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Nucleic Acids Research Advance Access originally published online on September 18, 2006
Nucleic Acids Research 2006 34(17):4943-4959; doi:10.1093/nar/gkl620
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Nucleic Acids Research, 2006, Vol. 34, No. 17 4943-4959
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Survey and Summary

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

Sigrid D. Auweter1,2, Florian C. Oberstrass1,2 and Frédéric H.-T. Allain1,*

1 Department of Biology, Institute for Molecular Biology and Biophysics ETH Zürich, CH-8093 Zürich, Switzerland 2 Molecular Life Science PhD Program Zürich, Switzerland

*To whom correspondence should be addressed. Tel: +41 44 633 3940; Fax: +41 44 63 31294; Email: allain{at}mol.biol.ethz.ch

Received July 5, 2006. Revised August 8, 2006. Accepted August 8, 2006.

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.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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