Synthesis and hybridization properties of polyamide based nucleic acid analogues incorporating pyrrolidine-derived nucleoammino acids

Bioorganic and Medicinal Chemistry Letters

Volumn 10, Issue 9, 2000, Pages 929-933

  Altmann, Karl Heinz ^a   Hüsken, Dieter ^c   Cuenoud, Bernard ^b   García Echeverría, Carlos ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

^b Respiratory Disease TA   (United Kingdom)

^c Functional Genomics Area   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; NUCLEIC ACID; NUCLEOSIDE ANALOG; POLYAMIDE; PYRROLIDINE DERIVATIVE;

ARTICLE; DNA BINDING; DNA HYBRIDIZATION; DNA SYNTHESIS;

AMINO ACIDS; CHEMISTRY, PHYSICAL; DNA, COMPLEMENTARY; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACIDS; NYLONS; PYRROLIDINES; RNA, COMPLEMENTARY; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 0343963246     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-894X(00)00121-9     Document Type: Article

References (40)

1. For recent reviews on antisense technology and the importance of structural modifications of oligonucleotides for antisense applications cf., e.g.: a Crooke, S. T. Med. Res. Rev. 1996, 16, 319.
2. (b) Matteucci, M. D. Persp. Drug Disc. Des. 1996, 4, 1.
3. (c) Altmann K.-H.; Cuenoud, B.; von Matt, P. In Applied Antisense Oligonucleotide Technology; Stein, C. A.; Krieg, A. M., Eds.; Wiley-Lyss: New York, 1997; pp 73-107.
4. For recent reviews on backbone modified oligonucleotides cf., e.g.: (a) De Mesmaeker, A.; Häner, R.; Martin, P.; Moser, H. E. Acc. Chem. Res. 1995, 28, 366.
5. (b) De Mesmaeker, A.; Altmann, K.-H.; Waldner, A.; Wendeborn, S. Curr. Opinion Struct. Biol. 1995, 5, 343.
6. For recent reviews on PNA cf., e.g.: (a) Nielsen, P. Curr. Opin. Struct. Biol. 1999, 9, 353.
7. (b) Hyrup; B.; Nielsen, P. E. Bioorg. Med. Chem. 1996, 4, 5.
8. Cf., e.g.: (a) Schah, V. J.; Cerpa, R.; Kuntz, I. D.; Kenyon, G. L. Bioorg. Chem. 1996, 24, 201.
9. (b) Petersen, K. H.; Buchardt, O.; Nielsen, P. E. Bioorg. Med. Chem. Lett. 1996, 6, 793.
10. (c) Lenzi, A.; Reginato, G.; Taddei, M. Tetrahedron Lett. 1995, 36, 1713; Lenzi, A.; Reginato, G.; Taddei, M.; Trifilieff, E. Tetrahedron Lett. 1995, 36, 1717.
11. (c) Lenzi, A.; Reginato, G.; Taddei, M. Tetrahedron Lett. 1995, 36, 1713; Lenzi, A.; Reginato, G.; Taddei, M.; Trifilieff, E. Tetrahedron Lett. 1995, 36, 1717.
12. (d) Garner, P.; Yoo, J. U. Tetrahedron Lett. 1993, 34, 1275.
13. (e) Lewis, I. Tetrahedron Lett. 1993, 36, 5697.
14. (f) Hudziak, R. M.; Barofsky, E.; Douglas, F.; Weller, D. L.; Huang, S.-B.; Weller, D. D. Antisense Nucleic Acid Drug Dev. 1996, 6, 267. For a review on earlier attempts to construct polyamide-based nucleic acid analogues see: Jones, S. A. Int. J. Biol. Macromolecules 1979, 1, 194.
15. (a) Lowe, G.; Vilaivan, T.; Westwell, M. S. Bioorg. Chem. 1997, 25, 321.
16. (b) Jordan, S.; Schwemler, C.; Kosch, W.; Kretschmer, A.; Stropp, U.; Schwenner, E.; Mielke, B. Bioorg. Med. Chem. Lett. 1997, 7, 687.
17. (a) Altmann, K.-H.; Schmit Chiesi, C.; García-Echeverría, C. Bioorg. Med. Chem. Lett. 1997, 7, 1119.
18. (b) García-Echeverría, C.; Schmit Chiesi, C.; Hüsken, D.; Altmann, K.-H. Bioorg. Med. Chem. Lett. 1997, 7, 1123.
19. Related structures have recently been described (cf. ref. 5).
20. The term nucleoamino acid is meant to signify amino acids with side chains bearing nucleic acid bases.
21. Baker G.L., Fritschel S.J., Stille J.R., Stille J.K. J. Org. Chem. 46:1981;2954.
22. Jenny T.F., Horlacher J., Previsiani N., Benner S.A. Helv. Chim. Acta. 76:1993;248.
23. Sigler G.F., Fuller W.D., Chaturverdi N.C., Goodman M., Verlander M. Biopolymers. 22:1983;2157.
24. 4-isobutyryl cytosine predominantly resulted in O-2 alkylation (Altmann, K.-H., unpublished results).
25. Divakar, K. J.; Reese, C. B. J. Chem. Soc. Perkin Trans. 1 1982, 1171.
26. Wünsch, E.; Graf, W.; Keller, O.; Keller, W.; Wersin, G. Synthesis 1986, 958.
27. Watkins, B. E.; Kiely, J. S.; Rapaport, H. J. Org. Chem. 1982, 104, 5702. For use of this reagent in the synthesis of PNA building blocks cf.: Egholm, M.; Behrens, C.; Christensen, L.; Berg, R. H.; Nielsen, P. E.; Buchardt, O. J. Chem. Soc., Chem. Commun. 1993, 800.
28. Watkins, B. E.; Kiely, J. S.; Rapaport, H. J. Org. Chem. 1982, 104, 5702. For use of this reagent in the synthesis of PNA building blocks cf.: Egholm, M.; Behrens, C.; Christensen, L.; Berg, R. H.; Nielsen, P. E.; Buchardt, O. J. Chem. Soc., Chem. Commun. 1993, 800.
29. 2 (u=I-U), which incorporates pyrimidine- as well as purine-derived building blocks.
30. Rink, H. Tetrahedron Lett. 1987, 28, 3787. Syntheses were carried out on a semi-automated peptide synthesizer using 140-190 mg of resin.
31. Knorr R., Trzeciak A., Bannwarth W., Gillesen D. Tetrahedron Lett. 30:1989;1927.
32. Efficient incorporation of the N-terminal lysine residue in general required double-coupling.
33. Atherton, E.; Sheppard, R. C. In Solid Phase Peptide Synthesis: A Practical Approach; IRL Press, Oxford, 1989.
34. m measurements cf.: Lesnik, E. A.; Guinosso, C. J.; Kawasaki, A. M.; Sasmor, H.; Zounes, M.; Cummins, L. L.; Ecker, D. J.; Cook, P. D.; Freier, S. M. Biochemistry 1993, 32, 7832.
35. m measurements cf.: Lesnik, E. A.; Guinosso, C. J.; Kawasaki, A. M.; Sasmor, H.; Zounes, M.; Cummins, L. L.; Ecker, D. J.; Cook, P. D.; Freier, S. M. Biochemistry 1993, 32, 7832.
36. Tam J.P., Heath W.F., Merrifield R.B. J. Am. Chem. Soc. 108:1986;5242.
37. The terms 'antiparallel' and 'parallel' RNA/DNA complement refer to the Watson-Crick alignment of oligomer A in the N→C direction with the RNA (DNA) in the 3′→5′ ('antiparallel') and 5′→3′ ('parallel') direction, respectively.
38. 5] is of 1/1 stoichiometry.
39. m of 30 °C. However, no cooperative transition was observed upon cooling the sample. Furthermore, subsequent re-heating did not reproduce the original transition curve, but merely resulted in a virtually monotonous increase in absorption.
40. m-values of 52 and 48°, respectively).