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Blocking transcription through a nucleosome with synthetic DNA ligands

Gottesfeld, Joel M. and Belitsky, Jason M. and Melander, Christian and Dervan, Peter B. and Luger, Karolin (2002) Blocking transcription through a nucleosome with synthetic DNA ligands. Journal of Molecular Biology, 321 (2). pp. 249-263. ISSN 0022-2836. doi:10.1016/S0022-2836(02)00598-3.

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Pyrrole-imidazole (Py-Im) polyamides are synthetic ligands that bind in the minor groove of DNA. Previous studies have established that sites on nucleosomal DNA facing away from the histone octamer, or even partially facing the histone octamer, are fully accessible for molecular recognition by Py-Im polyamides, and that nucleosomes remain fully folded upon ligand binding. Two polyamides that bind within the sea urchin 5S gene nucleosome positioning sequence inhibit both heat-induced nucleosome sliding and transcription by bacteriophage T7 RNA polymerase from the nucleosomal template, but not from histone-free DNA. These polyamides prevent repositioning of the histone octamer by RNA polymerase, and thereby inhibit passage of the elongating polymerase through nucleosomal DNA. These results establish unambiguously the requirement for octamer mobility for transcription of nucleosomal templates by T7 RNA polymerase.

Item Type:Article
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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2002 Elsevier Science Ltd. Received 28 February 2002; received in revised form 11 June 2002; accepted 13 June 2002. This work was supported by grants from the National Institutes of Health (GM57148 to J.M.G. and P.B.D., and GM61909 to K.L.). C.M. was supported by an NIH postdoctoral fellowship (GM19789) and J.M.B. was supported by a predoctoral fellowship from the Ralph M. Parsons Foundation. We thank R. Edayathumangalam for technical assistance. We thank Dr Peter Stockley for the gift of the T7-5 S DNA and for valuable suggestions in the early phase of this work, and Dr Jeff Hayes for helpful advice with hydroxyl radical footprinting. We also thank Dr Peter Geiduschek for discussions.
Funding AgencyGrant Number
NIH Postdoctoral FellowshipGM19789-02
Ralph M. Parsons FoundationUNSPECIFIED
Subject Keywords:nucleosome; transcription; pyrrole-imidazole polyamide
Issue or Number:2
Record Number:CaltechAUTHORS:20160510-081403900
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Official Citation:Joel M. Gottesfeld, Jason M. Belitsky, Christian Melander, Peter B. Dervan, Karolin Luger, Blocking Transcription Through a Nucleosome with Synthetic DNA Ligands, Journal of Molecular Biology, Volume 321, Issue 2, 9 August 2002, Pages 249-263, ISSN 0022-2836, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66813
Deposited By: Victoria Brennan
Deposited On:18 May 2016 18:52
Last Modified:11 Nov 2021 00:03

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