Predicting RNA-RNA Interactions Using RNAstructure.
RNA-RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA-RNA hybridization sites is challenging because of the competition between intramolecular and intermolecular structure formation. A complete picture of RNA-RNA binding includes an understanding of single-stranded folding and binding site accessibility, and is strongly concentration-dependent. This chapter provides guidance for using RNAstructure to predict RNA-RNA binding sites and RNA-RNA structures, utilizing free energy minimization and partition function calculations. RNAstructure is freely available at http://rna.urmc.rochester.edu/RNAstructure.html .
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.|Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
Laura
L
DiChiacchio
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.|Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
David H
DH
Mathews
D000465:Algorithms; D020029:Base Pairing; D019295:Computational Biology / Q000379:methods; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
D012313:RNA
Bimolecular RNA structure; RNA Duplex Formation; RNA hybridization