Published online 7 August 2006
Nucleic Acids Research, 2006, Vol. 34, No. 13 3755-3761
© 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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An RNA aptamer that interferes with the DNA binding of the HSF transcription activator
Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University Ithaca, NY 14853, USA 1 Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine 812-815 Stellar-Chance, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
*To whom correspondence should be addressed. Tel: +1 607 255 2442; Fax: +1 607 255 6249; Email: JTL10{at}Cornell.edu
Received May 7, 2006. Revised June 20, 2006. Accepted June 20, 2006.
Heat shock factor (HSF) is a conserved and highly potent transcription activator. It is involved in a wide variety of important biological processes including the stress response and specific steps in normal development. Reagents that interfere with HSF function would be useful for both basic studies and practical applications. We selected an RNA aptamer that binds to HSF with high specificity. Deletion analysis defined the minimal binding motif of this aptamer to be two stems and one stem–loop joined by a three-way junction. This RNA aptamer interferes with normal interaction of HSF with its DNA element, which is a key regulatory step for HSF function. The DNA-binding domain plus a flanking linker region on the HSF (DL) is essential for the RNA binding. Additionally, this aptamer inhibits HSF-induced transcription in vitro in the complex milieu of a whole cell extract. In contrast to the previously characterized NF-
B aptamer, the HSF aptamer does not simply mimic DNA binding, but rather binds to HSF in a manner distinct from DNA binding to HSF.
Present address: Hua Shi, Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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