Sequence-specific DNA-binding small molecules that can permeate human cells potentially could regulate transcription of specific genes. Multiple cellular DNA-binding transcription factors are required by HIV type 1 for RNA synthesis. Two pyrrole-imidazole polyamides were designed to bind DNA sequences immediately adjacent to binding sites for the transcription factors Ets-1, lymphoid-enhancer binding factor 1, and TATA-box binding protein. These synthetic ligands specifically inhibit DNA-binding of each transcription factor and HIV type 1 transcription in cell-free assays. When used in combination, the polyamides inhibit virus replication by >99% in isolated human peripheral blood lymphocytes, with no detectable cell toxicity. The ability of small molecules to target predetermined DNA sequences located within RNA polymerase II promoters suggests a general approach for regulation of gene expression, as well as a mechanism for the inhibition of viral replication.Simple rules have been developed to rationally control the sequence specificity of minor-groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids (1-6). DNA recognition depends on a code of side-by-side aromatic amino acid pairings in the minor groove. A pyrrole opposite an imidazole (Py͞Im pairing) targets a C⅐G bp whereas Im͞Py targets a G⅐C bp. A Py͞Py pair binds both A⅐T and T⅐A pairs. These compounds represent the only class of synthetic small molecules that can bind predetermined DNA sequences with affinities and specificities comparable to DNA-binding proteins (7). The DNA-binding activity of the 5S RNA genespecific transcription factor TFIIIA was inhibited by an eightring hairpin polyamide that bound within the recognition site of zinc finger four in the DNA minor groove. As a result, transcription of 5S RNA genes by RNA polymerase III was suppressed in vitro and in cultured Xenopus cells (8). The question arises whether polyamides can permeate human cells and specifically regulate genes transcribed by pol II (RNA polymerase II). As a first case study, we examined the ability of polyamides to inhibit HIV type 1 (HIV-1) transcription in cell-free assays and viral replication in human lymphocytes.The HIV-1 enhancer͞promoter element contains binding sites for the cell-encoded proteins upstream stimulatory factor, Ets-1, lymphoid-enhancer binding factor 1 (LEF-1) the nuclear factors NF-B, Sp1, and TATA-box binding protein (TBP) (Fig. 1 A) (9). To shut-down the promoter, polyamides were designed to target the transcription factors TBP, LEF-1, and Ets-1 simultaneously. TBP is indispensable for initiation of HIV-1 transcription, and LEF-1, considered to be an architectural protein, plays a central role in coordinating activities of multiple transcription factors (10). Both TBP and LEF-1 bind the minor groove of DNA and are likely to be inhibited by the minor groove binding polyamides. Ets-1 predominantly contacts the major groove in the center of its binding site, with additional flanking contacts that are possibly in the m...