DIELECTRIC RESPONSE OF TRIPLEX DNA IN IONIC SOLUTION FROM SIMULATIONS

We have analyzed a 1.2-ns molecular dynamics simulation of 51 mM d(CG- G), with 21 Na+ counter-ions and 1 M NaCl in water. Via the dipole flu ctuations, the dielectric constant for the DNA is found to be around 1 6, whereas that for the bases and sugars combined is only 3. The diele ctric constant for water in this system is 41, which is much smaller t han 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Also addres sed in the present work are several technical issues related to the ca lculation of the dipole moment of an ionic solution from molecular dyn amics simulations using periodic boundary conditions.