  The structure and dynamics of negatively charged nucleic acids strongly
correlate with the concentration and charge of the oppositely charged
counter-ions. It is well known that the structural collapse of DNA is favored
in the presence of additional salt, a source of excess oppositely charged ions.
Under such conditions single stranded DNA adopts a collapsed coil like
conformation, typically characterized by stacking base pairs. Using atomistic
molecular dynamics simulation, we demonstrate that in the presence of
additional divalent salt (MgCl2) single stranded DNA (Dickerson Drew dodecamer)
initially collapses and then expands with increasing salt concentration. This
is due to the overcharging induced DNA chain swelling, a dominant factor at a
higher divalent salt concentration. In a nutshell, our simulations show how in
the presence of divalent salt, non-sequential base stacking and overcharging
competes and affect single stranded DNA dynamics unlike a monovalent salt.
