Optimization of interstrand hydrophobic packing interactions within unnatural DNA base pairs

Journal of the American Chemical Society

Volumn 126, Issue 44, 2004, Pages 14419-14427

  Matsuda, Shigeo ^a   Romesberg, Floyd E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENETIC ALGORITHMS; SYNTHESIS (CHEMICAL);

GENETIC ALPHABETS; PHENYL RINGS; PRIMER TERMINUS; UNNATURAL BASE PAIRS;

HYDROPHOBICITY;

AROMATIC COMPOUND; DNA; DOUBLE STRANDED DNA; HYDROGEN;

AMINO TERMINAL SEQUENCE; ARTICLE; BASE PAIRING; BINDING AFFINITY; CHEMICAL INTERACTION; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; DNA SYNTHESIS; GENETIC ALPHABET; GENETIC ANALYSIS; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR STABILITY; REACTION OPTIMIZATION;

BASE PAIRING; CIRCULAR DICHROISM; DNA; HYDROPHOBICITY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOSIDES; OLIGONUCLEOTIDES; THERMODYNAMICS;

EID: 7744230597     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja047291m     Document Type: Article

References (45)

1. Berger, M.; Ogawa, A. K.; McMinn, D. L.; Wu, Y.; Schultz, P. G.; Romesberg, F. E. Angew. Chem., Int. Ed. 2000, 39, 2940-2942.
2. Berger, M.; Luzzi, S. D.; Henry, A. A.; Romesberg, F. E. J. Am. Chem. Soc. 2002, 124, 1222-1226.
3. Henry, A. A.; Yu, C.; Romesberg, F. E. J. Am. Chem. Soc. 2003, 125, 9638-9646.
4. Matsuda, S.; Henry, A. A.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2003, 125, 6134-6139.
5. McMinn, D. L.; Ogawa, A. K.; Wu, Y.; Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 1999, 121, 11585-11586.
6. Ogawa, A. K.; Wu, Y.; McMinn, D. L., Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 3274-3287.
7. Ogawa, A. K.; Wu, Y.; Berger, M.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 8803-8804.
8. Tae, E. L.; Wu, Y. Q.; Xia, G.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2001, 123, 7439-7440.
9. Wu, Y.; Ogawa, A. K.; Berger, M.; McMinn, D. L.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 7621-7632.
10. Yu, C.; Henry, A. A.; Romesberg, F. E.; Schultz, P. G. Angew. Chem., Int. Ed. 2002, 41, 3841-3844.
11. Switzer, C.; Moroney, S. E.; Benner, S. A. J. Am. Chem. Soc. 1989, 111, 8322-8323.
12. Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature 1990, 343, 33-37.
13. Switzer, C. Y.; Moroney, S. E.; Benner, S. A. Biochemistry 1993, 32, 2, 10489-10496.
14. Horlacher, J.; Hottiger, M.; Podust, V. N.; Hübscher, U.; Benner, S. A. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 6329-6333.
15. Lutz, M. J.; Held, H. A.; Hottiger, M.; Hübscher, U.; Benner, S. A. Nucleic Acids Res. 1996, 24, 1308-1313.
16. Lin, K.-Y.; Matteucci, M. D. J. Am. Chem. Soc. 1998, 120, 8531-8532.
17. Flanagan, W. M.; Wolf, J. J.; Olsen, P.; Grant, D.; Lin, K. Y.; Wagner, R. W.; Matteucci, M. D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3515-3518.
18. Kool, E. T.; Morales, J. C.; Guckian, K. M. Angew. Chem., Int. Ed. 2000, 39, 990-1009.
19. Kool, E. T. Chem. Rev. 1997, 97, 1473-1487.
20. Ahmadian, M.; Zhang, P.; Bergstrom, D. E. Nucleic Acids Res. 1998, 26, 3127-3135.
21. He, J.; Seela, F. Nucleic Acids Res. 2002, 30, 5485-5496.
22. Seela, F.; Zulauf, M. Helv. Chim. Acta 1999, 82, 1878-1898.
23. Bergmann, E. D.; Weiler-Feilchenfeld, H. In The Dipole Moments of Purines; Bergmann, E. D., Pullman, B., Eds.; The Israel Academy of Sciences and Humanities: Jerusalem, 1971; pp 21-28.
24. Lister, J. H. The Purines. Supplement 1; John WiLey and Sons: New York, 1996; Vol. 54.
25. Hurst, D. T. An Introduction to the Chemistry and Biochemistry of Pyrimidines, Purines and Pteridines; Page Bros.: Norwich, Great Britain, 1980.
26. Gilchrist, T. L. Heterocyclic Chemistry; Longman Scientific & Technical: Essex, 1985.
27. Bugg, C. E. In Solid-State Packing Patterns of Purine Bases; Bergmann, E. D., Pullman, B., Eds.; The Israel Academy of Sciences and Humanities: Jerusalem, 1971; pp 178-204.
28. Farr, R. N.; Outten, R. A.; Cheng, J. C. Y.; Daves, G. D. Organometallics 1990, 9, 3151-3156.
29. Zhang, H. C.; Daves, G. D. J. Org. Chem. 1992, 57, 4690-4696.
30. Hsieh, H. P.; McLaughlin, L. W. J. Org. Chem. 1995, 60, 5356-5359.
31. Zhang, H. C.; Brakta, M.; Daves, G. D. Nucleosides Nucleotides 1995,14, 105-116.
32. Cameron, M. A.; Cush, S. B.; Hammer, R. P. J. Org. Chem. 1997, 62, 9065-9069.
33. Wichai, U.; Woski, S. A. Org. Lett. 1999, 1, 1173-1175.
34. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
35. Ferguson, D. M.; Kollman, P. A. J. Comput. Chem. 1991, 12, 620-626.
36. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440-467.
37. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
38. Shih, P.; Pedersen, L. G.; Gibbs, P. R.; Wolfenden, R. J. Mol. Biol. 1998, 250, 421-430.
39. Marky, L. A.; Breslauer, K. J. Biopolymers 1987, 26, 1601-1620.
40. Schweitzer, B. A.; Kool, E. T. J. Am. Chem. Soc. 1995, 117, 1863-1872.
41. Guckian, K. M.; Morales, J. C.; Kool, E. T. J. Org. Chem. 1998, 63, 9652-9656.
42. Brotschi, C.; Haberli, A.; Leumann, C. J. Angew. Chem., Int. Ed. 2001, 40, 3012-3014.
43. Brotschi, C.; Leumann, C. J. Angew. Chem., Int. Ed. 2003, 42, 1655-1658.
44. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M. Science 2003, 299, 1212-1213.
45. Henry, A. A.; Olsen, A. G.; Matsuda, S.; Yu, C; Geierstanger, B. H.; Romesberg, F. E. J. Am. Chem. Soc. 2004, 126, 6923-6931.