Monte carlo simulation for single RNA unfolding by force

¹ Center for Advanced Study
² Chinese Academic of Sciences

^* To whom correspondence should be addressed. E-mail: liufei{at}tsinghua.edu.cn.

Submitted on July 8, 2004
Revised on August 10, 2004
Accepted on 4 October 2004

	Abstract

Using polymer elastic theory and known RNA free energies, we construct a Monte Carlo algorithm to simulate the single RNA folding/unfolding by mechanical force on the secondary structure level. For constant force ensemble, we simulate the force-extension curves of p5ab, p5abcA, and p5abc molecules in equilibrium. For constant extension ensemble, we focus on the mechanical behaviors of RNA p5ab molecule, which include the unfolding force dependence on the pulling speed,force-hysteresis phenomenon and the coincidence of stretching-relaxing force-curves in thermal equilibrium. We particularly simulate the time traces of the end-to-end distance of p5ab under constant force in equilibrium, which also has been recorded in the recent experiment [Science 292, 733-737(2001)]. The reaction rate constants for folding and unfolding are calculated. Our results show that the agreement between the simulation and the experimental measurements is satisfactory.

Key Words: Force, Force-extension curves, Monte Carlo algorithm, Reaction rates, Single RNA, Time traces

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