FIGURE 1.

Flap-out and flap-in nucleosome substrates. A, schematic of DNA oligonucleotides used to assemble the 154-bp flap-out and flap-in substrates. Substrates are based on the Xenopus 5S nucleosome positioning element. The length of the ligated oligos used to anneal each template are indicated in italics. The location of the flap, the EcoRV cleavage site, and predicted orientation of the flaps (right) are indicated. B, nucleosomes reconstituted on control (Con, no flap), flap-out (FO), and flap-in (FI) substrates were run on a 0.7% agarose nucleoprotein gel along with a 154-bp naked DNA control (DNA). C, flap-out and flap-in substrates labeled on either the top (flap) or bottom strands were run on a 5% polyacrylamide nucleoprotein gel. D, nucleosomes reconstituted on flap-out and flap-in templates were separated over sucrose gradients, and fractions were analyzed on 0.7% agarose nucleoprotein gels. Autoradiographs of the dried gels are shown.