Sequence dependent ultrafast electron transfer of nile blue in oligonucleotides

In this contribution we report studies on the nature of binding of nile blue (NB), a well known DNA intercalating drug, with three synthetic DNA oligonucleotides, (CGCAAATTTGCG) ₂, (GCGCGCGCGCGC) ₂ and (ATATATATATAT) ₂. The nature of fluorescence quenching of the ligand upon complexation with the DNAs has been studied using steady state and picosecond-resolved optical spectroscopic techniques. The geometrical restriction on the probe in the DNA microenvironment is measured using picosecond-resolved rotational anisotropy measurements. Our experiments identify both non-specific electrostatic and intercalative modes of interaction of the probe with the DNAs at lower and higher DNA concentrations, respectively. This dual nature of binding is also confirmed through gel electrophoresis experiments. The nature of electron transfer (ET) reaction of GC base pairs with intercalated NB has also been explored. Competitive binding study reveals that binding affinity of the probe is higher with SDS micelles than with the DNAs within its structural integrity in presence of the micelles, as evidenced from circular dichroism (CD) measurements. The complex rigidity of NB with various DNAs and its fluorescence quenching with DNAs elucidate a strong recognition mechanism between NB and DNA.