Cleavage of an RNA analog by mononuclear zinc(II) macrocyclic complexes and metal ion and metallodrug interactions with deoxyribonucleic acids
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A series of five mononuclear Zn(II) macrocycle complexes were designed and synthesized for the catalyzed cleavage of the RNA analog, 2-hydroxylpropyl-4-nitrophenyl phosphate ( HpPNP ). The Zn(II) macrocylces include Zn(II) 1,4,7,10-tetraazacyclododecane ( Zn ( 1 )), Zn(II) 1-oxa-4,7,10-triazacyclododecane ( Zn ( 2 )), Zn(II) 1,5,9-triazacyclododecane ( Zn ( 3 )), Zn(II) 1-hydroxyethyl-1,4,7-triazacyclononane ( Zn ( 4 )) and Zn(II) N'-methyl-1-oxa-4,7,10-triazacyclododecane ( Zn ( 5 )). The second-order rate constants were measured for each of the catalysts as a function of pH, where a downward break is centered at the p K a for the zinc aqua ligand. The macrocyclic Zn(II) complexes were compared to the free ion, Zn(H 2 O) 6 2+ , and found to only moderately increase and decrease the transition state stabilization energy. Inhibition studies at pH = 7.6, involving a ground state phosphodiester mimic ( DEP ), a transition state mimic ( MP 2- ), a coordination probe ( Ox 2- ) and the nucleobase uridine ( U ) were used to examine various properties of the Zn(II) complexes. All of the Zn(II) macrocycles displayed weak binding to DEP , while Zn(4) exhibited the weakest binding to MP 2- and U , which is attributed to its inability to bind anions tightly at lower pH. Zn(1) displayed weak inhibition to the known bidentate chelator, Ox 2- , which suggests that it cannot accommodate as many substrate binding sites or aqua ligands. The pH-Inhibition profile of Zn(2) and MP 2- shows that weaker binding to the inhibitor is shown at higher pH because of competition with hydroxide anions, which suggests that the aqua form of the catalyst is in fact the active species in the phosphodiester catalysis of HpPNP . The interactions of metal ions and a metallodrug with various structures of DNA were studied. Lanthanide luminescence and lanthanide induced shifts of 1 H NMR were examined to determine the location of metal ion and metallodrug binding within DNA. The studies shows that weak, non-specific binding is observed for Eu(III) and Eu(CPFX) to single stranded pentamers containing the same nucleobase. Eu(III) and Ce(III) binding to long, double stranded duplex structures were much stronger and the ions remained hydrated. The steady-state luminescence excitation spectrum of Eu(CPFX) show that all of the Eu(CPFX) 2 is converted to the Eu(CPFX) species when interacting with the duplex DNA. The weakest interactions of Eu(CPFX) are observed with d(AATT) 6 . Binding within the Dickerson-Drew dodecamer (5'-GCGCAATTGCGC-3') show that Ce(CPFX) prefers binding in the dodecamer GCGC domains. Thymine hairpins were also studied, which display specific Eu(III) and Eu(CPFX) binding that is accompanied by partial dehydration of inner sphere aqua ligands. Based on the lanthanide induced shifts observed in the NMR spectrum, Ce(III) shows greater selectivity for the T3 and T4 hairpin loops, whereas the Ce(CPFX) displays binding to the 5'-GCGC-3' stem and weaker specific binding to the thymine hairpin. The ciprofloxacin ligand appears to block deeper penetration of the metallodrug complex into the hairpin structure. The Ce(CPFX) induces shifts of all the thymine residues of the T4 hairpin suggesting a less specific interaction takes place with the Ce(CPFX) than Ce(III).