Hydrodynamics of confined DNA knots

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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.