A clonal cell line (56-42) that was stably and exclusively resistant to the toxic effects of the antileukemic agent 5-aza-2'-deoxycytidine (5-aza-CdR) was derived from C3H 10T1/2 C18 cells after multiple treatments with 5-aza-CdR. The 50% lethal dose of 5-aza-CdR for these cells was 1.3 ,uM, which was 15-fold greater than that for the parental cells. Cell line 56-42 was slightly cross-resistant to the ribo-analog 5-azacytidine, but was sensitive to the nucleoside analog 1-4-D-arabinofuranosylcytosine and to colcemid. Both parental and resistant cell lines incorporated equimolar amounts of 5-aza-CdR into DNA. Resistance was therefore not due to decreased activation, increased detoxification, or reduced incorporation of the drug. The overall level of cytosine methylation in the resistant cione was 80% lower than the level in the sensitive cells. Therefore, the potential number of hemimethylated sites created by the incorporation of equivalent amounts of 5-aza-CdR into the DNA of the two cell types was much greater in the sensitive cells. Furthermore, 5-azacytosine-substituted DNA from the sensitive cells bound 100% more nuclear protein in the form of highly stable complexes. The incorporation of 5-azg-CdR opposite methylated cytosine residues in DNA of the sensitive cells thus resulted in increased nuclear protein binding -at hemimethylated sites. This relative increase in tight-binding protein complexes was shown to occur in livlng cells and may well disrupt replication and transcription and instigate cell death. The differential binding of proteins to hypomethylated, azacytosine-containing DNA may thus mediate a novel mechanism of drug resistance.The methylation of specific cytosine residues in DNA is thought to play a role in the transcriptional regulation of certain genes in eucaryotic cells (3,4,15,25). The deoxycytidine analog 5-aza-2'-deoxycytidine (5-aza-CdR) has been widely used as an inducer of suppressed genetic information (13,14,16). The analog is thought to act by incorporating into DNA (5) where it inhibits the postreplicative methylation of cytosine residues (10, 30). The resulting hypomethylation of the genome has been associated with the activation of certain genes (11, 14).5-Aza-CdR is also an effective antileukemic agent in both humans (36) and rmice (23,28,34). The antineoplastic action of the drug is related to its incorporation into DNA (31) and may be mediated through its ability to inhibit DNA methylation (33, 37). In contrast to our present understanding of the mechanisms of 5-aza-CdR-induced gene activation, virtually nothing is known about the mechanisms of drug cytotoxicity. The elucidation of such a mechanism is especially itnportant since the development of resistance to 5-aza-CdR is a major problem in the treatment of leukemias (32).We previously derived a series of cell lines that were resistant to 5-aza-CdR and reported the initial characterization of these cells (12). In this study, we isolated clones from a mass culture of 5-aza-CdR-resistant cells and characterized the mode of ...