10 March 2017

Inlaid with gold by DNA

DNA will become the basis of unprecedented complex synthetic crystals

Nadezhda Bessonova, N+1

Physicists used gold nanoparticles and the "smart glue" of DNA to create a colloidal analogue of the so-called lattice clathrate. The resulting crystals are interesting in themselves for their impressive complexity of structure, potentially they can be used to protect the environment from pollution and in medicine for virus recognition. The description of the work is published in the journal Science (Lin et al., Clathrate colloidal crystals).

A clathrate lattice created from gold nanoparticles
(here and below are drawings from an article in Science)

Clathrate is a compound in which molecules of one variety ("guests") are enclosed in cavities formed by molecules of another variety ("hosts"). An important example of a lattice clathrate is methane hydrate, in which methane molecules are enclosed in the voids of the crystal lattice of ice. This compound is widespread in nature; methane reserves at the bottom of the oceans probably significantly exceed the reserves of gas in the free state. If the clathrate structure is able to "absorb" sufficiently large organic molecules, it can be used in environmental protection products – for example, to collect pollutants.

Creating clathrates from nanoparticles is a difficult task, since obtaining the correct crystal structure depends on the exact size and shape of the nanoparticles, which are quite difficult to control. In the new work, the researchers created a computer model and demonstrated in the laboratory the process of creating an accurate clathrate structure of unprecedented complexity based on gold nanoparticles and "glue" from DNA chains.

A group of scientists at Northwestern University in the USA has been studying the possibilities of synthetic DNA for binding nanoparticles into programmable designs for about ten years. For the new experiment, they synthesized bipyramidal gold nanoparticles consisting of two tetrahedra connected by a common face; the dimensions of the sides of the nanoparticle are 250 and 177 nanometers. After purification by centrifugation and washing with buffered saline solution, the obtained particles were connected to modified DNA strands of various lengths.


The process of self-assembly of a clathrate crystal. a) Geometry and electron microscopy of gold nanoparticles. b - d) Scheme of connection of nanoparticles with a DNA chain. e-f) Electron microscopy of the obtained material with a different approximation.

Experiments have shown that sufficiently long DNA chains ensure the creation of a high-quality crystal structure: for example, when using DNA with 4-block segments, a clear clathrate structure was observed, images of which can be obtained using electron microscopy, however, the dimensions of the structure were relatively small. Crystals of the highest quality were obtained using DNA with 5-block segments: in this case, the resulting clathrate crystals reached tens of micrometers in size.


The effect of the length of the DNA chain on the resulting structure: the use of (A) zero-, (B), one-, (C), two-, (D), three-, (E) four-, and (F) five-block DNA segments. The quality of the structure obviously increases with the growth of the chain length.

Computer simulation of the process showed the formation of cluster types of formed crystal lattices in the form of stellate polyhedra: dodecahedron, icosahedron, icosododecahedron, which correlate with known types of clathrate lattices.


Determination of the three main clathrate structures. The experimental data revealed structures similar to the clathrate lattice of type I (A-C), type IV (D-F) and type II (G-I). Schemes A, D, G: local geometry of structures. Schemes B, E, H: cavities of the clathrate structure. C, F, I: electron microscopy images with varying degrees of approximation.

According to scientists, the resulting clathrate structures can be used in environmental protection systems, as well as in medicine: for example, they can be used to recognize viruses and proteins. In addition, since the sizes of nanoparticles used in clathrates are comparable to the wavelength of visible light, complex clathrate structures can be useful in light-controlled devices such as lenses, lasers and masking materials.

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