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

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. 1. Introduction Hairpin loops are a common form of nucleic acid secondary structure and are crucial for tertiary structure and function [1]. They are known to play a key role in a number of biological processes such as gene expressions, DNA recombination, and DNA transposition [2–4]. In RNA molecules hairpins act as nucleation sites for RNA folding into final conformations [5–7] and play a critical role in RNA-protein recognition and gene regulation [8, 9]. Furthermore, due to the specificity of probe/target hybridization determined as a match-versus-mismatch discrimination, hairpin DNA oligomer probes have become an important tool in modern biotechnology and diagnostics [10, 11]. The thermodynamics and kinetics of hairpin formation, hairpin binding to complementary nucleic acids, and hairpin-ligand associations have been studied extensively [12–21]. There is no doubt that studies of hairpin-to-coil transitions and hairpin-ligand binding affinity and specificity have greatly enhanced our understanding of structural features and function of the naturally occurring nucleic acids [22, 23]. However, despite extensive biophysical research on the systems involving hairpin structures that produced a number of high-quality explanations and evaluations on properties and behavior of nucleic acids containing hairpin formations, there are still many unresolved questions. As pointed out by Marky et al. [24] the most suitable hairpin molecules for studying the thermodynamics of their conformational transitions and ligand binding are the single-stranded hairpin molecules. They form stable partially paired duplexes that tend to melt in simple monomolecular transitions. Furthermore, their conformational stability and ligand binding properties are easily compared with