= Solution
\b[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.
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