Noise-synchronized Electrophoretic Manipulation in Nanoporous Hydrogels

1160010乌干达拟议的工作旨在展示如何利用控制全球气候变化和感官感知等各种现象的相同动态来指导大分子在纳米孔环境中的传输。研究人员的目标是在凝胶电泳的背景下，通过在熵捕获运输机制中建立一个共振条件来证明这一点，该机制同步了DNA在基质中的孔之间的噪声不相关的运动。利用这一独特效应的令人惊讶的结果包括不同大小的分子在相反方向上的同时传输，以及与直觉相反的分离效率的反尺寸依赖。这种共振效应可以通过调整周围凝胶基质的驱动电场和孔径分布来精确操纵。在有希望的初步研究的基础上，将进行新的基础研究，旨在了解如何定制水凝胶的纳米级孔形态，以充分利用基于熵捕获的大分子传输的独特特征。目前缺乏的这些信息，是在实际环境中充分利用这种共振效应的好处的关键。首先，将应用机械、量热和基于电子显微镜的研究相结合的方法，开发基于产生的输入的预测传输模型，以量化在广泛的基质配方中的纳米尺度孔尺寸分布。这些结果将使我们能够合理地定制凝胶组成和聚合条件，以实现针对特定大小的大分子分析物的最佳共振同步。其次，通过应用新的光引发剂和凝胶组合物以获得更大的平均孔径，并通过在单分子可视化研究的输入的传输模型中加入额外的激活模式，结果将扩展到更广泛的分析物范围。第三，在目标1和2中获得的基本见解将被调整为现实的分离，包括对STR/SNP产物、长DNA和蛋白质的分析。获得解释全球气候变化事件的相同动力学并将其应用于描述纳米级大分子运输的能力在智力上是耐人寻味的，在已发表的文献中几乎没有类似之处。凝胶电泳的无处不在为共振现象的实际应用提供了一个相关的背景，通过在具有特定孔径分布的凝胶中简单地施加周期性电场来实现极大地改进的分级。及时而深远的影响包括建立设计规则来构建最佳地定制以利用这些效应的基质结构，以及在其他新兴的纳米级势井陷阱的适应中实现新的操纵和分类功能。这种共振同步效应以前被认为只有在理想化的纳米机械拓扑中才可能实现，但在广泛使用的聚合物水凝胶中可以很容易地获得，尽管它们是异质纳米孔排列。拟议中的研究将为矩阵架构的设计建立规则，该架构以最佳方式量身定做，以利用这种独特的运输模式。通过提供一种在普通水凝胶中获得这些现象的新途径(而不是理想化的平面纳米机械拓扑结构)，存在着一条史无前例的途径，使这项研究的结果几乎可以在任何分子生物学实验室中直接实施。这些效应还可能极大地拓宽在3-D纳米环境中对大分子和粒子进行同步操作的可能性。这项技术通过显著提高电泳分离效率，具有巨大的潜力来影响分子生物学。我们建议将这种仪器集成到简单的设备中，允许在教室中查看和研究DNA分离过程。研究人员计划利用这一系统的便携性和易操作性来开发针对从K-12到大学的学生的各种适应，以及更多的外展机会(为高中生和教师举办的讲习班、少数族裔外展、研究生院招聘等)。这项研究将被整合到本科生和研究生的课程中，利用PI参与多项REU努力，并担任以生物技术为重点的专业科学硕士项目的主席。

1160010 UgazThe proposed work aims to show how the same dynamics governing phenomena as diverse as global climate change and sensory perception can be exploited to direct macromolecular transport through nanoporous surroundings. The researchers aim to demonstrate this in the context of gel electrophoresis by establishing a resonance condition in an entropic trapping transport regime that synchronizes the otherwise noisy uncorrelated motion of DNA between pores in the matrix. Surprising consequences of exploiting this unique effect include simultaneous transport of different-sized molecules in opposite directions, and a counterintuitive inverted size dependence of separation efficiency. This resonance effect can be precisely manipulated by adjusting the driving electric field and pore size distribution of the surrounding gel matrix.Building on the foundation of promising preliminary studies, new fundamental research will be performed aimed at understanding how the nanoscale pore morphology of hydrogels can be tailored to fully harness the unique features of entropic trapping-based macromolecular transport. This information, currently lacking, is a key to fully exploiting the benefits of this resonance effect in practical settings. First, a predictive transport model based on input generated will be developed by applying a combination of mechanical, calorimetric, and TEM-based studies to quantify the nanoscale pore size distribution across a broad range of matrix formulations. These results will allow us to rationally tailor gel compositions and polymerization conditions to achieve optimal resonance synchronization targeting macromolecular analytes of specific size. Second, the results will be extended to a broader range of analytes by applying new photoinitiator and gel compositions to obtain larger average pore sizes, and by incorporating additional activation modes into the transport model with input from single molecule visualization studies. Third, the fundamental insights gained in Objectives 1 and 2 will be adapted toward realistic separations involving analysis of STR/SNP products, long DNA, and proteins.The ability to access the same dynamics that explain global climate change events and apply them to describe macromolecular transport at the nanoscale is intellectually intriguing, with few parallels in published literature. The ubiquity of gel electrophoresis casts a relatable backdrop for the practical use of resonance phenomenon to achieve vastly improved fractionation by simply applying a periodic electric field in a gel with a specific pore size distribution. Timely far-reaching implications include establishing design rules to construct matrix architectures optimally tailored to exploit these effects, and enabling new manipulation and sorting functionalities in other emerging adaptations of nanoscale potential well traps.This resonant synchronization effect, previously thought possible only in idealized nanomachined topologies, can be readily accessed in widely used polymeric hydrogels despite their heterogeneous nanopore arrangement. The proposed research will establish rules for design of matrix architectures optimally tailored to exploit this unique transport mode. By providing a new avenue to access these phenomena in ordinary hydrogels (as opposed to idealized planar nanomachined topologies), an unprecedentedly pathway exists for the results of this research to be directly implemented in virtually any molecular biology lab. These effects are also likely to significantly broaden the possibilities to execute synchronized manipulation of macromolecules and particles in 3-D nanoenvironmentsThis technology has enormous potential to impact molecular biology by enabling significant improvements in electrophoretic separation efficiency. We propose to incorporate this instrumentation into simple devices that allow the DNA separation process to be viewed and studied in the classroom. The researchers plan to harness the portability and ease of operation of this system to develop numerous adaptations aimed at students ranging from K-12 through college, as well as additional outreach opportunities (workshops for high school students and teachers, minority outreach, graduate school recruiting, etc.). This research will be integrated into curriculum at both the undergraduate and graduate levels, leveraging the PI's involvement in multiple REU efforts and as chair of a biotechnology-focused professional science master's program.