Stochastic Dynamic Simulation Study on the DNA Adsorption by the Lipid Monolayer by Using Coarse-Grained Model

• Main Authors: Po-Wei Yang, 楊博偉
• Other Authors: 林滄浪
• Format: Others
• Language: zh-TW
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/86746613014945972261

碩士 === 國立清華大學 === 工程與系統科學系 === 95 === At present, gene therapy is a very promising curing diseases. Because of the potential of non-viral gene vectors, the cat-ion lipid and DNA complexes were widely used for gene transfer studies that show high transfect efficiency. Lipid is one kind of amphiphilic molecules. The characteristics of having the hydrophilic and hydrophobic parts enable the lipids to self-assembly into specific conformation in the solution. Molecular dynamics (MD) simulations is a well established method tool to understand the properties of the complex bio-molecules system. To simplify the simulation, we simulated DNA interaction with cat-ions lipid monolayer without solvent particles by using stochastic dynamics method with the coarse-grained model. In this thesis, we investigated the phenomenon of DNA adsorption by the cat-ion lipid monolayer at air-water interface with and without divalent salt. First we observed how DNA moves to the charged planar surface by electrostatic attraction between negative DNA and opposite charged plane. Single layer of DNA was absorbed to the lipid monolayer. The absorbed DNA form locally ordered arrays. Longer DNA has batter ordering than shorter DNA when they form adsorbed layer. When divalent ions were added to the system, the DNA adsorbed on the lipid monolayer would rearrange to more compact ordering (small DNA to DNA distance) and some DNA would form two layer clusters. The divalent ions play the role of gluing the DNA together and to induce the formation of closely packed clusters. More DNA can be absorbed to the lipid monolayer with the addition of divalent ions.