272903 Optimally Designed Capillary Networks for Rapid DNA Separation by Micelle End-Labeled Free Solution Electrophoresis

Wednesday, October 31, 2012: 3:45 PM
411 (Convention Center )
James W. Schneider, Max A. Fahrenkopf, Stephen Istivan, Angela Jones and B. Erik Ydstie, Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA

We have recently developed a novel means to rapidly separate DNA oligomers in electric fields using end-attached surfactant micelles (“micelle-ELFSE”). The method relies on statistical fluctuations in micelle size to provide highly uniform drags for each oligomer in a population, and has long DNA elute before short DNA.  Experiments verify that the method provides single-base resolution of Sanger sequencing products, up to 410 bases in length, in less than 20 minutes.  An additional order-of-magnitude improvement in throughput can be realized by carefully selecting tag size, electric field, electro-osmotic flow, and capillary length for desired separation schemes.  Here we present results from an optimization-based analysis of key parameters in the micelle-ELFSE process to obtain best-possible designs for micelle-ELFSE in both bench-top capillary electrophoresis (CE) and microfluidic formats.

We define a peak-dispersion model for the micelle-ELFSE system and implement the global optimization software package BARON1, designed for non-convex, non-linear optimization problems. This optimization framework also allows us to investigate the performance of alternative capillary configurations such as parallel capillaries, microfluidic serpentines and spirals.

An important insight is that the electric field must not be so large that the oligomers fail to statistically sample an adequate number of micelle sizes during the run.  This effect, which limits runtime, is more pronounced for the longer populations in the sample.  Runtime can be greatly decreased by reversing elution order so that the longest DNA has the greatest residence time for sampling purposes.  We present physically plausible schemes that utilize electro-osmotic counterflows to achieve this goal.  Run times can be further decreased using micelles with a slight negative charge, to hasten the elution of lagging short DNA.  Taken together, these refinements bring runtime for single-base resolution of 410 bases to less than 4 minutes in a bench-top CE format.

  1. N.V. Sahinidis, M. Tawarmalani Mathematical Programming 2005, 103, 2, 225-249

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