1 DNA fluorescence probes based on N-[5-(11-functionalised-undecylamino)- 9H-benzo[a]phenoxazin-9-ylidene]propan-1-aminium chlorides Sarala Naik, M. Sameiro T. Gonçalves and Paulo J. G. Coutinho a * Centro de Química, Universidade do Minho, Gualtar, 4710-057 Braga, Portugal a Centro de Física, Universidade do Minho, Gualtar, 4710-057 Braga, Portugal e-mail: pcoutinho@fisica.uminho.pt Abstract: Several fluorescent benzo[a]phenoxazinium chlorides possessing undecylamino chains with non-functionalised (methyl group) or functionalised terminals (hydroxyl, carboxylic acid and the ester group) as substituents at the 5-position of the heterocycles were used in photophysical studies with DNA. It was found that the functionalised terminal has a dramatic influence on the type of interaction with the hydroxyl group promoting intercalation, while the ester group promotes groove binding. Keywords: Benzo[a]phenoxazinium dyes; Nile Blue; DNA probes; Near-Infrared fluorophores; 1. Introduction Fluorescent probes offer a wealth of information in various fields. The strong influence of the surrounding medium on fluorescence emission, lead the fluorescent molecules to be used as probes for the investigation of physicochemical, biochemical and biological systems. The solubility of the probes and the resulting specific interactions that can be established with the system to be probed are governed by their chemical nature; the hydrophobic, hydrophilic or amphiphilic character of the probe is essential in this regard. Studies on the interaction between DNA and ligands are particularly important for therapeutic 1 and scientific reasons. 2,3 Among other molecules, Nile Blue, a benzo[a]phenoxazinium dye with a planar and rigid structure, has been reported as DNA probe, 4 and was considered a good intercalator of DNA double helix. 5 Mitra and collaborators clearly identified non-specific electrostatic and intercalative modes of interaction of the label with DNA at lower and higher DNA concentrations, respectively. 6 Minor or major groove DNA binding of molecules is another possibility of interaction with nucleic acids. 7,8