Modelling RNA folding under mechanical tension

Abstract

We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transition force for unfolding, the end-to-end distribution function and its variance, as well as kinetic information, for a representative RNA sequence and for a sequence containing two homopolymer segments: A·U and G·C.

Acknowledgements

One of us (IT) has been a colleague and friend of Bob Harris for over 40 years. He is the person who has always been willing to explain quantum mechanics, statistical mechanics, and the meaning of life. Bob is a rare and valuable treasure.

Also, we would like to thank Laurent Lacroix and Sophie Dumont for their critical reading of the manuscript. This work was supported by NIH Grant GM-10840. JV was partially funded by a NSF Graduate Research Fellowship.