It is well known that two major factors contribute to the stability of DNA double helix: base stacking and base pairing. Using PAGE we were able to separately characterize heterogeneous stacking interactions for all contacts in DNA duplex (1). This approach is grounded on the assumption that DNA nick exists as an equilibrium between the stacked (straight) and unstacked (kinked) conformations. PAGE mobility of DNA molecules with solitary sequence-specific nicks and gaps is used to assess the occupancies of the two states of the nicked dinucleotide stack yielding stacking free energy parameters for each contact.

This approach provides with a unique opportunity of direct determination of the stacking free energy under the chosen ambient conditions (first of all temperature). Here we explore the effect of ambient conditions on the stacked/unstacked equilibrium at the DNA nick as well as on a cumulative stacking contribution and base-pairing contribution to the DNA stability. We report the temperature dependence of the stacking parameters within the range of physiological temperatures.

References and Footnotes

1. Protozanova, E., Yakovchuk, P., and Frank-Kamenetskii, M. D. J. Mol. Biol. 342, 775-85 (2004).