Redox properties of green fluorescent proteins and their chromophores

To further study why ssDNA is easier bound to silica surface than dsDNA, we designed an in silico comparion. We captured a phosphate-silanol binding case for dsDNA. Then we removed one chain of the dsDNA to make a ssDNA. The binding free energy was also determined for the remaining chain, which contained the phosphate group bound to silica surface. The free energy of the dsDNA showed increased repulsion far from the surface exhibited greater repulsion between 0.55 nm and 0.9nm, which we interpreted in terms of increased electrostatic repulsion between the negatively charged surface and a negatively charged polyelectrolyte with twice as much charge density. When the DNA oligomers are close enough to surface, specific interactions (phosphate-silanol, hydrophobic interactions) play a main role and the potential of mean force contains a local minimum. In this particular case, the repulsion makes the difference between a stable binding site for ssDNA and a metastable binding site for dsDNA, each with a similar point of attachment to the silica surface.