The folded state of long duplex-DNA chain reflects its solution history

The higher-order structure of compacted single giant DNA induced by complexation with polypeptide (poly-Arg) in NaCl solution was investigated using fluorescence microscopy. As the poly-Arg concentration increased, the mean size of extended DNA chains gradually decreased. In the presence of excess poly-Arg, individual DNA chains collapsed into compact globules, and the degree of collapse of the DNA chains depended not only on the concentration of poly-Arg, but also on the time course of the addition of poly-Arg and NaCl, indicating that the structure of the collapsed DNA is not determined simply according to the minimum free energy. We discuss theoretically the presence of multiple stationary states based on a consideration of simple kinetics in the process of binding. Depending on the past history, the number of poly-Arg and Na⁺ that bind to each DNA changes markedly. This interesting characteristic of long DNA is discussed in relation to the possible mechanism of self-regulation of gene expression in living cells.