An investigation on interaction between 14mer DNA oligonucleotide and CTAB by fluorescence and fluorescence resonance energy transfer studies

Abstract

Possible interaction mechanisms between oligonucleotide (DNA) of 14 base pairs with cetyl trimethyl ammonium bromide (CTAB) were postulated based on fluorescence and fluorescence resonance energy transfer (FRET) studies. Detailed FRET investigations were carried out by fluorometric titrations of the surfactant with various oligonucleotide duplexes with 5′-tagged fluorescein (donor) (DD), 5′-tagged TAMRA (acceptor) (D_A) and both (D_DA). In general, fluorescence spectra of the duplexes (D_D, D_A and D_DA) revealed a reduction in the fluorescence intensities of 5′-fluorescein as well as 5′-TAMRA and thereafter an attainment of saturation with increase in the surfactant concentration. The observed changes in the oligonucleotide fluorescence intensities for the duplexes under investigation could be attributed to the microenvironmental changes during the oligonucleotide−CTAB interaction. Considering together, it appeared that the interaction is a three-stage process, wherein the initial addition of surfactant caused neutralization of the 14mer at Z_±¹ = 0.8, which is manifested by a slight reduction in fluorescence intensity. Further, addition of the surfactant molecules sharply reduced the fluorescence intensity of the oligonucleotide depicting oligonucleotide induced self-assembly until the second break point (Z_±² = 1.7). From the second break point, a striking resonance energy transfer was observed from donor to acceptor, which revealed shortening of distance between 5′ ends of the oligonucleotides that attained a saturation at Z_±³ = 2.5. Similar three-stage interaction of oligonucleotide with the surfactant has also been observed through fluorometric titrations in the presence of NaCl. However, in the presence of the salt, neutralization of oligonucleotide, surfactant aggregation and FRET occurred at higher charge ratios due to the screening effect of Na⁺ ions followed by an increase in critical association concentration (CAC) of the surfactant. Overall, investigations probe possible structural changes in the 14mer oligonucleotide−CTAB complex upon increase in the surfactant concentration.