CMU MEMS Laboratory Publication Abstract


in M.S. Thesis, August 2004, Carnegie Mellon University, Pittsburgh, PA.
A nanoelectrode lined nanochannel for single-molecule DNA sequencing
P. Schmidt
This thesis presents a novel idea for a device for single-molecule DNA sequencing. The device consists of a nanometer scale water channel embedded in glass, with an array of evenly spaced nanoelectrodes running at a 90 degree angle with the channel and terminating on both sides of it. These nanoelectrodes permit an electric characterization of the DNA, differentiating between the bases on the basis of their permanent dipoles. The contribution of the DNA’s charged backbone is easily eliminated by clever choice of applied signal and signal processing.

Whereas traditional DNA sequencing methods rely on costly chemical reactions and unscalable machinery, the device only uses DNA and water and allows system-on-a-chip identification. Our theoretical analysis, supported by finite element data, shows that it surpasses the capabilities of all other non-traditional DNA sequencing technologies: We show that a feasibly manufacturable device should be able to classify with approximately 2~19 base accuracy a DNA molecule of arbitrarily long length comprised of two concatenated strands of a single base type.

We also discuss the manufacturing process, the tolerance in the various physical design parameters and their effects on performance. As current molecular dynamics technology is insufficient to accurately capture all the intricacies of the system, we present sufficient information for a full molecular dynamics simulation to be implemented in future work.

© 2004 Carnegie Mellon University, Department of Electrical and Computer Engineering.
Full paper (PDF) (opens in new window).

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