423417 Equilibrium Properties of DNA Confined in Nanochannels: A Monte Carlo Chain Growth Approach

Monday, November 9, 2015
Exhibit Hall 1 (Salt Palace Convention Center)
Abhiram Muralidhar1, Douglas R. Tree2 and Kevin D. Dorfman1, (1)Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, (2)Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA

Recent developments in next-generation sequencing (NGS) techniques have opened the door for low-cost, high-throughput sequencing of genomes. However, these developments have also exposed the inability of NGS to track large-scale genomic information, which is extremely important to understand the relationship between genotype and phenotype. Genome mapping offers a reliable way to obtain information about large-scale structural variations in a given genome. A promising variant of genome mapping involves confining single DNA molecules in nanochannels whose cross-sectional dimensions are approximately 50 nm. Despite the development and commercialization of nanochannel-based genome mapping technology, the polymer physics of DNA in confinement remains poorly understood. In this poster, we show results of our studies on the equilibirum and near-equlibrium properties of DNA confined in nanochannels. We performed large-scale Monte Carlo simulations of a coarse-grained model of DNA via the pruned-enriched Rosenbluth method (PERM). In addition, we combined our PERM simulations with computational fluid dynamics (CFD) calculations of the hydrodynamic tensor to estimate the diffusivity of confined DNA. We elucidate our results in the context of existing theories in polymer physics, and discuss how our work can be used to engineer better conditions for genome mapping technology. 

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