A rapid field-use assay for mismatch number and location of hybridized DNAs

Lab Chip. 2010 Apr 7;10(7):828-31. doi: 10.1039/b925854j. Epub 2010 Feb 23.

Abstract

Molecular dielectrophoresis (DEP) is employed to rapidly (<ms) trap ssDNA molecules in a flowing solution to a cusp-shaped nanocolloid assembly on a chip with a locally amplified AC electric field gradient. By tuning AC field frequency and DNA DEP mobility relative to its electrophoretic mobility due to electrostatic repulsion from like-charged nanocolloids, mismatch-specific binding of DNA molecules at the cusp is achieved by the converging flow, with a concentration factor about 6 orders of magnitude higher than the bulk, thus allowing fluorescent quantification of concentrated DNAs at the singularity in a generic buffer, at room temperature within a minute. Optimum flow rate and the corresponding hybridization rate change by nearly a factor of 2 with a single mismatch in the 26 base docking sequence and are also sensitive to the mismatch location. This dielectrophoresis and shear enhanced pico-molar sensitivity and SNP selectivity can hence be used for field-use DNA detection/identification.

Publication types

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

MeSH terms

  • Base Pair Mismatch*
  • DNA / chemistry*
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis / methods*
  • Time Factors

Substances

  • DNA