Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. Journal Article uri icon



  • The ability of DNA-binding proteins to recognize their cognate sites in chromatin is restricted by the structure and dynamics of nucleosomal DNA, and by the translational and rotational positioning of the histone octamer. Here, we use six different pyrrole-imidazole polyamides as sequence-specific molecular probes for DNA accessibility in nucleosomes. We show that sites on nucleosomal DNA facing away from the histone octamer, or even partially facing the histone octamer, are fully accessible and that nucleosomes remain fully folded upon ligand binding. Polyamides only failed to bind where sites are completely blocked by interactions with the histone octamer. Removal of the amino-terminal tails of either histone H3 or histone H4 allowed these polyamides to bind. These results demonstrate that much of the DNA in the nucleosome is freely accessible for molecular recognition in the minor groove, and also support a role for the amino-terminal tails of H3 and H4 in modulating accessibility of nucleosomal DNA.

publication date

  • June 8, 2001

has subject area

Full Author List

  • Gottesfeld JM; Melander C; Suto RK; Raviol H; Luger K; Dervan PB

Other Profiles

Additional Document Info

start page

  • 615

end page

  • 629


  • 309


  • 3