Efficient new ribozyme mimics: Direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts

Nucleic Acids Research

Volumn 29, Issue 10, 2001, Pages 2199-2204

  Putnam, William C ^a,c   Daniher, Andrew T ^a   Trawick, Bobby N ^a,d   Bashkin, James K ^a,b  

^a WASHINGTON UNIVERSITY   (United States)

^b PFIZER INC   (United States)

^c MIDWEST RESEARCH INSTITUTE   (United States)

^d MetaPhore Pharmaceuticals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1,10 PHENANTHROLINE; 2,9 DIMETHYL 1,10 PHENANTHROLINE; LIGAND; PYRIDINE DERIVATIVE; REAGENT; RIBOZYME; RNA;

ARTICLE; CATALYSIS; CATALYST; CONTROLLED STUDY; GENE SEQUENCE; MACROMOLECULE; MOLECULAR MIMICRY; MOLECULAR SIZE; PRIORITY JOURNAL; RNA CLEAVAGE;

EID: 0035873532     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.10.2199     Document Type: Article

References (41)

1. Dreyer, G.B. and Dervan, P.B. (1985) Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA Fe(II). Proc. Natl Acad. Sci. USA, 82, 968-972.
2. Dervan, .B. (1992) Reagents for the site-specific cleavage of magabase DNA. Nature, 359, 87-88.
3. Meijler, M.M, Zelenko, O. and Sigman, D.S. (1997) Chemical mechanism of DNA scission by (1,10-phenantholine)copper. Carbonyl oxygen of 5-methelenefuranone os derived from water. J. Am. Chem. Soc., 119, 1135-1136.
4. Sigman, D.S. (1986) Nuclease activity of 1,10-phenanthroline-copper ion. Acc. Chem Res., 19, 180-186.
5. Sigman, D.S., Mazumder, A. and Perrin, D.M. (1993) Chemical nucleases. Chem. Rev., 93, 2295-2316.
6. n+. J. Am. Chem. Soc., 109, 7548-7550.
7. Basile, L.A., Raphael, A.L. and Barton, J.K. (1987) Metal-activated hydrolytic cleavage of DNA. J. Am. Chem. Soc., 109, 7550.
8. Gallagher, J., Chen, C.B., Pan, C.Q., Perrin, D.M., Cho, Y.-M. and Sigman, D.S, (1996) Optimizing the targeted chemical nuclease activity of 1,10-phenanthroline-copper by ligand modification. Bioconj. Chem., 7,413-420.
9. Trawick, B.N., Daniher, A.T. and Bashkin, J.K. (1998) Inorganic mimics of ribonucleases and ribozymes: from random cleavage to sequence-specific chemistry to catalytic antisense drugs. Chem. Rev., 98, 939-960.
10. Bashkin, J.K., Xie, J., Daniher, A.T., Jenkins, L.A. and Yeh, G.C. (1996) Ribozyme mimics for catalytic antisense strategies. Nato Asi Ser. Ser. C, 479, 355-366.
11. Cech, T.R. (1988) Ribozymes and their medical implications. J. Am. Med. Assoc., 260, 3030-3034.
12. Cohen, J.S. (1989) Oligodeoxynucleotides: Antisense Inhibitors of Gene Expression. CRC Press, Boca Raton, FL.
13. Haner, R. and Hall, J. (1997) The sequence-specific cleavage of RNA by artificial chemical ribonucleases. Antisense Nucleic Acid Drug Dev., 7, 423-430.
14. Morrow, J.R., Buttrey, L.A., Shelton, V.M. and Berback, K.A. (1992) Efficient catalytic cleavage of RNA by lanthanide(III) macrocyclic complexes: toward synthetic nucleases for in vivo applications. J. Am. Chem. Soc., 114, 1903-1905.
15. Bashkin, J.K., Frolova, E.I. and Sampath. U. (1994) Sequence-specific cleavage of HIV mRNA by a ribozyme mimic. J. Am. Chem. Soc., 116, 5981-5982.
16. Matsumura, K., Endo, M. and Komiyama, M. (1994) Lanthanide complex-oligo-DNA hybrid for sequence-selective hydrolysis of RNA. J. Chem. Soc. Chem. Commun., 2019-2020.
17. Magda, D., Miller, R.A., Sessler, J.L. and Iverson, B.L. (1994) Site-specific hydrolysis of RNA by europium(III) texaphyrin conjugated to a synthetic oligodeoxyribonucleotide. J. Am. Chem. Soc., 116, 7439-7440.
18. Hall, J., Husken, D., Pieles, U., Moser, H.E. and Haener, R. (1994) Efficient sequence-specific cleavage of RNA using novel europium complexes conjugated to oligonucleotides. Chem. Biol., 1, 185-190.
19. Hovinen, J., Guzaev, A., Azhayeva, E., Azhayev, A. and Lönnberg, H. (1995) Imidazole tethered oligodeoxyribonucleotides: synthesis and RNA cleaving activity. J. Org. Chem., 60, 2205-2209.
20. Oivanen, M., Kuusela, S. and Lonnberg, H. (1998) Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by bronsted acids and bases. Chem. Rev., 98, 961-990.
21. Hall, J., Husken, D. and Haner, R. (1997) Sequence-specific cleavage of RNA using macrocyclic lanthanide complexes conjugated to oligonucleotides: a structure activity study. Nucl. Nucl., 16, 1357-1368.
22. Magda, D., Crofts, S., Lin, A., Miles, D., Wright, M. and SesslerJ.L. (1997) Synthesis and kinetic properties of ribozyme analogs prepared using phosphoramidite derivatives of dysprosium(III) texaphyrin. J. Am. Chem. Soc., 119, 2293-2294.
23. Baker, B.F., Lot, S.S., Kringel, J., Cheng-Floumoy, S., Villiet, P., Sasmor, H.M., Siwkowski, A.M., Chappel, L.L. and Morrow, J.M. (1999) Oligonucleotide-europium complex conjugate designed to cleave the 5′ cap structure of the ICAM-1 transcript potentiates antisense activity in cells. Nucleic Acids Res., 27, 1547-1551.
24. Reynolds, M.A., Beck, T.A., Say, P.B., Schwartz, D.A., Dwyer, B.P., Daily, W.J., Vaghefi, M.M., Metzler, M.D., Klem, R.E. and Arnold, L.J., Jr (1996) Antisense oligonucleotides containing an internal, non-nucleotide-based linker promote site-specific cleavage of RNA. Nucleic Acids Res., 24, 760-765.
25. Bashkin, J.K., Xie, J., Daniher, A.T., Sampath, U. and Kao, J.L.-F. (1996) Building blocks for ribozyme mimics: conjugates of terpyridine and bipyridine with nucleosides. J. Org. Chem., 61, 2314-2321.
26. Liu, S. and Hamilton, A.D. (1997) Catalysis of phosphodiester transesterification by Cu(II)-terpyridine tomplexes with peripheral pendent base groups: implications for the mechanism. Tet. Lett., 38, 1107-1110.
27. 11 complex. Angew. Chem. Int. Ed. Engl., 34, 472-474.
28. Stern, M.K., Bashkin, J.K. and Sall, E.D. (1990) Hydrolysis of RNA by transition metal complexes. J. Am. Chem. Soc., 112, 5357.
29. Modak, A.S., Gard, J.K., Merriman, M.C., Winkeler, K.A., Bashkin, J.K. and Stern, M.K. (1991) Toward chemical ribonucleases. 2. Synthesis and characterization of nucleoside-bipyridine conjugates; hydrolytic cleavage of RNA by their copper(II) complexes. J. Am. Chem. Soc., 113, 283.
30. Jenkins, L.A., Bashkin, J.K., Pennock, J.D., Florian, J. and Warshel, A. (1999) Catalytic hydrolysis of adenosine 2′,3′-cyclic monophosphate by Cu(II)terpyridine. Inorg. Chem., 38, 3215-3222.
31. Jenkins, L.A., Bashkin, J.K. and Autry, M.E. (1996) The embedded ribonucleotide assay: a chimeric substrate for studying cleavage of RNA by transesterification. J. Am. Chem. Soc., 118, 6822-6825.
32. Jenkins, L.J. and Bashkin, J.K. (1997) Transesterification of RNA by Cu(II) terpyridine. Inorg. Chim. Acta, 263, 49-52.
33. Daniher, A.T. and Bashkin, J.K. (1998) Precise control of RNA cleavage by ribozyme mimics. Chem. Commun., 1077-1078.
34. Fukui, K., Morimoto, M., Segawa, H., Tanaka, K. and Shimidzu, T. (1996) Synthesis and properties of an oligonucleotide modified with an acridine derivative at the artificial abasic site. Bioconj. Chem., 7, 349-355.
35. Lecompte, J.-P., De Mesmaeker, A.K., Demeunynck, M. and Lhomme, J. (1993) Synthesis and characterization of a new DNA-binding bifunctional ruthenium(II) complex. J. Chem. Soc. Faraday Trans., 89, 3261-3269.
36. Smith, G.F. and Cagle, F.W. (1947) Improved synthesis of 5-nitro-1,10-phenanthroline. J. Org. Chem., 12, 781-784.
37. Dalcanale, E. and Mantanari, F. (1986) Selective oxidation of aldehydes to carboxylic acids with sodium chlorite-hydrogen peroxide. J. Org. Chem., 51, 567-569.
38. Constable, E.C. and Ward, M.D. (1990) Synthesis and coordination behavior of 6′,6″-bis(2-pyridyl)-2,2′:4,4″:2″,2‴- quaterpyridine; 'back-to-back' 2,2′:6′,2″-terpyridine. J. Chem. Soc. Dalton Trans., 1405-1409.
39. Putnam, W.C. and Bashkin, J.K. (2000) De novo synthesis of artificial ribonucleases with benign metal catalysts. Chem Comm., 9, 767-768.
40. Kierzek, R. (1992) Nonenzymic hydrolysis of oligoribonucleotides, Nucleic Acids Res., 20, 5079-5084.
41. Kierzek, R. (1992) Hydrolysis of oligoribonucleotides: influence of sequence and length. Nucleic Acids Res., 20, 5073-5077.