Statistical properties of the electrophoretic collision of a long DNA molecule with a small obstacle

Abstract

We present experimental results for the collision of a single λ-DNA molecule with isolated cylindrical nanoposts whose radii range from 350 nm to 1.37 μm. The experimental apparatus was fabricated in oxidized silicon using a plasma-thinning method. The probability density for the dimensionless holdup time is described by a gamma distribution, which accurately represents the behavior of the probability density for X collisions and U/J collisions for short-lived and long-lived collisions, respectively. The shape parameter of the gamma distribution reflects the nature of the short-lived collisions, whereas the scaling parameter captures the role of the finite size of the post on the U/J collisions. When rendered in an appropriate dimensionless form, the existing models for the role of electric field gradients extend to all post sizes, indicating that 350 nm is still well above the point-sized limit. Our experiments provide insights into a regime that is very challenging for numerical simulations but highly relevant for separation processes.

Experimental study of the effect of disorder on DNA dynamics in post arrays during electrophoresis

“…At this dye ratio, YOYO-1 bisintercalation into the DNA backbone saturates and external binding to the DNA molecule begins [21]. We have found that a relatively high dye ratio is useful for high spatial and temporal resolution of single molecules based on our previous work [18,22]. While such a high dye ratio was not necessary for data acquisition in the 5-reservoir device, we used a constant dye ratio for both the single molecule and the ensemble level experiments to facilitate comparison between them.…”

“…Neutral, adsorbed polymers suppress electroosmotic flow (EOF) during electrophoresis by forming a dynamic surface coating [23]. While several polymers have been shown to reduce EOF in capillaries [24], we chose PVP based on its success in microfluidic devices [1,5,6,14,18,20,22,25,26]. The device can be conditioned with the polymer overnight to develop a uniform surface coating [22,27,28]; however, several groups have had success conditioning the device for less than one minute [24], or simply including polymer in the running buffer [6,14,20,25,26].…”

“…The high salt concentration of this buffer reduces the size of the electric double layer and is commonly used in microfluidic electrophoresis experiments [14,17,18,20,22,25,26]. Before DNA loading, we heated 200 µL of a solution of approximately 0.1 µg/mL λ DNA in running buffer at 70…”

“…confidence level. The data follow the gamma distribution as was the case for DNA collisions with an isolated post [22] and in a nanofence geometry [20]. From the stationary stage data we were able to estimate the collision probability for the DNA in each of the arrays at 10 V/cm from the number of collisions observed as molecules passed through the viewing window divided by the number of rows in the viewing window.…”

New directions in single polymer dynamics

“…More recently, Doyle and Dorfman formulated new models describing polymer-obstacle collisions based on single molecule data. [46][47][48][49][50] Nanoconfinement Polymer chains in confined geometries have been observed to adopt similar conformations to polymer chains in strong extensional flows. 51 Polymer confinement is typically described using three variables: channel dimension d, polymer persistence length p, and polymer radius of gyration R g .…”