Local control of polymer chain conformation upon adsorption onto surfaces is one of the central issues in biosensing, biomineralization and biocompatability. One of the possible ways of controlling the conformation of adsorbed biomolecules is via engineering the properties of the surface. Self-assembled monolayers, with a well developed patterning protocols, offer a versatile system for designing different surface functionalities. We have considered the specific adsorption of DNA molecule on a surface of patterned self-assembled monolayers and studied the dependence of the conformation on the size of the pattern. Due to the size and heterogeneity of the system, the problem requires the developments of new simulation techniques. We propose the following method.
In order to model the interactions of large organic molecules, such as DNA or proteins, with surfaces it is essential to adequately describe short- and long-range interactions with the surface. We will show that the long-range forces can be described on the mesoscopic level of theory. The comparison of the results of mesoscopic calculations, based on the mean-field DLVO theory, with the experimental data for DNA on mica surface in aqueous salt solutions shows that the theory is able to capture the conformational behaviour of the DNA molecule on the surface.
In order to treat the short-range part of interactions, responsible for specific binding of biomolecules to surfaces, we have developed an embedded cluster model. In this model the region of interest is considered quantum mechanically, while the rest of the atomistic system is treated on the molecular mechanical level.
Combining the mesoscopic and the embedded cluster approaches allows us modelling biomolecules on surfaces. Using this technique we have found the optimum size of pattern of mixed self-assembled monolayers required for DNA adsorption in almost unperturbed solution conformation, while maximising the density of DNA molecules on the surface. |