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

Abstract

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.

Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, and DNA Stretching

“…We have focused thus far on separations that rely in some way on the ordered packing of colloidal particles, but there are also a number of studies that have used micelle-forming block polymers such as pluronics, − liquid crystals, − and core–shell nanospheres to create alternatives to agarose gels that exhibit useful properties (such as thermoswitchable viscosities) along with packings that are similar to colloidal crystals. We focus here on the DNA separations in nanospheres .…”

Bicontinuous Cubic Phase of Monoolein and Water as Medium for Electrophoresis of Both Membrane-Bound Probes and DNA

“…Our main aim was to investigate if the monoolein cubic phase can be used as a medium for electrophoresis of membrane-bound molecules and to compare it in this respect to a conventional hydrogel of similar pore size. The type of agarose we use here is modified in order to obtain comparable pore size to the cubic phase and is well-suited as hydrogel control because it follows 19 the Rodbard-Chrambach-Ogston model commonly used for conventional agarose gels. The average pore radius in the 5% gel used here (3.7 nm) is somewhat larger than the 2.5 nm of the cubic phase, but reproducing the cubic-phase value would require about 12% agarose gel, and such solutions are too viscous to handle.…”