Motion of DNA in confinement-induced ionic gradients

DNA undergoes conformational changes when confined to small fluidic channels. In particular, confinement of long (> 10 kbp) double-stranded DNA to channels with a cross-section of less than (100 nm)² causes elongation of DNA. It has commonly been observed that long DNA has a tendency to drift within channels, even without an applied flow or electric field. Here we demonstrate that this effect is due to the non-homogeneouos ionic strength within the channel, where anions are depleted compared to the bulk solution, resulting in a lower ionic strength. We combine finite element modeling with single-molecule experiments to show that the motion of DNA is consistent with a drift of DNA from regions of lower to higher ionic strength.