Purification of in organello formaldehyde-fixed mtDNA–protein complexes. (A) Flow diagram of the formaldehyde crosslinking procedure. (B) Time course of in organello crosslinking. Mitochondria were treated for increasing lengths of time with 1% formaldehyde, quenched with glycine, and lysed with sarkosyl. The lysate was applied directly to CsCl gradients (RI = 1.37) and, after centrifugation, the distribution of mtDNA was determined by dot blots using a COXII probe. (C) Formaldehyde-dependent crosslinking of Abf2p to mtDNA. mtDNA, crosslinked for 16 h and prepared as described in A (▴), was separated from free (untreated) mtDNA (□) in CsCl gradients (RI = 1.365). In addition to the presence of free Abf2p at the top of the gradient (fractions 8–10), some Abf2p cosediments with mtDNA (peak = fraction 3) after formaldehyde treatment and is released by a 30-min heat treatment, but not by SDS alone or SDS and 0.5 min heating (Inset).