Sensors for DNA detection: theoretical investigation of the conformational properties of immobilized single-strand DNA

A major challenge in the design and creation of biomolecular sensors is the development of efficient strategies using both existing synthetic technologies and novel fabrication methods to effectively adsorb and assemble different molecular species on suitable substrates. In order to generate stable and effective biodevices it is fundamental to understand the mechanisms responsible for the formation of the supramolecular structures, to evaluate to what extent the function and conformation of the adsorbed macromolecules are influenced by their interactions with the substrates and the environment and to identify possible causes of disruption, with the ultimate aim of suggesting and selecting appropriate methodologies to design highly efficient systems. Here in silico modeling comes into play, provided that realistic models and reliable computational strategies are employed. This paper is focused on DNA detection systems based on the hybridization between a DNA target and its complementary probe, which is present either in solution or on a solid support. MD simulations of the fully hydrated single strand attached to an allylamine functionalized Si(111) surface in aqueous solution are presented. A reliable and high quality picture of the structural flexibility and dynamic properties of the modified and unmodified DNA segment in solution together with the ability of DNA to rearrange its structure due to environmental effects is given and clarified.