Cleavage by calicheamicin gamma 1I of DNA in a nucleosome formed on the 5S RNA gene of Xenopus borealis

Abstract

The cleavage by calicheamicin gamma 1I (CLM gamma 1I) of a nucleosome formed on the 5S RNA gene of Xenopus borealis was studied in vitro as a first step toward the understanding of CLM gamma 1I-chromatin interactions within the cell. The drug does not cleave in the region of the dyad axis of the nucleosome. Outside of this region, double-stranded cleavage occurs with a periodicity of 10-11 bp. The sites of cleavage correspond to DNA sequences facing outward in the nucleosome. The drug shows some sequence preference of cleavage within these accessible sites. The predominant cleavage event within this nucleosome occurs at -1 helical turn from the dyad axis. This site constitutes a "hot spot" for CLM gamma 1I cleavage within the 5S nucleosome. We observe an overall footprinting effect whereby the drug preferentially cleaves DNA located outside the nucleosome core (analogous to the linker DNA of chromatin) as compared to cleavage within the nucleosome core. We discuss the importance of accessibility, structural deformations of DNA within the nucleosome, and steric constraints posed by sequence, in the recognition and cleavage of nucleosomal DNA by calicheamicin.