Stability of a Short DNA Duplex as a Function of Temperature: the Effect of ∆Cp and Added Salt Concentration†

Igor Drobnak, Mojca Seručnik, Jurij Lah* and Gorazd Vesnaver*
University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia.
Jurij Lah, phone: +386 1 2419 414, fax: +386 1 2419 425, e-mail: jurij.lah@fkkt.uni-lj.si;
Gorazd Vesnaver, phone: +386 1 2419 402, fax: +386 1 2419 425, e-mail: gorazd.vesnaver@fkkt.uni-lj.si;

Abstract
Recently, it has been shown that ∆cp effects accompanying the helix-to-coil transitions of DNA duplexes are not negligible. To find out if this is the case also with a short model (5’-CGAATTCG-3’)2 duplex we studied its thermal unfolding by high sensitivity differential scanning calorimetry (DSC) at 0, 0.1, 0.3 and 1 M added NaCl. We succesfully described the measured DSC thermograms by the model function that is based on the two-state approximation of the unfolding process and contains three adjustable parameters: T_1/2 – the melting temperature, ∆H_(T1/2) – enthalpy of unfolding at T_1/2 and ∆cp – the change of heat capacity upon DNA unfolding. These ∆H_(T1/2) values are in good agreement with those obtained by the straightforward integration of the DSC thermograms. From the available experimental data a ∆H_(T1/2) versus T_1/2 plot was constructed and ∆cp was obtained as a slope of the observed linear relationship. We believe that excellent agreement between this ∆cp and the one obtained as adjustable parameter from fitting the experimental DSC thermograms strongly supports our suggestion that ∆cp accompanying unfolding of DNA is independent of temperature an added salt concentration and may be accurately determined from the described fitting procedure. Analysis of our results shows that even for short DNA duplexes the errors in the nearest-neighbor estimates of ∆G(25 °C), ∆H(25 °C) and ∆S(25 °C) of unfolding based on the ∆cp = 0 assumption may be significant. It also shows that the experimental T_1/2 versus ln[Na+] slope depends on the salt concentration and agrees reasonably well with the one predicted by the electrostatic polyelectrolyte theory.

Keywords: DNA, thermodynamics, differential scanning calorimetry, heat capacity, stability.