DNA ANALYSIS IN A NANOFLUIDIC DEVICE

There has been an increasing interest in developing “lab-on-a-chip” devices, which would allow for DNA analysis in the order of minutes instead of hours, in addition to decreasing sample size and the reagent consumption, therefore dramatically reducing cost.

The purpose of our investigation is to inform future experiments involving the analysis and detection of DNA and single nucleotide polymorphisms (SNP). We start by determining the resolution at which DNA and SNPs can be separated and detected using nanofluidic devices, and determine optimal conditions for successful experiments.  Industry standard DNA ladder solutions are electrokinetically manipulated by applied electric fields within an etched fused silica nanochannel. The movement of fluorescently labeled DNA molecules ranging from 25-300 base pairs is tracked and measured by recording intensity profiles using an EMCCD camera and microscope. These results are used to quantitatively characterize the separation capacity of nanofluidic devices.

Preliminary results show that fluorescently labeled DNA has a tendency to accumulate in the channel and coat the channel walls, and that electroosmotic flow dominates over the electrophoretic movement of DNA in the nanochannels.  To alleviate these obstacles and improve performance, we will repeat our experiments using channels coated with hydrophilic neutral silane.