Cleavage of a RNA analog containing uridine by a bifunctional dinuclear Zn(II) catalyst

• Published in: Journal of inorganic biochemistry 2009, Vol.103 (1), p.64-71
• Main Authors: Rossiter, Clifford S., Mathews, Ryan A., del Mundo, Imee Marie A., Morrow, Janet R.
• Format: Article
• Language: English
• Subjects: Catalysis; Cleavage of RNA; Kinetics; Ligands; Organometallic Compounds - chemical synthesis; Organometallic Compounds - chemistry; RNA - chemistry; Uridine - chemistry; Zinc - chemistry; Zinc complexes
• ISSN: 0162-0134; 1873-3344
• DOI: 10.1016/j.jinorgbio.2008.09.004

The macrocyclic ligand, 1,4-bis((1-oxa-4,7,10-triazacyclododecan-7-yl)methyl)benzene ( L1) is prepared. L1 binds two Zn(II) ions at neutral pH to form Zn 2( L1) as studied by using pH-potentiometric titrations. Zn 2( L1) binds two uridines at pH 7.0, I = 0.100 M (NaCl) and the mononuclear analog Zn( L2) ( L2 = 1-oxa-4,7,10-triazacyclododecane) binds a single uridine; dissociation constants for both complexes are in the millimolar range. Both complexes promote the cleavage of a simple RNA analog lacking a nucleobase ( HpPNP = 2-hydroxypropyl-4-nitrophenylphosphate), and a uridine containing RNA analog UpPNP (uridine-3′-4-nitrophenylphosphate). Plots of the first-order rate constant for cleavage of HpPNP as a function of Zn( L2) concentration from 0.5 mM to 20.0 mM are linear, consistent with weak complexation to substrate K d > 20 mM. In contrast, first-order rate constants for cleavage of UpPNP by Zn( L2) or Zn 2( L1) over similar concentration ranges exhibit a downward curvature, consistent with the formation of a complex between catalyst and UpPNP. Comparison of second-order rate constants ( k 2 = k cat/ K d) shows that the dinuclear complex Zn 2( L1) is a better catalyst than Zn( L2) for both HpPNP and UpPNP cleavage.