title: Sequence-specific binding of single-stranded RNA: is there a code for recognition?
abstract: A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Sigrid D
authors.initials: SD
authors.lastname: Auweter
authors.forename: Florian C
authors.initials: FC
authors.lastname: Oberstrass
authors.forename: Frédéric H-T
authors.initials: FH
authors.lastname: Allain
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D008958:Models, Molecular; D011485:Protein Binding; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA