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The DNA-binding domain supports site occupancy, while the region for homotypic protein interaction permits much larger assemblies. With the truncated protein, the faster complex 4 appears at low protein:DNA ratios and gives way to the slower complex 3 as protein increases. A natural assignment is occupancy of one and then both recognition repeats by functional binding units. A binding unit could itself be a protein dimer; a native gel does not determine the number of polypeptide chains from mobility alone. Loss of free probe with increasing protein supports binding, and failure to shift the zero-repeat probe supports sequence preference under these conditions.

Full-length protein instead produces the very slow complex 1 already at relatively low ratios, followed by more of complex 2 at high ratios. homotypic protein interactions can make cooperative higher-order assemblies and can bridge different probe molecules. At protein excess, separate saturation of available sites can reduce productive bridging, explaining why the largest species need not increase monotonically. Complex 2 is compatible with a smaller saturated full-length assembly; assigning its exact stoichiometry requires an independent measurement. protein size also contributes to the difference between full-length and truncated complexes, but size alone does not explain the concentration-dependent redistribution into the exceptionally slow species. The experiment supports assembly dependent on protein oligomerization rather than a unique structure for every numbered band.

At low concentration, the array with more and higher-affinity binding sites is preferentially occupied, giving one visible protein cluster on an otherwise extended DNA molecule. At higher concentration the weaker origin array also becomes occupied. homotypic protein interactions between proteins at the two arrays can bridge them, trapping the intervening DNA through DNA looping. This explains why the electron-dense protein cluster lies at the loop junction rather than uniformly coating the entire molecule.

The high-affinity array can stabilize weak-site occupancy through tethering: once one partner is anchored, the second site experiences a high effective local concentration and several contacts can contribute avidity. This reconciles stable looped assemblies with the vulnerability of the isolated weak site to nonspecific competitor DNA. The images support intramolecular DNA bridging, but selected micrographs do not measure its frequency or exclude some intermolecular associations. A high local density of protein need not imply biomolecular phase separation. The printed scale-bar unit appears implausible for a kilobase-scale DNA substrate; the mechanistic inference uses topology and site positions rather than that unit.