Thermodynamic Parameters of Specific and Nonspecific Protein-DNA Binding

Linda Jen-Jacobson*, Lisa E. Engler, Jennifer T. Ames, Michael R. Kurpiewski, Arabela Grigorescu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


Proteins that bind preferentially to specific recogntion sites on DNA also bind more weakly to nonspecific DNA. We have studied both specific and non-specific binding of the EcoRI and BamHI restriction endonucleases, and determined enthalpic and entropic contributions to binding free energy (ΔGobind) using both the van't Hoff method and isothermal titration calorimetry. Specific binding is characterized by a strongly negative ΔCop and can be either enthalpy-driven or entropy-driven, depending on temperature. Nonspecific binding has ACop ≈ 0 and is enthalpy-driven. A strongly negative ΔCop is the "thermodynamic signature" of site-specific binding, because it reflects the characteristics of a tight complementary recognition interface: the burial of previously hydrated nonpolar surface and restriction of configurational-vibrational freedoms of protein, DNA, and water molecules trapped at the protein-DNA interface. These factors are absent in nonspecific complexes. We probed the contributions to ΔCop by varying the sequence context surrounding the recognition site. As ΔGobind improves, ΔCop, ΔHo and ΔSo all become more negative, and there is a linear correlation between ΔHo and ΔSo (enthalpy-entropy compensation). Because these context variations do not change the protein-base or protein-phosphate contacts, the hydrophobic contribution or the number of trapped water molecules at the interface, we conclude that a better sequence context improves the "goodness of fit" in the interface and and thus increases the magnitude of the negative configurational-vibrational contribution to ΔCop.

Original languageEnglish (US)
Pages (from-to)143-160
Number of pages18
JournalSupramolecular Chemistry
Issue number2
StatePublished - 2000


  • Enthalpy-entropy compensation
  • Heat capacity change
  • Nonspecific protein-DNA complexes
  • Specific protein-DNA complexes
  • Thermodynamics

ASJC Scopus subject areas

  • Chemistry(all)


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