Structure and thermodynamic properties of complexes of DNA and synthetic polynucleotides complexes with dodecylamine and dodecyltrimethylammonium bromide as studied by spectral methods

The interactions of the cationic amphiphiles of dodecylamine (DDA) and dode cyltrimethylammonium bromide (DTAB) with native and denatured DNA, single-s tranded polyribonucleotides of polyA and polyU, and a double polyA-polyU he lix were studied by using a pyrene fluorescent probe and UV and CD spectros copies. It was shown that DDA and DTAB are bound cooperatively with DNA and polynucleotides, yielding complexes containing hydrophobic micelle-like cl usters. The critical micelle concentration (CMC) for DDA and DTAB in the pr esence of DNA and polynucleotides was found to decrease by a factor of 30 t o 50 in comparison with the CMCs for the free amphiphiles in solution. An a nalysis of isotherms of binding based on the model for the cooperative bind ing of low-molecular-weight ligands with linear polymers made it possible t o determine the thermodynamic parameters for the process of complexation. T he contribution from the electrostatic interaction of the amphiphile fragme nt with the nucleic acid monomer and from the hydrophobic interaction of th e hydrocarbon chains to the stability of the complex were determined. It wa s shown that the contribution from the electrostatic interaction to the sta bility of the complex is predominant for DNA complexes with DDA; for DNA co mplexes with DTAB, the contributions of the intensity of electrostatic and hydrophobic interactions are comparable. Opposite effects of DDA and DTAB o n the double helix were revealed: DTAB stabilizes the DNA helix, whereas DD A destabilizes it. The latter effect was attributed to the replacement of t he intramolecular hydrogen bonds in A-T and G-C pairs for intermolecular II -bonds of the nucleic bases with the nonsubstituted NH3+ groups of DDA.