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. Author manuscript; available in PMC: 2015 Oct 15.
Published in final edited form as: J Phys Condens Matter. 2014 Sep 19;26(41):413101. doi: 10.1088/0953-8984/26/41/413101

Figure 17.

Figure 17

The type of monovalent ions affect the translocation velocity of DNA. (a) A snapshot from an MD simulations illustrating binding of Li+ ions to dsDNA. DNA is shown in gray, lithium is shown in yellow, and water is shown in red and white. Only those water molecules involved in the lithium-DNA bonds are shown. (b) A toy model describing ion binding to DNA. Red and black lines schematically represent 1D potentials describing affinity of two different cations to DNA. The depth of the free-energy minima are the same and so is the instantaneous number of ions bound to DNA. The barrier for hopping between the adjacent sites along DNA varies with the ion size and so is the strength of the bond. (c) The barrier height (the strength of the cation-DNA bond) affects the effective charge of DNA. The effect of water flow is neglected in this model. Adapted with permission from Ref. [319]. Copyright 2012 American Chemical Society.