Today, we put 2 new #CDlab papers on the @arxiv preprint server – which both report, in different ways, on demonstrating nanoscale rotary motors that are driven by a flow through a nanopore.
arxiv.org/pdf/2206.06612…
arxiv.org/pdf/2206.06613…
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arxiv.org/pdf/2206.06612…
arxiv.org/pdf/2206.06613…
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@arxiv Such rotors are inspired by the awesome F0F1 ATPase motor protein in our cells. Here, a proton gradient drives rotation of F0 which induces conformational changes in F1 that catalyze production of ATP, which is the fuel for most processes in our body.
Video credit Biovisions
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Video credit Biovisions
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We built similar rotary motors synthetically from the bottom up, using ‘DNA origami’ in great collaboration with @hendrik_dietz lab. These motor structures dock onto a nanopore and autonomously show sustained unidirectional rotations where a rod rotates at >10 rotations/sec.
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@hendrik_dietz In a first approach (paper 1 arxiv.org/abs/2206.06613), we demonstrate a self-organized artificial nanoscale rotary machine, where a simple DNA bundle acts as the rotor that self organizes onto a nanopore in a thin solid-state membrane that serves as stator and flow generator.
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Video’s often tell the story in less words – so here’s a movie where you see the fluorescently labelled end of a rotating DNA bundle that is observed to move in a circle around the nanopore that is located at the center.
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Energy is provided by applying a static applied DC voltage.
Or even simpler: by merely having different salt concentration on the two sides of the membrane (think salt water versus fresh water)!
The latter directly mimics F0F1 where a concentration gradient drives rotation.
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Or even simpler: by merely having different salt concentration on the two sides of the membrane (think salt water versus fresh water)!
The latter directly mimics F0F1 where a concentration gradient drives rotation.
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So how is this rotation driven?
As the elastic and highly charged bundle docks on the pore, it gets compressed by the field into a chiral shape. This asymmetrically couples to the radial water flow out of the pore, which exerts an angular force that drives the rotation.
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As the elastic and highly charged bundle docks on the pore, it gets compressed by the field into a chiral shape. This asymmetrically couples to the radial water flow out of the pore, which exerts an angular force that drives the rotation.
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Like in this simulation movie…
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We deduced this self-organized rotor mechanism in a wonderful collaboration with the @RGolestanian lab who did extensive simulations on this – see the results for different initial docking configurations where bundles are placed off center in various ways
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@RGolestanian Read all about these self-organized DNA rotors in our preprint (soon to be published in Nature Physics):
arxiv.org/pdf/2206.06613…
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arxiv.org/pdf/2206.06613…
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In a second paper (arxiv.org/pdf/2206.06612…), advanced rational origami design by the @hendrik_dietz lab defined a true nanoscale turbine, with right-handed or left-handed chiral blades.
Its mere ~20 nm scale mimics the size of the F0F1 ATPase.
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Its mere ~20 nm scale mimics the size of the F0F1 ATPase.
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@hendrik_dietz Upon applying a (reinforced 16hb) DNA rod as load, we again measured sustained unidirectional rotations.
And now, the rotation direction was set by chirality! Lefthanded turbines rotated clockwise; righthanded ones rotated anticlockwise
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And now, the rotation direction was set by chirality! Lefthanded turbines rotated clockwise; righthanded ones rotated anticlockwise
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And, very surprising:
In high salt buffer, the DNA nanoturbines rotated in the opposite direction compared to rotation in low salt!
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In high salt buffer, the DNA nanoturbines rotated in the opposite direction compared to rotation in low salt!
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Here, full-atom MD simulations by @aksimentievLab (with 4.3 million atoms!) came to the rescue, as they showed the flow-driven rotation as well as the rotation-direction reversal at high salt, caused by a different ion distribution near the DNA that reverses the force on it.
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This was all really a technical tour-de-force: from the origami design, to docking turbines correctly, to nanoscale detection, and to puzzling out the mechanisms involved.
Very gratifying that 7 years after the conception of these ideas, this now materialized in 2 papers!
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Very gratifying that 7 years after the conception of these ideas, this now materialized in 2 papers!
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Our nanoturbines are the first-ever experimental realization of flow-driven rotors at the nanoscale, constituting a new class of molecular motors. These synthetic machines convert energy from a static electrochemical gradient into useful mechanical work.
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These artificial turbines operate autonomously in physiological conditions. Next to better understanding motor proteins such as F0F1 ATPase, the results open new perspectives for engineering active robotics at the nanoscale.
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NB All this was teamwork (see above), but most credits go to 1st author @xinshi_d, who led this challenge as postdoc in our #CDlab
Xin is on the job market now and will continue this work as tenure track assistant professor. I greatly recommend him, so get him while you can!
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Xin is on the job market now and will continue this work as tenure track assistant professor. I greatly recommend him, so get him while you can!
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