722c Coarse-Grained Simulation of DNA Dynamics in Sub-Persistence Length Nanochannels

Yeng-Long Chen, Institute of Physics and Research Center for Applied Science, Academia Sinica, 128 Academia Rd Sec. 2, Nangang, Taipei, Taiwan

Recent advances in optical tools and microscopy techniques have spurred investigation of single DNA molecules in micron- and nano-scale fluidic channels. Classical polymer physics has been shown to be extremely successful in predicting the polymer conformation and dynamics of DNA in various experiments. In sub-100nm channels, it has become possible to study the conformation and dynamics of DNA at and below the length scale of the DNA persistence length (~50nm). We employ Brownian dynamics simulations to investigate DNA dynamics in nanochannels. Our study explores how the bending and thermal energy, the conformational entropy, and the DNA-surface interactions contribute to the macromolecular dynamics. Our simulation results are compared to the predictions of the Odijk theory for confined polymers,and we found that the confinement strongly affects the persistence length segment relaxation, which could affect how double stranded DNA interact with enzymes and proteins in biological processes.