An experimental study of DNA rotational relaxation time in nanoslits

The longest relaxation time (tau(1)) of DNA confined in nanoslits is characterized, and its dependence on molecular weight (M) and channel height (h) is investigated. The relaxation time is extracted from the rotational autocorrelation function obtained from time-sequence images of confined DNA at equilibrium using fluorescence microscopy. We find that tau(1) similar to M(2.45)h(-0.92) , in partial agreement with the predictions of the blob theory (tau(1) similar to M(5/2)h(-7/6)). The experimental results suggest that the assumptions of both a 2-dimensional self-avoiding walk of blobs and a 3-dimensional self-avoiding walk of polymer segments within blobs are valid, while the assumption of nondraining blobs is compromised. We also find (tau(1)/tau(1,bulk)) similar to M-0.1(R-g,R-bulk/h)(0.92), where tau(1,bulk) is the bulk relaxation time and R-g,R-bulk the bulk radius of gyration. Because of the very weak M dependence in above scalings, a master plot of (tau(1)/tau(1,bulk)) vs (R-g,R-bulk/h) is constructed and is used to compare our results to other studies. The plot also provides a convenient way to estimate the relaxation time of DNA in varying degrees of confinement. Using the measured relaxation time and blob theory, we explain recent observations that a very large shear rate is required to deform DNA when it is confined to channels with a dimension comparable to or smaller than the bulk radius of gyration.