(549f) Relationship Between Frequency and Deflection Angle in the DNA Prism

The DNA prism is a microfluidic method for separating DNA under the influence of an asymmetric pulsed electric field. In contrast to conventional pulsed field gel electrophoresis, where the DNA all migrate in the same direction, the DNA prism leads to deflection angles that are a function of the molecular weight of the DNA. As a result, the DNA prism permits the simultaneous sizing and continuous separation of large DNA.  While the original DNA prism used an ordered array of microfabricated posts (Huang et al., Nature Biotech., 2004), recent experiments have implemented this strategy in colloidal crystals (Zeng et al., Angew Chem. Int. Ed., 2008, Nazemifard et al., ibid, 2010) with different pore spacings. In relatively large pores, the DNA deflection angle exhibits a maximum as a function of frequency. In very small pore spacing, however, the deflection angle increases monotonically to a plateau, which is what we might expect from predictions of the switchback mechanism (Southern et al., Nucleic Acids Res., 1987).

We will illustrate the origin of the maximum in the deflection angle as a function of frequency by simulating the DNA prism using a sparse array of posts and a Brownian dynamics algorithm. By analyzing the microscopic details of the transport process, we show that the maximum in the deflection angle arises when the electric field changes direction with a frequency that is close to the inverse of the reorientation time. Remarkably, for frequencies near the maximum deflection angle, the DNA prism also features much stronger stretching of the DNA than we observe during dc electrophoresis in the same system. Thus, although the dc electrophoresis is well described by a geometration-like mechanism, the migration in the DNA prism is much closer to classical reputation even if the pore sizes are larger than the radius of gyration of the DNA.