Flexible elements in the structure of promoter DNA as probed by cationic surfactant binding

Adsorption of DNA and dodecyl trimethylammonium bromide mixtures at the air/water interface: a neutron reflectometry study

The interactions between dodecyl trimethylammonium bromide (C12TAB) and two samples of DNA with widely differing molecular weights have been studied using surface tension and neutron reflectometry. Neutron reflection data show that the surfactant and polymer are adsorbed together in a highly cooperative fashion over a 1000-fold change in surfactant concentration. Furthermore, the shorter DNA fragments adsorb with C12TAB as trilayers at higher surfactant concentrations, with overall layer thicknesses of 65-70 A. The high molecular weight DNA, however, shows only approximate monolayer adsorption with thicknesses varying from 19 to 26 A over the entire range of C12TAB concentrations. The difference in behavior between the different samples is believed to be a result of the rigid double helical structure of DNA which makes the formation of bulk phase polymer/micelle aggregates much less favorable for the short fragments. The resulting increase in the critical aggregation concentration (CAC) then leads to the adsorption of additional surfactant/polymer complex to the underside of the initial stable surface active DNA/C12TAB complex. Comparison with previous results obtained for synthetic polyelectrolytes shows that DNA/C12TAB complexes are not capable of reducing the surface tensions to the extent that other mixtures such as the poly(styrene sulfonate)/C12TAB mixtures do. A possible reason for this is the high rigidity of DNA combined with the fact that its hydrophobic moieties are positioned within the double helix so that the external molecule is largely hydrophilic.

Cationic lipids and cationic ligands induce DNA helix denaturation: detection of single stranded regions by KMnO4probing

Cationic lipids and cationic polymers are widely used in gene delivery. Using 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) as a cationic lipid, we have investigated the stability of the DNA in DOTAP:DNA complexes by probing with potassium permanganate (KMnO4). Interestingly, thymidines followed by a purine showed higher susceptibility to cationic ligand-mediated melting. Similar studies performed with other water-soluble cationic ligands such as polylysine, protamine sulfate and polyethyleneimine also demonstrated melting of the DNA but with variations. Small cations such as spermine and spermidine and a cationic detergent, cetyl trimethylammonium bromide, also rendered the DNA susceptible to modification by KMnO4. The data presented here provide direct proof for melting of DNA upon interaction with cationic lipids. Structural changes subsequent to binding of cationic lipids/ligands to DNA may lead to instability and formation of DNA bubbles in double-stranded DNA.