Mapping the landscape of potentially primordial informational oligomers: (3′→2′)-D-phosphoglyceric acid linked acyclic oligonucleotides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements

Chemistry - An Asian Journal

Volumn 6, Issue 5, 2011, Pages 1252-1262

  Hernández Rodríguez, Marcos ^a   Xie, Jian ^a   Osornio, Yazmin M ^a   Krishnamurthy, Ramanarayanan ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

aminopyrimidines; base pairing; nucleic acids; oligonucleotides; RNA

Indexed keywords

AMINOPYRIMIDINES; BASE PAIRING; DEPROTECTION; GLYCERIC ACID; HEXAMERS; LOCKED NUCLEIC ACID; PEPTIDE NUCLEIC ACID; PHOSPHATE BACKBONE; PHOSPHODIESTERS; PROTECTING GROUP; RECOGNITION ELEMENT; RNA SEQUENCES;

BIOMOLECULES; DEGRADATION; DNA SEQUENCES; HYDROGEN; OLIGOMERS; OLIGONUCLEOTIDES; RNA;

NUCLEIC ACIDS;

GLYCERIC ACID; LOCKED NUCLEIC ACID; OLIGONUCLEOTIDE; ORGANOPHOSPHORUS COMPOUND; PEPTIDE NUCLEIC ACID; PHOSPHORAMIDOUS ACID; PYRIMIDINE DERIVATIVE; RNA;

ARTICLE; BASE PAIRING; CHEMISTRY; SYNTHESIS; TRANSITION TEMPERATURE;

BASE PAIRING; GLYCERIC ACIDS; OLIGONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; PEPTIDE NUCLEIC ACIDS; PYRIMIDINES; RNA; TRANSITION TEMPERATURE;

EID: 79955591544     PISSN: 18614728     EISSN: 1861471X     Source Type: Journal    
DOI: 10.1002/asia.201000828     Document Type: Article

References (45)

1. G. F. Joyce, L. E. Orgel, in The RNA World, Vol2 (Eds.:, RF. Gesteland, JF. Atkins,), Cold Spring Harbor Lab, Cold Spring Harbor, NY, 1993, pp 1-25
2. nd ed., (Eds.: RF. Gesteland, TR. Cech, JF. Atkins,), Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY, 1999, pp 49-77.
3. L. E. Orgel, F. H. Crick, FASEB J. 1993, 7, 238
4. S. L. Miller, Nat. Struct. Biol. 1997, 4, 167
5. J. P. Ferris, Origins Life Evol. Biosphere 1993, 23, 307
6. L. E. Orgel, Crit. Rev. Biochem. Mol. Biol. 2004, 39, 99
7. J. D. Sutherland, Cold Spring Harbor Perspect. Biol. 2010, 2, 1.
8. A. G. Cairns-Smith, in Genetic Takeover and the Mineral Origin of Life, Cambridge University Press, Cambridge, 1982
9. G. F. Joyce, A. W. Schwartz, S. L. Miller, L. E. Orgel, Proc. Natl. Acad. Sci. USA 1987, 84, 4398
10. A. Eschenmoser, Origins Life Evol. Biosphere 1997, 27, 535
11. K. E. Nelson, M. Levy, S. L. Miller, Proc. Natl. Acad. Sci. USA 2000, 97, 3868.
12. A. Eschenmoser, Origins Life Evol. Biosphere 2004, 34, 277
13. A. Eschenmoser, Tetrahedron 2007, 63, 12821
14. G. K. Mittapalli, K. R. Reddy, H. Xiong, O. Munoz, B. Han, F. De Riccardis, R. Krishnamurthy, A. Eschenmoser, Angew. Chem. 2007, 119, 2522
15. Angew. Chem. Int. Ed. 2007, 46, 2470
16. G. K. Mittapalli, Y. M. Osornio, M. Guerrero, K. R. Reddy, R. Krishnamurthy, A. Eschenmoser, Angew. Chem. 2007, 119, 2530
17. Angew. Chem. Int. Ed. 2007, 46, 2478.
18. Independently, Orgel had also suggested a polymer based on the phosphoglyceric acid backbone, but tagged with canonical nucleobases (personal communication, A. Eschenmoser); see also:, L. E. Orgel, PLoS Biol. 2008, 6, e 18.
19. V. Kolb, L. E. Orgel, Origins Life Evol. Biosphere 1996, 26, 7.
20. S. Miyakawa, H. J. Cleaves, S. L. Miller, Origins Life Evol. Biosphere 2002, 32, 209.
21. A. Eschenmoser, Chimia 2005, 59, 836.
22. H. Wippo, F. Reck, R. Kudick, M. Ramaseshan, G. Ceulemans, M. Bolli, R. Krishnamurthy, A. Eschenmoser, Bioorg. Med. Chem. 2001, 9, 2411.
23. K. U. Schöning, P. Scholz, S. Guntha, X. Wu, R. Krishnamurthy, A. Eschenmoser, Science 2000, 290, 1347
24. K. U. Schöning, P. Scholz, X. Wu, S. Guntha, G. Delgado, R. Krishnamurthy, A. Eschenmoser, Helv. Chim. Acta 2002, 85, 4111.
25. L. Zhang, A. Peritz, E. Meggers, J. Am. Chem. Soc. 2005, 127, 4174
26. M. K. Schlegel, A. E. Peritz, K. Kittigowaittana, L. Zhang, E. Meggers, ChemBioChem 2007, 8, 927
27. M. K. Schlegel, L.-O. Essen, E. Meggers, Chem. Commun. 2010, 46, 1094
28. E. Meggers, L. Zhang, Acc. Chem. Res. 2010, 43, 1092.
29. B. M. S. Choudary, M. R. Sarma, A. D. Prasad, N. Narender, Indian J. Chem. Sect. B 1994, 33, 152.
30. D. J. Brown, J. Appl. Chem. 1957, 7, 109
31. P. C. Ratsep, R. C. Pless, J. Org. Chem. 1998, 53, 3241; of the three amino groups, the 5-amino group is expected to be the most nucleophilic; see references and commentary in footnote [9] in reference [4d].
32. C. Bleasdale, S. B. Ellwood, B. T. Golding, J. Chem. Soc. Perkin Trans. 1 1990, 803.
33. Y. Hayakawa, S. Wakabayashi, H. Kato, R. Noyori, J. Am. Chem. Soc. 1990, 112, 1691.
34. T. B. Johnson, C. O. Johns, Am. Chem. J. 1905, 34, 554.
35. G. L. Tong, W. W. Lee, L. Goodman, J. Am. Chem. Soc. 1964, 86, 5664.
36. SL. Beaucage in e-EROS Encyclopedia of Reagents for Organic Synthesis, Wiley, Chichester, UK,.
37. See footnote 25 (page 4295) of, S. Pitsch, S. Wendeborn, R. Krishnamurthy, A. Holzner, M. Minton, C. Miculca, N. Windhab, R. Micura, M. Stanek, B. Jaun, A. Eschenmoser, Helv. Chim. Acta 2003, 86, 4270.
38. 2-benzoyl group; see references [10] and [19]; fortunately these backbones were stable to the deprotecting conditions.
39. M. Manoharan, Y. Lu, M. D. Casper, G. Just, Org. Lett. 2000, 2, 243.
40. M. Egholm, O. Buchardt, P. E. Nielsen, R. H. Berg, J. Am. Chem. Soc. 1992, 114, 1895.
41. S. K. Singh, A. A. Koshkin, J. Wengel, P. Nielsen, Chem. Commun. 1998, 455.
42. Y. W. Yang, S. Zhang, E. McCullum, J. Chaput, J. Mol. Evol. 2007, 65, 289.
43. M. Egli, P. S. Pallan, R. Pattanayek, C. J. Wilds, P. Lubini, G. Minasov, M. Dobler, C. J. Leumann, A. Eschenmoser, J. Am. Chem. Soc. 2006, 128, 10847
44. P. S. Pallan, P. Lubini, M. Bolli, M. Egli, Nucl. Acids Res. 2007, 35, 6611
45. M. Egli, P. S. Pallan, Chem. Biodiversity 2010, 7, 60.