  The stability and dynamics of a double-stranded DNA (dsDNA) is affected by
the preferential occupancy of small monovalent molecular ions. Small metal and
molecular ions such as sodium and alkyl ammonium have crucial biological
functions in human body, affect the thermodynamic stability of the duplex DNA
and exhibit preferential binding. Here, using atomistic molecular dynamics
simulations we investigate the preferential binding of metal ion such as Na+
and molecular ions such as tetramethyl ammonium (TMA+) and
2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double stranded DNA. The
thermodynamic driving force for a particular molecular ion- DNA interaction is
determined by decomposing the free energy of binding into its entropic and
enthalpic contributions. Our simulations show that each of these molecular ions
preferentially binds to the minor groove of the DNA and the extent of binding
is highest for CHO+. The ion binding processes are found to be entropically
favourable. In addition, the contribution of hydrophobic effects towards the
entropic stabilization (in case of TMA+) and the effect of hydrogen bonding
contributing to enthalpic stabilization (in case of CHO+) have also been
investigated.
