Uridine Binding by Zn(II) Macrocyclic Complexes:  Diversion of RNA Cleavage Catalysts

Abstract

Zn(II) complexes of 1-oxa-4,7,10-triazacyclododecane (12[ane]N3O), 1,5,9-triazacyclododecane (12[ane]N3), and 1-hydroxyethyl-1,4,7-triazacyclononane (9[ane]N3OH) promote cleavage of the RNA analogue, 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) at pH 8.0, I=0.10 M (NaCl), 25 degrees C with second-order rate constants of 8.9x10(-3), 9.0x10(-3), and 3.3x10(-3) M-1 s-1, respectively. Cleavage of HpPNP by these catalysts is inhibited by uridine with inhibition constants (Ki) of 1.2, 0.46, and 45 mM, respectively, under these conditions. Binding constants derived from these inhibition constants are 2-200-fold larger than those for binding of related Zn(II) complexes to phosphate diesters under similar conditions, suggesting that uridine sequences in RNA will inhibit Zn(II)-catalyzed cleavage by competing with phosphate diester binding sites. Further studies are carried out that utilize pH-potentiometric titrations to monitor uridine binding to five Zn(II) macrocyclic complexes in aqueous solution at 25 degrees C, I=0.10 M (NaCl). The data are consistent with binding of the Zn(II) complexes to the N3-deprotonated form of uridine to give log KU.-values of 5.29, 4.57, 4.56, 3.47, and 2.65 for the Zn(II) complexes of 12[ane]N3, 12[ane]N4, 12[ane]N3O, 15[ane]N3O2, and 9[ane]N3OH, respectively (12[ane]N4=1,4,7,10-tetraazacyclododecane, 15[ane]N3O2=1,4-dioxa-7,10,13-triazacyclopentadecane). For the five Zn(II) complexes studied, there is a linear relationship between uridine anion binding constants and hydroxide binding constants.

Cleavage of an RNA analog by Zn(II) macrocyclic catalysts appended with a methyl or an acridine group

“…We have recently shown that the magnitude of the uridine anion binding constant correlates strongly to the hydroxide binding constant for a series of structurally distinct Zn(II) macrocyclic complexes. This suggests that the Zn(II) anion interaction dominates and that hydrogen bonding is not an important contribution in recognition [19]. Consistent with this correlation, Zn (2) and Zn(3) have similar hydroxide binding constants and similar uridine binding constants.…”

“…A characteristic property of the Zn(3) complex is its tight (millimolar) binding to uridine nucleobases through interaction with the N3 of uridine [19,47]. This interaction competes with binding of the catalyst to the phosphate ester and leads to inhibition of catalysis.…”

“…Both Zn(2) and Zn(3) bind to uridine with millimolar affinity. Inhibition constants for uridine (K i ) are a measure of binding affinity and are 1.5 mM with I = 0.100 M (NaNO 3 ) and K i = 1.2 mM, I = 0.100 (NaCl) at pH 8.0 [19], respectively, for the two Zn(II) complexes. This shows that the methyl group in Zn(2) does not markedly affect binding of the complex to uridine and that alkylated macrocyclic complexes will retain this recognition property.…”

“…Efforts to design structure specific cleaving agents based on Zn(II) complexes are complicated by the nucleoside binding properties of the macrocyclic complex even without attached recognition agents [19][20][21][22][23][24]. Zn(II) complexes bind to uridine or uridine-rich sequences, diverting the catalyst from interacting with the more weakly binding phosphate ester.…”

Template synthesis, spectroscopic studies, antimicrobial, nematicidal and pesticidal activities of chromium(III) macrocyclic complexes

“…7 Nowadays interest is focused on the synthesis of macrocyclic complexes with potential medicinal applications, as contrast-enhancing agents in magnetic resonance imaging (MRI), 8 as N.M.R shift and relaxation reagents 9 and as RNA cleavage catalyst. 10,11 Macrocyclic complexes of transition metals exhibit antibacterial, 12 anticarcinogenic, 13 antifertility, 14 and antifungal 15 activities.…”