Abstract
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.
Highlights
RNAs can fold into complex three-dimensional (3D) structures to carry out their various biological functions [1]
Several computational models have been developed to predict 3D structures for RNA pseudoknots to further unveil the mechanisms of their functions, these structure prediction models seldom consider ion conditions departing from the high salt (e.g., 1M NaCl) and temperatures from the room temperature
Based on our comprehensive analyses for extensive pseudoknots and the wide range of monovalent/divalent ion conditions, we confirmed that the thermally unfolding pathway of RNA pseudoknots is mainly determined by the relative stability of intermediate states, which has been proposed by Thirumalai et al Our analyses show that the thermally unfolding pathway of RNA pseudoknots could be apparently modulated by the sequences and ion conditions
Summary
RNAs can fold into complex three-dimensional (3D) structures to carry out their various biological functions [1]. An RNA pseudoknot is formed when a sequence of nucleotides within a single-stranded loop region forms base pairs with a complementary sequence outside that loop [2,3,5,6]. Many experiments have shown that this special 3D topology is key to realize the various functions of RNA pseudoknots [2,3,4]. To determine 3D structures and quantify stability of RNA pseudoknots is essential to unveil the mechanisms of their functions and to further aid the related drug design [5,9]
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