(142cb) Understanding DNA in Nanoconfinement Through Monte Carlo Simulations and Scaling Theory

DNA behavior in nanoconfinement is a burgeoning research area. Nanodevices with well-defined geometries are particularly useful in DNA separations and single molecule genomic assays. In pursuit to better control DNA in these nanodevices, it is crucial to systematically understand DNA behavior under various degrees of confinement. DNA behavior in moderate and strong confinement regimes have been well understood from the blob theory and deflection theory, respectively. However, the transition regime between those two regimes is unclear. In particular, some contradictory results from experiments exist in literatures. We perform Monte Carlo simulations of DNA in slits and tubes, spanning from very weak to very strong confinement, with special focus on the transition regime. We find that the competition of three lengths (persistence length, chain width, slit height / tube diameter) results in some sub-regimes in addition to the Odijk regime ( strong confinement ) and the classic de Gennes regime ( moderate confinement ).