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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.

With nucleosomes alone, neither competitor substantially removes the main nucleosome band, although some free labelled DNA is present. With nucleosome–NVNA1 complexes, increasing specific competitor DNA removes the extra shifts and restores the nucleosome band. The starting shifted complexes therefore contained histones as well as NVNA1: competitor recognition sites draw NVNA1 away while leaving labelled DNA associated with histones.

nonspecific competitor DNA gives a different endpoint. The shifted population changes to a band matching the far-right NVNA1–naked-DNA control, rather than returning mainly to the nucleosome position. The labelled DNA remains bound to NVNA1 while histones can transfer to the excess competitor DNA. NVNA1 binding destabilizes the nucleosome against competitor-induced histone displacement. Remaining shifted DNA is not evidence that the histone octamer remained: its mobility must be compared with both controls. The nucleosome-only competition lanes show that competitor DNA alone is insufficient to cause the same conversion. Histone-specific detection would confirm the inferred component loss. A closely analogous ternary-complex and competition analysis was demonstrated for EBNA1; it provides a methodological precedent without establishing the identity of NV.^[ref]