Figure 3.

Holliday junction-specific DNA binding by Rap. (A) Gel retardation assay showing binding of Rap 29K and Rap 17K to synthetic X junction. Reaction mixtures contained 0.4 ng of ³²P-labeled J3 DNA and various amounts of Rap protein in binding buffer incubated on ice for 15 min. Protein–DNA complexes were resolved by 4% PAGE in low ionic strength buffer. Lanes b–e and g–j contained Rap protein at 6.25, 12.5, 25, and 50 nM. (B) Gel retardation assay with Rap 29K and Rap 17K on linear duplex DNA. Reaction mixtures contained 0.3 ng of ³²P-labeled duplex DNA. Lanes l–o and q–t contained Rap protein at 6.25, 12.5, 25, and 50 nM. Concentrations of Rap 17K are approximate, as the molecular masses of the binding species are unknown.