Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

Elife. 2018 Apr 11;7:e32963. doi: 10.7554/eLife.32963.


Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS.

Keywords: DNA recognition; biochemistry; chemical biology; enthalpy; entropy; epistasis; human; molecular biophysics; structural biology; thermodynamics; transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CDX2 Transcription Factor / chemistry
  • CDX2 Transcription Factor / genetics
  • CDX2 Transcription Factor / metabolism*
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism*
  • Entropy*
  • Homeodomain Proteins / chemistry
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism*
  • Humans
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • Substrate Specificity
  • Thermodynamics*


  • CDX2 Transcription Factor
  • CDX2 protein, human
  • HOXB13 protein, human
  • Homeodomain Proteins
  • DNA

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.