Physics of Biological Systems: From Molecule to The Cell

生物系统物理学：从分子到细胞

• 批准号: 14340119
• 负责人: SANO Masaki
• 金额: $ 9.47万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2002
• 资助国家: 日本
• 起止时间: 2002 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-14340119/
• 关键词: Dynamical Systems; Biological Systems; Condensation of DNA; Single Molecular Measurement; Genetic Networks; レーザーピンセット; DNAの凝縮転移; Worm Like Chain; リエントラント転移; カルシウム波

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

本研究的成果可概括为三部分：1.DNA的塌陷转变是本研究的重点之一。为了探索DNA分子的单分子动力学，我们开发了双光束激光镊子和微流体池，在力测量过程中可以交换离子溶液。通过使用该装置，我们测量了在多价阳离子亚精胺 (SPD3+) 存在下塌陷 DNA 的机械响应。我们发现了非线性响应，例如力延伸曲线中的平台和粘杆释放模式。这些反映了 DNA 沿弧长的折叠状态和拉长状态的共存。我们还发现单分子DNA的可重入塌陷转变，这意味着塌陷的DNA在很高浓度的SPD下再次变成卷曲状态。论文发表了。2.我们还研究了遗传网络的问题。数学模型能够在多大程度上预测细胞过程的动态是生物物理学的基本问题。为此，我们合成了一个由正反馈组成的简单遗传网络模块，并通过使用带有绿色荧光蛋白（GFP）的报告系统测量了其动态。测量基因开关启动后基因表达的时间进程并与数学模型进行比较。反应的生物物理参数通过独立实验确定。我们发现，与无反馈系统相比，正反馈模块会产生响应延迟。响应函数和延迟时间与模型的预测非常吻合。论文已提交发表。3.我们开发了原子力显微镜来探索单分子蛋白质的展开动力学。 SNase 被用作最简单的蛋白质来测试解折叠过程。当我们拉伸 SNase 时，观察到高度非线性、棒状释放型响应。力延伸曲线中峰的数量和高度与AFM的拉伸速度有很强的相关性，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。较少的

项目成果

佐野雅己 他: "スペクトル解析ハンドブック"朝倉書店. 640 (2004)

佐野正美等：《光谱分析手册》朝仓书店 640 (2004)。

M.Mashiko, Y.Tsuji T.Mizuno, M.Sano: "Measurement of Velocity Fields in Thermal Turbulence in Mercury by Ultrasonic Doppler Method"Theoretical and Applied Mechanics Japan. 53(印刷中). (2004)

M.Mashiko、Y.Tsuji T.Mizuno、M.Sano：“通过超声波多普勒方法测量水银中的热湍流速度场”《日本理论与应用力学》53（出版中）。

Y.Murayama, Y.Sakamaki, M.Sano: "Elastic Response of Single DNA Molecules Exhibits a Reentrant Collapsing Transition"Physical Review Letters. 90. 018102 (2003)

Y.Murayama、Y.Sakamaki、M.Sano：“单个 DNA 分子的弹性响应表现出重入折叠转变”物理评论快报。

H.Wada, Y.Murayama, M.Sano: "Model of Elastic Response of Single DNA Molecules in Collapsing Transition"Physical Review E. 66. 061902 (2002)

H.Wada、Y.Murayama、M.Sano：“折叠转变中单个 DNA 分子的弹性响应模型”物理评论 E. 66. 061902 (2002)

Y.Murayama, Y.Sakamaki, M.Sano: "Elastic Response of Single DNA Molecules Exhibits a Reentrant Collapsing Transition"Phys.Rev.Lett.. 90,1. 018102-1-018102-4 (2003)

Y.Murayama、Y.Sakamaki、M.Sano：“单个 DNA 分子的弹性响应表现出重入折叠转变”Phys.Rev.Lett.. 90,1。