Abstract
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 ~ 10 6- 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 ∼ 10 6 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.
Original language | English (US) |
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Pages (from-to) | 162-171 |
Number of pages | 10 |
Journal | Biophysical Chemistry |
Volume | 159 |
Issue number | 1 |
DOIs | |
State | Published - Nov 2011 |
Keywords
- DNA hydration
- DNA stem-loop motifs
- DSC and ITC calorimetries
- Density and ultrasound velocity techniques
- Netropsin binding
ASJC Scopus subject areas
- Biophysics
- Biochemistry
- Organic Chemistry