Selective interactions of a few acridinium derivaties with single strand DNA: Study of photophysical and DNA binding interactions

Abstract

Novel acridinium derivatives 1-3,wherein steric factors have been varied systematically through substitution at the ninth position of the acridinium ring, were synthesized and their interactions with stand and double strand DNA have been investigated through photophysical, biophysical and microscopic techniques. The acridinium derivative 1 exhibited quantitative fluorescence yields (ff@ 1) and high lifetime of 35 ns, while significantly lower fluorescence yields of 0.11 and 0.02 and lifetimes of 3.5 and 1.2 ns were observed for 2 and 3 respectived. The derivatives 1 and 2 having 2-methylphenyl and 2,4 - dimithylphenyl substituents at the ninth position of the acridinium ring showed selective interactions with single strand DNA (ssDNA) with association constants of KggDNA = 6.3-6.6 x 104 M-1, while negligible interactions were observed with double strand DNA (dsDNA). In contrast, the derivative 3 with 2,6-dimethylphenyl substitution showed negligible interactions with both ssDNA and dsDNA. Studies with a series of 19-mer oligonucleotides indicate that these derivatives exhibit significant selectivity for the sequences rich in guanosine (ca. 3-fold) as compared between ssDNA and dsDNA through changes influorescence emission can be used as fluorescent probes for understanding the role of ssDNA in various biological processes and to study various DNA - ligand interactions.