In situ analysis of the higher-order genome structure in a single Escherichia coli cell

We developed a novel method for the in situ analysis of the higher-order structure of an individual genome from a single Escherichia coli cell using laser tweezers. Initially, condensed DNA was stably grasped by a laser without any chemical modification and without physical attachment to an artificial object such as micro-plastic beads. Under optical transport, the trapped genome gradually unfolded in solution due to viscous friction. Interestingly, the nucleoid DNA from a log-phase cell is almost fully elongated, whereas in the stationary phase, unfolding of the nucleoid is characterized by step-wise elongation of 1.7–5.1 μm, corresponding to a size of 5–15 kbp, and a few tightly packed domains remain along the DNA chain. This suggests the coexistence of tightly packed and swollen domains in the genome in the stationary phase.