Single Molecule Force Measurements of DNA and RNA Hairpin Structures

Abstract

DNA and RNA hairpins contribute to fundamental mechanisms of molecular biology, for instance to the regulation of transcription and translation. Moreover, the hairpin secondary structure is a model system for studying the dynamic assembly of nucleic acid structures. Using a high-precision dual-trap optical tweezers setup, we performed a quantitative investigation of the folding dynamics of hairpins under mechanical load.A hairpin structure is composed of a double-helical stem and a single-stranded loop. Two different hairpins were studied, each one as a DNA and as an RNA molecule. They have the same stem of 13 basepairs, but exhibit loops of 10 and 18 nucleotides respectively. Significant differences are observed, not only between the two hairpins but also between DNA and RNA. As illustrated in the figure, hysteresis between unfolding and refolding curves is much stronger for RNA than for DNA. For narrow-loop hairpins, flipping between folded and unfolded states is observed for DNA and RNA. The wide-loop hairpins, however, show flips only for DNA. Altogether, our results show that the RNA molecule is more easily driven out-of-equilibrium by an external perturbation than DNA.View Large Image | View Hi-Res Image | Download PowerPoint Slide