Structure and nuclease activity of simple dinuclear metal complexes: Quantitative dissection of the role of metal ions

Accounts of Chemical Research

Volumn 32, Issue 6, 1999, Pages 485-493

  Williams, Nicholas H ^a   Takasaki, Bryan ^a   Wall, Mark ^a   Chin, Jik ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CERIUM; COBALT COMPLEX; COPPER ION; DNA; HYDROXIDE; LANTHANUM; MAGNESIUM ION; METAL COMPLEX; METAL ION; ORGANOPHOSPHATE; PEROXIDE; PHOSPHINIC ACID DERIVATIVE; RNA;

ARTICLE; CATALYSIS; CATALYST; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DNA CLEAVAGE; EPOXIDATION; ESTERIFICATION; HALF LIFE TIME; HYDROLYSIS; RNA CLEAVAGE; X RAY CRYSTALLOGRAPHY;

EID: 0032839614     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar9500877     Document Type: Article

References (50)

1. DeRose, V. J.; Liu, K. E.; Lippard, S. J.; Hoffman, B. M. Investigation of the dinuclear Fe center of methane monooxygenase by advanced paramagnetic resonance techniques on the geometry of dmso binding. J. Am. Chem. Soc. 1996, 118, 121.
2. (a) Sträter, N.; Lipscomb, W. N.; Klabunde, T.; Krebs, B. Two-metal catalysis in enzymatic acyl-and phosphoryl-transfer reactions. Angew. Chem., Int. Ed. Engl. 1996, 35, 2024.
3. (b) Wilcox, D. E. Binuclear metallohydrolases.Chem. Rev. 1996, 96, 2435. In the case of RNase H, there is some controversy as to whether it is a mononuclear or a dinuclear metalloenzyme: Black, C. B.; Cowan, J. A. Magnesium activation of ribonuclease-H - evidence for one catalytic metal-ion. Inorg. Chem. 1994, 33, 5805.
4. (b) Wilcox, D. E. Binuclear metallohydrolases.Chem. Rev. 1996, 96, 2435. In the case of RNase H, there is some controversy as to whether it is a mononuclear or a dinuclear metalloenzyme: Black, C. B.; Cowan, J. A. Magnesium activation of ribonuclease-H - evidence for one catalytic metal-ion. Inorg. Chem. 1994, 33, 5805.
5. Pratviel, G.; Bernadou, J.; Meunier, B.: DNA and RNA cleavage by metal complexes. Adv. Inorg. Chem. 1997, 45, 251.
6. Chin, J.: Developing artificial hydrolytic metalloenzymes by a unified mechanistic approach. Acc. Chem. Res. 1991, 24, 145.
7. Perreault, D. M.; Anslyn, E. V. Unifying the current data on the mechanism of cleavage - transesterification of RNA. Angew. Chem., Int. Ed. Engl. 1997, 36, 432 and references therein.
8. Järvinen, P.; Oivanen, M.; Lönnberg, H. Interconversion and phosphoester hydrolysis of 2′,5′-dinucleoside and 3′, 5′-dinucleoside monophosphates-kinetics and mechanisms. J. Org. Chem. 1991, 56, 5396.
9. a of the 2′-hydroxyl group were independently extrapolated to 25 °C.
10. Westheimer, F. H. Why nature chose phosphates. Science 1987, 235, 1173.
11. (a) Davis, A. M.; Hall, A. D.; Williams, A. Charge description of bse-catalyzed alcoholysis of aryl phosphodiesters: a ribonuclease model. J. Am. Chem. Soc. 1988, 110, 5105.
12. (b) Usher, D. A.; Richardson, D. I.; Oakenfull, D. G. Models of ribonuclease action II. Specific acid, specific base and neutral pathways for hydrolysis of a nucleotide diester analogue. J. Am. Chem. Soc. 1969, 92, 4699.
13. Rate constants for 1 are as determined by Cheung, W. M. Sc. Thesis, Department of Chemistry, McGill University, Canada.
14. Guthrie, J. P. Hydration and dehydration of phosphoric acid derivatives: Free energies of formation of the pentacoordinate intermediates for phosphate ester hydrolysis and of monomeric metaphosphate. J. Am. Chem. Soc. 1977, 99, 3991.
15. A significantly shorter half-life had been proposed but subsequently retracted. Wolfenden, R.; Ridgway, C.; Young, G. Spontaneous Hydrolysis of Ionized Phosphate Monoesters and Diesters and the Proficiencies of Phosphatases and Phosphodiesterases as Catalysts. J. Am. Chem. Soc. 1998, 120, 833.
16. Molenveld, P.; Kapsabelis, S.; Engbersen, J. F. J.; Reinhoudt, D. N. Highly efficient phosphate diester transesterification by a calix[4]arene-based dinuclear zinc(II) catalyst. J. Am. Chem. Soc. 1997, 119, 2948 and references therein.
17. Fife, T. H.; Przystas, T. Effects of divalent metal ions on the hydrolysis of esters of 2-(hydroxyethyl)-picolinic acid. J. Am. Chem. Soc. 1982, 104, 2251.
18. (a) Jou, R.; Cowan, J. A. Ribonuclease-H activation by inert transition-metal complexes-mechanistic probes for metallocofactors-insights on the metallobiochemistry of divalent magnesium-ion. J. Am. Chem. Soc. 1991, 113, 6685.
19. (b) Yeh, G. C.; Beatty, A. M.; Bashkin, J. K.: Synthesis and characterization of cobalt-cage complexes with pendant phenol groups. Inorg. Chem. 1996, 35, 3828.
20. Williams, N. H.; Chin, J. Metal-ion catalyzed phosphate diester transesterification: quantifying double Lewis-acid activation. J. Chem. Soc., Chem. Commun. 1996, 131.
21. Williams, N. H.; Cheung, W.; Chin, J. Reactivity of phosphate diesters doubly coordinated to a dinuclear cobalt(III) complex: dependence of the reactivity on the basicity of the leaving group. J. Am. Chem. Soc. 1998, 120, 8079.
22. Hendry, P.; Sargeson, A. M. Base hydrolysis of the penta-ammine(trimethyl phosphate)iridium(iii) ion. J. Chem. Soc., Chem. Commun. 1984, 164. Metal ions such as Mg(II), Ca(II), or Zn(II) that are commonly found in living organisms are poorer Lewis acids than Co(III) and are thus expected to provide somewhat less of a rate acceleration as Lewis acid activators.
23. Hendry, P.; Sargeson, A. M. Reactivity of coordinated phosphate esters: pentaaminecobalt(III) complexes. Inorg. Chem. 1990, 29, 92.
24. 31 to act as a general base catalyst here. Jencks, W. P. General Acid-Base Catalysis of Complex reactions in Water. Chem. Rev. 1972, 72, 705.
25. Wahnon, D.; Lebuis, A.-M.; Chin, J. Hydrolysis of a phosphate diester coordinated to a dinuclear cbalt-(III) complex: a novel mechanism. Angew. Chem., Int. Ed. Engl. 1995, 34, 2412.
26. Connolly, J.; Kim, J. H.; Banaszczyk, M.; Drouin, M.; Chin, J. Factors affecting chelation of carboxylates to cis-diaqua Co(III) complexes. Inorg. Chem. 1995, 34, 1094.
27. Chin, J.; Banaszczyk, M. Highly efficient hydrolytic cleavage of adenosine-monophosphate resulting in a binuclear Co(III) complex with a novel doubly bidentate μ-4-phosphato bridge. J. Am. Chem. Soc. 1989, 111, 4103.
28. Connolly, J. A.; Banaszczyk, M.; Hynes, R. C.; Chin, J. Reactivity of a chelated phosphate ester. Inorg. Chem. 1994, 33, 665.
29. Linkletter, B.; Chin, J. Rapid hydrolysis of RNA with a Cu complex. Angew. Chem., Int. Ed. Engl. 1995, 34, 472.
30. Chin, J.; Banaszczyk, B.; Jubian, V.; Zou, X. Co(III) complex promoted hydrolysis of phosphate diesters. J. Am. Chem. Soc. 1989, 111, 186.
31. The phosphates in 11, 15, and 16 have been replaced with dimethyl phosphate, dibenzyl phosphate, and diphenyl phosphinate in 11′, 15′, and 16′, respectively. The bridging O-P-O bond angles in the three compounds are comparable (11′, 117.4°; 15′, 117.9°; 16′, 116.8°). For compound 16′, there are two bridging phosphinates in the original structure. The one in the front has been omitted in Figure 2 for clarity of view.
32. Wall, M.; Hynes, R. C.; Chin, J. Double Lewis acid activation in phosphate diester cleavage. Angew. Chem., Int. Ed. Engl. 1993, 32, 1633.
33. (a) Young, M. J.; Chin, J. Dinuclear copper(II) complex that hydrolyzes RNA. J. Am. Chem. Soc. 1995. 117, 10577.
34. (b) Young, M. J. Ph.D. Thesis, Department of Chemistry, McGill University, Canada, 1996.
35. It should be noted that intramolecular general base catalysts provide only moderate rate acceleration over intermolecular general base catalysts. Kirby, A. J. Effective molarities of intramolecular reactions. Adv. Phys. Org. Chem. 1980, 17, 183.
36. 3+ (triole) mit säure. Helv. Chim. Acta 1974, 57, 802.
37. Kim, J. H.; Chin, J. Dimethyl phosphate hydrolysis at neutral pH. J. Am. Chem. Soc. 1992, 114, 9792.
38. Young, M. J.; Wahnon, D.; Hynes, R. C.; Chin, J. Reactivity of copper(II) hydroxides and copper(II) alkoxides for cleaving an activated phosphate diester. J. Am. Chem. Soc. 1995, 117, 9441.
39. 2-) group transfer from an oxygen donor. J. Org. Chem. 1984, 49, 1200.
40. Steitz, T. A. A mechanism for all polymerases. Nature 1998, 391, 231.
41. Mechanism 24 has been proposed for a simple model system without any evidence. Yashiro, M.; Ishikubo, A.; Komiyama, M. Preparation and study of a dinuclear zinc(II) complex for the efficient hydrolysis of the phosphodiester linkage in a diribonucleotide. J. Chem. Soc., Chem. Commun. 1995, 1793.
42. Bracken, K.; Moss, R. A.; Ragunathan, K. G. Remarkably rapid cleavage of a model phosphodiester by Complexed Ceric Ions in aqueous micellar solutions. J. Am. Chem. Soc. 1997, 119, 9323 and references therein.
43. (a) Takasaki, B. K.; Chin, J. La(III)-hydraogen peroxide cooperativity in phosphate diester cleavage: a mechanistic study. J. Am. Chem. Soc. 1995, 117, 8582.
44. 3+ and hydrogen-peroxide. J. Am. Chem. Soc. 1994, 116, 7893.
45. Barnes, J. C.; Blyth, C. S.; Knowles, D. Sodium salts of the bis-μ-peroxo-hexacarbonatodicerate(IV) anion. Inorg. Chim. Acta 1987, 126, L3.
46. Takasaki, B. K. Ph.D. Thesis, Department of Chemistry, McGill University, Canada, 1995.
47. Hurst, P.; Takasaki, B. K.; Chin, J. Rapid cleavage of RNA with a La(III) dimer. J. Am. Chem. Soc. 1996, 118, 9982.
48. Structures other than 28 that have a metal-tohydroxide ratio of 2:5 are also possible.
49. (a) Takasaki, B. K.; Chin, J. Cleavage of the phosphate diester backbone of DNA with cerium(III) and molecular oxygen. J. Am. Chem. Soc. 1994, 116, 1121.
50. (b) Komiyama, M.; Matsumura, K.; Yonezawa, K.; Matsumoto, Y. Consecutive catalysis by cerium-(III) ion for complete hydrolysis of phosphodiester linkage in DNA. Chem. Express 1993, 8, 85.