- 學位論文
利用分子模擬探討甲基化對雙股螺旋核酸結構機械性質之影響
Using Molecular Simulation to Study the Effects of Methylation on the Structural and Mechanical properties of Double-Stranded Nucleic Acid
摘要
DNA甲基化是一種表觀遺傳化學修飾的方式，可以在不改變DNA序列的情況下調節基因表達或改變細胞表型。DNA胞嘧啶(cytosine)經過甲基化會吸引相關抑制基因表達的蛋白質或是直接抑制轉錄因子與DNA的結合達到調節基因表達的功能。DNA甲基化對於生物體會產生諸多影響，如生物體的細胞發育、分化以及許多疾病都與DNA甲基化的調控有關。在此論文研究中，我們利用分子動態模擬計算未甲基化的DNA以及甲基化DNA (meDNA)在水溶液中的動態與機械性質的變化，並分析DNA螺旋結構是否受到甲基化影響使兩者在結構上產生差異。我們透過分析DNA螺旋的持續長度(persistence length)、主次溝、Zp值、骨架扭轉角$delta$和$chi$以及糖基皺褶(sugar puckering)這幾個結構參數來暸解甲基化對於DNA結構的影響，結果顯示甲基化除了增加DNA的結構剛性與主次溝的大小，也使DNA的A型構型比例上升。知道甲基化會影響DNA構型後，我們也想知道甲基化對於鹼基對之間結構的影響，所以我們對鹼基對之間的六個主要的結構參數Shift、Slide、Rise、Tilt、Roll、Twist分析甲基化對於鹼基對的影響。計算鹼基對之間結構參數得到的結果顯示，甲基化DNA在這六個鹼基對參數方面產生不同程度的變化。因此我們想知道鹼基對之間的變化對於整體DNA結構拉伸柔性的影響，這部分我們透過計算DNA的輪廓長度與結構的螺旋扭曲值暸解鹼基對變化對於節透的影響，分析的結果顯示甲基化DNA的輪廓長度受到鹼基對之間的變化影響而縮短，而累積螺旋扭曲值則是增加。從分析Zp值、骨架扭轉角與糖基皺褶的結果知道甲基化使DNA出現A構型比例上升，以及使得鹼基對之間結構產生變化，這也影響DNA的輪廓長度與結構的螺旋扭曲值，因此通過分子模擬甲基化對於DNA結構產生影響的結果，能有助於暸解DNA甲基化如何導致基因沉默。
並列摘要
DNA methylation is an epigenetic chemical modification, which can regulate gene expression without changing the DNA sequence. Methylation DNA will attract related proteins that inhibit gene expression or directly inhibit the combination of transcription factors with DNA to regulate gene expression. For example, the development of organisms and many diseases are related to DNA methylation. In the study, the dynamic and mechanical properties of DNA in aqueous solution are calculated by molecular dynamic simulation and analyze the DNA helical structure is affected by methylation. We analyze the structural parameters of the DNA helix persistence length, primary and secondary grooves, Zp value, skeleton torsion angles $delta$ and $chi$, and sugar puckering. The effect of methylation on the structure of DNA shows that methylation not only increases the structural rigidity of DNA and the size of the primary and secondary grooves, but also increases the proportion of A-form conformation of DNA. We also want to know the effect of methylation between base pairs. Therefore, we analyzed the six structural parameters of base pairs: Shift, Slide, Rise, Tilt, Roll, Twist. The results show that methylation increases the flexibility of base pairs. In the last, we calculated the DNA contour length and the cumulative helical twist to understand the effect of the flexibility between base pairs on the mechanical properties of the DNA structure. The result shows that the changes in base pairs decrease the contour length of DNA, and increase the cumulative helical twist. It is shown that methylation increases the proportion of A conformation in DNA, and change the structure status between base pairs. And, effects the contour length of the DNA and the cumulative helical twist of DNA. Therefore the results of molecular simulations of methylation DNA can help to understand how DNA methylation leads to gene silencing.