Transcriptional regulators bind to specific cis-regulatory sequences in theDNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that bind to a sequence twice as long as a monomer binds, increasing the sequences and reducing the chances of random binding. Transcription regulator dimers can be homodimers or heterodimers. In solution, these cooperative regulators exist either as monomers or weakly linked dimers. However, when these monomers bind to an extended cis-regulatory sequence on the DNA, they form stable dimers.

Cooperativity is a phenomenon where the binding of a monomeric protein causes structural changes to the DNA and increases the regulatory sites’ affinity for other monomers. This enables the monomers to bind as dimers on the cis-regulatory sequence. This phenomenon also helps regulators access sites located on DNA that is tightly bound to histone proteins in the nucleosome, which would otherwise be inaccessible. The first binding usually occurs at the DNA at the end of the nucleosome, where it is not tightly bound. Binding at this site leads to the DNA moving away from the histones, thereby leading to the unpacking of the nucleosome. This unpacking increases access to the other regulatory sites. In eukaryotes, transcription factor binding predominantly depends on cooperativity. Although cooperativity can occur in some cases, most of the binding of transcriptional regulators in prokaryotes is non-cooperative. In such cases, the regulators exist as stable dimers held together by several non-covalent interactions.

Whether an unknown regulator binds cooperatively or non-cooperatively can be determined by plotting the number of occupied binding sites on the DNA against the protein concentration. If the plot is an S-shaped curve, it indicates that the regulator binds cooperatively to the binding sites. If the curve rises steadily before leveling off as it approaches all of the binding sites being occupied, it indicates that binding is non-cooperative.