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Nucleic Acids Research 2005 33(3):838-845; doi:10.1093/nar/gki212
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Published online 8 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Distinct transcriptional responses of RNA polymerases I, II and III to aptamers that bind TBP

Xiaochun Fan, Hua Shi and John T. Lis*

Department of Molecular Biology and Genetics, Cornell University Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +1 607 255 2442; Fax: +1 607 255 6249; Email: jtl10{at}cornell.edu

Received November 5, 2004. Revised January 9, 2005. Accepted January 9, 2005.

The TATA-binding protein (TBP) is a general factor that is involved in transcription by all three types of nuclear RNA polymerase. To delineate the roles played by the DNA-binding surface of TBP in these transcription reactions, we used a set of RNA aptamers directed against TBP and examined their ability to perturb transcription in vitro by the different RNA polymerases. Distinct responses to the TBP aptamers were observed for transcription by different types of polymerase at either the initiation, reinitiation or both stages of the transcription cycle. We further probed the TBP interactions in the TFIIIB•DNA complex to elucidate the mechanism for the different sensitivity of Pol III dependent transcription before and after preinitiation complex (PIC) formation. Lastly, the aptamers were employed to measure the time required for Pol III PIC formation in vitro. This approach can be generalized to define the involvement of a particular region on the surface of a protein at particular stages in a biological process.

Present address: Xiaochun Fan, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA


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 Proc. Natl. Acad. Sci. USAHome page
H. Shi, X. Fan, A. Sevilimedu, and J. T. Lis
RNA aptamers directed to discrete functional sites on a single protein structural domain
PNAS, March 6, 2007; 104(10): 3742 - 3746.
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