P elements are a family of transposable elements found in Drosophila that move using a cut-and-paste mechanism and which encode a transposase protein that uses guanosine triphosphate (GTP) as a cofactor for transposition. Here, we use atomic force microscopy (AFM) to visualize the initial interaction of transposase protein with P element DNA. The transposase first binds to one of the two P element ends, in the presence or absence of GTP, prior to synapsis. In the absence of GTP these complexes remain stable but do not proceed to synapsis. In the presence of GTP or non-hydroyzable GTP analogs, synapsis happens rapidly, while DNA cleavage is slow. Both AFM and standard biochemical methods have been used to show that the P element transposase exists as a pre-formed tetramer that initially binds to either one of the two P element ends in the absence of GTP prior to synapsis. This initial single-end binding may explain some of the aberrant P element-induced rearrangements observed in vivo, such as hybrid end insertion (HEI). The allosteric effect of GTP in promoting synapsis may be to orient a second site-specific DNA binding domain in the tetramer allowing recognition of a second high affinity transposase binding site.