Optically Patterned DNA Prism

描述（由申请人提供）：DNA凝胶电泳可以说是分子生物学中最广泛的实验室方法，是大量分析和制备任务的基础。DNA棱镜是一种按大小连续分离DNA混合物的微流控方法，它可以大大提高这一过程的速度和效率。该装置提供(i)组分的分子量（分析任务）和（ii）出口纯化组分（制备任务）。现有的DNA棱镜是通过熔融二氧化硅的光刻和反应离子蚀刻或胶体自组装制备的。不幸的是，这两种方法都不足以使DNA棱镜进入生物学实验室的常规应用。这项研究计划的长期目标是开发新的纳米结构介质，与凝胶电泳相比，这种介质可以在分离速度和分辨率方面提供数量级的提高。这一特殊应用的目的是：(i)开发一种适合于大规模生产DNA棱镜电泳芯片的工艺，该芯片包含一个大的、完全有序的、均匀的、亚微米孔的三维阵列；（ii）证明这种介质分离DNA的能力。为了实现这些目标，将使用光学图型方法在光刻胶中制造纳米结构，纳米结构将集成到提供脉冲电场的微通道中，并且将使用DNA梯子建立该装置的分离能力。为了帮助该装置的工程设计，光学理论将用于设计结构，蒙特卡罗模拟模型将用于预测与特定孔隙结构的分离。因此，研究计划分为两个具体目标：具体目标1：通过光学图形制作DNA棱镜并展示其分离能力。特定目标2：设计最佳的DNA棱镜来分离不同的DNA大小范围。这项研究意义重大，因为它将大大减少DNA分离所需的成本和时间。光学图型介质应该(i)与凝胶电泳相比，在分离时间和分辨率上有明显的改进，同时（ii）比现有的用于DNA分离的纳米流体装置更容易制造和更坚固。这项研究生产的设备将影响分子生物学，特别是基因组学，为大规模生产用于测定DNA大小和收集产品的芯片提供了一条途径。这项工作是创新的，因为它使用了光子晶体领域发展起来的方法，为生物分子电泳提供了新的介质。作为一个整体，该研究计划将通过提供创建三维有序介质的方法，影响生物微流体和纳米流体的更大领域。

DESCRIPTION (provided by applicant): DNA gel electrophoresis is arguably the most widespread laboratory method in molecular biology, underlying an enormous range of analytical and preparative tasks. The speed and efficiency of this process could be greatly advanced by the DNA prism, a microfluidic method for continuously separating a mixture of DNA by size. This device provides (i) the molecular weight of the components (the analytical task) and (ii) purified components at the outlets (the preparative task). Existing DNA prisms were fabricated via photolithography and reactive ion etching of fused silica or by colloidal self-assembly. Unfortunately, neither of these methods is sufficient to move the DNA prism into routine use in biology labs. The long-term goal of this research program is to develop new nanostructured media that can provide order of magnitude improvements in separation speed and resolution when compared to gel electrophoresis. The objectives of this particular application are to (i) develop a process that is suitable for mass-production of DNA prism electrophoresis chips containing a large, three-dimensional array of perfectly ordered, uniform, sub-micron pores and (ii) demonstrate the ability of this medium to separate DNA. To accomplish these goals, an optical patterning method will be used to fabricate nanostructures in photoresist, the nanostructures will be integrated into a microchannel that provides a pulsed electric field, and the separating power of the device will be established using DNA ladders. To aid in the engineering of this device, optical theory will be used to design the structures and a Monte Carlo simulation model will be used to predict the separation from a particular pore structure. The research plan is thus divided into two specific aims: Specific Aim 1: Fabricate a DNA prism through optical patterning and demonstrate its separation ability. Specific Aim 2: Engineer optimal DNA prisms for separating different DNA size-ranges. This research is significant because it will lead to substantial reductions in the cost and time required for DNA separations. Optically patterned media should (i) exhibit marked improvements in separation time and resolution when compared to gel electrophoresis while (ii) being much easier to fabricate and more robust than existing nanofluidic devices for DNA separations. The devices produced by this research will impact molecular biology in general and genomics in particular by providing a route towards mass-produced chips for sizing DNA and collecting the products. The work is innovative because it uses methods developed in the field of photonic crystals to provide novel media for biomolecule electrophoresis. Taken as a whole, this research program will impact the larger field of biomicrofluidics and nanofluidics by providing approaches to create three-dimensional ordered media. PUBLIC HEALTH RELEVANCE: The proposed work will lead to improved nanoscale systems for rapid and high-resolution separations of DNA. These devices will accelerate a number of key genomics applications, such as DNA fingerprinting of infectious organisms and genome assembly.