The antileukemic agent 6-thioguanine (TG) is thought to inhibit DNA synthesis as a result of its incorporation into DNA. In the present study we have examined the nature of this inhibition, using replication of SV40 viral DNA as a model system. Addition of TG to SV40-infected CV1P cells from 22 to 24 hr post infection causes a dose-dependent inhibition of viral DNA synthesis. This inhibition plateaus between 250 and 2500 microM TG, resulting in a maximum decrease of viral DNA synthesis of about 50%. Pulse-chase experiments showed no detectable slowing of elongation of nascent DNA chains, whereas measurement of the conversion of incorporated 3H-dThd into supercoiled viral DNA suggested that elongation might be slightly inhibited, but by no more than 20%. Since inhibition of elongation could not account for the total depression of DNA synthesis, we hypothesized that inhibition of initiation of DNA replication takes place. This hypothesis was tested by radioactively labeling newly synthesized viral DNA and then assessing the ability of these molecules to reenter the replicating pool by density labeling with bromodeoxyuridine. The fraction of TG-containing molecules able to re-initiate replication was decreased 15%, compared to control. This effect, which was dependent on the concentration of TG added to the medium, was closely correlated to the extent of TG incorporation into the viral genome. We concluded that a portion of SV40 viral DNA synthesis inhibited by TG is due to an effect on initiation, and hypothesized that this effect may be caused by the substitution of TG for guanine in critical recognition sequences at the origin of replication. We proceeded to test this hypothesis by constructing SV40 origin sequences containing TG and then measuring their ability to bind T-antigen in vitro. The necessary deoxynucleoside triphosphate, TdGTP, was obtained by chemical phosphorylation of thiodeoxyguanosine. In order to selectively place TG within the desired region, a plasmid containing the T-antigen binding sequences was linearized so as to place these sequences at one end of the molecule, and then digested briefly with exonuclease III. The excised strand was resynthesized by use of the Klenow fragment of DNA polymerase I along with various nucleotide mixtures. Although resynthesis with mixtures containing TdGTP in place of dGTP was impeded somewhat, it was possible to achieve complete resynthesis with this analog.(ABSTRACT TRUNCATED AT 400 WORDS)