Dynamics and Solvent Effects in Functionalized DNA Sensing Nanogaps

The potential of reading-out DNA molecules, using functionalized electrodes embedded in nanopores, is discussed here. Focus is given on a functionalization using tiny diamond-like hydrogenated cages, the diamondoids. A derivative (known as memantine) of the smallest diamondoid is taken. This offers hydrogen bonding possibilities to DNA molecules. Accordingly, we place a small DNA unit, a nucleotide, within the functionalized nanogap. Based on quantum-mechanical calculations, we discuss the alteration in the electronic features of the electrodes by varying the relative arrangements of the nucleotides between these electrodes. Quantum transport calculations were also performed and have shown distinct features among the nucleotides revealing the high sensitivity of the electrodes in distinguishing the nucleotide identity. At a next step, the effect of an aqueous environment was taken into consideration through quantum-mechanical/molecular-mechanics simulations. This effect is discussed in view of the water structuring close to the electrodes and their influence on the device characteristics. These results would be highly relevant in detecting DNA using novel nanopore sequencers.