Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs

•The role of water in binding events provides insight into thermodynamic profiles.•ΔS values were negative for nogalamycin binding and positive for doxorubicin binding.•Whether water is released or taken up depends on both binding mode and sequence.

Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater < 0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater > 0 for CT DNA and Δnwater < 0 for poly(dG·dC). For poly(dA·dT), Δnwater ~ 0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions.

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