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Volumn 126, Issue 13, 2004, Pages 4145-4156

Covalent Schiff Base Catalysis and Turnover by a DNAzyme: A M 2+-Independent AP-Endonuclease Mimic

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CONDENSATION; DNA; HYDROLYSIS;

EID: 1842607442     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja037625s     Document Type: Article
Times cited : (60)

References (135)
  • 52
    • 0000917638 scopus 로고    scopus 로고
    • Reviewed in: (a) Breaker, R. R. Chem. Rev. 1997, 97, 371-90.
    • (1997) Chem. Rev. , vol.97 , pp. 371-390
    • Breaker, R.R.1
  • 55
    • 1842461741 scopus 로고    scopus 로고
    • note
    • The distinction is perhaps a subtle one. Self-modifying sequences that have been selected for enhanced nucleophilicity have been described as "catalysts". If turnover is a desirable quality to be pursued in the development of a catalyst. then in some cases it can be "engineered" by divorcing the nucleophile from the catalytic domain to provide for a catalyzed bimolecular condensation between nucleophile and electrophile. Consequent to the engineering step that provides for turnover, the term "nucleophilic catalysis" loses pertinence because the nucleophile consequently resides on the newly appointed substrate and no longer on what had been the self-modifying strand. We would like to distinguish cases of enhanced nucleophilicity that result in irreversible self- modification from cases where a nucleophilic attack precedes a second critical bond making/breaking step and where the covalent adduct that forms is used to lower the activation energy in this second step. Although the issue of turnover is not addressed in this description, its relation to the definition of catalysis is generally considered integral.
  • 56
    • 1842461742 scopus 로고    scopus 로고
    • note
    • An exception to this statement would be a catalyst that used an unbound amino cofactor to promote a Mannich or Stork enamine reaction involving a resonance-stabilized anion but where the cofactor is released from the product and recycled (turnover).
  • 58
    • 1842566307 scopus 로고    scopus 로고
    • note
    • Although unexamined in ref 16c, the thioester of a self-acylating ribozyme will hydrolyze to regenerate free thiol and catalyze acyl transfer with turnover.
  • 91
    • 1842513906 scopus 로고    scopus 로고
    • note
    • Piperidine treatment confirmed 100% abasic site conversion on S2.
  • 92
    • 1842513932 scopus 로고    scopus 로고
    • note
    • -1 (0.1 M KCI. 0.05 M Hepes-KOH. 0.5 mM EDTA pH 7.4. extrapolated from 70 °C back lo 22 °C) measured by Lindahl and Andersson. ref 6. It is difficult to consider rate enhancements of two reactions that do not operate via the same mechanism.
  • 95
    • 0035906731 scopus 로고    scopus 로고
    • This assumes that there are no slow steps to achieving catalytically competent conformations. See: Russell, R.; Herschlag, D. J. Mol. Biol. 2001, 308, 839-51 for a nice treatment of these effects.
    • (2001) J. Mol. Biol. , vol.308 , pp. 839-51
    • Russell, R.1    Herschlag, D.2
  • 96
    • 1842618440 scopus 로고    scopus 로고
    • note
    • 3 trapping experiments would exclude this possibility.
  • 100
    • 1842566327 scopus 로고    scopus 로고
    • note
    • 3 inhibited the RNaseA-like reaction catalyzed by C1, presumably due to cyanoboranation of the imidazoles, of amines, or both.
  • 108
    • 1842618441 scopus 로고    scopus 로고
    • note
    • cat would be further diminished.
  • 126
    • 0028820909 scopus 로고
    • Koch, T.; Reymond, J.-L.; Lerner, R. A. J. Am. Chem. Soc. 1995, 117, 9383-7. provides an interesting exception where neither a divalent metal cation nor a Schiff base is observed.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 9383-9387
    • Koch, T.1    Reymond, J.-L.2    Lerner, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.