Selection and characterization of anti-NF-κB p65 RNA aptamers
Abstract
NF-κB transcription factors include a group of five mammalian proteins that form hetero- or homodimers and regulate hundreds of target genes involved in acute inflammation, HIV-1 transcription activation, and resistance to cancer therapy. We previously used in vitro selection to develop a small RNA aptamer (anti-p50) that binds the DNA-binding domain of NF-κB p502 with low nanomolar affinity but does not bind NF-κB p652. Here, we report the in vitro selection of anti-NF-κB p65 RNA aptamers using parallel in vitro selections with either a fully randomized RNA library or a degenerate RNA library based on the primary sequence of the 31-nucleotide anti-p50 RNA aptamer. We report the characterization of these aptamers with respect to NF-κB target specificity, affinity, minimal sequence requirements, secondary structure, and competition with DNA κB sites. These results expand opportunities for artificial inhibition of NF-κB transcription factor dimers containing p65 subunits.
Keywords
Footnotes
-
Reprint requests to: L. James Maher III, Department of Biochemistry and Molecular Biology, 200 First Street SW, Rochester, MN 55905, USA; e-mail: maher{at}mayo.edu; fax: (507) 284-2053.
-
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.878908.
-
- Received October 16, 2007.
- Accepted February 18, 2008.
- Copyright © 2008 RNA Society