Static and dynamic properties of DNA-based polymer structures under constraints and confinement

基于 DNA 的聚合物结构在约束和约束下的静态和动态特性

• 批准号: 58098735
• 负责人: Professor Dr. Frank Cichos
• 金额: --
• 依托单位: Professur für Physikalische Chemie, Mess- und Sensortechnik
• 依托单位国家: 德国
• 项目类别: Research Units
• 财政年份: 2007
• 资助国家: 德国
• 起止时间: 2006-12-31 至 2014-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/58098735?language=en
• 关键词: Static; dynamic; properties; DNA; based

The proposed project is a follow-up application for the second funding period of the Forschergruppe merging the main scientific activities of the currently running projects P1 and P2 into a joint project. The main objective of the joint project P2 is to explore the static and dynamic behaviour of complex, DNA-based polymer structures in liquid environment under simultaneous application of constraints and confinement.We will apply advanced optical methods in combination with force-sensitive (Seidel) techniques to study the local fluctuations of single molecules in one-dimensional confining geometries. We explore properties like internal friction in supercoiled molecules, while changing the degree of confinement systematically. The investigations in confined geometries will be carried out under both, equilibrium conditions, without applying external forces, and application of force fields like hydrodynamic drag and electrical fields. As polymers we will use linear, double-stranded DNA, plasmids and artificially designed DNA assemblies such as branched DNA structures. Implementing local optical probes (fluorescent dyes and/or quantum dots) in a site-specific manner into the molecular structures under investigation, will allow us to study the influence of such particular properties of the polymer like flexural rigidity and morphology on the statistical mechanical behaviour of the complex DNA structures in confined geometries. In particular, by controlling the degree of supercoiling of plasmids, we aim to investigate the direct relationship between topology, rigidity and morphology of the molecule in confinement. The planned studies are of importance from the physics as well as from the engineering perspective, because cognition of the Brownian dynamics of both constrained and confined molecules is also critical for the device design, potentially leading to new applications in nanoconfinement and singlemolecule detection. Here we will concentrate on restriction enzyme mapping and melting of single DNA molecules in nanochannels.

拟议项目是研究小组第二个供资期的后续申请，将目前正在进行的项目P1和P2的主要科学活动合并为一个联合项目。合作项目P2的主要目的是探索复杂的DNA聚合物结构在液体环境中同时应用约束和限制的静态和动态行为。我们将应用先进的光学方法结合力敏（Seidel）技术来研究一维限制几何中单个分子的局部波动。我们探索超螺旋分子的内部摩擦等性质，同时系统地改变限制程度。在有限的几何形状的调查将进行两个，平衡条件下，不施加外力，并施加力场，如水动力阻力和电场。作为聚合物，我们将使用线性双链DNA，质粒和人工设计的DNA组装体，如分支DNA结构。实施本地光学探针（荧光染料和/或量子点）以位点特异性的方式进入正在调查的分子结构中，将使我们能够研究聚合物的这种特定性质的影响，如弯曲刚度和形态对复杂的DNA结构的统计力学行为在受限的几何形状。特别是，通过控制超螺旋的质粒的程度，我们的目标是调查的拓扑结构，刚性和形态的分子限制之间的直接关系。计划的研究是重要的，从物理学以及从工程的角度来看，因为认知的布朗动力学的约束和限制的分子也是至关重要的设备设计，可能导致新的应用在nanoconfinement和singlemolecule检测。在这里，我们将集中在限制性内切酶图谱和纳米通道中单个DNA分子的熔化。