Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.

ABSTRACT: This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one of 10 base pairs in length, are measured and characterized by isothermal titration calorimetry (ITC) as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔG^S) is large and unfavorable. The duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔG^S = +460 kcal·mol^-1per base pair at 25 °C. A van't Hoff analysis of the data is complicated by the varying degree of intramolecular base stacking w

SUBMITTER: Harmon C 

PROVIDER: S-EPMC11532980 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature