Ion Detection in a DNA Nanopore FET Device

<br/>Significant strides have been made to integrate biotechnology with semiconductor nanotechnology, but the ability to directly interface with living cells is still an emerging area of research. Such devices are being developed for interfacing directly with neurons, which can help monitor and treat chronic pain and Parkinson’s disease. In this pursuit, an ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine the sensitivity of the nanodevice to the local cellular environment.<br/>Our design employed an "artificial gap junction" constructed using a DNA origami nanopore on a CMOS device as a direct interface between the cell and the electronic device. Inspiration for using a DNA Nanopore comes from naturally occurring transmembrane nanopores, such as the protein Gramicidin, which have been modeled as ion channels. In this work, we have modeled a synthetic nanopore pore that uses a six-helix bundle of DNA that has been previously synthesized as a cylindrical nanopore structure that spans a bilipid membrane. The DNA-origami structure is bio-compatible and can also be modified with ligands to anchor to the lipid bi-layer on a cell. This self-assembling structure would be compatible with the living system and convert signals generated by ionic currents directly into an electrical signal using a gated ion-selective field effect transistor. While typical nanopore sensors detect single molecules and ions by measuring the change in ion flow across a membrane, the proposed device would detect the ions as a buildup of charge across the gate of the FET. A blanket of ions (electrical double layer) would form on the nanopore inner wall and over the gate oxide in a manner dependent on the local environment, and the resulting source-drain current can be used to measure the presence of ions in the cell.<br/>A continuum model was used to account for the ions in the electrolyte. Modeling of an electron distribution with the electric double layer theory was applied to verify the applicability of the model to a bio-sensing environment. The FinFET architecture was shown to increase sensitivity to ions even with a low drain-source bias. The device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. The logarithmic relationship found between ion concentration and FET current generates almost a microampere of current difference across varying concentrations with a small applied bias.<br/>Our findings illuminate a promising pathway for refining cellular interfacing, potentially catalyzing advancements in in-vivo sensing technologies for biomedical applications.<br/>We acknowledge the NSF SemiSynBio 2027165 grant.