DNA melting in slit pores: A reaction density functional theory

Abstract

A reaction density functional theory (R-DFT) is developed for chemical reactions in confined space by integrating reaction thermodynamics and DFT for chain fluids. The theory is applied to investigate DNA melting in slit pores, with nucleotides represented by coarse-grained charged Lennard-Jones particles. Three types of slit pores are considered for DNA melting: repulsive pore, attractive pore, and under electric field. In repulsive pores, the melting temperature increases slightly with reducing pore width, and the increase magnitude is nearly the same for DNA of different chain lengths. The double-strand DNA (dsDNA) and single-strand DNA (ssDNA) are located in the slit center, particularly for long DNA due to the effect of configuration entropy. In attractive pores, the melting temperature increases with increasing wall-fluid interaction. The DNA chains are preferentially adsorbed near the slit walls with a strong wall-fluid interaction. Under electric field, the melting temperature increases slightly and is more distinct for shorter DNA. © 2011 American Chemical Society.