Abstract:
:The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, three-dimensional (3D) conformation-based computational method for modeling salt concentration-dependent conformational distributions and the detailed 3D structures for a set of three RNA hairpins that contain a variable, 15-nucleotide loop sequence. For a given RNA sequence, the new, to our knowledge, method integrates a Vfold2D two-dimensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carlo tightly bound ion estimations of ion-mediated electrostatic interactions. The model predicts free-energy landscapes for the different RNA hairpin-forming sequences with variable salt conditions. The theoretically predicted results agree with the experimental fluorescence measurements, validating the strategy. Furthermore, the theoretical model goes beyond the experimental results by enabling in-depth 3D structural analysis, revealing energetic mechanisms for the sequence- and salt-dependent folding stability. Although the computational framework presented here is developed for RNA hairpin systems, the general method may be applied to investigate other RNA systems, such as multiway junctions or pseudoknots in mixed metal ion solutions.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Zhao C,Zhang D,Jiang Y,Chen SJdoi
10.1016/j.bpj.2020.07.042subject
Has Abstractpub_date
2020-10-06 00:00:00pages
1439-1455issue
7eissn
0006-3495issn
1542-0086pii
S0006-3495(20)30675-5journal_volume
119pub_type
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