Hydrodynamics of confined DNA knots

随机的热波动可以在DNA等聚合物中形成结，就像震动耳机会在电线上造成结一样。因此，结在长聚合物链中很常见。结也可以由流体流动产生。该项目的目的是进行实验，揭示流体中结是如何形成的，以及结后结是如何去除的。从广义上讲，结聚合物对生物学的基础问题和生物技术的应用课题都很重要。这个问题的直接技术影响在于两种新兴的长读基因组技术：基因组图谱和纳米孔测序。DNA中的打结在生物学中也具有更广泛的重要性，特别是对基因组的调节。这个项目通过实验解决了与长聚合物结相关的两个关键科学问题，使用DNA作为模型系统。第一部分的重点是如何在纳米流体界面上的DNA产生结，重点是通过荧光显微镜发展机制的见解。第二部分着重于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”来分离结内部的流体动力学相互作用和结与链其余部分之间的流体动力学相互作用。通过这项工作，该项目的研究生将接受洁净室制造方法、荧光显微镜、图像处理以及流体动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外展项目，为高中生开发与研究相关的科学展览项目。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.