371781 A Re-Examination of Strongly Confined DNA in Nanoslits

Monday, November 17, 2014
Galleria Exhibit Hall (Hilton Atlanta)
Douglas R. Tree, Wesley F. Reinhart and Kevin D. Dorfman, Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN

DNA mapping and barcoding are important complimentary technologies to traditional high-throughput sequencing for assessing structural variation in large genomes. Linearization of the wormlike polymer, DNA, is a key step in these techniques and is often accomplished through confinement of the polymer in a nanoscale device. However, fundamental properties such as the root-mean-square end-to-end distance for highly confined polymers in even the most basic slit geometry are still not completely understood. This is largely due to the large separation of length scales between the monomer size, confinement length scale and contour length that must be spanned in order to properly account for the entropy of the polymer. To address this, we have directly computed polymer statistics for very long wormlike chains confined in slits using an off-lattice implementation of the pruned-enriched Rosenbluth method (PERM). Unlike the Metropolis algorithm, PERM is a chain-growth method that efficiently generates statistics for confined chains for over four orders of magnitude in contour length. From our calculations, we find that a strongly confined wormlike chain can be thought of as a nearly two-dimensional wormlike chain composed of deflection segments. This description is in contrast to a prior theoretical description of this regime, which attempted to map the behavior directly to a two-dimensional self-avoiding walk. Using our computational results, we show that the latter approach incorrectly treats the excluded volume, which results from three dimensional interactions between deflection segments.

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