A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Abstract

The separation of DNA fragments by gel electrophoresis has been studied extensively over the last two decades. More recently, similar studies have been carried out to characterize the separation achieved by the current capillary array electrophoresis systems and their sieving polymer solutions. In all cases, at least three different mobility regimes have been shown to exist: the Ogston regime when the radius of gyration of the DNA fragment is smaller than the pore size, the reptation regime when the DNA is larger than the pore size but remains in a random coil conformation, and finally the reptation-with-orientation regime where the DNA orients in the field direction and essentially all resolution is lost. Unfortunately, although theory helps us understand the different regimes and how to properly exploit them, we still have no theory-based general equations that would apply to all regimes. Such equations would be especially useful to analyze data, optimize separation systems and interpolate mobilities to estimate unknown molecular sizes. Recently, van Winkle, Beheshti and Rill (Electrophoresis 2002, 23, 15-19) proposed an intriguing empirical formula that seems to adequately fit the mobility of dsDNA fragments across all three regimes. In this paper, I investigate the relation between this empirical formula and the known theories of gel electrophoresis, and I study the dependence of its fitting parameters upon the experimental conditions. Finally, I examine how this equation may need to be modified to capture the more subtle details predicted by fundamental theories of DNA gel electrophoresis.

Network Formation and Sieving Performance of Self-Assembling Hydrogels

“…The actual data could be described empirically by the following "vWBR" formula: 22 where R, β, and γ are fitting parameters that have recently been related to the known gel electrophoresis theories. 23 In contrast to previously studied PEO solutions, the present R f -PEG hydrogels show a very different relationship between the electrophoretic mobility and DNA size. The curves are no longer sigmoidal shaped and cannot be fitted properly with the empirical vWBR formula (Figure 4).…”

“…The relationship between mobility, μ, and double-stranded DNA length, N base pairs, shows the typical sigmoidal shape attributed to three successive regimes: the Ogston regime (A), the reptation regime (B), and the reptation-with-orientation regime (C). The actual data could be described empirically by the following “vWBR” formula: where α, β, and γ are fitting parameters that have recently been related to the known gel electrophoresis theories 3 Mobility vs base pairs for dsDNA migration through an entangled PEO solution.…”

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

“…Nevertheless, Slater [132] recently showed that this function is related to the equations predicted by theory for the three regimes mentioned above. Amazingly, Eq.…”

Capillary zone electrophoresis and polymer dynamics

“…For electrophoresis in agarose gels, Van Winkle et al propose a functional form that describes well the dependence of μ on DNA size for a wide range of DNA lengths. Slater has discussed this form in terms of expected mobility mechanisms, and proposed extensions and further experimental tests.…”