以蒙地卡羅法研究ssDNA模型分子在有障礙物的平板中之電泳行為

Abstract

本論文利用蒙地卡羅法及尺度分析，探討了二個主題。第一部份是研究單股DNA模型分子所形成可逆環狀結構的靜態及動態性質。我們所模擬的單股DNA尾端具有一對互補鹼基對，其作用位能為 ，並利用蠕蟲模型來描述其角度彎曲的能量；而開啟-閉合之間的轉換，可由開啟狀態機率隨溫度變化之曲線(Po vs. T)來表現，模擬中發現不論鏈長為何，其開啟狀態的機率會隨著溫度升高而變大，模擬結果指出從閉合狀態到開啟狀態，只與鍵結能量有關，而從開啟狀態到閉合狀態，除了亂度外，還必需考慮到角度彎曲的能量。 第二部份則為研究單股DNA模型分子於有障礙物的平板中之電泳行為，利用放置障礙物阻礙分子鏈的前進速度不一，來達到分離的效果，其作用方式與凝膠電泳相同；經由模擬發現當平板距離太大時，其障礙物相較之下顯得太小，因此並沒有很好的分離效果，但平板距離太小時會發生特殊的現象，即較長的分子鏈由於壓縮變形成長條狀後，反而移動速度比短的分子鏈還快，其鏈長對速度的圖形會呈現打勾的形狀，由於同一個速度下會有二種不同鏈長的分子鏈出現，這對於分離是相當不方便的，因此利用障礙物於平板中的分離效果並不如預期的好。 接下來，我們嘗試在原有的障礙物系統，於帶電分子鏈尾端接上了不帶電的粒子，探討所謂的末端效應。結果顯示，與原有方式得到不同的速度分佈，即分子鏈越長的其移動速度越快，代表末端接上不帶電粒子的效應大於原有的障礙物效應，且其分離的效果會比單純使用障礙物的系統更好，但其整體速度變慢，會拉長分離所需的時間。

There are two topics studied in this work on the basis of Monte Carlo simulation and scaling analysis. Firstly, the diffusion-limited loop formation is investigated for the ssDNA owing to the reversible intrachain reaction. The ssDNA modeled as worm-like chain has reactive sites at both ends with binding energy . The open-to-closed crossover is characterized by the probability curve which depicts the variation of the open-state probability with temperature. According to our study, we find the open-state probability increases as temperature increases. The two-state model is found to be valid. The chain needs to overcome only the binding energy for closed-to-open transition. However, the energy barrier for the open-to-closed transition is found to include both the entropy effect and bending energy. In the second part of the work, we study the electrophoresis of model ssDNA between two parallel plates with barriers. The barriers can hinder the movements of the chains to achieve the purpose of separation. If the distance between plates (dp) is large compared to the barrier height, the result is similar to the free solution electrophoresis. For small dp, the mobility of the chains decreases at first and then increases as chain length increases. This phenomenon may be attributed to the different degree of compression to the chains of different lengths. An uncharged drag-tag attached to the charged chain is also applied in the work. We find that the end-labeled effect is more significant than the barriers effect. However, the mobility of the end-labeled chain becomes slower and thus it needs more time to separate chains of different sizes.