Catch-Slip Transition in DNA Duplex

Abstract

DNA experiences a wide range of mechanical stress in cells. Structural transitions of DNA under mechanical stresses have thus been a subject of intensive study. We recently used a single-molecule FRET assay to study sequence-dependent looping of double-stranded DNA (dsDNA). In this method, a 100-200 bp long dsDNA is terminated with single-stranded overhangs (∼10-bp) that are complementary to each other. When DNA loops spontaneously, these two sticky ends can base pair and stabilize the DNA in the looped state. The stiffness of the DNA then exerts a restoring force on the duplex and induces unlooping. We found an unexpected relationship between the loop size and the unlooping rate: the duplex formed between the sticky ends ruptured more slowly with decreasing loop size. This phenomenon is reminiscent of a catch bond which becomes stronger under tension. We also observed a transition from a catch bond-like to a normal slip bond-like behavior for an 8-bp duplex. We present a catch mechanism based on the coupling between stretching and twisting of dsDNA to explain this counterintuitive phenomenon.