O2-and 04-alkyldeoxythymidine are among the four O-alkyl base-modified derivatives produced by the reaction of N-nitroso alkylating agents with nucleic acids in vitro and in vivo. We find.that both O2-and 04-methyl-dTTP can substitute for dTTP in alternating poly(dA-dT)-primed DNA synthesis. Up to 22% of the pyrimidines in the newly synthesized polymer were found by HPLC analysis to be O-methyldeoxythymidine. Little polymer synthesis was observed in the absence of dTTP. However, the O-methyl-dTTPs did not inhibit polymerization of dATP and dTTP. Polymers containing O2_ or 04-methyldeoxythymidine were obtained in good yield, retaining the secondary structure of alternating poly(dA-dT). This was shown by the data for thermal transition under different conditions. In contrast, poly(dA-dT)-poly(dA-dT) methylated or ethylated to less than 4% total modification by alkylnitrosoureas had a distinctly less stable structure. Neither O2-nor 04-methyldeoxythymidine can form more than one hydrogen bond with adenosine. The unchanged secondary structure of polymers containing these modified thymidines indicates that stacking interactions must play a major role in helix stabilization. O-Alkyldeoxythymidine may be formed by N-nitroso carcinogens that react intracellularly. We have shown that the triphosphates can be utilized by Escherichia coli DNA polymerase I as dTTP. The incorporated 04-methyl-dT causes misincorporation of G, both in transcription and synthesis. When 02-methyldT is present, less, but definite, misincorporation results.The structural and mutagenic effects of many alkyl derivatives formed by carcinogens in vivo have been investigated in vitro in various ways. Substitution of a noncomplementary nucleotide has been used as a test of whether the modification causes transcriptional errors and whether it changes the ability to form a normal base pair (1-3). There is little information on the use of modified deoxynucleotide triphosphates (dNTPs) in primed DNA synthesis using DNA polymerases, particularly those with high fidelity resulting from their associated proofreading function (4). It has been reported that N6-methyl-dATP can replace dATP in Escherichia coli DNA polymerase I (pol I)-catalyzed synthesis of the alternating copolymer poly(dA-dT) (5). However, this derivative has the ability to form a normal A-T base pair because the methyl group is oriented anti to the WatsonCrick side when the triphosphate is incorporated. Similarly, 5-substituted pyrimidine dNTPs can also be used by pol I because the modification does not interfere with base pairing (6).Carcinogen-modified deoxynucleotides have been incorporated into random single-stranded polymers by using terminal deoxynucleotidyltransferase or specific modifications have been introduced. Such polymers were transcribed or replicated to ascertain whether misincorporations occur, but no data were given on the possible structural alterations in either the template or the resulting polymer. The derivatives studied in this way include 06-methyldeoxyguanosin...