FIG. 3.

(A) Native gel analysis of native and tailless nucleosomes. Native histones (N), histones digested with clostripain to generate tailless tetramers (-tet) or tailless octamers (-oct) and histones digested with trypsin to generate fully tailless octamers (tryp) were reconstituted with the T7 transcription template DNA and purified by sucrose gradient ultracentrifugation. Individual positioning isomers were isolated by native gel purification. The resulting samples were analyzed by native gel electrophoresis. Approximately 100 ng of naked DNA or the different nucleosome preparations in sucrose loading buffer (10% sucrose in 5 mM NaCl and 0.5× TE) was run on a 5% acrylamide gel in 1/3× TBE at 10 V cm⁻¹ and exposed to a phosphorimager plate for analysis. Naked DNA (D) was included as a mobility reference. (B) Native gel analysis of native and trypsinized nucleosomes singly end labeled on the left or right 5′ end. Native and trypsinized histones were reconstituted with template DNA labeled on the left or right 5′ end for studies with exonuclease III and DNase I and were analyzed on a 5% polyacrylamide–1/3× TBE gel. Lanes contain naked DNA (D), native nucleosomes (N) and trypsinized nucleosomes (T); the end containing the label is designated below the lane labels.