10 January 2018

Origami by algorithm

Scientists have developed an algorithm for DNA origami


Stages of the algorithm operation 
(Roman Reshetnikov, Artur Zalevsky)

The staff of the Faculty of Bioengineering and Bioinformatics of Lomonosov Moscow State University together with colleagues from several Russian scientific institutes and the University of Pennsylvania proposed an algorithm for computer modeling of three-dimensional structures made of DNA. Such nanorobots can be used in electronics and medicine, for example, for drug delivery. An article with the results of the scientists' work was published in the journal Nuclear Acids Research (Reshetnikov et al., A coarse-grained model for DNA origami). The research was supported by a grant from the Russian Science Foundation (RNF).

DNA origami technology allows you to create various constructions from DNA chains, including three-dimensional and controllable ones. This is possible due to the fact that these long molecules consist of nucleotides forming pairs: adenine with thymine, cytosine with guanine. By setting the sequence of nucleotides in the chain, it can be achieved that it will fold and fasten in the right places and at the right angle.

"It is very difficult to draw a project of complex DNA origami structures, especially volumetric and dynamic ones, for example, boxes for drug delivery that will open and close, because the program for creating such projects assumes that you draw two-dimensional scans there. If the project is complex, it is very easy to mess something up somewhere and generate a project that simply won't come together," explained Artur Zalevsky, a graduate student of the Faculty of Bioengineering and Bioinformatics at Moscow State University.

The calculations that are required to create a working project are quite large-scale. They are complicated by the fact that it is necessary to take into account the movement of a large number (about a million) of particles and calculate their pairwise interactions. Therefore, scientists use a simplified version of the algorithm, in which groups of atoms are combined into conditional particles and described as a single whole, which makes it possible to repeatedly reduce the size of systems. To develop the program, scientists used the power of the Lomonosov-2 Moscow State University supercomputer.

The algorithm shows whether the design created by the project will be able to collapse in principle and how it will move, open and close. Its advantage over similar services is that it takes into account all kinds of interactions between particles, describes the movements of structural elements better and more fully, shows them more natural.

"A scientist uploads a project file containing a two–dimensional description of the system there, and at the output receives a full-fledged three-dimensional animated structure on which he can see how this system moves," added Artur Zalevsky.

To assess the accuracy of the algorithm, scientists conducted a series of experiments by examining the position and shape of molecules using an atomic force microscope. The authors compared the distributions of configurations generated by the algorithm and obtained during experiments. According to them, during this check, the algorithm proved its effectiveness.

One of the possible applications of DNA origami technology is the use of structures as containers that can deliver and release drugs in a targeted manner. For example, with the help of such nanorobots, it is possible to dissolve a blood clot without diluting the blood throughout the body, or to direct drugs precisely to the cells of a cancerous tumor. Such a targeted effect allows you to reduce the dose of drugs and mitigate side effects. In addition, DNA objects can capture individual molecules, which makes it possible to study particle interactions at the molecular level.

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