Dielectrophoretic trapping and polarizability of DNA: the role of spatial conformation

Abstract

Dielectrophoresis is a convenient tool for controlled manipulation of DNA with numerous applications, including DNA trapping, stretching, and separation. However, the mechanisms behind the dielectrophoretic properties of DNA are still under debate, and the role of conformation has not been addressed yet. Here, we quantify dielectrophoretic effects on DNA by determining its polarizability from microfluidic single molecule trapping experiments. We systematically study different DNA configurations (linear and supercoiled, 6-164 kbp) and demonstrate that the polarizability strongly depends on the specific conformation and size of the DNA molecules. The connection to its spatial extension is established by measuring diffusion coefficients and from that the radii of gyration; details about the spatial DNA structure are obtained from atomic force microscopy images. For linear and supercoiled DNA fragments, we found a power-law scaling for the polarizabilities and the diffusion coefficients. Our results imply a scaling of the polarizability with the radius of gyration, alpha approximately Rg0.9+/-0.1 and alpha approximately Rg1.6+/-0.2 for linear and supercoiled DNA, respectively. As an application, we demonstrate the separation of DNA topoisomers based on their dielectrophoretic properties, achieving baseline resolution within 210 s. Purified DNA samples of specific configuration may be of great importance for DNA nanoassembly or future DNA vaccines.