We asked ourselves, why the miRNA2911 has the amazing property of being extremely heat stable as well as RNase resistant. We hypothesized, that the 3D structure might play a key role in this, which is why we simulated the folding of the RNA molecule de novo based on the sequence, using a Monte Carlo simulated annealing method.

We used the SimRNA software package by Janusz Bujnicki and simulated 200,000 steps of the RNA folding, starting from a circular default structure. After 10,000 steps a stable helix had formed. You can see the first 10,000 simulation steps in the following video, animated with the Visual Molecular Dynamics package by the theorectical and computational biophysics group at the University of Illinois [2].

We extracted the minimum free energy (MFE) structure from the simulation trajectory. It can be plainly seen, that the number of basepairs and stacked pi-electron-systems is maximized:

To confirm the predicted structure, one could use X-ray crystallography, to which we unfortunately did not have access. If this structure does form in vivo however, that could explain the enhanced stability of the molecule.

In order to reconfirm the alignments of the miRNA with the influenza genes, we did some alignments ourselves, using RNAhybrid [3]. The respective virus strains and genes are indicated in the figure.

H1N1, MP gene
H5N1, NA gene
H7N9, PA gene

As you can see, the miRNA 2911 binds well to different genes in different virus strains.

  1. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Michał J. Boniecki, Grzegorz Łach, Konrad Tomala, Wayne Dawson, Paweł Łukasz, Tomasz Sołtysiński, Kristian M. Rother, and Janusz M. Bujnicki. (to be published).
  2. Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
  3. Rehmsmeier, Marc and Steffen, Peter and Hoechsmann, Matthias and Giegerich, Robert Fast and effective prediction of microRNA/target duplexes RNA, RNA, 2004

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