Separation of single-stranded DNA fragments at a 10-nucleotide resolution by stretching in microfluidic channels

Abstract

We report a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its size. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Here we show that this method, originally proposed for separation of long double-stranded DNA chains (>10,000 base pairs), is also applicable to single-stranded (ss) DNA fragments with less than 100 nucleotides (nt). Theoretical analysis indicates that the separation resolution is limited by the fluctuation forces on tethered DNA chains. By employing a microfluidic platform with narrow channels filled with a buffer of low ionic conductivity, we are able to apply a strong electric field to the DNA fragments with negligible Joule heating. Upon stepwise increments of the electric field, we demonstrate efficient separation of short ssDNA fragments at a 10-nt resolution.