Molecular simulations of DNA transport in solution

Abstract

A proposed novel nanotechnology concept utilizes tunneling conductance measurements across nanoelectrodes to identify individual nucleotides as a DNA strand crosses its path. Such a device offers the possibility of unprecedented rapidity in the detection of DNA sequences. Preliminary simulations of this device have indicated that single-stranded (ss)-DNA sequences behave differently depending on the location of the molecule within the device. Motivated by the similarity of the comparison of the transport properties of the ss-DNA molecule in bulk solution to experimental capillary electrophoresis data, we performed molecular dynamics (MD) simulations of ss-DNA and double-stranded (ds)-DNA in free solution to directly compare electrophoretic mobility as calculated by simulation. Drift velocity at the lowest magnitude applied electric field was consistent with expected experimental data; however, at the larger applied fields necessary under timescale constraints, drift velocity appeared inconsistent with extrapolated experimental values. The simulated electrophoretic mobility values resulting from the drift velocity calculations were also smaller than experiment.

Keywords:

• Molecular dynamics
• DNA
• Electrophoresis
• Genome sequencing

Acknowledgements

We would like to thank Dr Paul Crozier for valuable discussions regarding the use of simulation codes. These simulations were performed using the ACCRE computational facilities at Vanderbilt University, Nashville, TN. Financial support from the NIH (1R21HG003578-01) and DOE CSGF fellowship support (DE-FG02-97ER25308) is gratefully acknowledged.