Nanopores that act like electrical gates pave way for ion-based computing

Pore-forming proteins are found throughout nature. In humans, they play key roles in immune defense, while in bacteria they often act as toxins that punch holes in cell membranes. These biological pores allow ions and molecules to pass through membranes. Their unique ability to control molecular transport has also made them powerful nanopore tools in biotechnology, for example in DNA sequencing and molecular sensing.

Despite their importance and impact on biotechnology, biological nanopores can also show complex, unpredictable behavior; for example, scientists still don’t fully understand how ions move through them or why the flow of ions sometimes stops.

Two phenomena have especially puzzled researchers for years: rectification, where ion flow differs depending on the “sign” (plus or minus—positive or negative) of voltage applied, and gating, where the flow reduces abruptly. Both effects, especially gating, interfere with sensing applications but have remained poorly understood.

Now, a team led by Matteo Dal Peraro and Aleksandra Radenovic at EPFL has uncovered the physical basis for these effects. By combining experiments, simulations, and theory, the researchers show that both rectification and gating are controlled by the electrical charges of the nanopore itself, and how those charges interact with ions flowing through the pore.

The work has been published in Nature Nanotechnology.

The researchers focused on aerolysin, a bacterial pore often used in sensing. By systematically mutating charged amino acids along the pore’s inner surface, they created 26 nanopore variants with different charge patterns. They then measured how ions flowed through these mutant pores under various conditions.

The scientists applied alternating voltage signals to probe the system at different timescales. This allowed them to separate rectification from gating, which takes place mainly at longer time scales. Finally, the scientists used biophysical models to interpret the data and identify underlying mechanisms.

Mimics of synaptic plasticity

The study found that rectification happens because of the way the electric charges lining the inside of the pore influence ion movement. The charge distribution makes it easier for ions to pass in one direction than the other, like a one-way valve. Gating, on the other hand, occurs when a large flow of ions leads to a charge imbalance that structurally destabilizes the pore, which causes part of the pore to temporarily collapse, blocking the flow of ions.

Both effects depend not just on the amount of charge, but where it is exactly localized in the nanopore and whether it is positive or negative. By changing charge “sign,” the scientists could tune when the pore gates and under what conditions. They also found that if the pore’s structure is made more rigid, it stops gating altogether, confirming that pore flexibility plays a key role.

The study’s findings offer a way to fine-tune biological nanopores for specific tasks. For example, engineers can now design pores that largely avoid gating in nanopore sensing, while for other applications like bio-inspired computing, gating can be harnessed.

In fact, the researchers built a nanopore that mimics synaptic plasticity, “learning” from voltage pulses like a neural synapse. Such systems could one day form the basis of ion-based processors.