Theory of DNA electrophoresis: A look at some current challenges

Abstract

Although electrophoresis is one of the basic methods of the modern molecular biology laboratory, new ideas are being suggested at an accelerated rate, in large part because of the pressing demands of the biomedical community. Although we now have, at least for some methods, a fairly good theoretical understanding of the physical mechanisms that lead to the observed peak spacings, widths and shapes, this knowledge is often too qualitative to be used to guide further technical developments and improvements. In this article, we review some selected elements of the current state of our theoretical ignorance, focusing mostly on DNA electrophoresis, and we offer several suggestions for further theoretical investigations.

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

“…Clearly, the first two have units of inverse mobility while the last one has units of DNA molecular size. The various theories of gel electrophoresis also require three parameters because one needs to parameterize the solvent, the sieving matrix and the electric forces that control the dynamics of the DNA fragments during the separation process [1][2][3].…”

“…Therefore, b = b(C) should presumably give the inverse mobility 1/m s (C) of a DNA fragment of "zero" size in a gel of concentration C. Note that this is not the DNA free-solution mobility m 0 commonly used in the field [1][2][3], although these two parameters should be closely related. This will be examined later.…”

“…Although polymer solutions and capillaries have now largely replaced polyacrylamide gel slabs, the physical mechanisms responsible for the separation of charged polyelectrolytes seem to be somewhat similar in both cases. Several excellent reviews have described the empirical and theoretical understanding that has been developed over the last decade and the challenges that remain (see, e.g., [1][2][3]). These theories, however, often make predictions for restricted ranges of experimental parameters because they are based on models that apply only under certain idealized conditions.…”

“…In spite of the fact that current theories are rather successful at predicting the correct power laws and overall curve shapes, they do not provide the user with a useful interpolation formula m = m (M, E, C) that could be used to fit all the data with a small subset of parameters. Similarly, there is no such formula for the diffusion coefficient D (M, E, C), although theoretical scaling laws and experimental data agree here as well [1][2][3][4][5].…”

Continuous separation of biomolecules by the laterally asymmetric diffusion array with out-of-plane sample injection

“…Many other types of devices have successfully exploited the novel effects that arise in a microfabricated environment and are simply not accessible on a larger scale [10,11]. Ideally these devices would be able to deal with of a variety of molecular sizes, ranging from the large chromosomal length DNA molecules to the much smaller single-stranded DNA [12,13] and protein molecules [14]. On a much larger scale, handling of whole cells would also be highly desirable.…”