Effects of chain length, temperature, and ionic strength on association and dissociation thermodynamics of DNA

• We analyzed binding thermodynamics of oligonucleotides to form DNA. • The affinity depends on chain length and ionic strength. • The Δ C p changes from negative to positive at a temperature close to T m . In this study, association of oligonucleotides of length 8-22 bases and their complementary oligonucleotides to form DNA was analyzed using isothermal titration calorimetry. Additionally, dissociation of DNA into its respective oligonucleotides was analyzed using differential scanning calorimetry. The effects of chain length, temperature, and ionic strength on the association and dissociation of DNA were evaluated using thermodynamic analyses. At 25 °C, the association of 10-base oligonucleotides largely depended on ionic strength, however, for oligonucleotides of 12-base and above, association was independent of ionic strength. In oligonucleotides of length 12-, 16-, and 22-bases, both binding enthalpy and entropy changes decreased with increase in chain length around 25 °C, providing similar binding affinity. The highest association constant was approximately 1 × 10 9 M –1 . During association of DNA oligonucleotide of the same chain length, binding enthalpy change gradually decreased with increase in temperature, indicating a negative heat capacity change around 25 °C. As the temperature increased close to the melting temperature, the binding enthalpy change increased, indicating a positive heat capacity change. The temperature-dependent binding enthalpy change was apparently extrapolated to the calorimetric enthalpy change of DNA at the melting temperature. At the melting temperature, the effect of chain length and ionic strength could be observed clearly; the stability of DNA increased with increasing chain length and ionic strength.