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Can gel concentration gradients improve two‐dimensional DNA displays?
Author(s) -
Sean David,
Wang Yixuan E.,
Slater Gary W.
Publication year - 2014
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.201300412
Subject(s) - fragment (logic) , porosity , gel electrophoresis of nucleic acids , electrophoresis , temperature gradient gel electrophoresis , gel electrophoresis , dna , materials science , chromatography , chemical physics , biological system , chemistry , computer science , algorithm , biology , biochemistry , 16s ribosomal rna , composite material , gene
The abrupt reduction in gel electrophoretic mobility that is observed when a dsDNA fragment is partially denatured has recently been predicted to exhibit a dependence upon the gel pore size. Using theoretical modeling, we demonstrate that this dependence can be exploited and used to improve the performance of 2D display of DNA. We report experimental evidence of this dependence and propose a new separation system in which a gel porosity gradient is utilized in a way analogous to temperature or denaturant gradients in traditional 2D display. Such gel porosity gradients can also be used in conjunction with denaturant gradients to improve 2D display results. We test these new ideas by modeling the fragment mobilities and computing the final fragment positions to find optimal 2D separation conditions.