Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides

Tetrahedron Letters

Volumn 45, Issue 11, 2004, Pages 2457-2461

  Berry, David A ^a   Jung, Kee Yong ^a   Wise, Dean S ^a   Sercel, Anthony D ^a   Pearson, William H ^a   Mackie, Hugh ^b   Randolph, John B ^b   Somers, Robert L ^b  

^a Berry and Associates Inc   (United States)

^b Glen Research Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

6 METHYL 3 (2 DEOXY BETA DEXTRO RIBOFURANOSYL) 3H PYRROLO[2,3 D]PYRIMIDIN 2 ONE; CYANOETHYL PHOSPHORAMIDITE; CYTIDINE; DEOXYCYTIDINE; OLIGONUCLEOTIDE; OLIGORIBONUCLEOTIDE; PHOSPHORAMIDIC ACID DERIVATIVE; PYRROLE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; AUTOMATION; FLUORESCENCE; FLUORESCENCE IN SITU HYBRIDIZATION; FLUORESCENCE MICROSCOPY; MEASUREMENT; SYNTHESIS;

EID: 1242338125     PISSN: 00404039     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tetlet.2004.01.108     Document Type: Article

References (59)

1. Hermanson G.T. Bioconjugate Techniques. 1996;San Diego, Academic. Ch. 8.
2. O'Donnell M.J., McLaughlin L.W. Hecht S.M. Bioorganic Chemistry: Nucleic Acids. 1996;216-243 Oxford University, New York.
3. Wojczewski C., Stolze K., Engels J.W. Synlett. 1999;1667-1678.
4. Beaucage S.L. Kool E.T. DNA and Aspects of Molecular Biology. Vol. 7:2002;153-249 Pergamon, Amsterdam.
5. Haughland R.P. Handbook of Fluorescent Probes and Research Products. 9th ed. 2002;Molecular Probes, Eugene, Oregon. Ch. 8.
6. Jameson D.M., Eccleston J.F. Brand L., Johnson M.L. Methods in Enzymology. Vol. 278:1997;363-390 Academic, San Diego.
7. Rist M.J., Marino J.P. Curr. Org. Chem. 6:2002;775-793.
8. ′. See: Ren R.X.-.F., Chaudhuri N.C., Paris P.L., Rumney S., Kool E.T. J. Am. Chem. Soc. 118:1996;7671-7678.
9. Strässler C., Davis N.E., Kool E.T. Helv. Chim. Acta. 82:1999;2160-2171.
10. Kool E.T. Acc. Chem. Res. 35:2002;936-943.
11. Coleman R.S., Madaras M.L. J. Org. Chem. 63:1998;5700-5703.
12. Ward D.C., Reich E., Stryer L. J. Biol. Chem. 244:1969;1228-1237.
13. Glen Research Corporation Catalog; http://www.glenres.com.
14. For the deoxyriboside phosphoramidite, see: Fujimoto J., Nuesca Z., Mazurek M., Sowers L.C. Nucleic Acids Res. 24:1996;754-759. and references cited therein.
15. For the riboside phosphoramidite, see: Doudna J.A., Szostak J.W., Rich A., Usman N. J. Org. Chem. 55:1990;5547-5549.
16. Leonard N.J. Chemtracts - Biochem. Mol. Biol. 3:1992;273-297.
17. Srivastava S.C., Raza S.K., Misra R. Nucleic Acids Res. 22:1994;1296-1304.
18. Hawkins M.E., Pfleiderer W., Jungmann O., Balis F.M. Anal. Biochem. 298:2001;231-240.
19. Charubala R., Maurinsh J., Rösler A., Melguizo M., Jungmann O., Gottlieb M., Lehbauer J., Hawkins M., Pfleiderer W. Nucleos. Nucleot. 17:1997;1369-1378.
20. Hawkins M.E., Pfleiderer W., Balis F.M., Porter D., Knutson J.R. Anal. Biochem. 244:1997;86-95.
21. Driscoll S.L., Hawkins M.E., Balis F.M., Pfleiderer W., Laws W.R. Biophys. J. 73:1997;3277-3286.
22. Hawkins M.E. Cell Biochem. Biophys. 34:2001;257-281.
23. Godde F., Toulmé J.-J., Moreau S. Biochemistry. 37:1988;13765-13775.
24. Wu P., Nordlund T.M., Gildea B., McLaughlin L.W. Biochemistry. 29:1990;6508-6514.
25. Gildea B., McLaughlin L.W. Nucleic Acids Res. 17:1989;2261-2281.
26. Godde F., Toulmé J.-.J., Moreau S. Nucleic Acids Res. 28:2000;2977-2985.
27. Lin K.-Y., Jones R.J., Matteucci M. J. Am. Chem. Soc. 117:1995;3873-3874.
28. Matteucci also reported a version of 13a / 14a wherein X represents a direct connection between the aryl rings, that is a benzo version of pyrrolo-dC 1a , which was found to be an effective substitute for dC. Fluorescence properties were not mentioned. See: Matteucci M.D., von Krosigk U. Tetrahedron Lett. 37:1996;5057-5060.
29. Wilhelmsson L.M., Holmén A., Lincoln P., Nielsen P.E., Nordén B. J. Am. Chem. Soc. 123:2001;2434-2435.
30. Adams C.J., Murray J.B., Arnold J.R.P., Stockley P.G. Tetrahedron Lett. 35:1994;1597-1600.
31. Syntheses of dF and F: Bergstrom D.E., Inoue H., Reddy P.A. J. Org. Chem. 47:1982;2174-2178.
32. Incorporation into a dodecamer and hybridization studies: Inoue H., Imura A., Ohtsuka E. Nucleic Acids Res. 13:1985;7119-7128.
33. Alternate synthesis of F: Whale R.F., Coe P.L., Walker R.T. Nucleos. Nucleot. 11:1992;1425-1442.
34. Staubli A.B., Dervan P.B. Nucleic Acids Res. 22:1994;2637-2642.
35. Durland R.H., Rao T.S., Jayaraman K., Revankar G.R. Bioconjugate Chem. 6:1995;278-282.
36. Inoue H., Imura A., Ohtsuka E. Nippon Kagaku Kaishi. 7:1987;1214-1220.
37. Woo J., Meyer R.B. Jr., Gamper H.B. Nucleic Acids Res. 24:1996;2470-2475. These authors refer to the furo[2,3-d]pyrimidin-2(3H)-ones as 'dF' and the 3H-pyrrolo[2,3-d]pyrimidin-2-ones as dP, in contrast to the nomenclature used originally by Inoue and adopted in the current paper.
38. McGuigan and co-workers have examined the anitiviral properties of nucleosides bearing both furo[2,3-d]pyrimidin-2(3H)-ones and 3H-pyrrolo[2,3-d]pyrimidin-2-ones, the latter made by the action of ammonia on the former: McGuigan C., Pathirana R.N., Jones G., Andrei G., Snoeck R., De Clercq E., Balzarini P. J. Antiviral Chem. Chemother. 11:2000;343-348.
39. Hydrazine can be used instead of ammonia, producing pyrimidopyridazinones. See: Loakes D., Brown D.M., Salisbury S.A., McDougall M.G., Neagu C., Nampalli S., Kumar S. Tetrahedron Lett. 44:2003;3387-3389.
40. A full paper has appeared since the submission of our manuscript: Loakes D., Brown D.M., Salisbury S.A., McDougall M.G., Neagu C., Nampalli S., Kumar S. Helv. Chim. Acta. 86:2003;1193-1204. This paper also includes the transformation of 25 to 1a in a fashion similar to our method.
41. Randolph, J. B., Somers, R. L. unpublished results.
42. Liu C., Martin C.T. J. Mol. Biol. 308:2001;465-475.
43. Liu C., Martin C.T. J. Biol. Chem. 277:2002;2725-2731.
44. ′-deoxyuridines, although others had employed similar palladium-catalyzed reactions to accomplish this transformation. See the following and references cited therein: Robins M.J., Barr P.J. Tetrahedron Lett. 22:1981;421-424.
45. Robins M.J., Barr P.J. J. Org. Chem. 48:1983;1854-1862.
46. De Clercq E., Descamps J., Balzarini J., Giziewicz J., Barr P.J., Robins M.J. J. Med. Chem. 26:1983;661-666.
47. See also: Hobbs F.W. Jr. J. Org. Chem. 54:1989;3420-3422.
48. Robins M.J., Vinayak R.S., Wood S.G. Tetrahedron Lett. 31:1990;3731-3734. Note: Compound 24 has been made by a slightly different route. See reference (c) above.
49. Sonogashira K., Tohoda Y., Hagihara N. Tetrahedron Lett. 1975;4467-4470.
50. For the first reports of this cyclization, see Ref. 30 above. For subsequent work, see Refs. [26,27b,31c], and: Crisp G.T., Flynn B.L. J. Org. Chem. 58:1993;6614-6619.
51. McGuigan C., Yarnold C.J., Jones G., Velázquez S., Barucki H., Brancale A., Andrei G., Snoeck R., De Clercq E., Balzarini J. J. Med. Chem. 42:1999;4479-4484.
52. McGuigan C., Barucki H., Blewett S., Carangio A., Erichsen J.T., Andrei G., Snoeck R., De Clercq E., Balzarini J. J. Med. Chem. 43:2000;4993-4997.
53. Base-promoted cyclizations of other 5-substituted uracils and uridines have also afforded furo[2,3-d]pyrimidin-2(3H)-ones: Bleackley R.C., Jones A.S., Walker R.T. Tetrahedron. 32:1976;2795-2797.
54. Kumar R., Knaus E.E., Wiebe L.I. J. Heterocycl. Chem. 28:1991;1917-1925.
55. Eger K., Jalalian M., Schmidt M. J. Heterocycl. Chem. 32:1995;211-218.
56. Kumar R., Wiebe L.I., Knaus E.E. Can. J. Chem. 74:1996;1609-1615.
57. ′-deoxycytidine (CuI, DMF, 120°C).
58. Pitsch S., Weiss P.A., Jenny L., Stutz A., Wu X. Helv. Chim. Acta. 84:2001;3773-3795.
59. Pitsch S., Weiss P.A. Beaucage S.L., Bergstrom D.E., Glick G.D., Jones R.A. Current Protocols in Nucleic Acid Chemistry. 2001;3.8.1-3.8.15 John Wiley & Sons, New York.