Nucleic Acids Research Advance Access originally published online on March 17, 2009
Nucleic Acids Research 2009 37(8):e59; doi:10.1093/nar/gkp154
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Nucleic Acids Research, 2009, Vol. 37, No. 8 e59
© 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.
Methods Online |
Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers
Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
*To whom correspondence should be addressed. Tel: +1 212 342 5610; Fax: +1 212 305 3475; Email: rp2164{at}columbia.edu
Received January 8, 2009. Revised February 23, 2009. Accepted February 24, 2009.
The full understanding of dynamics of cellular processes hinges on the development of efficient and non-invasive labels for intracellular RNA species. Light-up aptamers binding fluorogenic ligands show promise as specific labels for RNA species containing those aptamers. Herein, we took advantage of existing, non-light-up aptamers against small molecules and demonstrated a new class of light-up probes in vitro. We synthesized two conjugates of thiazole orange dye to small molecules (GMP and AMP) and characterized in vitro their interactions with corresponding RNA aptamers. The conjugates preserved specific binding to aptamers while showing several 100-fold increase in fluorescence of the dye (the ‘light-up’ property). In the presence of free small molecules, conjugates can be displaced from aptamers serving also as fluorescent sensors. Our in vitro results provide the proof-of-concept that the small-molecule conjugates with light-up properties can serve as a general approach to label RNA sequences containing aptamers.