DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity

Sarah E. Ochmann, Himanshu Joshi, Ece Büber, Henri G. Franquelim, Pierre Stegemann, Barbara Saccà, Ulrich F. Keyser, Aleksei Aksimentiev, and Philip Tinnefeld
Nano Letters 21(20) 8634-8641 (2021)
DOI:10.1021/acs.nanolett.1c02584  BibTex

Highlight

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrate its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of ∼5% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.

Abstract

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrate its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of ∼5% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.

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mrDNA simulation of the DNA origami plate designed as a sensor of transmembrane potentials. The coarse-grained simulation starts with the caDNAno design of the origami plate which is first mapped into a 5-bp/bead model followed by a 1-bead/bp model. Finally, the all-atom model of the system was obtained by averaging equilibrated conformations in coarse-grained simulation. At the end, the all-atom model was simulated for couple of nanoseconds in vacuum using the network of elastic restraints.

All-atom molecular dynamics simulation of ATTO532 (yellow) and ATTO647N (red) dye molecules conjugated to dsDNA in purely aqueous solution. The movie illustrates MD trajectories of two independent simulation runs (run 1 and run 2) starting from the same initial configuration. Water and ions are not shown for clarity.

All-atom molecular dynamics simulation of ATTO532 (yellow) and ATTO647N (red) dye molecules conjugated to dsDNA anchored in DOPC lipid bilayer membrane. The movie illustrates MD trajectories of two independent simulation runs (run 1 and run 2) starting from the same initial configuration. Water and ions are not shown for clarity.