Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement
| Autor: | Guo-Jun Liao, 廖國鈞 |
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| Rok vydání: | 2013 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 102 We investigate nanoparticle-induced DNA condensation in a confined suspension of dilute DNA molecules and ideal nano-particles (NP) using Langevin dynamics simulation. DNA condensation has been observed in a solution of dilute DNA molecules (persistence length Lp ~ 50 nm) and high concentration of electrostatically neutral nano-particles (diameter Sigma_NP ~ 5 to 35 nm) in recent experimental measurements. It is believed that nano-particles entropically induce an attraction between DNA segments. For nano-particles much smaller than Lp, a DNA molecule can be considered as a chain of connected rods, and the nanoparticle-induced depletion attraction between DNA segments can be regarded as rod-rod attraction. Thus, the strength of the depletion attraction is proportional to the number of persistence length in a DNA chain, Np = L/Lp, the depletion volume NpLp^2(Sigma_ NP + Sigma_ M), and the NP volume fraction Phi, where L is the DNA contour length. We performed Langevin dynamics simulation with coarse-grained DNA molecules and accounted for the most important factors: (1) excluded volume forces between a DNA segment and NP, (2) elasticity of the semi-flexible DNA molecule, (3) bending rigidity of the DNA segment, and (4) steric repulsion between DNA segments. In nano-slit confinement with ionic strength corresponding to intra-cellular environment, owing to the repulsion from the walls, the local density of nano-particles near two walls is lower than the central region, which indicates the strength of intra-DNA attraction is weaker near walls. Thus, as the density of nano-particles Phi increases, the DNA chain will be pushed toward one wall. DNA conformation changes are much different from in an unconfined environment. The height of the nano-slit H relative to the nanoparticle size Sigma_ NP strongly influences the DNA conformation. For H/Lp ~ 1, DNA size decreases monotonically as Phi increases. In contrast, the dependence on Phi is non-monotonic for H/Lp ~ 6, due to the competition between DNA-DNA, DNA-NP, DNA-wall and NP-wall interactions. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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