The study on the stability of DNA structure by steered molecular dynamics simulations

Abstract

The stability of DNA double-stranded structure is examined by pulling atoms using steered molecular dynamics simulations. We use the base sequence to which DNA helicase binds; it acts to separate a double-stranded chain into single-stranded ones. The force is applied to atoms in the middle of the strand and they are pulled perpendicular to the helical axis of DNA. The force profile basically corresponds to the fraction of Watson-Crick hydrogen bonds which shows jumps and plateaus. The work for double-stranded separation can be interpreted in conjunction with the way to break hydrogen bonds. When some hydrogen bonds are broken at once, the bigger force is needed, and it leads to morework.