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

拟议的项目是Forschergruppe第二个资助期的后续申请，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。联合项目P2的主要目标是探索在约束和约束同时应用的液体环境中复杂的基于DNA的聚合物结构的静态和动态行为。我们将结合先进的光学方法和力敏感(Seidel)技术来研究一维限制几何中单分子的局部涨落。我们探索超螺旋分子的内耗等性质，同时系统地改变限制程度。受限几何的研究将在平衡条件下进行，不施加外力，以及在流体动力阻力和电场等力场的作用下进行。作为聚合物，我们将使用线性、双链DNA、质粒和人工设计的DNA组件，如分支DNA结构。将局部光学探针(荧光染料和/或量子点)以特定位置的方式安装到所研究的分子结构中，将使我们能够研究聚合物的特殊性质，如弯曲刚性和形态对受限几何结构中复杂DNA结构统计力学行为的影响。特别是，通过控制质粒的超卷曲程度，我们的目标是研究限制条件下分子的拓扑结构、刚性和形态之间的直接关系。计划中的研究从物理和工程角度都具有重要意义，因为对受限和受限分子的布朗动力学的认识对于器件设计也是至关重要的，这可能导致在纳米限制和单分子检测方面的新应用。在这里，我们将集中在限制酶图谱和单DNA分子在纳米通道中的融化。

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.