(211b) Dynamics of Single Tethered DNA In Shear Flow at High Weissenberg Numbers

Organic molecules as charge carriers play a key role in the developing field of “plastic electronics”. To test the electrical properties of organic single molecules, it is necessary to create a closed circuit containing the molecule. We wish to develop a simple, repeatable process to create such circuits using DNA as a scaffold. By using dip-pen nanolithography (DPN) we can control the tethering location of a 3 micron DNA-conducting organic molecule-DNA (DOD) sandwich. The single-tethered DOD is then exposed to shear flow stretching the chain and creating contact between the free end and a second electrode. The free end is subsequently tethered via an additional chemical functionalization and the DNA segments in the bridge are metallized, creating conducting wires separated by an organic single molecule. To make this process repeatable, we must understand the dynamics of a single tethered DNA molecule in shear flow, and in particular, how to effectively stretch DNA chains over a range of sizes to near their maximum extensibility. Moreover, we wish to understand the frequency of the chain end contacting the surface at a given flow Weissenberg number.

In this talk, we will examine the dynamics of a single tethered DNA molecule under the influence of shear flow by a) bead spring simulations, b) full Kratky-Porod simulations and c) single molecule experiments using etched quartz channels that allow visualization in the flow-gradient plan. We demonstrate that very high Weissenberg numbers are necessary to achieve 90+% stretch. Moreover, that, at these flow rates, we are able to achieve “overstretch” of the molecule which must be considered in detail if accurate models for chain end contact are to be developed. Finally, we demonstrate how the close proximity to the wall at high stretch affects the scaling for a number of important statistical properties including the frequency of end contact.