Beyond gel electrophoresis: Microfluidic separations, fluorescence burst analysis, and DNA stretching

Methods for obtaining sequence information directly from unamplified genomic length DNA are discussed. Three classes of analysis methods are considered, microfluidic separation methods, DNA stretching, and fluorescence burst measurements. Microfluidic separation methods approaches separate long DNA with higher resolution or higher speed than pulsed field gel electrophoresis. In DNA stretching, the DNA is extended from its bulk equilibrium conformation and imaged using a sensitive camera. Fluorescence burst measurements are essentially flow cytometry experiments using dyed DNA, where the size of each DNA fragment is inferred from the number of photons emitted as it passes by a detector. Combining nanochannel confinement with electrophoretic cytometry also introduces the possibility of obtaining high throughput data on the configurations and dynamics of confined DNA. An oscillating force field is another possible approach to precondition the DNA.