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The Behavior of Polymer Chains Translocation Through a Nanopore

Author: JiangShaoZuo
Tutor: ZhangLinXi
School: Zhejiang University
Course: Condensed Matter Physics
Keywords: Linear polymer Ring -type polymer Knotted polymers Folding polymer Langevin dynamics simulation Migration time Scaling behavior Distributed Sequencing
CLC: Q71
Type: Master's thesis
Year: 2009
Downloads: 42
Quote: 0
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Abstract


Many physiological processes in vivo are related to proteins, DNA, and RNA such as the migration of the polymer, such as, DNA and RNA through the nuclear pore, the protein through the membrane, the virus was injected into the cell and so on. Because of its important value in biotechnology, scientists across the nanopore of biological macromolecules is very interested in research. These migration process research helps us better understand the physiological processes, it will also generate some potential applications, for example, DNA sequencing, gene therapy and controlled drug delivery. In this chapter, we use molecular dynamics method for linear polymer chains through the pores in the process simulated. The results showed that the external electric field strength for different migration time scaling behavior have emerged crossover phenomenon, and in the short-chain compliance τ-N2v, in line with long-chain τ-N1 v. Statistical distribution of the migration time and found that the part before the peak close to the Gaussian distribution, the part after the peak exponential decay. In this chapter, we use molecular dynamics method ring, knotted and folded polymer chain through the pores in the process simulated. For ring polymers in different external electric field force, the migration time scaling behavior of cross phenomenon, and long-chain portion of the scaling exponent close to double-stranded DNA perforation experiments. Whether long-chain or short chain, its scaling exponent numerically than the linear polymer of the results to be small. Migration time behavior and distribution of the results of linear polymer showed a similar trend. For knotted polymers, their migration time novel bimodal distribution of the phenomenon appeared in the peak before the second peak occurred. When the electric field strength increases, the second peak gradually increases, then reaches a maximum, and then slowly decreases until it disappears. The folding polymer, symmetric and asymmetric folding folded migration time corresponding to the distribution of the polymer showed different trends. Fold symmetric distribution of molecular migration time ring polymer with similar results, and present a clear unimodal distribution. Asymmetric collapse polymer migration time distribution is no clear single peak. In mixed NDA perforation experiments, whether the distribution of migration time showed a single peak, can distinguish a polymer asymmetric fold, or fold symmetry or linear. In this chapter, we use molecular dynamics method for single-stranded DNA and other molecules through pores in the process was simulated, and the DNA monomer through the pores in the record time of stay, based on the DNA strand presents a sequence of projections approach. Application of this method to predict the twenty different strands of DNA sequences, the average accuracy rate of 94.7 percent. In the single-stranded DNA through the nanopore experiment, if we can accurately record the residence time of each monomer, the residence time from one figure to predict the entire sequence of the DNA strand, the DNA strand sequence of Sequencing provides an efficient, low-cost method.

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CLC: > Biological Sciences > Molecular Biology > The structure and function of biological macromolecules
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