A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport

Xiaoming Liu (), Fengyu Liu, Hemani Chhabra, Christopher Maffeo, Zhuo Chen, Qiang Huang, Aleksei Aksimentiev () and Tatsuo Arai
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Xiaoming Liu: Beijing Institute of Technology
Fengyu Liu: Beijing Institute of Technology
Hemani Chhabra: University of Illinois at Urbana Champaign
Christopher Maffeo: University of Illinois at Urbana Champaign
Zhuo Chen: Beijing Institute of Technology
Qiang Huang: Beijing Institute of Technology
Aleksei Aksimentiev: University of Illinois at Urbana Champaign
Tatsuo Arai: Beijing Institute of Technology

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Synthetic membrane nanopores made of DNA are promising systems to sense and control molecular transport in biosensing, sequencing, and synthetic cells. Lumen-tunable nanopore like the natural ion channels and systematically increasing the lumen size have become long-standing desires in developing nanopores. Here, we design a triangular DNA nanopore with a large tunable lumen. It allows in-situ transition from expanded state to contracted state without changing its stable triangular shape, and vice versa, in which specific DNA bindings as stimuli mechanically pinch and release the three corners of the triangular frame. Transmission electron microscopy images and molecular dynamics simulations illustrate the stable architectures and the high shape retention. Single-channel current recordings and fluorescence influx studies demonstrate the low-noise repeatable readouts and the controllable cross-membrane macromolecular transport. We envision that the proposed DNA nanopores could offer powerful tools in molecular sensing, drug delivery, and the creation of synthetic cells.

Date: 2024
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DOI: 10.1038/s41467-024-51630-0

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