An Improved Coarse Grain Model of DNA and Applications
Thomas A. Knotts IV, Aslin Izmitli, and Juan J. De Pablo. Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691
For several years, single molecule experiments have given insights into the stability of DNA. Many descriptions of DNA, from atomistic to continuum, have proven successful at reproducing observed behavior. We have found, however, that there is no suitable model for several problems of interest, including viral packaging of DNA, nano-fluidic devices, and microarray interactions, where the size of the molecules prohibits atomistic representations, but continuum and linear bead-spring models do not contain the required molecular level of detail. Previously, we described a new coarse grain model in an effort to investigate length scales in the 2 nm to 2 μm range. The model was remarkably successful at accurately predicting sequence specificity, persistence length, bubble formation, and low-concentration salt effects (using the Debye-Huckel approximation for coulombic interactions) in simulations of DNA up to a few microns in length. Despite this achievement, the model did possess some weaknesses which have since been addressed. After a brief introduction to the model, I will describe these corrective efforts as well as an extension of the model to include explicit counter-ions. The latter allows for study of DNA in conditions of higher salt concentration than Debye-Huckel theory allows. Specific emphasis is placed on validation of the model with experimental data. I will conclude with a discussion on including hydrodynamic interactions using Lattice Boltzmann methods to understand DNA flow in micro/nano-fluidic devices and the results of this effort.