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Journal of Nucleic Acids
Volume 2011, Article ID 513910, 9 pages
http://dx.doi.org/10.4061/2011/513910
Research Article

Influence of a Hairpin Loop on the Thermodynamic Stability of a DNA Oligomer

Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia

Received 13 April 2011; Accepted 16 May 2011

Academic Editor: Luis A. Marky

Copyright © 2011 Jurij Lah et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

DSC was used to evaluate the mechanism of the thermally induced unfolding of the single-stranded hairpin HP = 5′-CGGAATTCCGTCTCCGGAATTCCG-3′ and its core duplex D (5′-CGGAATTCCG-3′)2. The DSC melting experiments performed at several salt concentrations were successfully described for HP and D in terms of a three-state transition model (intermediate state) S (unfolded single-stranded state) and two state transition model , respectively. Comparison of the model-based thermodynamic parameters obtained for each HP and D transition shows that in unfolding of HP only the transition is affected by the TCTC loop. This observation suggests that in the intermediate state its TCTC loop part exhibits significantly more flexible structure than in the folded state while its duplex part remains pretty much unchanged.