Advertisement

Force Unfolding Single RNAs: From Equilibrium to Far-From Equilibrium

  • Fei Liu
  • Huan Tong
  • Zhong-Can Ou-Yang
Part of the Solid Mechanics and its Applications book series (SMIA, volume 144)

Abstract

We summarize our recent simulation progress of micromanipulation experiments on RNAs. We mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to protein cases, using the single polymer elastic theory and the well-known RNA secondary structure free energy knowledge, we can successively simulate various behaviors of force unfolding RNAs under different experimental setups from equilibrium to far-from equilibrium.

Key words

continuous time Monte Carlo method Jarzynski’s equality RNA single-molecule manipulation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Cech, T.R., The chemistry of self-splicing RNA and RNA enzymes, Science 236, 1987, 1532.CrossRefGoogle Scholar
  2. 2.
    Couzin, J., Small RNAs make big splash, Science 298, 2002, 2296.CrossRefGoogle Scholar
  3. 3.
    Harlepp, S., Marchal, T.M., Robert, J., Leger, J.F., Xayaphoummine, A., Isambert, H. and Chatenay, D., Probing complex RNA structures by mechanical force, European Physical Journal E 12, 2003, 605.CrossRefGoogle Scholar
  4. 4.
    Rief, M., Clausen-Schaumann, H. and Gaub, H.E., Sequence-dependent mechanics of single DNA molecules, Nature Structural & Molecular Biology 6, 1999, 346.CrossRefGoogle Scholar
  5. 5.
    Liphardt, J., Onoa, B., Smith, S.B., Tinoco, I. and Bustamante, C., Reversible unfolding of single RNA molecules by mechanical force, Science 292, 2001, 733.CrossRefGoogle Scholar
  6. 6.
    Liphardt, J., Dumont, B.S., Smith, S.B., Tinoco, I. and Bustamante, C., Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski’s equality, Science 296, 2002, 1832.CrossRefGoogle Scholar
  7. 7.
    Onoa, B., Dumont, S., Liphardt, J., Smith, S.B., Tinoco, I. and Bustamante, C., Identifying kinetic barries to mechanical unfolding of the T. thermophila Ribozyme, Science 299, 2003, 1892.CrossRefGoogle Scholar
  8. 8.
    Montanari, A. and Mezard, M., Hairpin formation and elongation of biomolecules, Physical Review Letter 86, 2001, 2178.CrossRefGoogle Scholar
  9. 9.
    Zhou, H., Zhang, Y. and Ou-Yang, Z.C., Stretch-induced hairpin-coil transitions in designed polynucleotide chains, Physical Review Letter 86, 2001, 356.CrossRefGoogle Scholar
  10. 10.
    Gerland, U., Bundschuh, R. and Hwa, T., Mechanically probing the folding pathway of single RNA molecules, Biophysical Journal 84, 2003, 2831.CrossRefGoogle Scholar
  11. 11.
    Lubensky, D.K. and Nelson, D.R., Single molecule statistics and the polynucleotide unzipping transition, Physical Review E 65, 2002, 031917.CrossRefGoogle Scholar
  12. 12.
    Liu, F., Dai, L.R. and Ou-Yang, Z.C., Theory for the force-stretched double-stranded chain molecule, Journal of Chemical Physics 119, 2003, 8112.CrossRefGoogle Scholar
  13. 13.
    Liu, F. and Ou-Yang, Z.C., Unfolding single RNA molecules by mechanical force: A stochastic kinetic method, Physical Review E 70, 2004, 0409011.Google Scholar
  14. 14.
    Liu, F. and Ou-Yang, Z.C., Monte Carlo simulation for single RNA unfolding by force, Biophysical Journal 88, 2005, 76.CrossRefGoogle Scholar
  15. 15.
    Flamm, C., Fontana, W., Hofacker, I. and Schuster, P., RNA folding at elementary step resolution, RNA 6, 2000, 325.CrossRefGoogle Scholar
  16. 16.
    Gillespie, D.T., Markov Process: An Introduction for Physical Scientists, Academic Press, San Diego, California, 1992.MATHGoogle Scholar
  17. 17.
    Jansen, A.P.J., Monte Carlo simulations of chemical reactions on surface with time-dependent reaction-rate constants, Computer Physics Communications 86, 1995, 1.CrossRefGoogle Scholar
  18. 18.
    Kawasaki, K., Diffusion constants near the critical point for time-dependent Ising models, Physcial Review 145, 1966, 224.CrossRefMathSciNetGoogle Scholar
  19. 19.
    Crooks, G.E., Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Physical Review E 60, 1999, 2721.CrossRefGoogle Scholar
  20. 20.
    Hofacker, I.L., The Vienna RNA secondary structure server, Nucleic Acids Research 31, 2003, 3429.CrossRefGoogle Scholar
  21. 21.
    Hmmer, G. and Szabo, A., Free energy reconstruction from nonequilibrium single-molecule pulling experiments, Proceedings of National Academy of Sciences, USA 98, 2001, 3658.CrossRefGoogle Scholar
  22. 22.
    Jarzynski, C., Equilibrium equality for free energy differences, Physical Review Letter 78, 1997, 2690.CrossRefGoogle Scholar
  23. 23.
    Ritort, F., Bustamante, C. and Tinoco, I.A., Two-state kinetic model for the unfolding of single molecules by mechanical force, Proceedings of National Academy of Sciences, USA 99, 2002, 3544.CrossRefGoogle Scholar
  24. 24.
    Cocco, S., Marko, J.F. and Monasson, R., Slow nucleic acid unzipping kinetics from sequence-defined barriers, European Physical Journal E 10, 2003, 153.CrossRefGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Fei Liu
    • 1
  • Huan Tong
    • 1
  • Zhong-Can Ou-Yang
    • 1
    • 2
  1. 1.Center for Advanced StudyTsinghua UniversityBeijingChina
  2. 2.Institute of Theoretical PhysicsThe Chinese Academy of SciencesBeijingChina

Personalised recommendations