DNA Binding to the Silica Surface

We
investigate the DNA–silica binding mechanism using molecular
dynamics simulations. This system is of technological importance,
and also of interest to explore how negatively charged DNA can bind
to a silica surface, which is also negatively charged at pH values
above its isoelectric point near pH 3. We find that the two major
binding mechanisms are attractive interactions between DNA phosphate
and surface silanol groups and hydrophobic bonding between DNA base
and silica hydrophobic region. Umbrella sampling and the weighted
histogram analysis method (WHAM) are used to calculate the free energy
surface for detachment of DNA from a binding configuration to a location
far from the silica surface. Several factors explain why single-stranded
DNA (ssDNA) has been observed to be more strongly attracted to silica
than double-stranded (dsDNA): (1) ssDNA is more flexible and therefore
able to maximize the number of binding interactions. (2) ssDNA has
free unpaired bases to form hydrophobic attachment to silica while
dsDNA has to break hydrogen bonds with base partners to get free bases.
(3) The linear charge density of dsDNA is twice that of ssDNA. We
devise a procedure to approximate the atomic forces between biomolecules
and amorphous silica to enable large-scale biomolecule–silica
simulations as reported here.