Elongation, alignment, and electrophoretic migration of double stranded DNA (ds-DNA) are investigated within flow aligned hexagonal Pluronic F127 mesophases contained in microfluidic channels. The DNA molecules are stained with YOYO-1 for visualization of their positions, conformations, and motions, which are recorded by wide-field fluorescence video microscopy. The videos show that the dsDNA molecules are elongated in flow aligned hexagonal F127 mesophases, with the long axis of the DNA molecules aligned parallel to the flow direction. Elongation and alignment are most prevalent near the channel surface in the hexagonal mesophase. In contrast, little or no alignment is observed for the cubic mesophase. DNA elongation and alignment may involve adsorption of one strand end to the glass surface, or its capture by an adsorbed, structured surface layer of F127. Subsequent stretching of the DNA would then occur within the steep flow profile that exists near the glass surface during filling of the microfluidic channels. Videos recorded under the influence of applied electric fields demonstrate that the electrophoretic motions of the elongated, aligned DNA are strongly guided by the hexagonal mesophase structure. Electrophoretic migration is observed to occur exclusively along the local flow alignment direction within hexagonal mesophases for fields applied at 0, 45 and 90 to the flow alignment direction. These results show that ds-DNA interacts strongly with the micelles comprising the gel. These observations will lead to a better understanding of macromolecular interactions with nanostructured gels like those now being investigated for use in drug delivery and chemical separations.