CAREER: Dynamics of DNA during Electrophoresis in Artificial Sieving Matrices

项目编号cts -0642794首席研究员：Kevin D. dorfman大学/机构：明尼苏达大学双城分校职业：人工筛分基质中电泳过程中的DNA动力学本项目涉及DNA微流体电泳的理论建模和实验研究。DNA电泳不仅是分子生物学和遗传学中最重要的工具之一，也是测试聚合物动力学基本理论和分离过程粗粒度平均的理想平台。拟议的研究将涉及与聚合物物理、随机过程和化学工程相关的主题，跨越多个长度尺度，将微观运动与宏观观察联系起来。研究部分是一个集成的理论和实验程序，解决了在微制造柱阵列中DNA分离过程中出现的一系列基本问题，包括外场中的受阻弛豫现象和柱晶格顺序的作用。这项研究的重点是在真实的分离装置中，由于哨所的接近而产生的影响，而现有的DNA碰撞知识体系并没有解决这一问题，孤立的哨所。实验工作跨越了多个尺度，结合了几毫米范围内输运的集合平均测量和大分子尺度上局部输运的详细单分子观察。微观洞察将用于构建基于连续时间随机游走理论的新理论模型，使集合平均实验结果合理化，并预测可以通过实验测试的新行为。除培养研究生外，本提案的教育内容包括三个部分：(i)开设电泳理论与芯片实验室技术的新课程；（ii）通过与波多黎各大学马亚圭斯分校的合作外展项目，为代表性不足的少数民族提供夏季研究机会；（iii）与明尼阿波利斯爱迪生高中（Edison High School）合作开展K-12外展计划。最重要的是，这项研究将在一个定义良好的微观结构环境中将理论与实验联系起来。这项工作将导致改进的DNA分离装置，适用于应用和基础研究。人工基质有望取代脉冲场凝胶电泳，在基因组定位和DNA指纹图谱中发挥重要作用，但对人工基质中DNA动力学的不完全理解阻碍了这项技术从原理验证阶段进入常规应用。基本结果也可能影响相关的分离技术，如电色谱和微流控高效液相色谱。与波多黎各大学马亚圭斯分校合作的暑期研究项目将提供计算和实验技术方面的高级培训，这些培训是这些学生在本国大学无法获得的。与明尼阿波利斯爱迪生高中的外展项目将把研究活动与K-12阶段的教育结合起来。

Proposal Number CTS-0642794Principal Investigator: Kevin D. DorfmanUniversity/Institution: University of Minnesota-Twin Cities CAREER: Dynamics of DNA during Electrophoresis in Artificial Sieving MatricesThis project involves theoretical modeling and experimental investigation of microfluidic electrophoresis of DNA. DNA electrophoresis remains not only one of the most important tools in molecular biology and genetics, but also an ideal platform for testing fundamental theories of polymer dynamics and coarse-grained averaging of separation processes. The proposed research will address topics relevant to polymer physics, stochastic processes, and chemical engineering, working across multiple length scales to connect microscopic motion to macroscopic observables. The research component is an integrated theoretical and experimental program that addresses a range of fundamental issues arising during DNA separations in microfabricated post arrays, including the hindered relaxation phenomena in an external field and the role of the order of the post lattice. The research focuses on effects that arise from the proximity of posts in real separation devices, which are not addressed by the existing body of knowledge on DNA collisions with a single, isolated post. The experimental work spans multiple scales, combining ensemble-averaged measurements of the transport over several millimeters with detailed single-molecule observations of the local transport at the macromolecular scale. The microscopic insights will be used to construct new theoretical models, based upon continuous-time random walk theory, that rationalize the ensemble-averaged experimental results and predict new behavior that can be tested experimentally. In addition to training graduate students, the education component of this proposal consists of three parts: (i) developing a new course on the theory of electrophoresis and lab-on-a-chip technology; (ii) summer research opportunities for underrepresented minorities through a collaborative outreach program with the University of Puerto Rico at Mayaguez; and (iii) a K-12 outreach program with Edison High School in Minneapolis.Most importantly, the research will link theory to experiment in a well-defined microstructured environment. The proposed work will lead to improved DNA separation devices, suitable for applied and fundamental research. Artificial matrices are poised to replace pulsed-field gel electrophoresis for important applications in genome mapping and DNA fingerprinting, but the incomplete understanding of the dynamics of DNA in artificial matrices has prevented this technique from moving beyond the proof-of-principle stage and into routine use. The fundamental results could also impact related separation techniques, such as electrochromatography and microfluidic HPLC. The summer research program with the University of Puerto Rico at Mayaguez will provide advanced training in computational and experimental techniques that are unavailable to these students at their home university. The outreach program with Edison High School in Minneapolis will integrate the research activities with education at the K-12 level.