FIG. 1.
INO80 preferentially binds to nucleosomes with extranucleosomal DNA. (A) The affinities of INO80 for end-positioned nucleosomes with various lengths of extranucleosomal DNA were measured by gel shift analysis on a 4% native PAGE with 1× TE. The binding reaction mixtures had 30 nM nucleosomes with end-labeled PCR DNA and increasing amounts of INO80 (2.5, 5, 10, 20, and 40 nM). These reaction mixtures did not contain any salmon sperm DNA. (B) The observed Kd values of INO80 for nucleosomes with different extranucleosomal DNA lengths was determined from the data shown in panel A and are plotted with respect to the length of extranucleosomal DNA. These data are from three independent binding titration experiments, and the standard deviations are shown.