Unfolding single RNA molecules by mechanical force: a stochastic kinetic method.
Using simple polymer elastic theory and known RNA free energies, we study the single RNA folding and unfolding on the secondary structure level under mechanical constant force by stochastic kinetic simulation. As a primary application, this method is used to simulate the experiment performed by Science 292, 733 (2001)]. The extension-force curves in equilibrium and kinetic reaction rate constants for folding and unfolding are calculated. Our results show that the agreement between simulation and experimental measurements is satisfactory.
Liu
Fei
F
Center for Advanced Study, Tsinghua University, Beijing 100084, People's Republic of China. liufei@tsinghua.edu.cn
Ou-Yang
Zhong-can
ZC
D003198:Computer Simulation; D004548:Elasticity; D007700:Kinetics; D008832:Microchemistry / Q000379:methods*; D008846:Micromanipulation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010812:Physical Stimulation / Q000379:methods; D012313:RNA / Q000032:analysis / Q000737:chemistry*; D013269:Stochastic Processes; D013314:Stress, Mechanical
D012313:RNA