Non-equilibrium forcing of DNA / RNA structures to twist, stretch, open, or melt

Mar 30, 2012, 1:00 PM
45m
132:028 (Nordita)

132:028

Nordita

Speaker

Prof. Lene Oddershede (Niels Bohr Institute, Copenhagen)

Description

In a living cell DNA and RNA are constantly subject to forces causing the nucleic acid structures to twist, bend, stretch, open, or melt. In order to understand important cellular processes and the physical mechanisms that nucleic acids obey, it is important to know how these nucleic acid structures comply to mechanical stress. By applying forces on individual DNA and RNA molecules, we investigated their response while being forced to undergo a non-equilibrium structural transition. Precise force-extension measurements performed on DNA by optical tweezers prompted a re-formulation of the celebrated worm-like chain model, our new model is denoted the 'twistable worm-like chain' and takes into account the observed twist-stretch coupling [1]. In the DNA overstretching regime, the so-called 'force-plateau', we consistently observed a reproducible rip-like structure in the data which originated from a mechanical unpeeling of the two strands [1]. RNA is another nucleic acid of poss ibly even more importance than DNA.. During translation mRNA pseudoknots are subject to a mechanical force acted upon the structure by the translating ribosome. This force causes the structure to open and occasionally the ribosome to shift reading frame. Using an optical trapping assay we mimicked the action of the ribosome by forcing mRNA pseudoknots to unfold in a non-equilibrium fashion. We found that the frameshifting efficiency correlates with the mechanical strength of the structure [2], however, the relation is not trivial as an inversion of the structure has a tremendous effect both on frameshifting rates, on Gibbs free energies, and on its mechanical strength. Occasionally, the mRNA pseudoknot is so strong that it efficiently acts as a roadblock for e the translating polymerase [3]. [1] Twist, stretch and melt: quantifying how DNA complies to tension. P. Gross, N. Laurens, L.B. Oddershede, U. Bockelmann, E.J.G. Peterman, G.J.L. Wuite, Nature Physics, vol.7 p.731 (2011). [2] Correlation between mechanical strength of messenger RNA pesudoknots and ribosomal frameshifting, T.M. Hansen, S.N.S. Reihani, L.B.Oddershede, M.A. Sørensen, PNAS vol.104 p.530 (2007). [3] mRNA pseudoknots act as ribosomal roadblocks, J. Tholstrup, L.B. Oddershede, M.A. Sørensen, Nucleic Acids Research vol.40 p.303-313 (2012).

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