The α-Helical Peptide Nucleic Acid Concept: Merger of Peptide Secondary Structure and Codified Nucleic Acid Recognition

Journal of the American Chemical Society

Volumn 126, Issue 14, 2004, Pages 4626-4640

  Huang, Yumei ^a   Dey, Subhakar ^a   Zhang, Xiao ^a   Sönnichsen, Frank ^b   Garner, Philip ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHEMICAL BONDS; DIMERS; DNA; METHANOL; PH EFFECTS; SYNTHESIS (CHEMICAL);

CIRCULAR DICHROISM (CD); SOLID PHASE SYNTHESIS;

NUCLEIC ACIDS;

AMINO ACID; CYTOSINE; DNA; NUCLEIC ACID BASE; PEPTIDE NUCLEIC ACID; SINGLE STRANDED DNA; THYMINE; URACIL;

ALPHA HELIX; ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; DENATURATION; GEL ELECTROPHORESIS; HYBRIDIZATION; PH; PROTEIN STRUCTURE; SYNTHESIS;

AMINO ACIDS; CIRCULAR DICHROISM; DNA, SINGLE-STRANDED; ELECTROPHORESIS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PEPTIDE NUCLEIC ACIDS; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY;

EID: 1842738560     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja038434s     Document Type: Article

References (87)

1. Zamecnik, P. C.; Stephensen, M. L. Proc. Natl. Acad. Sci. U. S. A. 1978, 75, 280.
2. (a) Antisense Technology Part A: General Methods, Methods of Delivery and RNA Studies; Phillips, M. I., Ed.: Academic Press: San Diego, CA, 2000; Methods in Enzymology. Vol. 313.
3. (b) Antisense Technology Part B: Applications; Phillips, M. I., Ed.; Academic Press: San Diego. CA, 1999: Methods in Enzymology, Vol, 314:
4. Fire, A.; Xu, S.; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; Mello, C. C. Nature 1998, 391, 806.
5. Hutvágner, G.; Zamore, P. D. Science 2002. 297, 2056.
6. Crooke, S. T., Ed. Antisense Drug Technology - Principles, Strategies and Applications; M. Decker: New York, 2001.
7. King, D. J.; Ventura, D. A.; Brasier, A. R.; Gorenstein, D. G. Biochemistry 1998, 37, 16489.
8. Summerton, J.; Weller, D. Antisense Nucleic Acid Drug Dev. 1997, 2375. 187.
9. Summerton, J.; Stein, D.; Huang, S.; Matthews, P.; Weller, D.; Partridge, M. Antisense Nucleic Acid Drug Dev. 1997, 7, 63.
10. (a) de Koning, H.; Pandit, U. K. Rec. Trav. Chim. 1971, 91, 1069.
11. (b) Buttrey, J. D.; Jones, A. S.; Walker, R. T. Tetrahedron 1975, 31, 73.
12. (c) Shvachkin, Yu. P. Zh. Obshch. Khim. 1979, 49, 1157.
13. For a comprehensive compilation of peptide-based nucleic acid surrogates up to 1999, see: Falkiewicz, B. Acta Biochim. Pol. 1999, 43, 509. (See also ref 15).
14. (a) Nielsen, P. E.; Egholm, M.; Berg, R. H.; Buchhardt, O. Science 1991, 254, 1497.
15. (b) Egholm, M.; Buchhardt, O.; Nielsem, P. E.; Berg, R. H. J. Am. Chem. Soc. 1992, 114, 1895.
16. (c) For a comprehensive review, see: Uhlmann, E.; Peyman, A.; Breipohl, G.; Will, D. W. Angew. Chem., Int Ed. 1998, 37, 2796n.
17. The idea of using N-(2-aminoethyl)glycine as a ribose phosphate replacement may actually be traced back to an article by Westheimer. See: Westheimer, F. H. Science 1987, 235, 1173.
18. (a) Sforza, S.; Haaima, G.; Marchelli, R.; Nielsen, P. E. Eur. J. Org. Chem. 1999, 197.
19. (b) Sforza, S.; Corradini, R.; Ghirardi, S.; Dossena, A.; Marchelli, R. Ibid. 2000, 2905.
20. Uhlmann, E.; Peyman, A.; Breipohl, G.; Will, D. W. Angew. Chem., Int. Ed. 1998, 37, 2796.
21. Garner, P.; Yoo, J. U. Tetrahedron Lett. 1993, 34, 1275.
22. Preliminary accounts of this work: (a) Garner, P.; Dey, S.; Huang, Y.; Zhang, X. Org. Lett. 1999, 1, 403.
23. (b) Garner, P.; Dey, S.; Huang, Y. J. Am. Chem. Soc. 2000, 122, 2405.
24. After our original αPNA communication appeared (ref 16a), Mihara and co-workers reported the incorporation of nucleobase-containing amino acids into both coiled-coils and α-helical peptides designed to recognize HIV-1 RRE RNA: (a) Matsumura, S.; Ueno, A.; Mihara, H. Chem. Commun. 2000, 1615.
25. (b) Takahashi, T.; Hamasaki, K.; Ueno, A.; Mihara, H. Bioorg. Med. Chem. 2001, 9, 991.
26. U = (S)-2-amino-3-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-ylmethoxy)propionic acid.
27. U-OMe was reported in the Russian chemical literature in another context: Timoshchuk, V. A.; Olimpieva, T. I. Zhurnal Obshei Khimii 1988, 58, 2404.
28. Curran, T.; Kerppola, T. K. Science 1991, 254, 1210.
29. (a) Olofsson, S.; Johansson, G.; Baltzer, L. J. Chem. Soc., Perkin Trans. 2, 1995, 2047.
30. (b) Broo, K. S.; Brive, L.; Ahlberg, P.; Baltzer, L. J. Am. Chem. Soc. 1997, 119, 11362.
31. Regan, L.; Degrado, W. F. Science 1988, 241, 976.
32. Park, C., Campbell, J. L.; Goddard, W. A., III. J. Am. Chem. Soc. 1995, 117, 6287.
33. Corey, D. R. J. Am. Chem. Soc. 1995, 117, 9373.
34. (a) Hwu, J. R.; Jain, M. L.; Tsay, S.-C.; Hakimelahi, H. Tetrahedron Lett. 1996, 37, 2035.
35. (b) Siro, J. G.; Martin, J.; Garcia, J. L.; Remuiñan, M. J.; Vaquero, J. J. Synlett 1998, 147.
36. (c) Ham, J.; Choi, K.; Ko, J.; Lee, H.; Jung, M. Protein Pept. Lett. 1998, 5, 257.
37. Median, J. C.; Salomon, M.; Kyler, K. S. Tetrahedron Lett. 1988, 29, 3773.
38. Sugimura, H.; Osumi, K.; Kodaka, Y.; Sujino, K. J. Org. Chem. 1994, 59, 7653.
39. Garner, P.; Park, J. M. J. Org. Chem. 1990, 55, 3772.
40. Ogilvie, K. K.; Nguyen-Ba, N.; Hamilton, R. G. Can. J. Chem. 1984, 62, 1622.
41. Tsantrizos, Y. S.; Lunetta, J. F.; Boyd, M.; Fader, L. D.; Wilson, M. C. J. Org. Chem. 1997, 62, 5451.
42. Huang, Y.; Dey, S.; Garner, P. Tetrahedron Lett. 2003, 44, 1441.
43. Bajwa, J. S. Tetrahedron Lett. 1992, 33, 2299.
44. Cheng, V.; Hughes, L.; Griffin, V. B.; Montserret, R.; Ollapally, A. P. Nucleosides Nucleotides 1986, 5, 223.
45. Kalinowski, H. O.; Berger, S.; Braun, S. Carbon-13 NMR Spectroscopy; Translated by Becconsall, J. K. Imprint Chichester; Wiley: New York, 1988; pp 441.
46. (a) Bax, A.; Summers, M. F. J. Am. Chem. Soc. 1986, 108, 2093.
47. (b) Huang, J. J.; Ragouzeos, A.; Rideout, J. L. J. Heterocycl. Chem. 1994, 31, 1685.
48. (c) Timár, Z.; Kovács, L.; Kovács, G.; Schmél, Z. J. Chem. Soc. Perkin Trans. 2000, 1, 19.
49. Paulsen, H.; Schleyer, A.; Mathieux, N.; Meldal, M.; Bock, K. J. Chem. Soc., Perkin Trans. 1 1997, 281.
50. Veber, D. F.; Milkowski, J. D.; Varga, S. L.; Denkewalter, R. G.; Hirschmann, R. J. Am. Chem. Soc. 1972, 94, 5456.
51. T-OMe indicated that exposure to 20% piperidine led to the elimination of free thymine.
52. Carpino, L. A. J. Am. Chem. Soc. 1993, 115, 4397.
53. (Rink amide linker = 4-(2′,4′ -dimethoxyphenylaminomethyl)phenoxy-acetamido) Rink, H. Tetrahedron Lett. 1987, 28, 3787,
54. Kamber, B.; Hartmann, A.; Eisler, K.; Riniker, B.; Rink, H.; Sieber, P.; Rittel, W. Helv. Chim. Acta 1980, 63, 899.
55. Freier, S. M.; Burger, B. J.; Alkema, D.; Neilson, T.; Turner, D. H. Biochemistry 1983, 22, 6198.
56. Von Hippel, P. H.; Schleich, T. Effects of Neutral Salts on the Structure and Conformational Stability of Macromolecules in Solution. In Structure and Stability of Biological Macromolecules; Timasheff, S. N., Fasman, G. D., Eds.; Biological Macromolecules: Vol. 2; M. Dekker Inc.: New York, 1969; p 417.
57. Tomac, S.; Sarkar, M.; Ratilainen, T.; Wittung, P.; Nielsen, P. E.; Nordén, B.; Gräslund, A. J. Am. Chem. Soc. 1996, 118, 5544.
58. (a) Record, M. T.; Anderson, C. F.; Lohman, T. M. Q. Rev. Biophys. II 1978, 2, 103.
59. (b) Manning, G. S. Ibid., 179.
60. (a) Taylor, J. D.; Ackroyd, A. J.; Halford, S. E. The Gel Shift Assay for the Analysis of DNA-Protein Interactions. In DNA-Protein Interaction: Principles and Protocols; Kneale, G. G., Ed.; Methods in Molecular Biology, Vol. 30: Humana Press Inc.: Totowa, NJ, 1994; p 263.
61. (b) Lane D.; Prentki, P.; Chandler, M. Microbiol. Rev. 1992, 56, 509.
62. Fasman, G. D., Ed. Circular Dichroism and the Conformational Analysis of Biomolecules; Plenum Press: New York, 1996.
63. Holzwarth, G.; Doty, P. J. Am. Chem. Soc. 1965, 87, 218.
64. Padmanabhan, S.; Baldwin, R. L. J. Mol. Biol. 1991, 219, 135.
65. Marqusee, S.; Baldwin, R. L. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 8898.
66. (a) Yasui, S. C.; Keiderling, T. A. J. Am. Chem. Soc. 1986, 108, 5576.
67. (b) Satake, I.; Yang, J. Biopolymers 1975, 14, 1841.
68. (c) Yaron, A.; Tal, N.; Berger, A. Biopolymers, 1972, 11, 2461.
69. Talanian, R. V.; McKnight, C. J.; Kim, P. S. Science 1990, 249, 769.
70. Sudha, T. S.; Vijayakumar, E. K. S.; Balaram, P. Int. J. Pept. Protein Res. 1983, 22, 464.
71. (a) Patel, L.; Abate, C.; Curran, T. Nature 1990, 347, 572.
72. (b) Weiss, M. A.; Ellenberger, T.; Wobbe, C. R.; Lee, J. P.; Harrison, S. C.; Struhl, K. Nature 1990, 347, 575.
73. Zlotnick, A.; Brenner, S. L.; J. Mol. Biol. 1988, 209, 447.
74. (a) Kim, S. K.; Nielsen, P. E.; Egholm, M.; Buchardt, O.; Berg, R. H.; Norden, B. J. Am. Chem. Soc., 1993, 115, 6478.
75. (b) Wittung, P.; Kim, S. K.; Buchardt, O.; Nielsen, P.; Norden, B. Nucleic Acid Res. 1994, 22, 5371.
76. (c) Wittung, P.; Nielsen, P.; Norden, B. J. Am. Chem. Soc., 1996, 118, 7049.
77. (d) Gray, D. M.; Hung, S.; Johnson, K. H. Methods Enzymol. 1995, 246, 19.
78. Wüthrich, K. NMR of Proteins and Nucleic Acids; Wiley & Sons: New York, 1986.
79. Leijon, M.; Gräslund, A.; Nielsen, P. E.; Buchardt, O.; Nordén, B.; Kristensen, S. M.; Eriksson, M. Biochemistry 1994, 33, 9820.
80. Altona, C.; Faber, D. H.; Hoekzema, A. W. Magnetic Reson. Chem. 2000, 38, 95.
81. Brown, S. C.; Thomson, S. A.; Veal, J. M.; Davis, D. G. Science 1994, 265, 777.
82. Alewood, P.; Alewood, D.; Miranda, L.; Love, S.; Meutermans, W.; Wilson, D. Methods Enzymol. 1997, 289, 14.
83. Sarin, K. V.; Kent, B. H. S.; Tam, P. J. Anal. Biochem. 1981 117, 6147.
84. Puglisi, J. D.; Tinoco, I., Jr. Methods Enzymol. 1989, 180, 304.
85. Sarin, V. K.; Kent, S. B.; Tam, J. P.; Merrifield, R. B. Anal. Biochem. 1981, 117, 147.
86. Chen, Y.; Yang, J. T.; Chau, K. H. Biochemistry 1974, 13, 3350.
87. Piotto, M.; Saudek, V.; Sklenar, V. J. Biomolecular NMR 1992, 2, 661.