New experimental concepts to study DNA dynamics in confined microstructures

我们的项目旨在对单个DNA分子在小通道、孔或狭缝中的运动和内部动力学进行实验研究。几何约束将被引入的微加工聚合物元件，以及通过图案化的水润湿层。为了精确地量化质量和约束依赖的自扩散以及DNA生物聚合物的内部结构弛豫的特征时间尺度，将采用荧光相关光谱（FCS）的各种复杂模式与基于荧光能量转移（FRET）的智能标记程序相结合。这些光谱技术提供了无与伦比的灵敏度，最小的侵入性，并获得数百纳秒和秒之间的动态时间尺度，并且可以很容易地与光学透明的微米和纳米结构相结合。在该项目的第一个资助阶段，将主要研究专门设计的纳米图案中DNA分子的移动性和灵活性，以测试几种理论模型的适用性。进一步概述了在这些条件下测试DNA生物功能的前景。这项工作将有助于一个基本的定性和定量的了解如何局部限制的大分子改变其流动性，内部动态，并最终其（生物）活动。然而，也存在实际相关性，因为复杂分子的分子运动的精确控制是基于大分子流动特性建立适合于分子分离过程的新的微流体和纳米流体部件的先决条件。

Our project aims at experimental studies on the motion and internal dynamics of single DNA molecules in small channels, pores or slits. The geometrical confinements will be introduced by microfabricated polymer elements as well as by patterned aqueous wetting as layers. To precisely quantify both mass and confinement-dependent self-diffusion as well as characteristic time scales of internal structural relaxation of DNA biopolymers, various sophisticated modes of fluorescence correlation spectroscopy (FCS) combined with smart labeling procedures based on fluorescence energy transfer (FRET) will be employed. These spectroscopic techniques provide unparalleled sensitivity, minimal invasiveness, and access to dynamic time scales between several hundred nanoseconds and seconds, and can be easily combined with optically transparent micro- and nanostructures. In the first funding phase of the project, mobility and flexibility of DNA molecules in specifically designed nanopatterns will be primarily investigated, to test several theoretical models for their applicabilitiy. The perspective of testing biological function of DNA under these conditions is further outlined. This work will contribute to a fundamental qualitative and quantitative understanding of how local confinement of macromolecules alters their mobility, internal dynamics, and finally their (biological) activity. However, there is also practical relevance as the precise control of molecular motion of complex molecules is a prerequisite to establish new micro- and nanofluidic components suitable for molecular separation processes, based on macro-molecular flow properties.