Nucleic Acids Research Advance Access originally published online on December 10, 2008
Nucleic Acids Research 2009 37(2):611-621; doi:10.1093/nar/gkn977
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Nucleic Acids Research, 2009, Vol. 37, No. 2 611-621
© 2008 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.
Chemistry and Synthetic Biology |
Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding
School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
*To whom correspondence should be addressed. Tel: +1 404 385 1162; Fax: +1 404 894 2295; Email: hud{at}chemistry.gatech.edu
Received October 21, 2008. Revised November 18, 2008. Accepted November 19, 2008.
A few drug-like molecules have recently been found to bind poly(A) and induce a stable secondary structure (Tm 
60°C), even though this RNA homopolymer is single-stranded in the absence of a ligand. Here, we report results from experiments specifically designed to explore the association of small molecules with poly(A). We demonstrate that coralyne, the first small molecule discovered to bind poly(dA), binds with unexpectedly high affinity (Ka >107 M–1), and that the crescent shape of coralyne appears necessary for poly(A) binding. We also show that the binding of similar ligands to poly(A) can be highly cooperative. For one particular ligand, at least six ligand molecules are required to stabilize the poly(A) self-structure at room temperature. This highly cooperative binding produces very sharp transitions between unstructured and structured poly(A) as a function of ligand concentration. Given the fact that junctions between Watson–Crick and A·A duplexes are tolerated, we propose that poly(A) sequence elements and appropriate ligands could be used to reversibly drive transitions in DNA and RNA-based molecular structures by simply diluting/concentrating a sample about the poly(A)-ligand ‘critical concentration’. The ligands described here may also find biological or medicinal applications, owing to the 3'-polyadenylation of mRNA in living cells.