A Method to Predict the Structure and Stability of RNA/RNA Complexes.
RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.
Department of Physics, Informatics Institute, University of Missouri, Columbia, MI, USA.|Department of Biochemistry, Informatics Institute, University of Missouri, Columbia, MI, USA.|Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.
Xiaojun
X
Xu
Department of Physics, Informatics Institute, University of Missouri, Columbia, MI, USA.|Department of Biochemistry, Informatics Institute, University of Missouri, Columbia, MI, USA.|Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.
Shi-Jie
SJ
Chen
D000465:Algorithms; D020029:Base Pairing; D019277:Entropy; D015497:HIV-1 / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D020871:RNA Stability; D012367:RNA, Viral / Q000737:chemistry
D012367:RNA, Viral; D012313:RNA
Partition function; RNA/RNA complex; Tertiary motif entropy; Two-step screening
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