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Published online 20 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 9 2802-2818
© 2004 Oxford University Press

Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates

Benjamin S. Edelson, Timothy P. Best, Bogdan Olenyuk, Nicholas G. Nickols, Raymond M. Doss, Shane Foister, Alexander Heckel and Peter B. Dervan*

Division of Chemistry and Chemical Engineering and The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA

*To whom correspondence should be addressed. Tel: +1 626 395 6002; Fax: +1 626 564 9297; Email: dervan{at}caltech.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
This article is dedicated to the memory of Prof. Claude Helene

Received March 19, 2004; Revised and Accepted April 22, 2004

A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein–DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a ß-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.


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