Intramolecular dynamics of dsDNA confined to a quasi-one-dimensional nanochannel

Abstract

The intramolecular dynamics of double-stranded DNA confined to a long, straight, and rectangular channel with a cross-sectional diameter of 125 nm (two times the persistence length) is measured with fluorescence microscopy. The derived intermediate dynamic structure factors show predominant odd modes associated with end-to-end fluctuation and typical stretched exponential relaxation behavior pertaining to Rouse dynamics. Major confinement-induced slowing down of intramolecular fluctuation is observed, which may have important implications in biology and biotechnology. As predicted for free-draining in a quasi-one-dimensional conformation, the Rouse times show a cube rather than the classical, blob model predicted square dependence on the molecular weight.