Silicon nanowire sensor for DNA detection and sequencing: an ab initio simulation

Electrical sensors able to detect DNA replication and determine its sequence would enable fast and relatively cheap diagnosis of gene-related vulnerabilities and cancers. At present, it is already possible to electrically monitor DNA replication events using a Klenow fragment of polymerase I attached to a carbon nanotube. Since devices based on Si nanowires would be much easier to produce in quantity, we examine theoretically the sensitivity of a Si nanowire/Klenow fragment for electrical detection of nucleotide addition. A highly parallel real-space multigrid code is used for DFT-based non-equilibrium Green's function calculations involving up to 16,000 atoms, employing highly-accurate variationally-optimized localized orbitals. We find that the “open” and “closed” Klenow fragment configurations, prior and during nucleotide addition, respectively, screen the Si nanowire differently and result in a detectable current difference. The sensitivity is the largest in the subthreshold regime while the absolute current difference is maximized in the turn-on state. The sensitivity decreases with an increase of the nanowire size, as expected, but the current difference between different enzymatic states is nearly independent on the nanowire size up to 800 \AA$^2$ cross section.