Artificial ion channels created using DNA origami

Nov 16, 2012 by Lin Edwards report
Scheme of a DNA-origami based ion channel. Credit: Technische Universität München

(Phys.org)—Researchers in Germany and the US have used scaffolded DNA origami techniques to create ion channels or pores that span and penetrate lipid membranes and mimic natural ion channels.

Prof. Dr. Friedrich Simmel and PhD student Martin Langecker of Technische Universität München (TUM) at Garching in Germany and their colleagues used a molecular self-assembly technique known as scaffolded , in which strands of DNA are folded to create three-dimensional . The strands are fixed in place by means of paired bases on short strands of DNA, and the base sequences determine exactly where the folds are fixed in place.

Scaffolding DNA origami has been used for several years and was described in this Phy.Org article. DNA origami has even been used to create nanoscale circuit boards, and has found application in cancer research.

Using this technique the team produced an artificial structure resembling a mushroom and comprising a 42-nanometer diameter stem and a barrel-shaped cap. The channel stem penetrated the while the cap was fixed to one side of the lipid membrane by attaching to 26 cholesterol groups within the synthetic membrane. The channels were subjected to electrochemical tests that showed the artificial channels allowed a current to flow, and could be exhibiting similar gating behavior to that found in natural ion channels.

TEM image of multiple DNA channels attached to a small lipid vesicle. Credit: Technische Universität München

Natural ion channels are basically proteins with holes down their middles, and they occur within the membranes enclosing all . The channels enable ions such as sodium, potassium, calcium and chloride to pass through what would otherwise be an impermeable lipid barrier, and can thus control the electrical current flow between the inside and outside of the cell. They are gated and can therefore be switched to open or closed, depending on the conditions and needs of the cell.

The researchers next made three versions of the artificial channel, with a short DNA strand protruding from the core of the channel in one of three different ways. These versions were then subjected to electrochemical testing. The tests revealed that the gating was more pronounced in the mutant versions, and the gating time was different for the three. These findings strongly suggest the gating is not an aberration produced by random thermal fluctuations, as might have been the case.

Possible applications for the artificial could include use in biosensors and in personalized medicine for delivering drugs directly to target cells. The paper was published in the journal Science.

Explore further: Scientists "resurrect" ancient proteins to learn about primordial life on Earth

More information: Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures, Science, 16 November 2012: Vol. 338 no. 6109 pp. 932-936. DOI: 10.1126/science.1225624

ABSTRACT
We created nanometer-scale transmembrane channels in lipid bilayers by means of self-assembled DNA-based nanostructures. Scaffolded DNA origami was used to create a stem that penetrated and spanned a lipid membrane, as well as a barrel-shaped cap that adhered to the membrane, in part via 26 cholesterol moieties. In single-channel electrophysiological measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-molecule translocation experiments show that the synthetic channels can be used to discriminate single DNA molecules.

Press release

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HannesAlfven
3 / 5 (2) Nov 16, 2012
Re: "The channels were subjected to electrochemical tests that showed the artificial channels allowed a current to flow, and could be exhibiting similar gating behavior to that found in natural ion channels."

From Gerald Pollack's "Cells, Gels and the Engines of Life", pages 11 - 12:

[...]

The existence of single ion channels appeared to be confirmed by groundbreaking experiments using the patch-clamp technique. In this technique the tip of a micropipette is positioned on the cell surface. Through suction, a patch of membrane is plucked from the cell and remains stuck onto the micropippete orifice ... A steady bias voltage is placed across the patch, and the resulting current flow through the patch is measured. The current is not continuous; it occurs as a train of discrete pulses. Because the pulses appear to be quantal in size, each pulse is assumed to correspond to the opening of a single ion channel.

[cont'd]
HannesAlfven
2.3 / 5 (3) Nov 16, 2012
[cont'd]

This dazzling result has so revolutionized the field of membrane electrophysiology that the originators of the technique, Erwin Neher and Bert Sakmann, were awarded the Nobel Prize. The observation of discrete events would seem to confirm beyond doubt that the ions flow through discrete channels.

Results from the laboratory of Fred Sachs, on the other hand, make one wonder. Sachs found that when the patch of membrane was replaced by a patch of silicon rubber, the discrete currents did not disappear (Sachs and Qin, 1993); they remained essentially indistinguishable from those measured when the membrane was present ... Even more surprisingly, the silicon rubber sample showed ion-selectivity features essentially the same as the putative membrane channel.

A similar troubling observation was made on polymer samples (Lev et al, 1993).

[...]

--

It appears that the cell biology textbooks might have left out some important details ...
flashgordon
not rated yet Nov 16, 2012
As I've remarked elsewhere, dna-nanomanufacturing has reached a stage where it's not just breakthroughs in making dna-nanomanufacturing possible, but that of using a dna-nanomanufacturing ability that is reliable enough for people to make admittedly limited nanotechnology almost at will; historians will have a tough time nailing down conclusions of when this happened; but, it's happened over the last few months, or this last year for sure!

Today, also, there was reported that dna-nanotechnology has been modified to allow it to do actual chemical reactions; before, dna-nanomanufacturing was restricted to just self-organisation purposes; with dna-nanomanufacturing being able to do actual chemical reactions, dna-nanomanufacturing is fast becoming capable to leading to a real nanotech world; one that can transform and recycle(in Eric Drexler's words) the industrial period of the last three hundred years! This now looks to happen almost certainly within a year!
flashgordon
not rated yet Nov 16, 2012
What's further remarkable is that at the same time dna-nanomanufacturing is showing that it can do nanomanufacturing(chemical reactions and self organisation), other enabling nanotechnology pathways are also looking to be able to make their mark in a year. This means this year is going to see an accellerated progress to the nano-era!

Dna-nanotechnology may still have en edge with its programmability and self-organisation ability. It's scalability.