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Improved nuclear localization of DNA-binding polyamides

Nickols, Nicholas G. and Jacobs, Claire S. and Farkas, Michelle E. and Dervan, Peter B. (2007) Improved nuclear localization of DNA-binding polyamides. Nucleic Acids Research, 35 (2). pp. 363-370. ISSN 0305-1048. PMCID PMC1802595.

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Regulation of endogenous genes by DNA-binding polyamides requires effective nuclear localization. Previous work employing confocal microscopy to study uptake of fluorophore-labeled polyamides has demonstrated the difficulty of predicting a priori the nuclear uptake of a given polyamide. The data suggest that dye identity influences uptake sufficiently such that a dye-conjugate cannot be used as a proxy for unlabeled analogs. Polyamides capable of nuclear localization unaided by fluorescent dyes are desirable due to size and other limitations of fluorophores. Recently, a polyamide-fluorescein conjugate targeted to the hypoxia response element (HRE) was found to inhibit vascular endothelial growth factor (VEGF) expression in cultured HeLa cells. The current study uses inhibition of VEGF expression as a biological read-out for effective nuclear localization of HRE-targeted polyamides. We synthesized a focused library of non-fluorescent, HRE-targeted polyamides in which the C-terminus ‘tail’ has been systematically varied. Members of this library bind the HRE with affinities comparable or superior to that of the fluorescein-labeled analog. Although most library members demonstrate modest or no biological activity, two non-fluorescent polyamides are reported with activity rivaling that of the previously reported fluorescein-labeled polyamide. We also show evidence that promoter occupancy by HIF-1, the transcription factor that binds the HRE, is inhibited by HRE-targeted polyamides.

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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Received September 17, 2006. Revised November 2, 2006. Accepted November 3, 2006. Nucleic Acids Research Advance Access originally published online on December 14, 2006. Mass spectrometry analyses were performed in the Mass Spectrometry Laboratory of the Division of Chemistry and Chemical Engineering at the California Institute of Technology, supported in part by the National Science Foundation Materials and Research Science and Engineering Program. The authors gratefully acknowledge the gift of U251 cells from Dr G. Melillo of the National Cancer Institute, and helpful discussions regarding chromatin immunoprecipitation with Dr E. Soragni and Prof. J. M. Gottesfeld of the Scripps Research Institute. We thank the National Institutes of Health for support (GM51747) and predoctoral training fellowships (C.S.J., M.E.F.). We also thank the Ralph M. Parsons Foundation for support (N.G.N.). Funding to pay the Open Access publication charges for this article was provided by NIH GM51747. Conflict of interest statement. None declared.
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NIH Predoctoral FellowshipUNSPECIFIED
Ralph M. Parsons FoundationUNSPECIFIED
Issue or Number:2
PubMed Central ID:PMC1802595
Record Number:CaltechAUTHORS:NICnar07
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Official Citation:Nicholas G. Nickols, Claire S. Jacobs, Michelle E. Farkas, and Peter B. Dervan Improved nuclear localization of DNA-binding polyamides Nucl. Acids Res. (2007) 35 (2): 363-370 first published online December 14, 2006 doi:10.1093/nar/gkl1042
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7579
Deposited By: Lindsay Cleary
Deposited On:06 Mar 2007
Last Modified:26 Nov 2019 11:15

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