Two different yeast two hybrid systems were used to examine interaction between the partition proteins SopA and SopB of F plasmid as well as their self association. In one system, the yeast Gal4 protein DNA binding domain (Gal4-BD) is fused to the N-terminus of the bait protein, and the Gal4 activation domain (Gal4-AD) is fused to the N-terminus of the target protein (1). In the other system, the target hybrid remains unchanged but E. coli LexA protein (LexA) is fused to the C-terminus of the bait protein (2). It is found that C-terminus part of SopB is involved in interaction with itself, as an N-terminal truncation of SopB, SopB-(120-323) remains capable of self association. For interaction between SopA, deletion of the N-terminal part weakens but does not abolish the interaction. Interaction between SopB and SopA protein was also detected, but only by the use of the second system. Full length SopB [SopB-(1-323)] or SopB-(1-180) lacking the C-terminal region beyond amino acid 180 can interact with full-length SopA-(1-383) protein. Copyright 1999 Academic Press.