37. Sawai H., Wada M., Kouda T., and Ozaki A.N. Nonenzymatic ligation of short-chained 2′-5′- or 3′-5′-linked oligoribonucleotides on 2′-5′- or 3′-5′-linked complementary templates. Chembiochem 7 (2006) 605-611
38. Schöning K., Scholz P., Guntha S., Wu X., Krishnamurthy R., and Eschenmoser A. Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3′->2′) oligonucleotide system. Science 290 (2000) 1347-1351
39. 2(001) single surface. Proc. Natl. Acad. Sci. USA 103 (2006) 1194-1198
40. Tohidi M., and Orgel L.E. Some acyclic analogues of nucleotides and their template-directed reactions. J. Mol. Evol. 28 (1989) 367-373
41. Usher D.A., and Mc Hale A.H. Nonenzymic joining of oligoadenylates on a polyuridylic acid template. Science 192 (1976) 53-54
42. van Holde K. In: Halvorson H.O., and van Holde K.E. (Eds). The Origins of Life and Evolution (1980), Alan R. Liss, Inc., New York 31
43. Verlander M.S., Lohrmann R., and Orgel L.E. Catalysts for the self-polymerization of adenosine cyclic 2′,3′-phosphate. J. Mol. Evol. 2 (1973) 303-316
44. Wachtershauser G. Pyrite formation, the first energy source for life: a hypothesis. Syst. Appl. Microbiol. 10 (1988) 207-210
45. Wang K.-J., and Ferris J.P. Catalysis and selectivity in prebiotic synthesis: initiation of the formation of oligo (U)s on montmorillonite clay by adenosine-5-methylphosphate. Orig. Life Evol. Biosph. 35 (2005) 187-212
46. Westheimer F.H. Why nature chose phosphates. Science 235 (1987) 1173-1178
47. Zanchetta G.J. Physical polymerization and liquid crystallization of RNA oligomers. J. Am. Chem. Soc. 130 (2008) 12804-12865