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

Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland.
Nucleic Acids Research (Impact Factor: 8.28). 02/2006; 34(17):4943-59. DOI: 10.1093/nar/gkl620
Source: PubMed

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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