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Originally published as Biophys J. BioFAST on October 22, 2004.
doi:10.1529/biophysj.104.049239
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Biophysical Journal 88:76-84 (2005)
© 2005 The Biophysical Society

Monte Carlo Simulation for Single RNA Unfolding by Force

Fei Liu * and Zhong-can Ou-Yang * {dagger}

* Center for Advanced Study, Tsinghua University, Beijing, China; and {dagger} Institute of Theoretical Physics, The Chinese Academy of Sciences, Beijing, China

Correspondence: Address reprint requests to Fei Liu, Center for Advanced Study, Tsinghua University, Beijing 100084, China. Tel.: 86-10-6277-1225 ext. 138; E-mail: liufei{at}tsinghua.edu.cn.

Using polymer elastic theory and known RNA free energies, we construct a Monte Carlo algorithm to simulate the single RNA folding and unfolding by mechanical force on the secondary structure level. For the constant force ensemble, we simulate the force-extension curves of the P5ab, P5abc{Delta}A, and P5abc molecules in equilibrium. For the constant extension ensemble, we focus on the mechanical behaviors of the RNA P5ab molecule, which include the unfolding force dependence on the pulling speed, the 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 the P5ab under the constant force in equilibrium, which also have been recorded in the recent experiment. The reaction rate constants for the folding and unfolding are calculated. Our results show that the agreement between the simulation and the experimental measurements is satisfactory.




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F. Liu, H. Tong, and Z.-c. Ou-Yang
Force Unfolding Single RNAs
Biophys. J., March 15, 2006; 90(6): 1895 - 1902.
[Abstract] [Full Text] [PDF]


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