Hydrodynamics of confined DNA knots

随机的热波动会在DNA等聚合物中形成结，就像摇晃耳机会在绳子上形成结一样。因此，长聚合物链中普遍存在打结现象。也可以通过流体流动来创建结。这个项目的目标是进行实验，揭示一个结是如何在流动中形成的，以及在形成后它是如何被移除的。广义地说，打结聚合物对于生物学的基本问题和生物技术的应用课题都是重要的。这个问题的直接技术影响在于两项新兴的长期阅读基因组学技术：基因组图谱和纳米孔测序。DNA打结在生物学中也具有更广泛的重要性，特别是对于基因组的调节。这个项目使用DNA作为模型系统，实验地解决了与长聚合物打结相关的两个关键科学问题。第一部分关注在纳米流体界面上停滞的DNA是如何产生结的，重点是通过荧光显微镜发展机制洞察力。第二部分主要研究DNA结的输运性质。这些实验利用纳米通道作为“流体动力学显微镜”，将结子内部的流体动力学相互作用与结子和链条其余部分之间的流体动力学相互作用隔离开来。通过这项工作，该项目的研究生将接受无尘室制造方法、荧光显微镜、图像处理以及流体力学和聚合物物理理论方面的培训。该项目还包括一个K-12推广项目，以开发与高中生研究相关的科学博览会项目。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Random thermal fluctuations can form knots in polymers such as DNA much like shaking headphones can cause knots in the cord. As a result, knots are common in long polymer chains. Knots also can be created by fluid flow. The objective of this project is to perform experiments that uncover how a knot is formed in a flow and how it is removed after formation. Broadly speaking, knotted polymers are important both to fundamental problems in biology and to applied topics in biotechnology. The immediate technological impacts of this problem lie in two emerging long-read genomics technologies: genome mapping and nanopore sequencing. Knotting in DNA also has a broader importance in biology, in particular for regulation of the genome.This project experimentally addresses two key scientific questions related to knotting of long polymers, using DNA as a model system. The first part focuses on how stalling DNA at a nanofluidic interface produces knots, focusing on developing mechanistic insights via fluorescence microscopy. The second part focuses on the transport properties of DNA knots. These experiments leverage nanochannels as a “hydrodynamic microscope” to isolate the hydrodynamic interactions within the knot from hydrodynamic interactions between the knot and the rest of the chain. Through this work, graduate students on the project will receive training in clean-room fabrication methods, fluorescence microscopy, image processing, and the theories of hydrodynamics and polymer physics. This project also involves a K-12 outreach project to develop science fair projects related to the research for high school students.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.