Collision of a DNA polymer with a small obstacle

Using single molecule fluorescence microscopy, we study the dynamics of an electric-field-driven DNA molecule colliding with a single stationary post. The radius of the obstacle is small compared to the contour length of the molecules. Molecules that achieve hooked configurations which span the obstacle were chosen for study. Four different types of hooked configurations were found: symmetric hairpins with constant extension during unhooking, asymmetric hairpins with constant extension during unhooking, asymmetric hairpins with increasing extension during unhooking, and rare multiply looped entangled configurations. The important physics describing the unhooking dynamics for each classification differ and models are proposed to predict unhooking times. Surprisingly, we find that most collisions do not follow classic rope-on-pulley motion but instead form hairpins with increasing total extension during the unhooking process (called X collisions). Last, we show that unraveling to form a hairpin and center-of-mass motion during unhooking affect the overall center of mass hold-up time during a collision process.