Treatment of human immunodeficiency virus type 1 (HIV-1)-infected patients with 3-azido-3-deoxythymidine (AZT) selects for mutant forms of viral reverse transcriptase (RT) with increased ability to remove chain-terminating nucleotides from blocked DNA chains. We tested various cell extracts for the presence of endogenous acceptor substrates for this reaction. ؉ or CD8 ؉ T cells, while PP i was present at 7 to 15 M. Under these conditions, the ATP-dependent reaction predominated, and excision by the AZT-resistant mutant RT was more efficient than wild type RT. Activated CD4 ؉ or CD8 ؉ T cells contained 1.4 to 2.7 mM ATP and 55 to 79 M PP i . These cellular PP i concentrations are lower than previously reported; nonetheless, the PP i -dependent reaction predominated in extracts from activated T cells, and excision by mutant and wild-type RT occurred with similar efficiency. While PP i -dependent excision may contribute to AZT resistance in vivo, it is likely that selection of AZT-resistant mutants occurs primarily in an environment where the ATP-dependent reaction predominates.Human immunodeficiency virus type 1 (HIV-1) replication is inhibited by the incorporation of chain-terminating nucleotide analogs at the 3Ј end of the nascent DNA chain during reverse transcription. Viral replication in the presence of these drugs results in selection of resistance mutations in the viral sequences encoding reverse transcriptase (RT), the replicative enzyme for HIV. Mutations at six codons in RT (M41L, D67N, K70R, L210W, T215Y or -F, and K219Q) are commonly selected by the nucleoside inhibitor 3Ј-azido-3Ј-deoxythymidine (AZT) and have been shown to confer AZT resistance through an increased ability to remove the chain terminator after it has been incorporated into DNA (1, 29, 46). These mutations are also correlated with significant resistance to other chain-terminating nucleosides (33,34,47).Excision has been shown to occur by RT-catalyzed transfer of the chain-terminating residue to a variety of acceptor substrates in vitro by a reaction that is related to pyrophosphorolysis (1,5,16,29,31,42,43). The intracellular acceptor for this reaction is unknown, but likely candidates include nucleoside triphosphates and nucleoside diphosphates as well as inorganic pyrophosphate (PP i ).In this report, we show that cell extracts contain a mixture of acceptor substrates for the excision reaction. ATP or PP i predominates depending on the cell type and its activation status. For these experiments, it was necessary to avoid errors in the measurement of PP i levels in the extracts, which can be affected by a number of factors: the breakdown of unstable intracellular compounds to form PP i during the extraction procedure, contaminating platelets, and cellular enzymes that alter PP i levels during the extraction process. Results obtained with an optimized extraction procedure disagree with widely quoted values of 130 to 150 M for intracellular PP i concentration in unstimulated lymphocytes (3); our results are more in agreement with the dat...