N-pent-4-enoyl (PNT) group as a universal nucleobase protector: Applications in the rapid and facile synthesis of oligonucleotides, analogs, and conjugates

Tetrahedron

Volumn 53, Issue 8, 1997, Pages 2731-2750

  Iyer, Radhakrishnan P ^a   Dong, Yu ^a   Habus, Ivan ^a   Nan Hui, Ho ^a   Johnson, Suzanne ^a   Devlin, Theresa ^a   Jiang, Zhiwei ^a   Zhou, Wen ^a   Jin, Xie ^a   Agrawal, Sudhir ^a  

^a HYBRIDON INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; DRUG SYNTHESIS; IN VITRO STUDY; METHODOLOGY; PRIORITY JOURNAL; REACTION ANALYSIS;

EID: 0031584876     PISSN: 00404020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0040-4020(97)00048-3     Document Type: Article

References (58)

1. 1. (a) Beaucage, S.L.; Caruthers, M. H. Tetrahedron Lett. 1981, 22, 1859-62;
2. (b) Adams, S. P.; Kavka, K.S.; Wykes, E. J.; Holder, S. B.; Galluppi, G. R. J. Am. Chem. Soc. 1983, 105, 661;
3. (c) McBride, L. J.; Caruthers, M. H. Tetrahedron Lett. 1983, 24, 245-248;
4. (d) Sinha, N. D.; Biernat, J. P.; McManus, J.; Koster, H. Nucl. Acids Res. 1984, 12, 4539;
5. (e) Caruthers, M. H. Science 1985, 230, 281-85;
6. (f) For a recent review see: Beaucage, S. L.; Iyer, R. P. Tetrahedron 1992, 48, 2223-2311.
7. 2. (a) Garegg, P. J.; Regberg, T.; Stawinski, J.; Stromberg, R. Chem. Scr. 1985, 25, 280-82;
8. (b) Froehler, B. C.; Ng, P. G.; Matteucci, M. D. Nucl. Acids Res. 1986, 14, 5399-5407.
9. 3. For reviews from a biological perspective, see: (a) Antisense Therapeutics, Agrawal, S. Ed.; Humana Press, Totowa, New Jersey, 1996;
10. (b) Pon, R. T.; Buck, G. A.; Niece, R. L.; Robertson, M.; Smith, A. J.; Spicer, E. Biotechniques, 1994, 17, 526-534.
11. For reviews from a chemical perspective see: (a) Uhlmann, E.; Peyman, A. Chem. Rev. 1990, 90, 544-84;
12. (b) Zon, G. Pharm. Rev. 1988, 5, 539-49;
13. (c) Miller, P. S. Bio/Technology 1991, 9, 358-62;
14. (d) Agrawal, S.; Iyer, R. P. Curr. Op. Biotech. 1995, 6, 12-19 and references therein;
15. (e) Thuong, N. T.; Helene, C. Angew Chem. Intl. Ed. Engl. 1993, 32, 666-690.
16. 4. For reviews see: (a) Beaucage, S. L.; Iyer, R. P. Tetrahedron, 1993, 49, 1925-63;
17. (b) Beaucage, S. L.; Iyer, R. P. Tetrahedron 1993, 49, 6123-94.
18. 5. For reviews of protecting groups in oligonucleotide synthesis, see: (a) Ref. 1f;
19. (b) Sonveaux, E. In Protocols for Oligonucleotides and Analogs; Agrawal, S., Ed.; Humana Press: New Jersey, 1993, pp.1-71.
20. 6. For recent studies in the rapid synthesis of oligonucleotides using tert-butylphenoxyacetyl (t-PAC)-protected nucleosides, see: (a) Boal, J. H.; Wilk, J.; Harindranath, N.; Max, E. E.; Kempe, T.; Beaucage, S. L. Nucl. Acids Res. 1996, 24, 3115-17 and references therein;
21. (b) For a comprehensive study, see: Sinha, N. D.; Davis, P.; Usman, N.; Perez, J.; Hodge, R.; Kremsky, J.; Casale, R. Biochimie, 1993, 75, 13-23;
22. Bz in the rapid synthesis of PO oligonucleotides, see: Reddy, M. P.; Hanna, N. B.; Farooqui, F. Tetrahedron Lett. 1994, 35, 4311-14;
23. (d) For a discussion of phenoxyacetyl (PAC) protecting groups in the rapid synthesis of oligonucleotides, see: (i) Schulhof, J. C.; Molko, D.; Teoule, R. Nucl. Acids Res. 1987, 15, 397-416; (ii) Chaix, C.; Molko, D.; Teoule, R. Tetrahedron Lett. 1989, 30, 71-74; (iii) Wu, T.; Ogilvie, K. K.; Pon, R. T. Nucl. Acids Res. 1989, 17, 3501-17;
24. (d) For a discussion of phenoxyacetyl (PAC) protecting groups in the rapid synthesis of oligonucleotides, see: (i) Schulhof, J. C.; Molko, D.; Teoule, R. Nucl. Acids Res. 1987, 15, 397-416; (ii) Chaix, C.; Molko, D.; Teoule, R. Tetrahedron Lett. 1989, 30, 71-74; (iii) Wu, T.; Ogilvie, K. K.; Pon, R. T. Nucl. Acids Res. 1989, 17, 3501-17;
25. (d) For a discussion of phenoxyacetyl (PAC) protecting groups in the rapid synthesis of oligonucleotides, see: (i) Schulhof, J. C.; Molko, D.; Teoule, R. Nucl. Acids Res. 1987, 15, 397-416; (ii) Chaix, C.; Molko, D.; Teoule, R. Tetrahedron Lett. 1989, 30, 71-74; (iii) Wu, T.; Ogilvie, K. K.; Pon, R. T. Nucl. Acids Res. 1989, 17, 3501-17;
26. (e) For a recent study related to the use of formamidino-protected nucleosides, see: Vu, H; McCollum, C.; Jacobson, K.; Theisen, P.; Vinayak, R.; Spiess, E.; Andrus, A. Tetrahedron Lett. 1990, 31, 7269-72;
27. (f) For other examples, see: reference 1f, pp. 2255-59.
28. 7. (a) Iyer, R. P.; Devlin, T.; Habus, I.; Ho, N.-H.; Yu, D.; Agrawal, S. Tetrahedron Lett. 1996, 37, 1539-42;
29. (b) Habus, I.; Devlin, T.; Iyer, R. P.; Agrawal, S. Bioorg. & Med. Chem. Lett. 1996, 6, 1393-98;
30. (c) Iyer, R. P.; Devlin, T.; Habus, I.; Yu, D.; Johnson, S.; Agrawal, S. Tetrahedron Lett. 1996, 37, 1543-46;
31. 2 analogs, see: Peyrottes, S.; Vasseur, J.-J.; Imbach, J.-L.; Rayner, B. Nucl. Acids Res. 1996, 24, 1841-48;
32. (e) Iyer, R. P.; Yu, D.; Jiang, Z.; Agrawal, S. Tetrahedron 1996, 52, 14419-36.
33. 8. (a) For the use of PNT protecting group in the synthesis of aminosugars see: Debenham, J. S.; Madsen, R.; Roberts, C.; Fraser-Reid, B. J. Am. Chem Soc. 1995, 117, 3302-03 and references therein.
34. (b) Madsen, R.; Roberts, C.; Fraser-Reid, B. J. Org. Chem. 1995, 60, 7920-26.
35. 9. Ti, G. S.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1982, 104, 1316-19.
36. 10. Cabre-Castellvi, J.; Palomo-Coll, A.; Palomo-Coll, A. L. Synthesis 1981, 616-618.
37. 11. Kuijpers, W. H. A.; Huskens, J.; Koole, L. H.; van Boeckel, C. A. A. Nucl. Acids Res. 1990, 18, 5197-5205
38. 12. (a) Hayakawa, Y.; Hirose, M.; Hayakawa, M.; Noyori, R. J. Org. Chem. 1995, 60, 925-30;
39. (b) Alul, R. H.; Singman, C. N.; Zhang, G.; Letsinger, R. L. Nucl. Acids Res. 1991, 19, 1527-32;
40. (c) Koole, L. H.; Moody, M. H.; Breeders, N. L. H. L.; Quaedflieg, P. J. L. M.; Kuijpers, W. H. A.; van Genderen, M. H. P.; Coenen, A. J. J. M.; van der Wal, S.; Buck, H. M. J. Org. Chem. 1989, 54, 1657-64.
41. 2 analogs, see: Letsinger, R. L.; Bach, S. A.; Eaddie, J. S. Nucl. Acids Res. 1986, 8, 3487;
42. (b) Tomasz, J. Nucleosides & Nucleotides 1983, 2, 51-58;
43. (c) Froehler, B. C. Tetrahedron Lett. 1986, 27, 5575-78;
44. 14. Beaucage, S. L. Oligodeoxyribonucleotide Synthesis: Phosphoramidite Approach. In Protocols for Oligonucleotides and Analogs; Agrawal, S., Ed.; Humana Press: Totowa, NJ, 1993; Vol. 20, pp. 33-61.
45. 15. (a) Froehler, B. C. Oligodeoxynucleotide Synthesis: H-phosphonate Approach. In Protocols for Oligonucleotides and Analogs; Agrawal, S., Ed.; Humana Press: New Jersey, 1993; pp. 63-80;
46. (b) Loading was carried out as described: Pon, R. T. Solid-Phase Supports for Oligonucleotide Synthesis. In Protocols for Oligonucleotides and Analogs; Agrawal, S., Ed.; Humana Press: Totowa, NJ, 1993; Vol. 20, pp. 469-72.
47. 3CN, pH 8.5; gradient: buffer A from 100% to 50%, buffer B from 100% to 50%, within 0 to 110 min; flow rate, 0.5 mL/min, column temperature 65 °C.
48. 17. For a discussion see: (a) (b) Iyer, R. P.; Yu, D.; Jiang, Z.; Agrawal, S. Nucleosides & Nucleotides, 1995, 14, 1349-57;
49. (b) Fearon, K. L.; Stults, J. T.; Bergot, B. J.; Christensen, L. M.; Raible, A. M. Nucl. Acids Res. 1995, 23, 2754-61;
50. (c) Temsamani, J.; Kubert, M.; Agrawal, S. Nucl. Acids Res. 1995, 23, 2754-61.
51. 18. Iyer, R. P.; Regan, J. B.; Egan, W.; Beaucage, S. L. J. Am. Chem. Soc. 1990, 112, 1253-54.
52. 19. CE analysis was done on a Beckman P/ace 2200 instrument operating at 14.1 Kv; before CE, the samples were desalted using a SEP-PAK cartridge.
53. 20. For an excellent summary see: Gait, M. J. An Introduction to Modern Methods of DNA Synthesis. In Oligonucleotide Synthesis: a Practical Approach, Gait, M. J., Ed.; IRL Press: New York, 1990; pp. 1-22;
54. 21. (a) Callahan, D. E.; Trapane, T. L.; Miller, P. S.; Ts'O, P. O. P.; Kan, L.-S. Biochemistry 1991, 30, 1650, and references therein;
55. (b) Agrawal, S.; Goodchild, J. Tetrahedron Lett. 1987, 28, 3539-42;
56. (c) Hogrefe, R. I.; Vaghefi, M. M.; Reynolds, M. A.; Young, K. M.; Arnold, L. J. Nucl. Acids Res. 1993, 21, 2031, and references therein.
57. 22. Agrawal, S.; Iyer, R. P. Drugs of the Future 1995, 20, 344-51.
58. 23. Iyer, R. P.; Yu, D.; Devlin, T.; Ho, N.-H.; Agrawal, S. Bioorg. Med. Chem. Lett. 1996, 6, 1917-22 and references therein.