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Methods Mol Biol. 2016;1490:51-62. doi: 10.1007/978-1-4939-6433-8_4.

Predicting RNA-RNA Interactions Using RNAstructure.

Author information

1
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
2
Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
3
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
4
Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.

Abstract

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 .

KEYWORDS:

Bimolecular RNA structure; RNA Duplex Formation; RNA hybridization

PMID:
27665592
DOI:
10.1007/978-1-4939-6433-8_4
[Indexed for MEDLINE]

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