Physics of Biological Systems: From Molecule to The Cell

本研究的成果可以概括为三个部分。1.本研究的重点之一是DNA的崩塌跃迁。为了探索DNA分子的单分子动力学，我们研制了双光束激光镊子和可以在测力过程中交换离子溶液的微流体池。利用该装置，我们测量了多价阳离子亚精胺(SpD3+)存在下塌陷DNA的机械响应。在力-伸长曲线上发现了平台型、粘滞型等非线性响应。这反映了DNA沿弧长的塌陷态和拉伸态共存。我们还发现了单分子DNA的重入塌陷转变，这意味着在很高的SPD浓度下，塌陷的DNA再次变成卷曲状态。论文发表了。2.我们还研究了遗传网络问题。数学模型能在多大程度上预测细胞过程的动力学是最基本的问题…生物物理学方面的更多内容。为此，我们合成了一个由正反馈组成的简单遗传网络模块，并用绿色荧光蛋白(GFP)的报告系统测量了它的动力学。测量了启动遗传开关后基因表达的时间进程，并与数学模型进行了比较。反应的生物物理参数由独立的实验确定。我们发现，与非反馈系统相比，正反馈模块使响应延迟。响应函数和延迟时间与模型的预测值吻合较好。3.我们研制了原子力显微镜来探索单分子蛋白质的展开动力学。以SNase作为最简单的蛋白质来测试其去折叠过程。当我们拉伸SNase时，观察到高度非线性的棒状释放类型的响应。力伸长曲线中峰的数目和高度与AFM的拉速有很强的相关性，可以反映折叠和展开过程的反应动力学路径。这个项目仍在进行中。较少

Achievements of this research can be summarized in three parts.1.One of the focuses in this research was collapsing transition of DNA. In order to explore a single molecular dynamics of DNA molecule, we developed double-beam laser tweezers and micro-fluidic cell in which ionic solution could be exchanged during force measurement. By using that apparatus, we measured mechanical response of collapsed DNA under the presence of multivalent cation, Spermidine(SPD3+). We found nonlinear response, such as plateau and stick-release pattern in force-extension curve. Those reflect the coexistence of collapsed state and elongated state of DNA along the arc length. We also found reentrant collapsing transition of single molecular DNA, implying that collapse DNA becomes coiled state again at very high concentration of SPD. Paper was published.2.We also worked on the problem of genetic networks. How far the mathematical model can predict the dynamics of the cellular process is the fundamental questi … More on in biophysics. For that purpose, we synthesized a simple genetic network module consists of a positive feedback, and measured its dynamics by using reporter system with Green Fluorescence Protein (GFP). The time course of the gene expression after the initiation of the genetic switch was measured and compared with mathematical model. Biophysical parameters of the reactions were determined by the independent experiments. We found that the positive feedback module makes a response delay compared with non-feedback system. The response function and the delay time agreed well with the prediction from the model. Paper has been submitted for publication.3.We developed an Atomic Force Microscope to explore the unfolding dynamics of single molecular protein. SNase was used as a simplest protein to test the unfolding process. Highly nonlinear, stick-release type response was observed when we stretch SNase. The number and height of the peaks in force extension curve has strong correlation with pulling speed of AFM, which may reflect reaction kinetic paths of folding and unfolding processes. This project is still going on. Less