Professor Pan Li – University of Albany
Title: Effect of Mg2+ ions on mechanical unfolding of a two-base-pair RNA kissing hairpin
Structure and function of RNA critically depend on ionic conditions. However, rigorous thermodynamic analysis of metal ions binding to polyelectric RNA remains a daunting task. To reduce complexity of this problem, we examined folding of a kissing complex with only two base pairs formed between two hairpins. Using optical tweezers, single kissing RNA molecules are stretched and relaxed from 5′- and 3′-ends. We can monitor folding of the kissing interaction in real time and distinguish its force and extension signals from those of secondary structure. We studied folding of this kissing complex under various Mg2+ ion concentrations. Mg2+ ions stabilize the kissing complex and speed its folding. However, Mg2+ ions have distinct effects on forward and reverse reactions. At saturation concentration of Mg2+ ions, the two-base-pair kissing complex breaks at >50 pN, whereas kissing forces merely change by ~5 pN. We will discuss how equilibrium, kinetic barrier and work dissipation change with concentration of Mg2+ ions and applied force. We will also discuss retrieval of equilibrium free energy under non-equilibrium pulling conditions.
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