Programming molecular noise with DNA nanopores

Overview

Living cells operate in a noisy molecular environment. Ion channels gate stochastically, and rather than suppressing this randomness, biology often exploits it for signal processing and decision-making. Synthetic cell platforms, by contrast, are almost always built around deterministic logic. Our group is developing a synthetic membrane pore whose gating noise can be programmed directly at the DNA sequence level, turning stochasticity from an experimental nuisance into a designable parameter.

Approach

We build membrane-spanning pores from DNA using the six-helix bundle (6HB) architecture, anchored into lipid membranes with cholesterol-TEG. We have established reproducible folding of these pores and confirmed their insertion into both liposomes and droplet hydrogel bilayers (DHBs).

To control gating, we design short oligonucleotide “lids” that partially occlude the pore lumen. By varying the GC content and complementarity length of each lid, we tune the stability of the lid duplex, and therefore how readily it opens and closes. Lids that bind near the operating temperature are predicted to fluctuate between open and closed states, producing tunable stochastic gating, while strongly or weakly binding lids remain persistently shut or open. Because the gating behaviour is encoded entirely in the lid sequence, noise becomes a property we can dial in by design.

Characterisation

We characterise pore behaviour using total internal reflection fluorescence (TIRF) microscopy on droplet hydrogel bilayers. This pairing gives single-molecule sensitivity at a defined planar bilayer, with full control over membrane composition and the straightforward introduction of membrane-bound components.

Why it matters

A pore whose gating statistics are set by sequence, independently of applied voltage or other external triggers, is a new kind of building block: not a switch, but a tunable noise source. We aim to use these pores as the input layer for synthetic signal transduction, where the noisiness of a molecular event, rather than the concentration of an analyte, shapes the downstream response. This work contributes to a broader effort to build bottom-up artificial cells that harness stochasticity the way living systems do.

People

This project is led by Aleksa Lakic in the SBC Lab, with collaborators in advanced light microscopy at UOW.