Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides

The ability of DNA-binding proteins to recognize their cognate sites in chr omatin is restricted by the structure and dynamics of nucleosomal DNA, and by the translational and rotational positioning of the histone octamer. Her e, we use six different pyrrole-imidazole polyamides as sequence-specific m olecular probes for DNA accessibility in nucleosomes. We show that sites on nucleosomal DNA facing away from the histone octamer, or even partially fa cing the histone octamer, are fully accessible and that nucleosomes remain fully folded upon ligand binding. Poly amides only failed to bind where sit es are completely blocked by interactions with the histone octamer. Removal of the amino-terminal tails of either histone H3 or histone H4 allowed the se polyamides to bind. These results demonstrate that much of the DNA in th e nucleosome is freely accessible for molecular recognition in the minor gr oove, and also support a role for the amino-terminal tails of H3 and H4 in modulating accessibility of nucleosomal DNA. (C) 2001 Academic Press.