In ̄uence of structural variation on nuclear localization of DNA-binding polyamide- ̄uorophore conjugates

A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-speci®c DNA-binding molecules that can enter live cells and traf®c to nuclei unaided. DNAbinding polyamides are a class of programmable, sequence-speci®c small molecules that have been shown to in ̄uence a wide variety of protein±DNA interactions. We have synthesized over 100 polyamidēuorophore conjugates and assayed their nuclear uptake pro®les 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 signi®cantly. Generally negative determinants for nuclear access include the presence of a b-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acidturn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological