TABLE 1.

Summary of Rep protein and DNA characteristics as determined by EM^a

Binding group (fragment size)	Protein/DNA mass ratio	Binding characteristics
		% Specific binding	% Nonspecific binding	% Free DNA
2.7 kb	1:1	40	16	44
1.7 kb	1:1	48.4	11	40.6
953 bp	1:1	0	0	100

^aThe 2.66-kb ch-19 integration contain an RBE located directly in the center of the fragment, while the 1.7-kb fragment contains an RBE located 180 nucleotides from one end of the fragment; the 953-bp fragment does not contain any known RBE. “Specific” was distinguished from “nonspecific” as any protein complex with the correct location on the 2.66-kb fragment. The same approach to analysis was used for the 1.7-kb fragment. Since the 953-bp fragment does not contain any known RBE, all Rep complex bound to this fragment was defined as nonspecific binding. A total of 100 DNA molecules were counted for each fragment. Binding was reflected as a percentage of the number of DNA molecules that were bound by Rep.