The distribution of DNA translocation times in solid-state nanopores

Jiali Li, David Talaga

Research output: Contribution to journalArticleResearchpeer-review

48 Citations (Scopus)

Abstract

This paper systematically investigates the effects of solution viscosity, applied voltage and DNA chain length on the distribution of DNA translocation times through 8 ± 2 nm diameter silicon nitride nanopores. Linear dsDNA translocation events were selected based on the magnitude of current blockage and accumulated into scatter plots of current blockage and event duration (translocation time). The translocation time distribution was fitted to the solution of a Smoluchowski-type equation for 1D biased diffusion to a sink. The DNA drifting speed under bias and diffusion constant were extracted from the fits as functions of solution viscosity, applied voltage and DNA chain length. Combined with the Einstein-Smoluchowski relation, this model allowed evaluation of the viscous drag force on DNA molecules. This model also allowed estimation of the uncertainty in determining the DNA chain length due to the influence of friction on the spread of translocation times in a nanopore measurement. The data analysis suggests that the simple 1D biased diffusion model fits the experimental data well for a wide range of conditions. Some deviations from predicted behavior were observed and show where additional phenomena are likely to contribute to the distribution of DNA translocation times.

Original languageEnglish
Article number454129
JournalJournal of Physics Condensed Matter
Volume22
Issue number45
DOIs
StatePublished - 17 Nov 2010

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Nanopores
DNA
deoxyribonucleic acid
solid state
Chain length
Viscosity
viscosity
viscous drag
Electric potential
electric potential
sinks
Silicon nitride
silicon nitrides
Drag
friction
plots
Friction
deviation
Molecules
evaluation

Cite this

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title = "The distribution of DNA translocation times in solid-state nanopores",
abstract = "This paper systematically investigates the effects of solution viscosity, applied voltage and DNA chain length on the distribution of DNA translocation times through 8 ± 2 nm diameter silicon nitride nanopores. Linear dsDNA translocation events were selected based on the magnitude of current blockage and accumulated into scatter plots of current blockage and event duration (translocation time). The translocation time distribution was fitted to the solution of a Smoluchowski-type equation for 1D biased diffusion to a sink. The DNA drifting speed under bias and diffusion constant were extracted from the fits as functions of solution viscosity, applied voltage and DNA chain length. Combined with the Einstein-Smoluchowski relation, this model allowed evaluation of the viscous drag force on DNA molecules. This model also allowed estimation of the uncertainty in determining the DNA chain length due to the influence of friction on the spread of translocation times in a nanopore measurement. The data analysis suggests that the simple 1D biased diffusion model fits the experimental data well for a wide range of conditions. Some deviations from predicted behavior were observed and show where additional phenomena are likely to contribute to the distribution of DNA translocation times.",
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The distribution of DNA translocation times in solid-state nanopores. / Li, Jiali; Talaga, David.

In: Journal of Physics Condensed Matter, Vol. 22, No. 45, 454129, 17.11.2010.

Research output: Contribution to journalArticleResearchpeer-review

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