Microscopy of DNA in dilute polymer solutions

The mechanism of separation of DNA in polymer solutions is not well understood. In this paper we use epifluorescence videomicroscopy to investigate the dynamic behavior of DNA electrophoresing through dilute polymer solutions. DNA collides with polymer obstacles, which cause the conformation of DNA to change from the globular, random coil conformation it takes in free solution. There are two main types of DNA-polymer collisions: U-shape collisions and brief collisions. In U-shape collisions, the DNA collides with a polymer obstacle, extends into a U-shape, and then slides around the polymer obstacle like a pulley. There are occasionally multiple entanglement points, causing the DNA to take more complex conformations, such as W-shapes. In the brief collision process, the DNA collides with a polymer obstacle and begins to extend but then collapses back into its globular conformation before a full U-shape is formed. The frequency of these interactions increases as the DNA size increases, and it also increases when the polymer size or concentration increases. These data support the transient entanglement coupling mechanism of separation of DNA, which states that entanglements between DNA and polymer molecules result in the separation of DNA.