Fluorescent probes based on side-chain chlorinated benzo[a]phenoxazinium chlorides: Studies of interaction with DNA

• Photophysical studies of the interaction of six benzo[a]phenoxazinium chlorides with DNA were performed.
• At low phosphate to dye ratios, electrostatic binding to DNA was observed.
• Fluorescence anisotropy measurements were used to confirm the binding mode to DNA.
• These compounds can be used as alternative candidates for DNA labeling in electrophoresis assays.

The interaction of DNA with six water soluble benzo[a]phenoxazinium chlorides mono- or di-substituted with 3-chloropropyl groups at the O and N of 2- and 9-positions, along with methyl, hydroxyl and amine terminal groups at 5-positions, was investigated by photophysical techniques. The results indicated that almost all compounds intercalated in DNA base pairs at phosphate to dye ratio higher than 5. At lower values of this ratio, electrostatic binding mode with DNA was observed. Groove binding was detected mainly for the benzo[a]phenoxazinium dye with NH2·HBr terminal. The set of six benzo[a]phenoxazinium chlorides proved successful to label the migrating DNA in agarose gel electrophoresis assays. These finding proves the ability of these benzo[a]phenoxazinium dyes to strongly interact with DNA.

The interaction of six water-soluble benzo[a]phenoxazinium chlorides with DNA was investigated, revealing a strong interaction of the dyes with this nucleic acid in several binding modes. These benzo[a]phenoxazinium chlorides can also act as fluorescent labels in agarose gel electrophoresis experiments.Figure optionsDownload as PowerPoint slide