Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions: Biophysical Journal

Significance

The knowledge of 3D structures and stabilities of RNA pseudoknots is extremely important for understanding their biological functions. Here, we have presented a coarse-grained model with salt effect to predict the structures and stabilities of complex RNA pseudoknots in ion solutions, beyond generally covered minimal H-type pseudoknots. The comparisons with experiments show that the model can successfully predict 3D structures of complex RNA pseudoknots including SARS-CoV-2 PFSE and Zika virus xrRNA from their sequences, and can reliably predict the stabilities of RNA pseudoknots of different sequences/lengths and the effects of monovalent/divalent ions. Furthermore, our analyses reveal that the thermally unfolding pathways of complex RNA pseudoknots such as SARS-CoV-2 FSE mainly depend on the relative stabilities of unfolded intermediates states.

DOI: https://doi.org/10.1016/j.bpj.2023.03.017