Fig. 3. Efficient ligation of a nick in a nucleosome. Nucleosomes were reconstituted with the 218 bp substrate containing three nicks and treated with human DNA ligase I as described in Materials and methods. Labeled reactants and products from the nucleosome (Nuc) or the free DNA (FD) were isolated from a 0.7% agarose gel and analyzed on a 6% sequencing gel. Lanes 1–5 and 6–10 contain ligation products from free DNA or nucleosomes generated after 0, 5, 10, 30 and 60 min, respectively. Oligonucleotides in the original substrate are shown in the schematic below the gel and the products of ligation at each of the three labeled sites (circles, schematic) are indicated alongside the gel.