RNA is a charged polymer; hence it is exquisitely sensitive to its ionic environment. Despite the presence of a series of negatively charged phosphodiester backbone, it folds into compact configurations in order to operate different functions. Folding of RNA pseudoknot into an ordered compact structure has often been attributed to the counter-ion condensation phenomena with substantial neutralization of the negative charges in the backbone. In this work, we present a new theoretical and computational approach integrating coarse-grained structure-based model of RNA and dynamic polyelectrolyte theory of RNA which has the potential to combat the challenges in the area of computer simulations to explore long-time scale and large-length scale phenomena. The model has been tested against various experimental results. Our model treats the Mg2+ ions explicitly to take into account the direct ion-ion correlations and KCl is treated implicitly using generalized Manning counter-ion condensation theory of polyelectrolyte. In this work, we have studied SARS-CoV-2 three-stemmed RNA pseudoknot (PK) where Mg2+ ions are found to play an important role in stabilizing the pseudoknot. We have also calculated small angle x-ray scattering (SAXS) intensity profile using simulation data in the absence of Mg2+. These SAXS results are consistent with experimental SAXS intensity profile which quantitatively ensures the reliability on our further predictions.

Development of Structure-Based Polyelectrolyte Theory Helps Capturing Ion-Environment Dependence of Viral RNA Pseudoknot of SARS-CoV-2

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27th CRSI National Symposium in Chemistry

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