三核苷酸重複序列的異常擴張容易引發許多神經退化性疾病，這些序列容易折疊成二級結構，導致 DNA 在複製、重組及修復時發生滑動，進而造成不正常擴張。人類複製蛋白 A (human replication protein A, hRPA) 是真核生物中含量最豐富的單股 DNA 結合蛋白，其功能在於幫助 DNA 保持在單股的狀態以維持基因組的穩定性，而其亦具有解開部分二級結構的能力並傾向從 5’ 端往 3’ 端解開。在本論文中，我們以 CTG 重複序列所形成的髮夾型結構作為模型系統，並利用單分子螢光共振能量轉移技術探討 hRPA 在不同方向性上對於 CTG 重複序列之解旋機制，首先我們發現人類複製蛋白 A 難以解開對齊髮夾型結構，因此我們將CTG 重複序列的髮夾結構末端，加上一段 10 個核苷酸的單股 DNA，形成突出型髮夾結構 (overhang hairpin)，以利 hRPA 的初始結合，而結果顯示 hRPA 只能部分解開 CTG 重複次數較多的髮夾型結構。我們進一步發現當一顆 hRPA 結合 CTG 重複序列後，髮夾型結構會發生滑動重組，導致形成 hRPA 難以解開的對齊髮夾型結構。然而，在單點突變抑制滑動的實驗中，我們卻發現了與 DNA 方向性有關的結果：當 hRPA 從 3’ 端的突出 DNA 入侵時，單點突變會使其更容易形成完全解開結構；但當 hRPA 從 5’ 端的突出 DNA 入侵時，卻發現其結果有著更低比例的完全解開結構。因此，我們提出了一個模型：在hRPA 從 3’ 端往 5’ 端解開 CTG 髮夾型結構，第二顆 hRPA 便會結合上另一股以 5’ 端往 3’ 端的方向進行更進一步的入侵並解開整個髮夾型解構。然而，在另一個相反的方向性中，第二顆的 hRPA 則不傾向結合上另一股以 3’ 端往 5’ 端的方向解開 CTG 髮夾型結構，進而降低完全解開的效率。因此，我們可以總結在不同的方向性中，hRPA 具有不同的解旋機制。

Abnormal expansions of trinucleotide repeats (TNRs) are responsible for many neurodegenerative disorders. TNRs usually fold into secondary structures that cause DNA slippage during DNA replication, recombination, or repair processes and ultimately lead to abnormal expansions. Human replication protein A (hRPA) is the most abundant single-stranded DNA binding protein in eukaryotes. Its major function is maintaining the single-stranded structure of DNA to keep genomic stability. It is also capable of resolving secondary structures with a polarity preference of 5’ to 3’. In the thesis, we used CTG repeat sequences, which fold into hairpins, as our model system to explore the mechanism of hRPA resolving CTG repeat hairpins in different polarities, utilizing single-molecule fluorescence resonance energy transfer (smFRET) microscopy. We found that hRPA cannot resolve the blunt-end hairpins. We then introduced a short (10-nt) random-coiled overhang to the hairpins for the initial binding of hRPA. The results revealed that hRPA partially resolves long hairpins. We further found that CTG repeat hairpin would undergo hairpin slippage and reorganize into blunt-end hairpin which prohibits the further invasion of hRPA. But when we introduced a single-point mutation to inhibit the slippage reconfiguration, we found polarity-dependent results: The point-mutation boosted the fully resolved hairpin when hRPA invaded from the overhang at 3’ end, while the lowered resolving efficiency was observed when hRPA invaded from the overhang at 5’ end. Hence, we proposed a model: After the hRPA resolves the CTG repeat hairpin from 3’ to 5’, the second hRPA binds to the other strand from 5’ to 3’ and further invades and fully resolves the hairpin. However, with the opposite polarity, the 3’ to 5’ invasion on the other stand is unfavorable and leads to a lowered resolving efficiency. Hence, we can conclude that hRPA has different resolving mechanisms in different polarities.

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