Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

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DOIResolve DOI: http://doi.org/10.1039/c4an01364f
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TypeArticle
Journal titleAnalyst
ISSN0003-2654
Volume139
Issue22
Pages60446051; # of pages: 8
AbstractWe investigate the trapping mechanism of individual DNA molecules in ordered nanoporous structures generated by crystalline particle arrays. Two requisites for trapping are revealed by the dynamics of single trapped DNA, fully-stretched U/J shapes and hernia formation. The experimental results show there is a stronger possibility for hernias to lead the reorientation upon switching directions of the voltage at high field strengths, where trapping occurs. Fully stretched DNA has longer unhooking times than expected by a classic rope-on-pulley model. We propose a dielectrophoretic (DEP) force reduces the mobility of segments at the apex of the U or J, where field gradients are highest, based on simulations and observations of the trapping force dependence on field strength. A modified model for unhooking time is obtained after the DEP force is introduced. The new model explains the unhooking time data by predicting an infinite trapping time when the ratio of arm length differences (of the U or J) to molecule length Δx/L < β, where β is a DEP parameter that is found to strongly increase with electric field. The DNA polarizability calculated with the DEP model and experimental value of β is of the same magnitude of reported value. The results indicate the tension at the apex of U/J shape DNA is the primary reason for DNA trapping during pulsed field separation, instead of hernias.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); Security and Disruptive Technologies
Peer reviewedYes
NPARC number21273053
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Record identifierf17c13d5-8ff0-4537-9ce7-6326c506d124
Record created2014-12-10
Record modified2016-05-09
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