DESIGN, SYNTHESIS, AND CHARACTERIZATION OF HIV-1 ENHANCER-BINDING POLYPEPTIDES DERIVED FROM BACTERIOPHAGE-434 REPRESSOR

We have designed and synthesized HIV-1 enhancer-binding polypeptides t hat were derived from bacterioph age 434 repressor. These peptides wer e 39-54 residues long and contained either the recognition helix or th e entire helix-turn-helix motif of the DNA-binding domain of 434 repre ssor. The dissociation constant of the complex formed between the stan dard peptide (R42) and a synthetic 70-bp HIV enhancer DNA was ca. 10(- 8) M. The specificity of the interaction of R42 with the two HIV enhan cers was demonstrated by competitive band shift assays, stepwise displ acement of the p50 subunit of transcription factor NF-kappa B from its two HIV enhancer binding sites, and DNase I footprinting; R42 seemed to protect best the two TTTCC sequences of the HIV enhancers against d igestion by DNase I. R42 analogues with mutated recognition helix had lower DNA binding specificity. It remains to be investigated whether o ur artificial HIV enhancer-binding polypeptides are active in vivo. (C ) Munksgaard 1995.