5'-peptidyl substituents allow a tuning of the affinity of oligodeoxyribonucleotides for RNA

Bioorganic and Medicinal Chemistry Letters

Volumn 8, Issue 18, 1998, Pages 2511-2516

  Sarracino, David A ^a   Steinberg, Joshua A ^a   Vergo, Maxwell T ^a   Woodworth, Graeme F ^a   Tetzlaff, Charles N ^a   Richert, Clemens ^a  

^a TUFTS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGODEOXYNUCLEOTIDE DERIVATIVE;

ARTICLE; DNA SEQUENCE; DRUG DNA INTERACTION; DRUG SYNTHESIS; RNA BINDING;

CIRCULAR DICHROISM; DIPEPTIDES; DNA; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; OSMOLAR CONCENTRATION; RNA; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 0032558529     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-894X(98)00449-1     Document Type: Article

References (34)

1. 1. Selected reviews on antisense therapy: (a) Uhlmann, E.; Peyman, A. Chem. Rev. 1990, 90, 544-584.
2. (b) Milligan, J. F.; Matteucci, M. D.; Martin, J. C. J. Med. Chem. 1993, 36, 1923-1937.
3. (c) Stein, C. A.; Cheng, Y.-C. Science 1993, 261, 1004-1012.
4. (d) DeMesmaeker, A.; Haener, R.; Martin, P; Moser, H. E. Acc. Chem. Res. 1995, 28, 366-374.
5. (e) Agrawal, S.; Iyer, R. P. Pharmacol. Ther. 1997, 76, 151-160.
6. 2. (a) Sanghvi, Y. S.; Cook, P. D., Eds.; Carbohydrate Modifications in Antisense Research; ACS Symposium Series: Washington, DC: 1994, pp 1-22.
7. (b) Hunziker, J.; Leumann, C. In Modern Synthetic Methods, Ernst, B.; Leumann, C., Eds.; Verlag Helvetica Chimica Acta: Basel, 1995; pp 333-417.
8. 3. Selected references: (a) Monia, B. P.; Lesnik, E. A.; Gonzalez, C.; Lima, W. F., McGee, D.; Guinosso, C. J.; Kawasaki, A. M.; Cook, P. D.; Freier, S. M. J. Biol. Chem. 1993, 168, 12514-14522.
9. (b) Manoharan, M.; Tivel, K. L.; Andrade, L. K.; Mohan, V.; Condon, T. P.; Bennett, C. F.; Dan Cook, P. Nucleosides Nucleotides 1995, 14, 969-973.
10. (c) Yu, D.; Iyer, R. P.; Shaw, D. R.; Lisziewicz, J.; Li, Y.; Jiang, Z. W.; Roskey, A.; Agrawal, S. Bioorg. Med. Chem. 1996, 4, 1685-1692.
11. (d) Szewczyk, J. W.; Baird, E. E.; Dervan, P. B. Angew. Chem. Int. Ed. Engl. 1996, 35, 1487-1489.
12. (e) Robles, J.; McLaughlin, L. W. J. Am. Chem. Soc. 1997, 119, 6014-6021.
13. 4. (a) Haralambidis, J.; Duncan, L.; Angus, K.; Tregear, G. W. Nucleic Acids Res. 1990, 18, 493-499.
14. (b) Arar, K.; Monsigny, M. Mayer, R. Tetrahedron Lett. 1993, 34, 8087-8090.
15. (c) Bongartz, J.-P.; Aubertin, A.-M.; Milhaud, P. G.; Lebleu, B. Nucleic Acids Res. 1994, 22, 4681-4688.
16. (d) Truffert, J.-C.; Lorthioir, O.; Asseline, U.; Thuong, N. T.; Brack, A. Tetrahedron Lett. 1994, 55, 2353-2356.
17. (e) Robles, J.; Pedroso, E.; Grandas, A. Nucleic Acids Res. 1995, 23, 4151-4161.
18. 5. (a) Bergmann, F.; Bannwarth, W. Tetrahedron Lett. 1995, 36, 1839-1842.
19. (b) Guibourdenche, C.; Seebach, D.; Natt, F. Helv. Chim. Acata 1997, 80, 1-13.
20. (c) Bruick, R. K.; Dawson, P. E.; Kent, S. B. H.; Usman, N.; Joyce, G. F. Chem. Biol. 1996, 3, 49-56.
21. 6. Tetzlaff, C. N.; Schwope, I.; Bleczinski, C. F.; Steinberg, J. A.; Richert, C. Tetrahedron Lett. 1998, 39, 4215-4218.
22. 3CN gradient/0.1 M TEAA). Tricationic peptidyl-DNA 5 required degradation of DNA failure products with calf spleen phosphodiesterase prior to HPLC purification to obtain the desired purity. Oligoribonucleotides 6 and 7 and RNA-DNA hybrids 12-14 were prepared using 2′-O-Fpmp phosphoramidite building blocks (Cruachem USA), and for the latter DNA phosphoramidite building blocks as given above. Chain assembly, deprotection, and purification were performed according to the supplier's recommendations (Cruachem Technical Bulletin No. 037R01). All oligonucleotides were characterized by MALDI-TOF mass spectrometry.
23. 8. Ho, W.; Steinbeck, C.; Richert, C., unpublished results.
24. 9. Saenger, W. Principles of Nucleic Acid Structure. Springer-Verlag: New York, 1983.
25. 10. Melting and cooling curves were measured at 260 nm in nuclease-free water with ammonium acetate buffer (Ambion, pH 6.0) at 0.1 mM EDTA over a temperature range of 5 to 65° C at a rate of 1 ° C per minute. Background absorbance changes, determined from the concurrent acquisition of a control sample containing buffer alone, were subtracted, and melting points were determined using Perkin Elmer UV TempLab® 1.2. Curves were smoothed with a 25 point moving average and melting points taken as the extrema of the 91 point first derivative.
26. 11. Zhu, T.; Wei, Z.; Tung, C-H.; Dickerhof, W. A.; Breslauer, K.; Georgopoulos, D. E.; Leibowitz, M. J.; Stein, S. Antisense Res. Dev. 1993, 3, 265-275.
27. 12. Wei, Z.; Tung, C.-H.; Zhu, T.; Dickerhof, W. A.; Breslauer, K. J.; Georgopoulos, D. E.; Leibowitz, M. J.; Stein, S. Nucleic Acids Res. 1996, 24, 655-661.
28. 13. Truffert, J. C.; Asseline, U.; Thuong, N. T.; Brack, A. Prof. Pept. Lett. 1995, 2, 419-424.
29. 14. Corey, D. J. Am. Chem. Soc. 1995, 117, 9373-9374.
30. 15. Schwope, I.; Bleczinski, C. F., Richert, C., unpublished results.
31. 16. (a) Orgel, L. E. J. Mol. Evol. 1989, 29, 465-474.
32. (b) Schimmel, P.; Henderson, B. S. Proc. Natl. Acad. Sci U.S.A. 1994, 97, 11283-11286.
33. (c) Di Giulio, M. J. Mol. Evol. 1997, 45, 571-578.
34. (d) Henderson, B. S.; Schimmel, P. Bioorg. Med. Chem. 1997, 5, 1071-1079.