Polymer Dynamics of Knotted DNA

Very long molecules, like polymers and DNA, can double over themselves and get entangled in knots. The goal of the proposed research is to study the processes of creating and relaxing these knots in single DNA molecules. Microfluidic channels and electric fields will be used to manipulate individual molecules. Discoveries from the project could impact the design of future instruments used in genomic analysis.

Knots are among the most ancient human tools used for hoisting of sails, suturing of wounds, and weaving of clothing. They also naturally occur in very long polymers such as DNA. The central goal of this project is to develop an understanding of knot dynamics on single polymer molecules. Single molecule DNA experiments, computer simulations, and scaling theory will be performed. The three main objectives of the project are: (1) understand how physical knots on DNA relax, (2) study how knots on a polymer move when pushed by fields or freely diffuse, and (3) develop nanofluidic devices to probe processes which couple knot relaxation and convection. The project will further engage high school teachers and undergraduates in research opportunities. Materials will be developed that can be used by grade school teachers to introduce concepts in knots and topology by linking them to everyday phenomena, such as the entangling strings and headphone cords.