Design and implementation of a highly selective minimal self-replicating system

Angewandte Chemie - International Edition

Volumn 45, Issue 38, 2006, Pages 6344-6348

  Kassianidis, Eleftherios ^a   Philp, Douglas ^a  

^a Fife   (United Kingdom)

Author keywords

Kinetics; Molecular modeling; Self replication; Supramolecular chemistry; Template synthesis

Indexed keywords

MOLECULAR MODELING; REACTION MIXTURES; SELF-REPLICATION; TEMPLATE SYNTHESIS;

AMPLIFICATION; FOCUSING; IMAGE ANALYSIS; REACTION KINETICS; SUPRAMOLECULAR CHEMISTRY;

IMAGING SYSTEMS;

MALEIMIDE; MALEIMIDE DERIVATIVE; NITROGEN OXIDE; NITRONES;

ARTICLE; CATALYSIS; CHEMICAL MODEL; CHEMISTRY; KINETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STEREOISOMERISM;

CATALYSIS; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MALEIMIDES; MODELS, CHEMICAL; NITROGEN OXIDES; STEREOISOMERISM;

EID: 33749260139     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200601845     Document Type: Article

References (77)

1. For examples of complex replicable entities, see: a) L.-H. Eckardt, K. Naumann, W. M. Pankau, M. Rein, M. Schweitzer, N. Windhab, G. von Kiedrowski, Nature 2002, 420, 286;
2. b) J. W. Szostak, D. P. Bartel, P. L. Luisi, Nature 2001, 409, 387-390;
3. c) N. C. Seeman, P. S. Lukeman, Rep. Prog. Phys. 2005, 68, 237-270;
4. d) R. Wick, P. Walde, P. L. Luisi, J. Am. Chem. Soc. 1995, 117, 1435-1436.
5. a) A. Mulder, J. Huskens, D. N. Reinhoudt, Org. Biomol. Chem. 2004, 2, 3409-3424;
6. b) G. M. Whitesides, M. Boncheva, Proc. Natl. Acad. Sci. USA 2002, 99, 4769-4774;
7. c) G. M. Whitesides, B. Grzybowski, Science 2002, 295, 2418-2421;
8. d) H. Cölfen, S. Mann, Angew. Chem. 2003, 115, 2452-2468;
9. Angew. Chem. Int. Ed. 2003, 42, 2350-2365;
10. e) I. W. Hamley, Angew. Chem. 2003, 115, 1730-1752;
11. Angew. Chem. Int. Ed. 2003, 42, 1692-1712;
12. f) G. W. Gokel, W. M. Leevy, M. E. Weber, Chem. Rev. 2004, 104, 2723-2750, and references therein;
13. g) J. W. Lee, S. Samal, N. Selvapalam, H.-J. Kim, K. Kim, Acc. Chem. Res. 2003, 36, 621-630, and references therein;
14. h) F. W. B. van Leeuwen, H. Beijleveld, H. Kooijman, A. L. Spek, W. Veboom, D. N. Reinhoudt, J. Org. Chem. 2004, 69, 3928-3936, and references therein;
15. J. Rebek, Jr., Angew. Chem. 2005, 117, 2104-2115;
16. Angew. Chem. Int. Ed. 2005, 44, 2068-2078;
17. j) M. Ruben, J. Rojo, F. J. Romero-Salguero, L. H. Uppadine, J.-M. Lehn, Angew. Chem. 2004, 116, 3728-3747;
18. Angew. Chem. Int. Ed. 2004, 43, 3644-3662;
19. k) O. Lukin, F. Vögtle, Angew. Chem. 2005, 117, 1480-1501;
20. Angew. Chem. Int. Ed. 2005, 44, 1456-1477;
21. A. Carbone, N. C. Seeman, Proc. Natl. Acad. Sci. USA 2002, 99, 12 577-12 582;
22. N. C. Seeman, A. M. Belcher, Proc. Natl. Acad. Sci. USA 2002, 99, 6451-6455;
23. n) S. Liao, N. C. Seeman, Science 2004, 306, 2072-2074;
24. o) H. Yan, Science 2004, 306, 2048-2049;
25. p) B. Samori, G. Zuccheri, Angew. Chem. 2005, 117, 1190-1206;
26. Angew. Chem. Int. Ed. 2005, 44, 1166-1181;
27. q) K. V. Gothelf, R. S. Brown, Chem. Eur. J. 2005, 11, 1062-1069.
28. a) G. Ashkenasy, R. Jegasia, M. Yadav, M. R. Ghadiri, Proc. Natl. Acad. Sci. USA 2004, 101, 10 872-10 877;
29. b) G. Ashkenasy, M. R. Ghadiri, J. Am. Chem. Soc. 2004, 126, 11 140-11 141.
30. a) D. S. Watts, S. H. Strogatz, Nature 1998, 393, 440-442;
31. b) S. H. Strogatz, Nature 2001, 410, 268-276;
32. c) H. Jeong, B. Tombor, R. Albert, Z. N. Oltval, A. L. Barabasi, Nature 2000, 407, 651-654;
33. d) E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, A. L. Barabasi, Science 2002, 297, 1551-1555;
34. e) M. Girvan, M. E. J. Newman, Proc. Natl. Acad. Sci. USA 2002, 99, 7821-7826;
35. f) R. Guimerà, L. A. N. Amaral, Nature 2005, 433, 895-900;
36. g) J. J. Perez, Chem. Soc. Rev. 2005, 34, 143-152;
37. h) K. Ding, H. Du, Y. Yuan, J. Long, Chem. Eur. J. 2003, 9, 2872-2884;
38. R. R. Breaker, Nature 2004, 432, 838-845;
39. j) C. M. Dobson, Nature 2004, 432, 824-828;
40. k) J. J. Lavigne, E. V. Anslyn, Angew. Chem. 2001, 113, 3212-3225;
41. Angew. Chem. Int. Ed. 2001, 40, 3118-3130.
42. M. Kindermann, I. Stahl, M. Reimold, W. M. Pankau, G. von Kiedrowski, Angew. Chem. 2005, 117, 6908-6913;
43. Angew. Chem. Int. Ed. 2005, 44, 6750-6755.
44. a) I. Saur, R. Scopelliti, K. Severin, Chem. Eur. J. 2006, 12, 1058-1066;
45. b) A. Buryak, K. Severin, Angew. Chem. 2005, 117, 8149-8152;
46. Angew. Chem. Int. Ed. 2005, 44, 7935-7938;
47. c) L. Vial, J. K. M. Sanders, S. Otto, New J. Chem. 2005, 29, 1001-1003;
48. d) P. T. Corbett, J. K. M. Sanders, S. Otto, J. Am. Chem. Soc. 2005, 127, 9390-9392;
49. e) P. T. Corbett, L. H. Tong, J. K. M. Sanders, S. Otto, J. Am. Chem. Soc. 2005, 127, 8902-8903.
50. a) J. D. Cheeseman, A. D. Corbett, J. L. Gleason, R. J. Kazlauskas, Chem. Eur. J. 2005, 11, 1708-1716;
51. b) J. D. Cheeseman, A. D. Corbett, R. Shu, J. Croteau, J. L. Gleason, R. J. Kazlauskas, J. Am. Chem. Soc. 2002, 124, 5692-5701.
52. a) G. von Kiedrowski, Angew. Chem. 1986, 98, 932-934;
53. Angew. Chem. Int. Ed. Engl. 1986, 25, 932-935;
54. b) G. von Kiedrowski, Bioorg. Chem. Front. 1993, 3, 113-146.
55. N. Paul, G. F. Joyce, Curr. Opin. Chem. Biol. 2004, 8, 634-639.
56. a) A. Robertson, D. Philp, N. Spencer, Tetrahedron 1999, 55, 11 365-11 384;
57. b) R. M. Bennes, B. M. Kariuki, K. D. M. Harris, D. Philp, N. Spencer, Org. Lett. 1999, 1, 1087-1090;
58. c) S. J. Howell, D. Philp, N. Spencer, Tetrahedron 2001, 57, 4945-4954;
59. d) R. J. Pearson, E. Kassianidis, D. Philp, Tetrahedron Lett. 2004, 45, 4777-4780.
60. Some recent examples include: a) E. Kassianidis; R. J. Pearson, D. Philp, Chem. Eur. J., 10.1002/chem.200600460;
61. b) R. J. Pearson, E. Kassianidis, A. M. Z. Slawin, D. Philp, Chem. Eur. J., 10.1002/chem.200501189;
62. c) E. Kassianidis, R. J. Pearson, D. Philp, Org. Lett. 2005, 7, 3833-3836;
63. d) R. J. Pearson, E. Kassianidis, A. M. Z. Slawin, D. Philp, Org. Biomol. Chem. 2004, 2, 3434-3441;
64. e) J. M. Quayle, A. M. Z. Slawin, D. Philp, Tetrahedron Lett. 2002, 43, 7229-7233;
65. f) X. Li, J. Chmielewski, J. Am. Chem. Soc. 2003, 125, 11 820-11 821;
66. g) S. Matsumura, T. Takahashi, A. Ueno, H. Mihara, Chem. Eur. J. 2003, 9, 4829-4837;
67. h) R. Isaac, J. Chmielewski, J. Am. Chem. Soc. 2002, 124, 6808-6809;
68. B. Wang, I. O. Sutherland, Chem. Commun. 1997, 1495-1496.
69. V. C. Allen, D. Philp, N. Spencer, Org. Lett. 2001, 3, 777-780.
70. 3 solvation model, Macromodel, version 7.1, Schrodinger Inc., USA, 2000) the minimum energy conformations of the both the endo and exo cycloadducts from all of the possible combinations of these six building blocks. Of the possible cycloadducts, only one combination, endo-3 from the reaction between 1 with 2, had the desired open template structure required for replication and warranted further investigation.
71. The ratio of endo-3 and exo-3 did not change upon heating the reaction mixtures to 60°C; additionally, heating endo-3 and exo-3 with N-phenylmaleimide did not result in any crossover products being formed. These results suggest that no thermodynamic equilibration between endo and exo cycloadducts occurs within the temperature range and on the timescale of our investigations.
72. Maximum rates (velocities) of reaction were calculated by determining the largest value of the first derivative of the function that describes the concentration-time profile for each reaction; for bimolecular reactions, this metric is equivalent to the initial rate; for autocatalytic reactions, this represents the point of inflection of the sigmoidal curve.
73. 1H NMR spectra (500 MHz) of the reaction mixtures, we estimate that our limit of detection for exo-3 is 100 μM. This analysis places a lower limit of 250:1 on the endo/exo selectivity generated by the recognition-mediated reaction.
74. The simple additivity calculation described herein will underestimate the stability of the duplex somewhat (C. A. Hunter, Angew. Chem. 2004, 116, 5424-5539;
75. a value of the duplex, which is then refined by iterative fitting.
76. The value of 22.7 M is higher than many simple synthetic systems that exploit recognition processes to achieve rate accelerations in cycloaddition reactions; for some comparison data, see: R. Cacciapaglia, S. Di Stefano, L. Mandolini, Acc. Chem. Res. 2004, 37, 113-122. The effective molarity observed in the system reported herein is of the same order of magnitude as that observed (Ref. [5]) by von Kiedrowski and co-workers in an almost exponentially replicating system based on the Diels-Alder reaction.
77. a value, we wished to use these means to explore this effect qualitatively. A detailed analysis of the effect of temperature on this system will be reported elsewhere. An alternative method of achieving the same effect is to change the solvent polarity; however, in practice, it is difficult to add a polar solvent without destroying recognition between the various components within the system completely.