Melting behavior and ligand binding of DNA intramolecular secondary structures

We use a variety of biophysical techniques to determine thermodynamic profiles, including hydration, for the unfolding of DNA stem-loop motifs (hairpin, a three-way junction and a pseudoknot) and their interaction with netropsin and random cationic copolymers. The unfolding thermodynamic data show that their helix-coil transition takes place according to their melting domains or sequences of their stems. All hairpins adopted the B-like conformation and their loop(s) contribute with an immobilization of structural water. The thermodynamic data of netropsin binding to the 5′-AAATT-3′/TTTAA site of each hairpin show affinities of ~ 106- 7 M− 1, 1:1 stoichiometries, exothermic enthalpies of − 7 to − 12 kcal mol− 1 (− 22 kcal mol− 1 for the secondary site of the three-way junction), and water releases. Their interaction with random cationic copolymers yielded higher affinities of ~ 106 M− 1 with the more hydrophobic hairpins. This information should improve our current picture of how sequence and loops control the stability and melting behavior of nucleic acid molecules.

Highlights► Unfolding of DNA stem-loop motifs shows transition(s) of their stem(s). ► Unfolding thermodynamic data consistent with DNA nearest-neighbor parameters. ► Incorporation of loops yielded an immobilization of structural water. ► Netropsin binding yielded conventional thermodynamic profiles and water releases. ► Interaction with copolymers yielded affinities of 105-6, highest with DNA Pseudoknot.