Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA-protein interactionsElectronic supplementary information (ESI) available: Additional figures and graphs, electrophoretic mobility shift assay of binding of p53 to DNA, copies of NMR spectra and selected MALDI analyses of the modified DNA. See DOI: 10.1039/c2sc20404e

• Main Authors: Riedl, Jan, Pohl, Radek, Ernsting, Nikolaus P, Orság, Petr, Fojta, Miroslav, Hocek, Michal
• Format: Article
• Language: English
• ISSN: 2041-6520; 2041-6539
• DOI: 10.1039/c2sc20404e

Solvatochromic fluorescent 4-aminophthalimide ( API ) and 4-( N , N -dimethylamino)phthalimide ( DAPI ) were attached covalently to 2-deoxycytidine or -adenosine via a non-conjugated propargyl linker by Sonogashira cross-coupling reactions of N -propargylphthalimides with halogenated nucleosides. The nucleosides were phosphorylated to triphosphates and enzymatically incorporated into oligonucleotides by DNA polymerases. API -labelled DNA was used for the detection of DNA protein interactions with either the sequence-specific p53 protein or a non-specific single strand binding (SSB) protein. Both proteins changed the polarity around the fluorophore and increased (2-3 fold) the intensity of API fluorescence. Solvatochromic fluorescent labels based on aminophthalimide were attached to nucleosides and dNTPs and enzymatically incorporated to DNA for studying of interactions with proteins.