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The following picture shows an inverted repeat sequence in a response element. Response element sequences for glucocorticoids, estrogen, and thyroid hormone show that they all contain inverse repeats. Why do these inverted repeats exist in so many response sequences? In other words, what advantage do they pose to the function of the response element?enter image description here

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Starting with prokaryotic (i.e., bacterial) transcription factors--which were the first to be characterized in depth, this type of pattern was noted. Even for the "classic" Type II Restriction Endonucleases used for molecular cloning have palindromic recognition sequences. In all three cases the answer is that the sequence-specific DNA binding protein binds as a dimer, and so each monomer is recognizing a "half-site" (one of the inverted sequences).

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  • $\begingroup$ Thanks for your answer. We do encourage links to external sources to support assertions in answers. That way the poster or interested readers can check whether or not they are correct, and learn more about a topic than may be appropriate to include in an answer. You can edit your answer at any time. $\endgroup$ – David Nov 25 '18 at 18:28
  • $\begingroup$ @RosieF In that case, is it essential that the repeated sequences be inverted? Wouldn't the DNA binding proteins still be able to bind as a dimer if it were just a sequence repeated without inversion? $\endgroup$ – Roxane Min Nov 26 '18 at 8:18
  • $\begingroup$ I think the most important concept here is that by having multiple binding sites concentrated in small region then this will effectively increase the concentration of the transcription factor. The more sites, the more specificity, and therefore more biological regulation is possible (e.g., ON vs. OFF). The location of the dimerization interface on the monomer will change if the recognition sites were direct repeats instead of inverted repeats. There are probably (?) examples of both. Certainly the first ones characterized were inverted. $\endgroup$ – RosieF Nov 27 '18 at 17:26

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