Lipoplex thermodynamics: determination of DNA-cationic lipoid interaction energies

An experimental study of the cationic lipid-DNA binding affinity is presented. The binding free energy was determined by monitoring lipoplex dissociation under conditions of increasing salt concentration. The primary procedure was based on the extent of quenching by energy transfer of fluorophores on DNA molecules by fluorophore on a lipid as these molecules came into close association in the lipoplex. Titration calorimetry on the Dickerson dodecamer was also done, with results that were in agreement with the fluorescence data. Measurements on short oligonucleotides allowed estimation of the binding energy per nucleotide. The binding free energy is approximately 0.6 kcal/mole nucleotide for the Dickerson dodecamer and declines for longer oligonucleotides. The entropy gained upon complex formation is approximately 1 entropy unit per released counterion. The method was applied to long DNA molecules (herring and lambda-phage DNA) and revealed that complete dissociation occurs at 750 mM NaCl. Likely contributions of macromolecular desolvation and DNA flexibility to the binding energy are discussed.