R21: DNA Electrophoresis on nanostructured surfaces

描述（由申请人提供）：我们提出开发一种新的方法，使用纳米结构表面分离DNA和相关的生物分子。我们将使用理论和实验相结合的方法来研究带电生物分子在图案化表面上的电泳。 我们的目标是了解控制表面附近的动态的基本机制，并制定预测模型，这将允许工程的高分辨率分离设备具有最佳的吞吐量和化学选择性。纳米级图案将使用聚合物自组装来压印，而具有拓扑和化学图案组合的更复杂的微米级结构将通过微接触印刷来制造。 将进行电泳，并通过共聚焦、近场显微镜或CCD耦合视频成像观察这些不同表面上DNA链的迁移率。 光漂白后荧光恢复（FRAP）与线性二色性检测（FDLD）相结合，将用于测量表面弛豫时间和扩散率。 将根据图案形态、缓冲液浓度、化学相互作用和链结构进行测量。 从这些测量，我们应该能够阐明表面相互作用，表面电荷，electrophortioc流量，和拓扑限制在带电分子的表面动力学的相对重要性。 由于问题的复杂性，将采用各种互补的理论处理，以获得一个定量模型。粗粒模型将用于将计算密集型分子模型的应用集中到控制系统行为的相空间区域。所使用的理论方法将从分子动力学模拟，缩放分析，到图案化介质上的流动研究。结果应该有广泛的适用性，包括微流控通道，微阵列，复合蛋白质和细胞材料的各种设备和分子。

DESCRIPTION (provided by applicant): We propose to develop a novel methodology to separate DNA and related biomolecules using nanostructured surfaces. We will use a combination of theoretical and experimental methods to study electrophoresis of charged biological molecules on patterned surfaces. The goal is to understand the fundamental mechanisms which control the dynamics near surfaces and to formulate predictive models which will allow the engineering of high resolution separation devices with optimum throughput and chemical selectivity. Nanoscale patterns will be imprinted using polymer self assembly, while more complicated micron scale structures with a combination of topological and chemical patterns will be manufactured by micro-contact printing. Electrophoresis will be performed and the mobility of DNA chains on these various surfaces will be observed either by confocal, near field microscopy, or CCD coupled video imaging. Fluorescence recovery after photobleaching (FRAP) coupled with Linear Dichroism detection (FDLD) will be used to measure surface relaxation times and diffusivity. The measurements will be performed as a function of pattern morphology, buffer concentration, chemical interactions, and chain structure. From these measurements we should be able to elucidate the relative importance of surface interactions, surface charges, electroosmotioc flow, and topological confinement in the surface dynamics of charged molecules. Due to the complexity of the problem, a variety of complementary theoretical treatments will be employed in order to obtain a quantitative model. Coarse grained models will be used to focus the application of more computationally intensive molecular models into those regions of phase space which control the behavior of the system. Theoretical methods used will range from Molecular dynamics simulations, to scaling analysis, to studies of flow on patterned media. The results should have broad applicability to a variety of devices and molecules including microfluidic channels, microarrays, complexed proteins, and cellular materials.