An experimental investigation of attraction between knots in a stretched DNA molecule

Abstract

It has been predicted through simulations that two knots in a stretched polymer will feel an attraction towards one another and will tend to be found in close proximity. Here, we examine data from experiments in which we stretched knotted DNA molecules and investigate a subset which contained two or more knots. In contrast to the expected behavior of an isolated knot in an elongational field, we observe that pairs of knots move towards each other from distant sections of the molecule. After meeting, pairs of knots fluctuate in and out of visual contact, and can remain in proximity for minutes at a time. Our experimental results suggest that knots on an extended polymer experience an attractive interaction.