Folding transition in single long duplex DNA chain

Abstract

Folding transition from elongated coil into compacted globule in a single polymer chain is discussed based on the results of our recent theoretical and experimental studies. As the theoretical approach to this problem, Monte Carlo simulation on the coil-globule transition for a neutral stiff polymer chain has been performed. It has become clear that toroid and rod are the two representative structures as the product of folding transition: toroid is the most stable and rod is a kinetically forzen metastable structure. As for the experimental methodology, single molecular observation with fluorescence microscopy was applied for the coil-globule transition of a single duplex DNA. With this experimental tool, it became evident that individual DNA chains undergo first-order phase transition. In contrast to this, the ensemble of DNA has the characteristics of diffuse or continuous transition. In other words, the coil-globule transition in the ensemble of the chains appears a kind of cooperative transition without any discrete character in spite of the large discrete change in the effective volume of the individual DNA chains. In order to gain further insight on the manner of folding in single chains, we have also performed electron microscopic observation on the morphology of the collapsed DNA chains.