Capillary electrophoresis sequencing of small ssDNA molecules versus the Ogston regime: Fitting data and interpreting parameters

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Abstract
We study the mobility of short ssDNA fragments (approximately 30–500 bases) separated by capillary electrophoresis in entangled polymer solutions. Although this corresponds to what is commonly called the Ogston regime, the corresponding sieving concept has never been defined properly nor tested quantitatively. We consider three formulas that have been suggested to fit data in this range of ssDNA sizes, and we discuss how their free parameters are related to actual physical parameters. We test these formulas with new data obtained in our laboratory using a commercial poly-N,N-dimethylacrylamide sieving matrix. Our results show that all three formulas provide decent fits. However, the traditional Ogston equation produces fitting parameters that appear to lack physical meaning. Surprisingly, all three approaches predict that the effective pore size and fiber radius are almost equal. This is the first step towards the development of a systematic approach to optimizing sequencing systems for this size range.