Reactions containing 8.6 M nM.HhaI, Metarrestin 2.4 M [methyl-3H]AdoMet, and indicated amounts of 2P-ODN inhibitor were incubated with increasing concentrations of substrate. enzymatic target site are competitive inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases. We determined that the ternary complexes between the enzymes, 2-(1H)-pyrimidinone inhibitor, and the cofactor [6-12] and [10-12]. ZCyd is phosphorylated by uridine-cytidine kinase and can be incorporated into both RNA and DNA whereas ZdCyd, which is phosphorylated by deoxycytidine kinase, is only incorporated into DNA [13, 14]. Once incorporated into DNA, azanucleoside analogs can effectively deplete the Metarrestin cell of active enzyme by forming irreversible covalent adducts with DNA C5-MTases, resulting in global hypomethylation. Despite the initial success of these agents for treating sickle cell anemia, myelodysplastic syndrome, and a number of other cancers [15-20], there are serious treatment-associated side effects. These include myelotoxicity and DNA mutations due to incorporation of the nucleosides into genomic DNA [21], a potential factor in cancer recurrence. Zebularine [2-(1H) pyrimidinone riboside] is a highly stable cytidine analog that is significantly less toxic than ZdCyd (Figure 1). First identified as a bacteriostat [22], zebularine was later found to act as a transition state inhibitor of cytidine deaminase (CDA) [23-27]. Open in a separate window Figure 1 The structure of (A) cytidine (Cyd), and its analogs (B) 2-(1H)-pyrimidinone ribonucleoside (zebularine), (C) 5-azacytidine (ZCyd), and (D) 5-aza-2′-deoxycytidine (ZdCyd). R=ribose and dR=2′-deoxyribose. At high micromolar concentrations zebularine has been shown to inhibit mammalian DNA C5-MTases in cultured cells and mammalian tumors after prolonged exposure [28-30]. studies have demonstrated the formation of stable inhibitory complexes between the bacterial DNA C5-MTases M.HgaI and M.MspI and synthetic oligodeoxyribonucleotides (ODNs) with the 2-(1H) pyrimidinone (2P) replacing C in their recognition site [30, 31]. experiments revealed several logs difference in potency between ZdCyd and zebularine on mammalian DNA methylation [28, 29], but no published studies have directly compared the interactions between Dnmt1 and DNA containing the two analogs. Therefore, we sought to directly compare the potency and inhibitory mechanisms of DNA containing ZdCyt or 2P on Dnmt1. We synthesized small ODN inhibitors containing either ZdCyt or 2P in place of the target C study DNA C5-MTase inactivation. Our analysis included determination of the kinetics of inhibition, thermal stability of complexes, and rate of dissociation in the presence and absence of cofactors. Here, we report that ODNs containing 2P at the enzymatic target site (Figure 2) are competitive inhibitors of both prokaryotic (M.HhaI) and mammalian DNA C5-MTases (Dnmt1). Moreover, we determined that the ternary complexes between M.HhaI:2P-ODN:strain ER1727 containing the pUHE25HhaI plasmid (generously provided by Dr. S. Kumar, New England Biolabs) and purified as described previously [35] using a HiTrap Sepharose SP HP column (cation exchange, Amersham Biosciences, Piscataway, NJ). Purified recombinant Dnmt1 was isolated as described previously [36]. 2.3 Assays determining inhibitor potency The procedure for measuring the rate of inactivation for M.HhaI has been previously described in detail [34]. Briefly, reaction mixtures containing increasing concentrations of substrate (AMp:A’) were incubated at 37 C in the absence or presence of ODN inhibitor (Figure 2). Reactions were terminated after 5 min, a time point within the linear range of the assay. Incorporation of methyl-H3 into DNA was quantified by liquid scintillation counting [37, 38]. Each reaction was performed in duplicate. Error bars indicate standard error from the mean of three independent experiments. The Km and Vmax Metarrestin data were determined using Graph Pad 3.0 software. A Lineweaver-Burk plot of the resulting data was prepared to determine kI values. Dnmt1 inactivation reactions containing 0.4-0.6 M enzyme were pre-incubated with 1-80 M ODN inhibitor (Figure Rabbit Polyclonal to FCGR2A 2) for 0-4 min at 22 C in imidazole buffer (100 mM imidazole, pH 7.5, 20 mM EDTA) containing 1.3 M DM7 (substrate), 50 M AdoMet, and 0.1 mg/ml BSA. Duplicate 1 l aliquots were removed after specified times of pre-incubation and diluted with 49 l of assay mixture containing 0.2 mg/ml BSA, 1.2 M AdoMet, 0.1 g poly dI-dC:dIdC (~3.45M dinucleotide), and 0.8 M 3H-AdoMet (specific activity 3015.5 GBq/mmol) in imidazole buffer. The diluted reactions were incubated for an additional 60 min at 37 C to determine the amount of Dnmt1 activity remaining. Substrate methylation was quantified as described above. For each concentration of inhibitor, the amount of remaining enzymatic activity was plotted versus the time of pre-incubation. The t1/2, or time necessary for each concentration of inhibitor to reduce the total activity by one-half was calculated using a fourth order polynomial regression. The t1/2 value was then plotted versus the inverse of the concentration of inhibitor, where kinactivation = ln2/slope. The KI was extrapolated from the resulting graph, with kI = -1/x-intercept. 2.4.