Interactions of Nucleotide Bases with Decorated Si Surfaces from Molecular Dynamics Simulations

Abstract

All-atom molecular dynamics simulations and potential of mean force calculations have been carried out to define a complete picture of the adsorption properties of the four nucleotide bases 9-methyladenine, 9-methylguanine, 1-methylthymine, and 1-methylcytosine on a Si(111) surface functionalized with alkyl-amine molecules in aqueous solution. A detailed knowledge of the interactions between the free or bound nucleotide groups and the decorated surfaces is important to design efficient and selective DNA-based sensors, which could be used as powerful biotechnological detection systems. Indeed, the conformation of a DNA strand tethered to an electrode (probe) depends on the strength of its interactions with the layer, which influences the probe capability to capture the target oligonucleotides. However, the arrangement of each single DNA base in close proximity to a substrate and how it may be controlled to improve sensor performance have not received much attention. The results of this investigation showed that all of the bases had favorable adsorption properties on the amine layer, and these interactions could be sometimes mediated by interposing water molecules. The plane of the nucleotide rings was inclined and oriented so as to maximize the number of hydrogen bonds with the surface and all the molecules adsorbed with a similar strength, but a slight preference for pyrimidine bases was observed.