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

Abstract

We 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.

Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap

“…These considerations are in agreement with the experimentally determined polarizabilities in this work (α 6HxB < α triangle ) and suggest that the DNA origami species behave like colloidal nanoparticles where the polarizability is largely influenced by the surface charge density . It is also interesting to note that the magnitude of α of the two origami species is approximately 1 order of magnitude smaller than that reported for similarly sized linear DNA , or supercoiled DNA . This could be attributed to the compact packing of the double stranded DNA in the case of the origamis compared to free-draining linear DNA or supercoiled DNA with hydrodynamic radii on the order of ∼1 μm. , …”