Comparison of oligonucleotide migration in a bicontinuous cubic phase of monoolein and water and in a fibrous agarose hydrogel.

Porous hydrogels such as agarose are commonly used to analyze DNA and water-soluble proteins by electrophoresis. More recently lyotropic liquid crystals, such as the diamond cubic phase formed by the lipid monoolein and water, has become a new type of well-defined porous structure of interest for both hydrophilic and amphiphilic analytes. Here we compare these two types of matrixes by investigating the nature of retardation they confer to an oligonucleotide that migrates in their respective aqueous phases. The retardation for a 25-mer oligonucleotide was found to be about 35-fold stronger in the cubic phase than in an agarose hydrogel modified to have the same average pore size. According to modelling, the strong retardation is primarily due to the fact that hydrodynamic interaction with the continuous monoolein membrane is a stronger source of friction than the steric interactions (collisions) with discrete gel fibres. A secondary effect is that the regular liquid crystal has a narrower pore-size distribution than the random network of the agarose gel. In agreement with experiments, these two effects together predict that the retardation in the cubic phase is a 30-fold stronger than in an agarose gel with the same average pore radius.