Efficient RNA hydrolysis by lanthanide(III)–hydrogen peroxide combinations. Novel aggregates as the catalytic species[hair space]1

(Note: The full text of this document is currently only available in the PDF Version )

Jun Kamitani, Jun Sumaoka, Hiroyuki Asanuma and Makoto Komiyama


Abstract

Combinations of lanthanum(III) ion and hydrogen peroxide efficiently hydrolyze RNA under physiological conditions, because of a synergetic cooperation. The rate constant for the hydrolysis of adenylyl(3′-5′)adenosine at pH 7.2 and 30 °C is 7.7 × 10–2 min–1, when [LaIII]0 = 10 and [H2O2]0 = 100 mM. This value is 460 times as great as that for the ApA hydrolysis by LaIII alone (1.7 × 10–4 min–1). Hydrogen peroxide is inactive when used separately. A similar synergism operates between NdIII and H2O2. According to the kinetic analysis and the potentiometric titration, a trimeric aggregate of [La(O–O)3La] complex is responsible for the RNA hydrolysis. This result is in contrast with the previous proposal on the hydrolysis of bis(4-nitrophenyl)phosphate that monomeric species of [La(O–O)2La]2+ is the active species (B. K. Takasaki and J. Chin, J. Am. Chem. Soc., 1995, 117, 8582). The discrepancy is ascribed to the difference in the basicities of the leaving groups in the substrates.


References

  1. A preliminary communication: M. Komiyama, J. Kamitani, J. Sumaoka and H. Asanuma, Chem. Lett., 1996, 869 Search PubMed.
  2. Reviews: (a) R. Breslow, Acc. Chem. Res., 1995, 28, 146 CrossRef CAS; (b) E. Kimura and T. Koike, Adv. Inorg. Chem., 1997, 44, 229 CAS; (c) M. Komiyama, J. Biochem., 1995, 118, 665 CAS; (d) D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432 CrossRef.
  3. (a) M. Komiyama, K. Matsumura and Y. Matsumoto, J. Chem. Soc., Chem. Commun., 1992, 640 RSC; (b) J. R. Morrow, L. A. Buttrey, V. M. Shelton and K. A. Berback, J. Am. Chem. Soc., 1992, 114, 1903 CrossRef CAS; (c) K. Matsumura and M. Komiyama, J. Biochem., 1997, 122, 387 CAS.
  4. (a) R. Breslow and D.-L. Huang, Proc. Natl. Acad. Sci. USA, 1991, 88, 4080 CAS; (b) M. Irisawa and M. Komiyama, J. Biochem., 1995, 117, 465 CAS; (c) M. Yashiro, A. Ishikubo and M. Komiyama, J. Biochem., 1996, 120, 1067 CAS; (d) P. Hurst, B. K. Takasaki and J. Chin, J. Am. Chem. Soc., 1996, 118, 9982 CrossRef CAS.
  5. (a) J. J. Butzow and G. L. Eichhorn, Biochemistry, 1971, 10, 2019 CrossRef CAS; (b) J. Ciesiolka, T. Marciniec and W. J. Krzyzosiak, Eur. J. Biochem., 1989, 182, 445 CAS; (c) Y. Matsumoto and M. Komiyama, J. Chem. Soc., Chem. Commun., 1990, 1050 RSC; (d) S. Kuusela and H. Lönnberg, J. Phys. Org. Chem., 1993, 6, 347 CrossRef CAS; (e) F. Chu, J. Smith, V. M. Lynch and E. V. Anslyn, Inorg. Chem., 1995, 34, 5689 CrossRef CAS; (f) M. Yashiro, A. Ishikubo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1995, 1793 RSC; (g) M. Irisawa, N. Takeda and M. Komiyama, J. Chem. Soc., Chem. Commun., 1995, 1221 RSC; (h) A. Ishikubo, M. Yashiro and M. Komiyama, Nucleic Acids Symp. Ser., 1995, 34, 85 Search PubMed; (i) B. Linkletter and J. Chin, Angew. Chem., Int. Ed. Engl., 1995, 34, 472 CrossRef CAS; (j) S. Kuusela, A. Guzaev and H. Lönnberg, J. Chem. Soc., Perkin Trans. 2, 1996, 1895 RSC; (k) M. J. Young and J. Chin, J. Am. Chem. Soc., 1995, 117, 10 577 CrossRef CAS.
  6. Artificial enzymes for sequence-selective RNA scission were prepared by attaching lanthanide complexes to DNA oligomers: (a) K. Matsumura, M. Endo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1994, 2019 RSC; (b) D. Magda, R. A. Miller, J. L. Sessler and B. L. Iverson, J. Am. Chem. Soc., 1994, 116, 7439 CrossRef CAS; (c) J. Hall, D. Hüsken and R. Häner, Nucleic Acid Res., 1996, 24, 3522 Search PubMed.
  7. Non-enzymatic hydrolysis of DNA was also achieved by lanthanide ions: (a) Y. Matsumoto and M. Komiyama, Nucleic Acids Symp. Ser., 1992, 27, 33 Search PubMed; (b) M. Komiyama, K. Matsumura, K. Yonezawa and Y. Matsumoto, Chem. Express, 1993, 8, 85 Search PubMed; (c) T. Shiiba, K. Yonezawa, N. Takeda, Y. Matsumoto, M. Yashiro and M. Komiyama, J. Mol. Catal., 1993, 84, L21 CrossRef CAS; (d) B. K. Takasaki and J. Chin, J. Am. Chem. Soc., 1994, 116, 1121 CrossRef CAS; (e) M. Komiyama, T. Shiiba, T. Kodama, N. Takeda, J. Sumaoka and M. Yashiro, Chem. Lett., 1994, 1025 CAS; (f) M. Komiyama, N. Takeda, Y. Takahashi, H. Uchida, T. Shiiba, T. Kodama and M. Yashiro, J. Chem. Soc., Perkin Trans. 2, 1995, 269 RSC; (g) J. Rammo, R. Hettich, A. Roigk and H.-J. Schneider, J. Chem. Soc., Chem. Commun., 1996, 105 RSC; (h) S. Hashimoto and Y. Nakamura, J. Chem. Soc., Perkin Trans. 1, 1996, 2623 RSC.
  8. Hydrolysis of other phosphodiesters: (a) K. Matsumura and M. Komiyama, J. Inorg. Biochem., 1994, 55, 153 CrossRef CAS; (b) Ref. 2.
  9. Phosphotriester hydrolysis: R. W. Hay and N. Govan, J. Chem. Soc., Chem. Commun., 1990, 714 Search PubMed.
  10. B. K. Takasaki and J. Chin, J. Am. Chem. Soc., 1993, 115, 9337 CrossRef CAS; 1995, 117, 8582.
  11. The La(ClO4)3–H2O2 combination was used as the catalytic site in an enyme model: R. Breslow and B. Zhang, J. Am. Chem. Soc., 1994, 116, 7893 Search PubMed.
  12. Takasaki and Chin noted in ref. 10 that ‘the dinuclear LaIII complex is unstable and loses activity after about 30 min’. In our experiments, however, no significant deterioration of the catalyst was observed even after 100 min of pre-incubation. As noted in the Experimental section, fairly good pseudo-first-order kinetics was obtained. The reason for the discrepancy is not clear.
  13. The pseudo-first-order rate constant of the hydrolysis of authentic sample of A > p by La(CIO4)3(10 mM) and H2O2(100 mM) at pH 7 and 30 °C is > 0.3s–1.
  14. In ref. 10, Takasaki and Chin examined the hydrolysis of BNPP with rather small LaIII concentrations (0.6–1.6 mM). However, Breslow et al. (ref. 11) reexamined the reaction in larger LaIII concentrations (0.1–4 mM), and obtained a similar result to Takasaki and Chin. Therefore, notable differences in the kinetic features between RNA hydrolysis and BNPP hydrolysis really come from the differences in the leaving group of substrates, and not simply from the differences in the reaction conditions employed.
  15. The possibility that either (OH)2 La(O–O) La(OH)2 or (OH)La(O–O)2La(OH) is formed is ruled out by the following pH titration. When [LaIII]0/[H2O2]0= 1, two protons (per LaIII ion) are released to the aqueous phase. This is contrast with three-proton release at [LaIII]0∶[H2O2]0 ratio of 0.05. Thus, all the protons are from hydrogen peroxide, and not from water molecules.
  16. The titration profile in Fig. 4 is significantly different from that reported by Takasaki and Chin (ref. 10). According to these authors, two protons were released on completion of complex formation. Based on this result, it was claimed that [La(O–O)2La]2+ is formed in the mixtures, as expressed by eqn. (6)(K′= 1.4 × 10–23M).
     
    2La3++ 2H2O2⇌[La(O–O)2]2++ 4H+(6)
    In contrast, our titration has shown absolutely that [La(O–O)3 La], rather than [La(O–O)2 La]2+, is formed in the solutions, at least under the conditions used for the present RNA hydrolysis. Probably, [La(O–O)2 La]2+ further reacts with another H2 O2 molecule to form [La(O–O)3 La], since the concentrations of both the LaIII salt and H2O2 are sufficiently great. The experimental points in Fig. 4 are far from the theoretical line (the broken one), which was calculated by using the parameters reported by Takasaki and Chin.
    .
  17. This conclusion was obtained under the hypothesis that eqn. (6)(for the formation of the dinuclear complex [La(O–O)2 La]2+) is the sole equilibrium in the mixture (this hypothesis is ruled out by the potentiometric titration). As estimated by using K′= 1.4 × 10–23 M, the equilibrium lies mostly in the right-hand side, so that the increase in [LaIII]0 causes only a small increase in the concentration of the dinuclear complex.
  18. Tetrameric (or even greater) aggregates of [La(O–O)3 La], in addition to [(La(O–O)3 La)3], might be making some contributions in the catalysis.
  19. M. L. Bender, R. J. Bergeron and M. Komiyama, The Bioorganic Chemistry of Enzymatic Catalysis, Wiley-Interscience, New York, 1984, p. 133 Search PubMed.
  20. The rate-limiting step in RNA hydrolysis was discussed in detail in ref. 3c. The decomposition of the pentacoordinated intermediates would be (at least partially) rate-limiting, since the substitution of 5′-O atom in RNA by 5′-S (replacement of the 59-OH with 5′-SH as a better leaving group) causes 104–106-fold acceleration of the hydrolysis of the corresponding linkage.
  21. N. Sträter, W. N. Lipscomb, T. Klabunde and B. Krebs, Angew. Chem., Int. Ed. Engl., 1996, 35, 2024 CrossRef.
  22. (a) R. G. Clewley, R. S. Brown and H. Slebockatilk, Inorg. Chim. Acta, 1989, 157, 223 CrossRef; (b) Y. Chung, E. U. Akkaya, T. K. Venkatachalam and A. W. Czarnik, Tetrahedron Lett., 1990, 31, 5413 CrossRef CAS; (c) S. Hikichi, M. Tanaka, Y. Moro-oka and N. Kitajima, J. Chem. Soc., Chem. Commun., 1992, 814 RSC; (d) D. H. Vance and A. W. Czarnik, J. Am. Chem. Soc., 1993, 115, 12 165 CrossRef; (e) N. Takeda, M. Irisawa and M. Komiyama, J. Chem. Soc., Chem. Commun., 1994, 2773 RSC; (f) J. A. Connolly, M. Banaszczyk, R. C. Hynes and J. Chin, Inorg. Chem., 1994, 33, 665 CrossRef CAS; (g) T. Koike, M. Inoue, E. Kimura and M. Shiro, J. Am. Chem. Soc., 1996, 118, 3091 CrossRef CAS.
Click here to see how this site uses Cookies. View our privacy policy here.