脫氧核糖核酸 (DNA) 的物理性質於基因工程中非常重要, 當中又以 DNA 的伸展性影響最為
廣泛。 舉例而言, DNA於複製過程中必須被拉伸至平直的 B 結構以利重組。 另一方面, 聚合酵素連鎖反應 (PCR) 常用於複製 DNA, 近年來更提出以自然對流式聚合酵素連鎖反應 (RB-PCR)連續反覆的複製特定 DNA。 故本研究採用數值方法, 探討 DNA 於 RB-PCR 反應中所產生的拉伸行為。

本研究使用粗粒化方法 (coarse-graining method) 將連續的真實 DNA 轉換為可數值模
擬的片段小珠彈簧模型 (bead-spring model), 粗粒化後獲得的物理參數將用以決定各小珠所受之力量。 隨後, 搭配朗之萬方程式 (Langevin equation) 可計算出各小珠的速度與位移。 藉由小珠彈簧模型的變化探討 DNA 與周圍流場的交互作用。

本研究模擬之 DNA 於均勻流中之伸長量與 Perkins et al. [1]的實驗結果接近。 同時, 獲得DNA 伸長量與均勻流入口速度、DNA 完全拉伸長度之關係。 隨後, 模擬完全拉伸長度44.0μm 之 DNA 於微型 RB-PCR 反應器中所產生的運動與拉伸。 根據模擬結果可以分析 DNA於反應器中之伸長量、 旋轉角度、 小珠彈簧模型之各彈簧長度、 作用於各小珠之水作用力與小珠的速度大小。 上述資訊可用以預測 DNA 於 RB-PCR 複製反應中可能出現的行為。

The physical properties of deoxyribonucleic acid(DNA) is important in genetic engineering. In particular, the extensibility of the DNA chain is considered in many DNA applications. For example, the DNA chain must be extended to a straight B-form for the recombination in the DNA replication. In addition, the DNA replication can be implemented by polymerase chain reaction (PCR). Recently, Rayleigh-B′enard polymerase chain reaction (RB-PCR) which is driven by natural convection was proposed.

In order to investigate the behavior of the DNA chain in the RB-PCR, the numerical simulation of the DNA chain stretched at the RB-PCR reactor is performed. In order to predict behavior of the DNA chain by the numerical analysis, the coarse-graining method that transfers a continuous real DNA chain into a sectional bead-spring model is implemented. Meanwhile, the physical parameters of the coarse-grained DNA chain can be determined and then the force exerted on a bead of the bead-spring model is derived. The Langevin equation is used to calculate the movement of those beads.

From the numerical results, the extension of the DNA chain in a uniform flow is
predicted and compared with Perkins’et al. [1] experimental data. Also, the relationship among the inlet velocity of the uniform flow, fully extended length and the extension of the DNA chain are obtained. Furthermore, the simulation of the DNA chain of L=44.0 μm stretched at a micron RB-PCR reactor is performed. As a result, the extension and rotated angle of the DNA chain are provided. Also, the length of the spring, hydrodynamic drag exerted on the bead and the magnitude of the velocity of the bead of the bead-spring model can be investigated. Those information could be use to predict the behavior of the DNA chain during the replication at the RB-PCR reactor.

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