(735f) Fluctuation Force On a Tethered DNA Chain
AIChE Annual Meeting
2010 Annual Meeting
Engineering Sciences and Fundamentals
Molecular Modeling and Simulation of Complex Molecules
Friday, November 12, 2010 - 10:35am to 11:00am
We are developing a novel DNA separation method by end tethering the DNA chains to a solid surface and stretching under an electric field (see Figure below). The anchor is such designed that the critical force to detach a DNA chain is independent of its length. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to perfect size-based removal of the DNA strands from the surface. With appropriate end labeling, DNA chains leaving the surface can be detected from their fluorescence signals, which can be used to determine the sequence. In this work, we studied the effects of the solvent-induced fluctuation forces on detachment of the tethered DNA chain by using Brownian dynamics simulations. We observed that the fluctuation force follows a Gaussian distribution with the average magnitude of fluctuation increasing with the chain length and approaching to a constant as the chain length goes to infinite. An empirical correlation is identified between the fluctuation force and the DNA chain length, which coincides with the fluctuation force in the Gaussian chain limit. We also studied the influence of solvent temperature, as well as that of the tethering details on the efficiency of the DNA separation. Understanding fluctuation force on end-tethered chain may help optimize the novel technique for separating long DNA chains. Figure. Schematics of DNA sequencing at a stretch. DNA separation is accomplished by end tethering to a solid surface and then stretching the DNA under an electric field. DNA strands leaving the surface can be detected either by observing the fluorescence signals on the surface or by reading fluorescence signals in a capillary tube that collects the detached DNA.