DNA-surfactant interactions

An electrode selectively responsive to an ionic ligand in equilibrium with ligands bound on a macromolecule can be utilized to construct binding isotherms.21 23,35 Dodecylpyridinium halide was chosen in this work as an amphiphilic ligand because an excellent electrode sensitive to it was found. This amphiphile is regarded as a model compound of many classes of biomedical molecules since it combines hydrophobic, aromatic, and polar (cationic) groups. The limited number of papers published on DNA-surfactant interaction,36 further prompted this work. 

Dias, R.S. DNA-surfactant interactions. Encyclopedia of Surface and Colloid Science, 2nd edn. Taylor Francis, London (2010)... 

In the context of DNA-surfactant interactions we will briefly comment on the amphiphilic nature of DNA and its consequences for the solution behavior In discussing the self-assembly behavior of DNA, we begin by broadly discussing other amphiphilic compounds and their self-assembly. Amphiphilic compounds - those that have distinct hydrophilic and lipophilic parts - range from low molecular weight molecules, like surfactants and lipids, to macromolecules, consisting of synthetic graft and block copolymers, and biomacromolecules, like proteins, lipopolysacchar-ides and nucleic acids. 

Complexes based on the double-helix DNA and oppositely charged surfactants are formed in aqueous solution due to Coulombic attraction between the polyanion chain units and surfactant ions, and they are stabilized by hydro-phobic interaction of nonpolar fragments of the surfactant [4-5]. One can expect that such amphiphilic structure of DNA-surfactant complexes will also promote solubility in low-polarity organic solvents. At present, there is lack of information on the behavior of DNA-surfactant complexes in nonaqueous organic solvents. However, some studies indicate that the complexes based on DNA and cationic dialkyl amphiphiles can be soluble in organic media in the presence of a small amount of water [6]. We... 

The effects of surface-active compounds on the thermal denaturation of DNA have been studied [90]. Anionic surfactants interact only weakly with DNA with the exception of N-lauroyl prolylprolylglycine and deoxycholic acid. Myristyl trimethylammonium chloride causes precipitation of DNA at the 1 mmoll level probably by interaction with the phosphate residues of the DNA. The conclusion of this preliminary study was that the structure of the surfactant rather than its surface activity was the determining factor for interaction and that typical surfactants were unlikely significantly to affect DNA structure. 

Interestingly, the cac is much lower when DNA is denaturated, and in the single-stranded conformation, than for the double-helix DNA, as illustrated by binding isotherms (curve 1 vs. curve 2 in Figure 10.2) [10] and in a recent study that deduced the cac from conductivity data [14]. This is a simple example of a stronger DNA-cationic surfactant interaction for ss- than for ds-DNA. 

Here we are interested in the differences in behavior between single- and double-stranded DNA when interacting with cationic surfactants. We have performed then two different studies within this system salt dependence and temperature dependence. 

Differences in CTAB-DNA interactions between the secondary structures of DNA are displayed during the swelling behavior experiments in the presence of high salt content. While CTAB-dsDNA particles placed in 150 mM NaBr monotonously dissolve with time, particles formed with denatured DNA show an initial swelling and dissolve only after 600 h. The observed response is related to the capacity to form stronger DNA-surfactant complexes in the latter system, to which both higher flexibility and amphiphilic character contribute. 

The collapse of the gels is reversible as can be inferred from Figure 10.15, which presents the volume change on addition of an anionic surfactant to a DNA gel, which was collapsed by a cationic surfactant the anionic surfactant interacts strongly with the cationic surfactant, forming different mixed aggregates, and effectively extracts the cationic surfactant from the gel. 

The electrochemical response of analytes at the CNT-modified electrodes is influenced by the surfactants which are used as dispersants. CNT-modified electrodes using cationic surfactant CTAB as a dispersant showed an improved catalytic effect for negatively charged small molecular analytes, such as potassium ferricyanide and ascorbic acid, whereas anionic surfactants such as SDS showed a better catalytic activity for a positively charged analyte such as dopamine. This effect, which is ascribed mainly to the electrostatic interactions, is also observed for the electrochemical response of a negatively charged macromolecule such as DNA on the CNT (surfactant)-modified electrodes (see Fig. 15.12). An oxidation peak current near +1.0 V was observed only at the CNT/CTAB-modified electrode in the DNA solution (curve (ii) in Fig. 15.12a). The differential pulse voltammetry of DNA at the CNT/CTAB-modified electrode also showed a sharp peak current, which is due to the oxidation of the adenine residue in DNA (curve (ii) in Fig. 15.12b). The different effects of surfactants for CNTs to promote the electron transfer of DNA are in agreement with the electrostatic interactions... 

FIGURE 15.13 Schematics of electrostatic interactions between surfactants adsorbed on CNTs and negatively charged DNA molecules. 

An alternative efficient approach to disperse CNTs relies on the use of synthetic peptides. Peptides were designed to coat and solubilise the CNTs by exploiting a noncovalent interaction between the hydrophobic face of amphiphilic helical peptides and the graphitic surface of CNTs (Dieckmann et al., 2003 Zoibas et al., 2004 Dalton et al., 2004 Arnold et al., 2005). Peptides showed also selective affinity for CNTs and therefore may provide them with specifically labelled chemical handles (Wang et al., 2003). Other biomolecules, such as Gum Arabic (GA) (Bandyopadhyaya et al., 2002), salmon sperm DNA, chondroitin sulphate sodium salt and chitosan (Zhang et al., 2004 Moulton et al., 2005), were selected as surfactants to disperse CNTs (Scheme 2.1). 

Common separation methods can be divided into chemical and physical routes. Chemical approaches rely on the interaction of the surface of different CNT types with surfactant molecules. Early work has shown that octadecylamine [94] and agarose gel [95] adsorb preferably on semiconducting SWCNTs, while diazonium reagents [96] and DNA [97, 98] show preference with metallic tubes. The assemblies with adsorbed molecular species are considerably larger and heavier than the indi-... 

The alternative noncovalent functionalization does not rely on chemical bonds but on weaker Coulomb, van der Waals or n-n interactions to connect CNTs to surface-active molecules such as surfactants, aromatics, biomolecules (e.g. DNA), polyelectrolytes and polymers. In most cases, this approach is used to improve the dispersion properties of CNTs [116], for example via charge repulsion between micelles of sodium dodecylsulfate [65] adsorbed on the CNT surface or a large solvation shell formed by neutral molecule (e.g. polyvinylpyrrolidone) [117] around the CNTs. 

DNA has also been immobilized on Au electrode by its interaction with gem-ini surfactants [216]. Moreover, inclusion complexes of viologen-attached alkanethi-ols and a- and /J-cyclodextrins that spontaneously assemble on Au electrodes have been studied [217, 218]. 

Ewert KK, Samuel CE, Safinya CR (2008) Lipid-DNA interactions structure-function studies of nanomaterials for gene delivery. In Dias R, Lindman B (eds) Interaction of DNA with surfactant and polymers. Blackwell, Boston, MA... 

The functionalization of the reverse micelles will create a novel application in bioseparation processes in the analytical and medical sciences. It is therefore important to reveal the recognition mechanism of proteins at the liquid-liquid interface in reversed micellar solutions. DNA is also successfully extracted in a few hours by reversed micelles formed by cationic surfactants in isooctane. The driving force of the DNA transfer is the electrostatic interaction between the cationic surfactants and the negatively charged DNA. Another important factor is the hydrophobicity of the cationic surfactants. Doublechain type cationic surfactants are found to be one of the best surfactants ensuring the efficient extraction of DNA. These results have shown that reverse micellar solutions will become a useful tool not only for protein separation, but also for DNA separation. 

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