FIG. 1.

Polyamide structures and binding sites. (A) Structures for polyamides ImPy-β-ImPy-γ-ImPy-β-ImPy-β-Dp (1), ImIm-β-ImIm-γ-PyPy-β-PyPy-β-Dp (2), and ImPy-β-PyIm-daba-PyIm-β-ImPy-β-Dp (3). Base sequence specificity depends on side-by-side pairing of Py and Im amino acids in the minor groove of DNA (6). Im-Py targets G·C base pairs and Py-Im targets C·G base pairs. Py-Py is degenerate and targets both A·T and T·A base pairs. The β-alanine-β-alanine pair also recognizes both A·T and T·A base pairs (42). Black and white circles, Im and Py rings, respectively; curved line, hairpin junction, which is formed with γ-aminobutyric acid or daba; diamonds, β-alanine; parenthesis with plus sign, Dp. The positive charge on the daba turn amino acid (3) is not shown. Me, methyl. (B) DNA sequences of the HIV-1 promoter constructs (from nucleotide positions −55 to +1, with respect to the transcription start site at +1), with polyamide binding sites at various distances upstream (U) or downstream (D) from the TATA box (boxed). Polyamide-binding models are shown.