Editing Transcription factor (section)

=== Response elements ===

The DNA sequence that a transcription factor binds to is called a [[transcription factor-binding site]] or [[response element]].<ref name="pmid15711128">{{Cite journal |vauthors=Wang JC |date=March 2005 |title=Finding primary targets of transcriptional regulators |url=http://www.landesbioscience.com/journals/cc/abstract.php?id=1521 |journal=Cell Cycle |volume=4 |issue=3 |pages=356–8 |doi=10.4161/cc.4.3.1521 |pmid=15711128 |doi-access=free}}</ref>

Transcription factors interact with their binding sites using a combination of [[Coulomb's law|electrostatic]] (of which [[hydrogen bond]]s are a special case) and [[Van der Waals force]]s.  Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner.  However, not all [[Base pair|bases]] in the transcription factor-binding site may actually interact with the transcription factor.  In addition, some of these interactions may be weaker than others.  Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction.{{cn|date=March 2024}}

For example, although the [[consensus sequence|consensus binding site]] for the [[TATA-binding protein]] (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA.{{cn|date=March 2024}}

Because transcription factors can bind a set of related sequences and these sequences tend to be short, potential transcription factor binding sites can occur by chance if the DNA sequence is long enough.  It is unlikely, however, that a transcription factor will bind all compatible sequences in the [[genome]] of the [[cell (biology)|cell]].  Other constraints, such as DNA accessibility in the cell or availability of [[cofactor (biochemistry)|cofactors]] may also help dictate where a transcription factor will actually bind.  Thus, given the genome sequence, it is still difficult to predict where a transcription factor will actually bind in a living cell.

Additional recognition specificity, however, may be obtained through the use of more than one DNA-binding domain (for example tandem DBDs in the same transcription factor or through dimerization of two transcription factors) that bind to two or more adjacent sequences of DNA.