Loop dependence of the stability and dynamics of nucleic acid hairpins

Hairpin loops are critical to the formation of nucleic acid secondary structure, and to their function. Previous studies revealed a steep dependence of single-stranded DNA (ssDNA) hairpin stability with length of the loop (L) as ∼L^8.5±0.5, in 100 mM NaCl, which was attributed to intraloop stacking interactions. In this article, the loop-size dependence of RNA hairpin stabilities and their folding/unfolding kinetics were monitored with laser temperature-jump spectroscopy. Our results suggest that similar mechanisms stabilize small ssDNA and RNA loops, and show that salt contributes significantly to the dependence of hairpin stability on loop size. In 2.5 mM MgCl₂, the stabilities of both ssDNA and RNA hairpins scale as ∼L^±0.5, indicating that the intraloop interactions are weaker in the presence of Mg²⁺. Interestingly, the folding times for ssDNA hairpins (in 100 mM NaCl) and RNA hairpins (in 2.5 mM MgCl₂) are similar despite differences in the salt conditions and the stem sequence, and increase similarly with loop size, ∼L^2.2±0.5 and ∼L^2.6±0.5, respectively. These results suggest that hairpins with small loops may be specifically stabilized by interactions of the Na⁺ ions with the loops. The results also reinforce the idea that folding times are dominated by an entropic search for the correct nucleating conformation.