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Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

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Cojocaru,  V.
Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society;

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Klement,  R.
Emeritus Group Laboratory of Cellular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Jovin,  T. M.
Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society;

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Citation

Cojocaru, V., Klement, R., & Jovin, T. M. (2005). Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Research, 33(10): doi:10.1093/nar/gki664, pp. 3435-3446. Retrieved from http://nar.oxfordjournals.org/cgi/content/full/33/10/3435.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0012-E8F3-0
Abstract
Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA (“k-e motion”) were identified using locally enhanced sampling molecular dynamics (LES-MD) simulations, results that agree with experiment. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and, modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.