Denaturation and renaturation behaviors of short DNA in a confined space

A deep understanding to the denaturation and renaturation behaviors of DNA in a confined state is fundamentally important to control the self-assembly of DNA in a chamber or channel for various applications. In this report, we study the denaturation and renaturation behaviors of short DNA confined in cylindrical and spherical spaces with the 3-Site-Per-Nucleotide coarse-grained DNA model applying the replica exchange molecular dynamics technology. It is found that as the confinement size decreases, the melting temperature T-m increases and the transition becomes broad. The analysis of the potential of mean force shows that the confinement increases the relative free energy of the denatured state of DNA and decreases the renaturation energy barrier. Besides the denatured and native states, the metastable parallel-stranded structure is also found. The simulation results show that the shapes of the confinement spaces and the short DNA sequences remarkably affect the renaturation behavior. In the cylindrical space, the DNA renaturation changes from random-binding to slithering-binding with the size of the confinement space decreasing. In contrast, the DNA renaturation in the spherical and symmetrical confinement space proceeds through strand binding and rolling. The relationship between the melting temperature and the confinement size, Delta T-m/T-m similar to R-c(-nu), is estimated and the exponential index nu equals about 1.32 and 1.75 in the cylindrical and spherical confinements, respectively. It is further compared with the theoretical result of the rigid rod model and a qualitative agreement with the simulation is achieved. (C) 2014 AIP Publishing LLC.