Synthesis and fluorescence studies of some new fluorophores and their effect on hybridization of oligodeoxyribonucleotides.

Some novel fluorophores, viz. 6-(6-isobutyrylamino-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)-hexanoic acid (1), 6-(6-dimethylamino-1,3-dioxo-1H, 3H-benzo[de]isoquinolin-2-yl)-hexanoic acid (2), 6-(6-benzoylamino-1, 3-dioxo-1H, 3H-benzo[de]isoquinolin-2-yl)-hexanoic acid (3), 6-(6-amino-1-oxo-1H, 3H-benzo[de]isoquinolin-2-yl)-hexanoic acid (4) and 6-(6-amino-1H,3H-benzo[de] isoquinolin-2-yl)-hexanoic acid (5) have been designed, synthesized and characterized. Their comparative fluorescence has been studied in different organic solvents and aqueous solutions containing inorganic ions. Out of these, two fluorophores, 1 and 2 have been used for labelling of nucleosides which were finally converted into their phosphoramidites, and used for labelling of oligodeoxyribonucleotides through covalent attachment. These fluorophores after attachment on oligodeoxyribonucleotides showed good fluorescence signals and higher hybridisation affinity than unlabelled oligodeoxyribonucleotides.