Protein–DNA interaction

A protein–DNA interaction is physical association between a protein and DNA. Contacts can depend on base sequence, DNA shape, charge or interactions with other bound factors. A transcription factor can recognize selected regulatory sites, while histones package much larger fractions of the genome. Detecting association establishes contact or proximity under the assay conditions; regulation, bending or bridging requires additional functional or structural evidence. ^[ref]

Simultaneous connection of separated DNA segments by a protein assembly. Intramolecular bridging produces a loop; intermolecular bridging connects distinct molecules.

A binding experiment challenging a labelled complex with unlabelled DNA. Specific and nonspecific competitors can distinguish sequence recognition from transfer of other DNA-bound components.

DNA that lacks the selected recognition sequence but can accept nonspecific interactions or transferred histones. Its effect must be interpreted against controls for all components.

Unlabelled DNA containing recognition sites for the protein being tested. Competition can draw that protein away from labelled DNA without necessarily removing other proteins from the labelled assembly.

An assembly of DNA and two distinguishable protein components. A mobility shift alone does not establish composition; selective competition and component-specific detection can test which components remain.