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Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture

Best, Timothy P. and Edelson, Benjamin S. and Nickols, Nicholas G. and Dervan, Peter B. (2003) Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture. Proceedings of the National Academy of Sciences of the United States of America, 100 (21). pp. 12063-12068. ISSN 0027-8424. PMCID PMC218713.

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A series of hairpin pyrrole-imidazole polyamide-fluorescein conjugates were synthesized and assayed for cellular localization. Thirteen cell lines, representing 11 human cancers, one human transformed kidney cell line, and one murine leukemia cell line, were treated with 5 muM polyamide-fluorescein conjugates for 10-14 h, then imaged by confocal laser scanning microscopy. A conjugate containing a beta-alanine residue at the C terminus of the polyamide moiety showed no nuclear localization, whereas an analogous compound lacking the beta-alanine residue was strongly localized in the nuclei of all cell lines tested. The localization profiles of several other conjugates suggest that pyrrole-imidazole sequence and content, dye choice and position, linker composition, and molecular weight are determinants of nuclear localization. The attachment of fluorescein to the C terminus of a hairpin polyamide results in an approximate ~10-fold reduction in DNA-binding affinity, with no loss of binding specificity with reference to mismatch binding sites.

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Additional Information:© 2003 by the National Academy of Sciences. Contributed by Peter B. Dervan, August 8, 2003. We thank M. Waring for helpful discussions. We are grateful to the National Institutes of Health for support (Grant GM57148) and for predoctoral support to T.P.B. (Grant T32-GM08501) and to the Howard Hughes Medical Institute for a fellowship to B.S.E. Mass spectral analyses were performed in the Mass Spectrometry Laboratory of the Division of Chemistry and Chemical Engineering of Caltech, supported in part by National Science Foundation Materials Research Science and Engineering program.
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32-GM08501
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:polymerase-II transcription, DNA-binding polyamides, solid-phase synthesis, minor-groove, recognition, inhibition, promoter, motif, drugs
PubMed Central ID:PMC218713
Record Number:CaltechAUTHORS:BESpnas03
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Official Citation:Timothy P. Best, Benjamin S. Edelson, Nicholas G. Nickols, and Peter B. Dervan Nuclear localization of pyrrole–imidazole polyamide–fluorescein conjugates in cell culture PNAS 2003 100 (21) 12063-12068; published ahead of print September 30, 2003, doi:10.1073/pnas.2035074100
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:929
Deposited By: Tony Diaz
Deposited On:09 Nov 2005
Last Modified:09 May 2016 20:52

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