Patrick S. Doyle, MIT, Room 66-456, Dept. of Chemical Engineering, 77 Massachusetts Ave, Cambridge, MA 02139, Anthony Balducci, Department of Chemical Engineering, MIT, Room 66-456, Dept. of Chemical Engineering, 77 Massachusetts Ave, Cambridge, MA 02139, Jongyoon Han, Department of Biological Engineering, MIT, Room 66-456, Dept. of Chemical Engineering, 77 Massachusetts Ave, Cambridge, MA 02139, and Pan Mao, Department of Electrical Engineering and Computer Science, MIT, Room 66-456, Dept. of Chemical Engineering, 77 Massachusetts Ave, Cambridge, MA 02139.
The ability to controllably position and manipulate molecules in confinement is important in biomolecular separations and direct visual mapping of DNA. In order to optimally design such devices, the dynamics of molecules and their interactions with the solvent in confined geometries must be understood. We present an experimental study of double-stranded DNA diffusion in slit-like channels under conditions of moderate (height ~ bulk radius of gyration of the DNA) to strong (height ~ persistence length) confinement. Scalings of diffusivity with channel height differ from blob model predictions. Scalings with molecular weight are indicative of hydrodynamic screening when the channel height is smaller than the bulk radius of gyration. We will discuss a scaling-level theory describing the origin of the observed free-draining diffusion dynamics. We find, after using a Zimm pre-average approximation, that hydrodynamic screening can result from a cancellation due to the unique symmetry of the disturbance flow-field in a slit as well as from the algebraic decay of the magnitude of the interactions.