Bending and Internal Tension of an Intramolecular Kissing Complex

Abstract

RNA tertiary base pairs are often bent and twisted by relative orientation of the interacting domains and by structures connecting these domains. Kissing complex, a basic RNA tertiary interaction, is formed by base pairing between distal hairpin loops. It remains unclear how much structure distortion a kissing complex can withstand. Crystal and NMR structures of several RNA kissing dimers show either a head-to-head coaxial helix or a slightly bent structure. An adenine riboswitch forms a well-bent two-base-pair kissing complex around its ligand. We designed two RNAs both consisting of a pair of hairpins connected by a single-strand. The two tetraloop hairpins in each RNA can form two GC kissing base pairs. The two RNAs, KC15 and KC30, have 15- and 30-nucleotide single-stranded linkers, respectively. Using optical tweezers, we examined mechanical folding of the two structures. With applied force, both RNAs can form an intramolecular kissing complex but show distinct mechanical unfolding patterns. Based on measured size and stability of the structures, we propose a mechanical model that such intramolecular kissing complexes, particularly the KC15, are bent to a blunt angle by internal tension of the single strand. Formation of such RNA triangle requires externally applied force by optical tweezers to offset the internal tension. Measurement of internal tension and structure distortion may facilitate understanding and prediction of tertiary interaction.