430989 Electrophoretic Segregation of DNA-Micelle Complexes in Concentrated Surfactant Solutions

Thursday, November 12, 2015: 9:15 AM
Canyon A (Hilton Salt Lake City Center)
James W. Schneider, Randall Gamble, Palak Pujara and Johnathan M. Goldman, Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA

Micelle end-labeled free solution electrophoresis (micelle ELFSE) is a rapid, gel-free DNA separation technique that can be used to quickly separate oligomers up to 500-700 bases with single-base resolution. Here, micelles serve as a drag tag for the DNA, which shifts the otherwise constant charge-to-friction ratio in a length-dependent way. We have been working to apply the method to separations of kilobase DNA, which are not possible in gel electrophoresis due to limits imposed by biased reptation. Micelle ELFSE does not suffer from biased reptation and is able to resolve kilobase DNA ladders an order of magnitude faster than gels do. The standard model that predicts DNA mobility in ELFSE separation,assumes that the DNA strand and its drag tag are hydrodynamically indistinct. Other models have been proposed that predict mobility in cases where the DNA and drag-tag are hydrodynamically distinct, and their individual friction coefficients are additive. This can occur when the DNA section is much smaller than the drag-tag (“steric segregation”) or when strong electric fields stretch the DNA away from the drag-tag (“field-induced segregation”).

We have recently observed DNA-drag-tag segregation effects that cannot be traced to either mechanism, and are only present using certain long-chain nonionic surfactant buffers. Segregation is identified by a scaling of electrophoretic mobility with the inverse square-root of the DNA length. This scaling is observed for surfactant buffers containing C16E6, but not for shorter nonionics. Interestingly, buffers that exhibit segregation give superior performance in separations, with separation of kilobase-length DNA ladders achieved in less than 3 minutes. We will discuss our efforts to describe this new segregation mechanism at a molecular level and offer insights into improved separations that may be realized under conditions of DNA-drag-tag segregation in micelle-ELFSE.

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