(462h) Exploiting the Entropic Trapping Regime to Enhance Separation Performance in Microchip Gel Electrophoresis

Electrophoretic DNA transport through nanoporous hydrogels is characterized by an entropic trapping (ET) mechanism when the DNA size is close to the gel pore size. This mode of transport can yield highly desirable transport properties (e.g., enhanced size dependences of mobility and diffusion for improved separations). But hydrogels have largely been ignored in efforts to understand and exploit ET effects, where the focus has instead centered on simpler idealized ?nanofilter? architectures based on arrays of alternating deep wells and narrow slits (i.e., describable by only two length scales). We have recently developed a new model that captures the inherently heterogeneous pore morphology comprising realistic hydrogel matrices, enabling key features of macromolecular transport in the ET regime to be successfully predicted. We can then directly apply these insights using microchip electrophoresis to measure the size dependence of these parameters (particularly diffusion, a seldom characterized parameter).

Here we use this approach to examine electrophoresis of double-stranded DNA in the 100 to 1000 bp size range under conditions favorable for ET-dominated migration. These experiments have led us to identify a range of conditions where a favorable interplay exists between these migration mechanisms, resulting in improved separation performance (e.g., resolving power that increases with DNA size, the opposite of what is conventionally observed). We also explore application of an oscillatory electric field at a specific frequency, in a specific gel morphology where ET effects dominate, to establish a resonance phenomenon that may significantly improve separation resolution. Our microchip electrophoresis experiments indicate that a significant increase in separation resolution occurs over a specific DNA size range relative to the continuous field case. The effect is tunable by adjusting the magnitude of the electric field to vary the window of DNA size where enhancement occurs. These insights may be useful in efforts to develop nanostructured sieving matrices tailored to exploit ET-dominated transport.