Formation of nucleation center in single double-stranded DNA chain

The dynamic process of compaction of long double-stranded DNA, T4DNA (166 kbp), was studied by the observation for individual DNA using fluorescence microscopy. We have observed the process of folding of metastable elongated DNA into compacted form in polyethylene glycol solution. During the thermal Brownian motion, the transition from the unfolded state into the compacted state is initiated by the formation of a nucleation center in the DNA chain. This center then grows along the DNA chain until the entire individual DNA takes the compacted state. The greatest probability for the formation of a nucleation center is at the ends of the DNA chain. In addition to the ends, nucleation is observed only in the region containing the positions with relatively high GC content region along the DNA chain.