An Experimental Study of DNA Rotational Relaxation Time in Nanoslits

Abstract

The longest relaxation time (τ 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 τ 1 ∼ M 2.45 h -0.92 , in partial agreement with the predictions of the blob theory (τ 1 ∼ 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 (τ 1 /τ 1,bulk ) ∼ M 0.1 (R g,bulk /h) 0.92 , where τ 1,bulk is the bulk relaxation time and R g,bulk the bulk radius of gyration. Because of the very weak M dependence in above scalings, a master plot of (τ 1 /τ 1,bulk ) vs (R g,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.

Electrophoretic Stretching of DNA Molecules in Cross-Slot Nanoslit Channels

“…36 Our epifluorescence microscopy and detection setup as well as data analysis and extraction of the extension and principal axis of the radius of gyration tensor are described elsewhere. 11,20 Electric Field Characterization. The electric field kinematics generated in the intersection region of all cross-slot devices were verified by tracking the center of mass of electrophoresing DNA under conditions in which they do not appreciably deform.…”

Nanofluidic structures with complex three-dimensional surfaces

“…This type of axial nanostructure has been applied to physical studies of DNA conformation and dynamics [10], diffusion [11], and electrokinetic mobility [12], as well as applications including DNA barcoding [13] and separation by analyte motion across boundaries formed by arrays of constrictions within a channel [14].…”

Simulation guided design of a microfluidic device for electrophoretic stretching of DNA

“…We also note that hydrodynamic interaction is neglected because the height of the testing devices is very close to or smaller than the natural size of DNA simulated. [35][36][37] A more detailed explanation is given later in the discussion section. During the simulations, if any bead moves across the boundary, it is moved back to the nearest wall.…”