Electrophoresis of ssDNA through nanoelectrode gaps from molecular dynamics: Impact of gap width and chain length

CM Payne and XC Zhao and PT Cummings, JOURNAL OF PHYSICAL CHEMISTRY B, 112, 12851-12858 (2008).

DOI: 10.1021/jp802258v

Molecular dynamics simulations were performed to study the translocation of single-stranded (ss) DNA through the nanoscale gap between the nanoscale electrodes of a proposed genomic sequencing device. An applied electric field forces the ssDNA to move in the direction of the nanoscale gap in platinum electrodes. A series of simulations utilizing eight different nanoscale gap distances as well as seven different nucleotide chain lengths were performed to determine the impact of these variables on the overall design of the sequencing device and the translocation behavior of ssDNA. The results clearly indicate a threshold value of the gap width below which the ssDNA will readily enter and traverse the nanoscale gap. Translocation velocities obtained for various chain lengths were consistent with simulated bulk data; however, successful translocation was inconsistent, possibly related to the sample's affinity for the metal electrodes. An attempt at overcoming this barrier was made through the implementation of shaped electrodes as well as prethreading of the ssDNA sample.

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