Wednesday, November 11, 2015: 8:30 AM
150A/B (Salt Palace Convention Center)
We will present a coarse-grained, Rouse-type model for the internal dynamics of a DNA molecule confined in a nanochannel. The model is multi-scale in nature, with the spring constants and friction coefficients in the Rouse-type model obtained from Pruned-Enriched Rosenbluth Method (PERM) simulations of a fine-scale, discrete wormlike chain model. In this way, we are able to span an enormous range of length scales, from the 5 nm beads used in the fine-scale model to the almost millimeter-long DNA molecules that are used in state-of-the-art genomics experiments. Indeed, our results are particularly important for the modeling of genome mapping technologies, where such long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distance between these probes (the so-called “DNA barcode”) are measured. The error in such measurements arises primarily from the dynamic fluctuations of DNA molecules in nanochannels. As these measurements are performed for the barcode distances or for the segments of different lengths, we focus on understanding the dynamics of various segments of the DNA chain. We find that the relaxation time of a segment of a particular size depends on the position of that segment in the chain. Interestingly, the relaxation time decreases as the segment position becomes close to the ends. This result suggests that the dynamic fluctuations are minimum at the ends and maximum at the center of the chain. These results on relaxation times and dynamic fluctuations can be useful in reducing the error in genomic measurements.