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Accessibility of nuclear chromatin by DNA binding polyamides

Dudouet, Brigitte and Burnett, Ryan and Dickinson, Liliane A. and Wood, Malcolm R. and Melander, Christian and Belitsky, Jason M. and Edelson, Benjamin and Wurtz, Nicholas and Briehn, Christoph and Dervan, Peter B. and Gottesfeld, Joel M. (2003) Accessibility of nuclear chromatin by DNA binding polyamides. Chemistry and Biology, 10 (9). pp. 859-867. ISSN 1074-5521. doi:10.1016/j.chembiol.2003.09.001.

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Pyrrole-imidazole polyamides bind DNA with affinities comparable to those of transcriptional regulatory proteins and inhibit the DNA binding activities of components of the transcription apparatus. If polyamides are to be useful for the regulation of gene expression in cell culture experiments, one pivotal issue is accessibility of specific sites in nuclear chromatin. We first determined the kinetics of uptake and subcellular distribution of polyamides in lymphoid and myeloid cells using fluorescent polyamide-bodipy conjugates and deconvolution microscopy. Then cells were incubated with a polyamide-chlorambucil conjugate, and the sites of specific DNA cleavage in the nuclear chromatin were assayed by ligation-mediated PCR. In addition, DNA microarray analysis revealed that two different polyamides generated distinct transcription profiles. Remarkably, the polyamides affected only a limited number of genes.

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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2003 Cell Press. Received 11 June 2003, Revised 9 July 2003, Accepted 24 July 2003, Available online 24 September 2003. Published: September 19, 2003. This work was supported by National Institutes of Health grants CA84192 (to J.M.G.), GM57148 (to J.M.G. and P.B.D.), and GM51747 (P.B.D). B.E. was supported by a Howard Hughes Medical Institute Predoctoral Fellowship, and R.B. was supported by NIH training grant T32 AI07354. We wish to thank Steve Head and members of The Scripps Research Institute DNA core facility for help with microarray analysis.
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Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIH Predoctoral FellowshipT32 AI07354
Issue or Number:9
Record Number:CaltechAUTHORS:20160510-080149335
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Official Citation:Brigitte Dudouet, Ryan Burnett, Liliane A. Dickinson, Malcolm R. Wood, Christian Melander, Jason M. Belitsky, Benjamin Edelson, Nicholas Wurtz, Christoph Briehn, Peter B. Dervan, Joel M. Gottesfeld, Accessibility of Nuclear Chromatin by DNA Binding Polyamides, Chemistry & Biology, Volume 10, Issue 9, September 2003, Pages 859-867, ISSN 1074-5521, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66798
Deposited By: Victoria Brennan
Deposited On:18 May 2016 00:06
Last Modified:11 Nov 2021 00:03

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