Expanding the Genetic Alphabet: Non-Epimerizing Nucleoside with the pyDDA Hydrogen-Bonding Pattern

Journal of Organic Chemistry

Volumn 68, Issue 25, 2003, Pages 9839-9842

  Huttert, Daniel ^a   Benner, Steven A ^a,b  

^a University of Florida ^*  (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; PH EFFECTS; SYNTHESIS (CHEMICAL);

GENETIC ALPHABET;

ORGANIC COMPOUNDS;

6 AMINO 3 (2' DEOXY BETA DEXTRO RIBOFURANOSYL) 5 NITRO 1H PYRIDIN 2 ONE; ACID; GLYCOSIDE; NUCLEOSIDE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; EPIMERIZATION; GENETIC ANALYSIS; HYDROGEN BOND; PH; PROTON TRANSPORT; SYNTHESIS;

BASE PAIRING; CATALYSIS; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; ISOMERISM; MOLECULAR STRUCTURE; NITRO COMPOUNDS; NUCLEOSIDES; PURINES; PYRIMIDINES;

EID: 0344235337     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo034900k     Document Type: Article

References (67)

1. (a) Watson, J. D.; Crick, F. H. C. Nature (London) 1953, 171, 737.
2. (b) Watson, J. D.; Crick, F. H. C. Nature (London) 1953, 171,964.
3. (a) Switzer, C. Y.; Moroney, S. E.; Benner, S. A. J. Am. Chem. Soc. 1989, 111, 8322.
4. (b) Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature (London) 1990, 343, 33.
5. (a) Piccirilli, J. A.; Krauch, T.; MacPherson, L. J.; Benner, S. A. Helv. Chim. Acta 1991, 74, 397.
6. (b) Voegel, J. J.; Altorfer, M. M.; Benner, S. A. Helv. Chim. Acta 1993, 76, 2061.
7. (c) Voegel, J. J.; von Krosigk, U.; Benner, S. A. J. Org. Chem. 1993, 58, 7542.
8. (d) Heeb, N. V.; Benner, S. A. J. Am. Chem. Soc. 1994, 116, 6929.
9. (e) Voegel, J. J.; Benner, S. A. J. Am. Chem. Soc. 1994, 116, 6929.
10. (f) von Krosigk, U.; Benner, S. A. J. Am. Chem. Soc. 1995, 117, 5361.
11. (g) Voegel, J. J.; Benner, S. A. Helv. Chim. Acta 1996, 79, 1863.
12. (h) Kodra, J. T.; Benner, S. A. Synlett 1997, 939.
13. (i) Jurczyk, S. C.; Battersby, T. R.; Kodra. J. T.; Park, J. H.; Benner, S. A. Helv. Chim. Acta 1999, 82, 1005.
14. (j) Jurczyk, S. C.; Horlacher, J.; Devine, K. G.; Benner, S. A.; Battersby, T. R. Helv. Chim. Acta 2000, 83, 1517.
15. (k) Rao, P.; Benner, S. A. J. Org. Chem. 2001, 66, 5012.
16. (a) Service, R. F. Science 2000, 289, 232.
17. (b) Wang, L.; Schultz, P. G. Chem. Commun. 2002, 1.
18. Modified H-bonding patterns: (a) Seela, F.; Wei, C. F. Chem. Commun. 1997, 1869.
19. (b) Seela, F.; He, Y. J. Org. Chem. 2003, 68, 367.
20. (c) Hirao, I.; Ohtsuki, T.; Mitsui, T. Yokoyama, S. J. Am. Chem. Soc. 2000, 122, 6118.
21. (d) Hirao, I.; Ohtsuki, T.; Fujiwara, T.; Mitsui, T.; Yokogawa, T.; Okuni, T.; Nakayama, H.; Takio, K.; Yabuki, T.; Kigawa, T.; Kodama, K.; Yokogawa, T.; Nishikawa, K.; Yokoyama, S. Nature Biotechnol. 2002, 20, 177.
22. (e) Searls, T.; McLaughlin, L. W. Tetrahedron 1999, 55, 11985.
23. (f) Chen, D. L.; McLaughlin, L. W. J. Org. Chem. 2000, 65, 7468.
24. (g) Roberts, C.; Banduru, R.; Switzer, C. J. Am. Chem. Soc. 1997, 119, 4640.
25. (h) Oyelere, A. K.; Strobel, S. A. J. Am. Chem. Soc. 2000, 122, 10259.
26. Hydrophobic base pairs: (a) Kool, E. T. Curr. Opin. Chem. Biol. 2000, 4, 602.
27. (b) Kool, E. T.; Morales, J. C.; Guckian, K. M. Angew. Chem., Int. Ed. 2000, 39, 990.
28. (c) Kool, E. T. Acc. Chem. Res. 2002, 35, 936.
29. (d) Ogawa, A. K.; Wu, Y.; McMinn, D. L.; Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 3274.
30. (e) Berger, M.; Luzzi, S. D.; Henry, A. A.; Romesberg, F. E. J. Am. Chem. Soc. 2002, 124, 1222.
31. Metal chelation: (a) Weizman, H.; Tor, Y. J. Am. Chem. Soc. 2001, 123, 3375.
32. (b) Zimmermann, N.; Meggers, E.; Schultz, P. G. J. Am. Chem. Soc. 2002, 124, 13684.
33. (c) Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shiro, M.; Shionoya, M. J. Am. Chem. Soc. 2002, 124, 12494.
34. Steitz, T. In Biological Organization: Macromolecular Interactions at High Resolution; Burnett, R. M., Vogel, H. J., Eds.; Academic Press: New York, 1987; pp 45-55.
35. pyDDA: Pyrimidine analogue carrying a H-bond donor-donor-acceptor motif proceeding from the major to the minor groove. puAAD: purine analogue carrying an H-bond acceptor-acceptor-donor motif.
36. (a) Kim, S. H.; Bartholomew, D. G.; Allen, L. B.; Robins, R. K.; Revankar, G. R.; Dea. P. J. Med. Chem. 1978, 21, 883.
37. (b) Rosemeyer, H.; Seela, F. J. Org. Chem. 1987, 52, 5136.
38. (c) Seela, F.; Amberg, S.; Melenewski, A.; Rosemeyer, H. Helv. Chim. Acta 2001, 84, 1996.
39. (a) Cohn, W. E. J. Biol. Chem. 1960, 235, 1488.
40. (b) Chambers, R. W.; Kurkov, V.; Shapiro, R. Biochemistry 1963, 2, 1192.
41. (a) Ohrui, H.; Jones, G. H.; Moffatt, J. G.; Maddox, M. L.; Christensen, A. T.; Byram, S. K. J. Am. Chem. Soc. 1975, 97, 4602.
42. (b) De Bernardo, S.; Weigele, M. J. Org. Chem. 1976, 41, 287.
43. (c) Pankiewicz, K.; Matsuda, A.; Watanabe, K. A. J. Org. Chem. 1982, 47, 485.
44. The different numbering systems of different heterocycles create confusion when attempting to compare substituents placed upon them. For this discussion, we use the pyrimidine numbering system by analogy to the pyridine rings that we describe.
45. (a) Ireland, R. E.; Thaisrivongs, S.; Vanier, N.; and Wilcox, C. S. J. Org. Chem. 1980, 45, 48.
46. (b) Larsen, E.; Jorgensen, P. T.; Sofan, M. A.; Pedersen, E. B. Synthesis, 1994, 1037.
47. (c) Walker, J. A., II; Chen, J. J.; Wise, D. S.; Townsend, L. B. J. Org. Chem. 1996, 61, 2219.
48. (d) Cameron, M. A.; Cush, S. B.; Hammer, R. P. J. Org. Chem. 1997, 62, 9065.
49. Deady, L. W. Synth. Commun. 1977, 509.
50. (a) Daeniker, H. U.; Druey, J. Helv. Chim. Acta 1958, 41, 2148.
51. (b) Taylor, E. C.; Driscoll, J. S. J. Org. Chem. 1960, 25, 1716.
52. (c) Markgraf, J. H.; Brown, Jr., H. B.; Mohr, S. C.; Peterson, R. G. J. Am. Chem. Soc. 1962, 85, 958.
53. (d) McKillop, A.; Bhagrath, M. K. Heterocycles 1985, 23, 1697.
54. (e) Sato, N.; Miwa, N.; Suzuki, H.; Sakakibara, T. J. Heterocycl. Chem. 1994, 31, 1229.
55. Radl, S.; Hradil, P. Collect. Czech. Chem. Commun. 1991, 56, 2420.
56. (a) Farr, R. N.; Outten, R. A.; Cheng, J. C.-Y.; Daves, G. D., Jr. Organometallics 1990, 9, 3151.
57. (b) Zhang, H.-C.; Daves, G. D., Jr. J. Org. Chem. 1992, 57, 4690.
58. (c) Zhang, H.-C.; Daves, G. D., Jr. Organometallics 1993, 12, 1499.
59. (a) Hsieh, H.-P.; McLaughlin, L. W. J. Org. Chem. 1995, 60, 5356.
60. (b) Chen, D. L.; McLaughlin, L. W. J. Org. Chem. 2000, 65, 7468.
61. (c) Searls, T.; Chen, D. L.; Lan, T.; McLaughlin, L. W. Biochemistry 2000, 39, 4375.
62. (d) Lan, T.; McLaughlin, L. W. Bioorg. Chem. 2001, 29, 198.
63. Coleman, R. S.; Madaras, M. L. J. Org. Chem. 1998, 63, 5700.
64. With 5′-OH protected: (a) Chen, J. J.; Walker, J. A., II; Liu, W.; Wise, D. S.; Townsend, L. B. Tetrahedron Lett. 1995, 36, 8363.
65. (b) Walker, J. A., II; Chen, J. J.; Hinkley, J. M.; Wise, D. S.; Townsend, L. B. Nucleosides Nucleotides 1997, 16, 1999.
66. Saenger, W. Principles of Nucleic Acid Structure; Springer: New York, 1984; p 107:
67. Baldwin, J. E.; Thomas, R. C.; Kruse, L. I.; Silberman, L. J. Org. Chem. 1977, 42, 3846.