Stretching DNA Molecules in Strongly Confining Nanofluidic Slits

Abstract

We experimentally investigate the stretching and relaxation of individual double-stranded DNA molecules in nanofluidic slits with depths that span the regime between moderate and strong confinement. DNA molecules are stretched by the application of a quadrupole-like homogeneous elongational electric field. In a moderately confining slit we verify the previously observed existence of two distinct relaxation times resulting from the transition from a bulk-like entropic spring force to one that is confinement dependent. In a strongly confining slit with a depth equal to one persistence length we observe the return to a coil–stretch transition that is governed by a single strain rate related to the confined spring constant. By measuring the equilibrium extension as a function of the applied strain rate as well as the relaxation dynamics from a highly stretched initial state, we are able to infer a hydrodynamic friction coefficient in the moderately and strongly confining slits that is in good agreement for a long DNA molecule. Our results are helpful for informing theoretical models of the force–extension relation for semiflexible polymers in quasi-two-dimensional space.