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Sequence-specific binding of single-stranded RNA: is there a code for recognition?

Sigrid D Auweter·Florian C Oberstrass·Frédéric H-T Allain
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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.

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Base SequenceBinding SitesModels, MolecularProtein BindingProtein EngineeringProtein Structure, TertiaryRNARNA-Binding ProteinsJournal ArticleResearch Support, Non-U.S. Gov'tReview

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Sigrid D Auweter, Florian C Oberstrass, Frédéric H-T Allain. 2006-09-18. Sequence-specific binding of single-stranded RNA: is there a code for recognition?. https://doi.org/10.1093/nar%2Fgkl620

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