BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 225, 796–800 (1996) ARTICLE NO. 1253 Formation of Nucleation Center in Single Double-Stranded DNA Chain Yukiko Matsuzawa,* Yasuo Yonezawa,² and Kenichi Yoshikawa‡ ,1 *Department of Ecological Engineering, Toyohashi University of Technology, 1-1, Tempaku-cho, Toyohashi 444, Japan; ² Graduate School of Science and Engineering, Ibaraki University, 4-12-1, Hitachi, Ibaraki 316, Japan; and ‡Graduate School of Human Informatics, Nagoya University, Nagoya 464-01, Japan Received June 14, 1996 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.  1996 Academic Press, Inc. In living cells, DNA usually exists in a highly compact state. For example, in bacteriophage capsid, DNA with a total stretched length of more than several tens of micrometers is compacted within a space of ca. 0.1 mm (1). As a model of the dense packing of DNA in a phage capsid, there have been numerous studies on the conformational change of a DNA molecule induced by cations and neutral polymers. Two important points have been noted in these past experimen- tal studies. First, DNA is compacted into a toroid or rod-like structure with cations or neutral polymers (2-6). In the case of a toroid, the diameter is on the order of 0.1 mm (7), which corresponds to the size of compacted DNA in a capsid. It has been confirmed that the secondary structure, the B-form, is preserved after the compaction (8). The second point is that, with an increase in the concentration of cations and neutral polymers, the higher order structure in DNA changes in a drastic manner, as has been indicated by the studies with CD spectroscopy and light-scattering (9-11). Recently, we found that individual double-stranded DNA chains undergo a marked discrete transition between an elongated coil and a compacted globule (12-14). In this transition, the term ‘‘coil’’ has a different meaning from that in the helix-coil transition, i.e., a ‘‘coil’’ in the coil-globule transition is a state in which a long double-stranded DNA chain is elongated as a random coil. On the other hand, the term ‘‘globule’’ indicates the state of collapsed DNA chain, being much small than the size of the corresponding ‘‘ideal’’ polymer chain with the same contour length. After experimental and theoretical studies on the coil-globule transition on individual single DNA chain (13,15), it has become clear that the transition of an individual chain is largely discrete with characteristics of a first-order phase transition. Actually, it was found that the effective volume changes as large as 10 4 -10 5 times accompanied with the coil- globule transition in a single T4 DNA (14). In relation to the first order transition, it has been discovered that a single long DNA molecule in a metastable state exhibits the process of nucleation center formation and successive crystal growth, the so-called ‘‘nucleation & growth’’ (14-16), just similar to the process of crystallization from a supersaturated solution. 1 Corresponding author. Fax: /81-53-789-4808. 0006-291X/96 $18.00 Copyright  1996 by Academic Press, Inc. All rights of reproduction in any form reserved. 796