Statics and dynamics of DNA in nanofabricated devices

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. For dsDNA confined in nanochannels below a critical width roughly twice the persistence length, there is a cross-over in the fundamental physics: a transition occurs between a regime dominated by self-exclusion interactions and a regime dominated by bending rigidity. Using a combination of electron beam lithography (EBL) and nano imprint lithography (NIL) channels have been fabricated that vary in width from 400nm down to 30 nm. The cross-over scale is identified by measuring the extension of DNA as a function of width: above the critical width, the stretch versus width curve has a power-law behavior which we identify with the self-exclusion regime. Below the crossover length, we observe a deviation from the self-exclusion power-law consistent with a theory developed by T. Odijk. The Brownian fluctuations of the confined DNA, which are critical for single molecule sequencing techniques, were also measured as a function of channel width. The relaxation time of the fluctuations exhibits a novel non-monotonic width-dependence: the relaxation time is maximized at the cross-over width.