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Sequence-specific binding of single-stranded RNA: is there a code for recognition?Auweter SD; Oberstrass FC; Allain FHNucleic Acids Res 2006[]; 34 (17): 4943-59A 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.|Base Sequence[MESH]|Binding Sites[MESH]|Models, Molecular[MESH]|Protein Binding[MESH]|Protein Engineering[MESH]|Protein Structure, Tertiary[MESH]|RNA-Binding Proteins/*chemistry/metabolism[MESH]|RNA/*chemistry/metabolism[MESH] |
