期刊
RNA
卷 15, 期 4, 页码 696-706出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.1429009
关键词
RNA folding; RNA pseudoknot; interhelix loop; structural predictions; folding thermodynamics
资金
- NIH [GM063732]
RNA pseudoknots play a critical role in RNA-related biology from the assembly of ribosome to the regulation of viral gene expression. A predictive model for pseudoknot structure and stability is essential for understanding and designing RNA structure and function. A previous statistical mechanical theory allows us to treat canonical H-type RNA pseudoknots that contain no intervening loop between the helices (see S. Cao and S.J. Chen [2006] in Nucleic Acids Research, Vol. 34; pp. 2634-2652). Biologically significant RNA pseudoknots often contain interhelix loops. Predicting the structure and stability for such more-general pseudoknots remains an unsolved problem. In the present study, we develop a predictive model for pseudoknots with interhelix loops. The model gives conformational entropy, stability, and the free-energy landscape from RNA sequences. The main features of this new model are the computation of the conformational entropy and folding free-energy base on the complete conformational ensemble and rigorous treatment for the excluded volume effects. Extensive tests for the structural predictions show overall good accuracy with average sensitivity and specificity equal to 0.91 and 0.91, respectively. The theory developed here may be a solid starting point for first-principles modeling of more complex, larger RNAs.
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