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

Lab Chip. 2011 Dec 7;11(23):4036-40. doi: 10.1039/c1lc20600a. Epub 2011 Oct 14.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biotin / chemistry
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / isolation & purification*
  • Electricity
  • Microfluidic Analytical Techniques / instrumentation
  • Microfluidic Analytical Techniques / methods*
  • Nucleotides / chemistry
  • Streptavidin / chemistry
  • Surface Properties

Substances

  • DNA, Single-Stranded
  • Nucleotides
  • Biotin
  • Streptavidin