DNA separation and analysis have advanced over recent years, benefiting from microfluidic systems that reduce sample volumes and analysis costs, essential for sequencing and disease identification in body fluids. We recently developed the μLAS technology that enables the separation, concentration, and analysis of nucleic acids with high sensitivity. The technology combines a hydrodynamic flow actuation and an opposite electrophoretic force in viscoelastic polymer solutions. Combining hydrodynamics first principles and statistical mechanics, we provide, in this paper, a quantitative model of DNA transport capable of predicting device performance with the exclusive use of one adjustable parameter associated with the amplitude of transverse viscoelastic forces. The model proves to be in remarkable agreement with DNA separation experiments, and allows us to define optimal conditions that result in a maximal resolution length of 7 bp. We finally discuss the usefulness of our model for separation technologies involving viscoelastic liquids.

We present µLAS, a lab-on-chip system that concentrates, separates, and detects DNA fragments in a single module. µLAS speeds up DNA size analysis in minutes using femtomolar amounts of amplified DNA. Here we tested the relevance of µLAS for sizing expanded trinucleotide repeats, which cause over 20 different neurological and neuromuscular disorders. Because the length of trinucleotide repeats correlates with the severity of the diseases, it is crucial to be able to size repeat tract length accurately and efficiently. Expanded trinucleotide repeats are however genetically unstable and difficult to amplify. Thus, the amount of amplified material to work with is often limited, making its analysis labor-intensive. We report the detection of heterogeneous allele lengths in 8 samples from myotonic dystrophy type 1 and Huntington disease patients with up to 750 CAG/CTG repeats in five minutes or less. The high sensitivity of the method allowed us to minimize the number of amplification cycles and thus reduce amplification artefacts without compromising the detection of the expanded allele. These results suggest that µLAS can speed up routine molecular biology applications of repetitive sequences and may improve the molecular diagnostic of expanded repeat disorders.

The dynamics of single DNA molecules conveyed in a viscoelastic fluid flow with an opposing electrophoretic force are investigated by fluorescence microscopy. For balanced hydrodynamic and electrophoretic forces, DNA is confined near the walls with a much smaller elongation than in bulk shear flows. Furthermore, we observe that DNA extension is characterized by intermittent fluctuations, the characteristic time scale of which depends on the flow velocity. A model based on Rouse dynamics explains the contraction of the molecule by the coupling of monomer motion in the transverse and longitudinal directions to the flow induced by transverse viscoelastic forces. Using simulations, we suggest that the occurrence of intermittent fluctuations is analogous to tumbling dynamics characterized by the cyclic spooling motion of end monomers about the molecule center of mass.