Electrophoresis of a Charged Polymer in a Nanopore
Date Issued
2008
Date
2008
Author(s)
Yu, Li-Wei
Abstract
A DNA molecule’s conformation and configuration as well as its number of bases and sequence are important characteristics that affects its functional properties. A simple method that can simultaneously determine DNA conformation and base number would be advantageous. Fologea and his coworkers proposed a method in which a nucleic acid polymer translocates through a pore in a voltage biased silicon nitride membrane. The ionic conductivity is partially blocked. Analyses of blockage amplitudes and blockage durations can reveal information about polymer length and conformation.n this work, Brown Dynamics was used to study the behavior of polyelectrolytes electrophoresed through a nanopore. It was found that the measured time integral of blocked ionic current, also known as the event-charge-deficit, ecd, for each translocation event was the same regardless of whether the molecules were in a linear or circular form. However, when polyelectrolytes containing different number of monomers were electrophoresed through a nanopore, the ecd depended strongly on the total length. Simulation results also showed that the magnitude of the current blockages was strongly affected by a molecule’s form. Circular polyelectrolytes blocked more ionic currents than linear ones did. Yet, the blockage duration times of circular polyelectrolytes were consistently shorter than those of the linear ones with identical chain length. Our simulation confirmed that it is possible to simultaneously determine both DNA conformation and base number by using a single nanopore assay.
Subjects
nanopore
charged polymer
electrophoresis
Type
thesis
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