208–12 NA linker DNA is accessible after assembly into supramolecular nucleoprotein complexes. (A) Aliquots of the intact 208–12 NA, 208–12 DNA, and trypsinized 208–12 NA complexes assembled at the indicated rSir3p were incubated with EcoRI at 37°C for 90 min. Undigested (−) and digested (+) samples were subsequently electrophoresed on a 1.0% agarose gel (1× TBE) as described in Materials and Methods. (B) Aliquots of the identical EcoRI-digested samples of intact 208–12 NA, 208–12 DNA, and trypsinized 208–12 NA from A were phenol-chloroform extracted to remove bound proteins and ethanol precipitated. Resuspended DNA was electrophoresed as in A. Lanes 2, 7, and 12 contain partial AvaI digests of pPol I 208–12, which generates a 208-bp DNA ladder. Arrowheads indicate the size of selected markers in base pairs.