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Nucleic Acids Research Advance Access originally published online on May 5, 2009
Nucleic Acids Research 2009 37(12):4022-4032; doi:10.1093/nar/gkp284
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Nucleic Acids Research, 2009, Vol. 37, No. 12 4022-4032
© 2009 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.

RNA

One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors

Zhen Huang1, Weimin Pei1, Yan Han1, Sabarinath Jayaseelan1, Alexander Shekhtman1, Hua Shi2 and Li Niu1,*

1Department of Chemistry and Center for Neuroscience Research and 2Department of Biological Sciences, University at Albany, SUNY, Albany, NY 12222, USA

*To whom correspondence should be addressed. Tel: +1 518 591 8819; Fax: +1 518 591 8820; Email: lniu{at}albany.edu

Received October 7, 2008. Revised April 11, 2009. Accepted April 14, 2009.

RNA is ideally suited for in vitro evolution experiments, because a single RNA molecule possesses both genotypic (replicable sequence) and phenotypic (selectable shape) properties. Using systematic evolution of ligands by exponential enrichment (SELEX), we found a single 58-nt aptamer sequence that assumes two structures with different functions, both of which are required to inhibit the GluR2 AMPA receptor channel. Yet, the two structures, once formed during transcription, appear to be incapable of interconverting through unfolding and refolding, presumably due to their extraordinary structural stability. Thus, our results suggest more broadly that natural RNA molecules can evolve to acquire alternative structures and associated functions. Such divergence of RNA phenotype may precede gene duplication at the genome level.


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