On the mechanism of electrophoretic migration of DNA in pluronic gels

Capillary electrophoresis of nucleic acids has recently employed gels of self-assembled uncharged triblock copolymers as sieving media. Pluronic F127 contains poly(ethylene oxide) (EO) and poly(propylene oxide) (PO) with the block structure (EO)(106)(PO)(70)(EO)(106). Aqueous solutions of 30% w/w of this polymer are liquids at low temperatures but above 11 degreesC the polymers assemble to micelles that pack into a locally cubic lattice forming a gel-like lyotropic liquid crystal phase. Here we use linear dichroism spectroscopy to study the orientation dynamics of double-stranded DNA molecules during the electrophoresis. In 30% Pluronic F127, a 5400 by DNA migrates with substantial perpendicular orientation of the helix axis, which is in contrast to electrophoresis in agarose gels where the helix axis of DNA is aligned parallel to the field direction. Comparison between linear and circular DNA indicates that neither DNA forth enters the cubic microcrystals at low fields, and when combined with velocity measurements the kinetics of alignment buildup and relaxation suggests that migration instead occurs in grain boundaries between domains of microcrystals.