Investigating Nucleosome Accessibility for MNase, FeII  Peplomycin, and Duocarmycin B2 by Using Capillary Electrophoresis.

Capillary electrophoresis, coupled with DNA 5' Texas Red labeling, was used to investigate the ability of MNase, FeII peplomycin, and duocarmycin B2 to access the nucleosome. Distinct accessibility patterns of these species to the nucleosome were observed. MNase was completely prevented from approaching the nucleosome core and exhibited a higher site specificity for targeting DNA sites located close to the core region. Intercalation of peplomycin in the nucleosomal core region was highly suppressed, but reaction sites located at the ends of the nucleosomal core remained accessible, which implied flexibility of the core DNA end. Duocarmycin B2 was able to enter and react in the core region, although its alkylating efficiency decreased significantly.