利用隨機動力學模擬方法及使用簡化模型研究DNA被脂質分子單層膜吸附作用現象

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

楊博偉(Po-Wei Yang)

指導教授 ： 林滄浪 ； 蕭百沂

國立清華大學/原子科學院/工程與系統科學系/碩士(2007年)

https://doi.org/10.6843/NTHU.2007.00405

摘要

目前，基因治療日益重要，由於以非病毒型基因為載體潛力無窮，以陽離子脂質分子聚集體作為DNA載體的研究日益受到重視。脂質為一兩性分子，自組裝成層狀結構，並進ㄧ步與DNA分子凝縮成三维的複雜體，其構型對於非病毒型基因載體的轉染效率有顯著的影響。而在分子尺度的模擬，分子動力學便成了一個好的研究工具。為了簡化系統，在系統中並未加入真實溶液分子，所以我們利用朗日凡模擬方法與簡化模型探討DNA分子吸附在脂質分子單層膜上的作用現象。
研究上首先探討DNA分子逐一吸附上分子單層膜的過程，包括DNA如何接近帶相反電性脂質分子平面以及未吸附DNA 與已吸附DNA之間的作用現象；另外透過計算吸附過程中各種分子隨距離表面位置之數量密度分佈情形，來探討反離子(counter-ion)與共同離子(co-ion)分別與DNA分子在帶電平面上的吸附位置分佈。同時也討論當吸附過程中，隨著被吸附DNA分子數目的增加，藉著計算DNA分子之質心在平面上的徑向分佈函數(radius distribution function)，得知吸附的DNA分子於帶電平面上具有區域規則排列的現象。待系統達吸附達平衡之後則觀察實際吸附數量與理論值的比例，吾人發現較長之DNA分子具有較高的吸附總值量，且整層吸附層區的電荷會略呈負電性，因此不會再繼續吸附第二層的DNA。
接著即討論額外加入的二價鹽類如何影響吸附的現象，包括加入二價的陽離子如何影響已經吸附上DNA分子的分佈情形，當加入二價陽離子，由於較強的靜電力作用緣故促使原本單層吸附在表面的分散DNA分子有些會局部堆疊成雙層，層與層之間有二價陽離子作為黏著，使得DNA上下層聚集在一起，其他未堆疊的DNA分子則排列成更緊密的狀態，所以加入二價陽離子可以顯著的改變DNA吸附的現象，增加吸附的密度與厚度。

關鍵字

分子動力學 ； 脂質

並列摘要

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.