Protein "paper clips" have been introduced into DNA origami

Vladimir Korolev, N+1

Chemists from the Technological University of Munich have developed a new modification of the DNA origami technique, in which protein fragments act as paper clips. According to the researchers, this expands the possibilities of DNA self–assembly - traditional techniques require a long single-stranded molecule as a basis, while in living organisms double helices of DNA are more common, with which the new technique can work. Scientists have managed to create rigid nanoparticles in the form of curved lines, squares, circles and frames. Research (Praetorius, Dietz, Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes) got on the cover of a magazine Science.

DNA origami is a technique of "folding" one long single-stranded DNA molecule into complex shapes of a pre–known shape, for example, sheets, boxes, "smileys", scissors and so on. It is based on the principle of complementarity: in DNA chains there are four types of "beads"-nitrogenous bases capable of forming pairs with each other in a strictly defined way. It is the formation of pairs that ensures the existence of a well-known double–stranded DNA helix, in which adenine is located opposite the "bead" - thymine, and cytosine is opposite guanine.

The DNA origami technique is quite simple. To a very long DNA molecule, short DNA "clips" are selected: half of the "clip" is complementary to one part of the original molecule, half to the other. The right set of such "paper clips" glues together the necessary fragments of a large molecule and it develops in the necessary scientific way.

However, it is very rare to find long single–stranded DNA molecules in living organisms - they are found, for example, in some viruses. In addition, the self-assembly process requires elevated temperatures that are incompatible with the vital activity of most organisms.

The scheme of DNA folding using TAL proteins
(here and below are drawings from an article in Science).

The authors of the new work proposed to rethink the original technique by replacing the "paper clips" from DNA with specially selected protein molecules. They are based on TAL effectors similar to transcription activators. These proteins are produced by pathogenic plant bacteria. They are able to control the expression (synthesis of proteins) from certain genes by joining their promoters (sites for the start of transcription), wrapping the double-stranded helix entirely. These proteins were chosen because scientists know very well which amino acid and in which position it is necessary to change so that the protein begins to "recognize" the required pair of nucleotides. TALS have a modular structure: they consist of several repeating parts, each of which "recognizes" its DNA base pairs. 

Scientists have created a "paper clip" of two TAL protein molecules connected by a special bridge. To test the efficiency of the approach, the authors developed 12 different "paper clips" that could recognize 24 specific sections of the DNA molecule and successfully self-assembled several test structures.

Structures that the authors managed to assemble
based on 12 protein "staples" and a DNA molecule.

For self–assembly in a physiological environment, the researchers used plasmids - short DNA chains encoding TAL proteins. Scientists placed plasmids corresponding to 12 "paper clips" in a medium containing ribosomes, amino acids, transport RNA, cofactors and other necessary substances, along with a folding double-stranded DNA molecule. Only six hours at room temperature was enough to form the required structures. They were examined using a transmission electron microscope.

Self-assembly based on plasmids encoding "paper clips";
ribosomes are indicated by asterisks on the micrograph.

The authors emphasize that "paper clips" can be developed for any desired sequence of pairs in DNA. In addition, existing techniques allow mass production of components for such nanoscale complexes. Among the possible applications of the updated DNA origami technique is the creation of platforms for targeted drug delivery.

Earlier, using the traditional DNA origami technique, Israeli scientists developed "nanorobots" to deliver drugs controlled by the power of thought. In addition, this technique can be used to create large-scale ordered objects, for example, chemists from the California Institute of Technology reproduced Van Gogh's painting "Starry Night" with its help.

Portal "Eternal youth" http://vechnayamolodost.ru  24.03.2017