26 June 2014

Nanorobots are coming!

Golakteko danger: DNA robots in a living organism

Anton Sergeev, "Biomolecule"In the era of electronic computers, it is difficult to imagine that anything other than a powerful computer can help a person in solving his problems.

Quantum computers are still exotic, inaccessible to mere mortals... Have you ever heard of molecular computers? Two decades have passed since scientists first solved a mathematical problem using DNA. To date, scientists have managed to move much further in this direction – the work of programmable nanorobots is already being tested on cockroaches. Do you still think the future is far away? Then we are coming to you!

A team of scientists from Israel and the USA set up a unique experiment – they launched nanorobots into live cockroaches and showed the effective operation of the structures they created. In fact, they created logic circuits that implement different outcomes depending on the molecular environment. The results are published in the journal Nature Nanotechnology (2014): Amir Y. et al., Universal computing by DNA origami robots in a living animal.

Nanorobots are specially constructed nanometer–scale objects consisting of various molecules or even individual atoms and performing predefined programmable operations. For the most part, they are the simplest molecular machines capable of performing a small set of elementary actions, such as movement in a given direction, cargo transfer and sensory functions. The emergence of DNA origami gave a huge impetus to the development of this scientific direction. The use of DNA origami has provided scientists with a reliable tool for building molecular structures of almost any complexity.

In their work, the scientists constructed three types of nanorobots: an effector robot E, which carried an antibody specifically binding to cockroach blood cells as a cargo, and two control robots - positive P and negative N (Fig. 1).

Figure 1. Effector robot E is a hexagonal prism, inside of which is hidden an "important cargo" – in this case, an antibody capable of binding to cockroach blood cells. The figure shows a screenshot of the caDNAno program, which allows you to model the structure of DNA origami and select the nucleotide sequences necessary for the design. (Here and below are the drawings from the article in Nature Nanotechnology).With the help of these elements, specifically interacting with each other and with substances in the environment, scientists managed to assemble a set of logic gates.

Logic gates are the basic elements of a digital circuit and are used to perform elementary logical operations. They have long been used by man in information technology, and are the basis of the architecture of computers.

The coordinated work of the effector robot E and its two regulators P and N imitated the work of the simplest computers, representing a fairly advanced version of a molecular computer or DNA computer. The interaction between DNA robots was carried out according to the principle of specific key-lock binding, through which they formed complex complexes.

During the experiment, a solution with E, P and N nanorobots was added to the blood of a live cockroach. Once inside the body, the effector robot E specifically interacted with molecules X and Y (let's call them that, because almost any compounds could act as X and Y) and underwent a conformational transition or, more simply, opened. Having opened, the robot released its molecular cargo – an antibody, which immediately recognized the cockroach's hemocytes and bound to them. At the same time, in order to open the robot and release the cargo, it was necessary to have both compounds in the blood – both X and Y.

However, in the presence of only one compound, the complex could also open up. To do this, he needed the help of a positive regulator P. This robot was loaded with a DNA key, and, depending on the design, released it when interacting with either X or Y. The DNA key opened robot E and started the process of formation of the E–hemocyte complex. Finally, the negative regulator N, when interacting with both compounds, did not allow the effector robot E to open and acted as an inhibitor of the formation of a complex with a blood cell.

All these processes can be illustrated using logic diagrams and presented in the form of elementary logical operations of the type "And" (both X and Y are needed), "OR" (either X or Y or both connections are needed), "exclusive OR" (either X or Y is needed, but not both connections). The output parameters FALSE (or 0) and TRUE (or 1) here are the presence of the E–hemocyte complex. These and other logic circuits are shown in Fig. 2.

Figure 2. Logic gates assembled by the authors of the article from nanorobots. The input signal can be represented by one bit (X) or two bits (X and Y), which are biological molecules. The output signal (one or two bits) represents the state of the effector robots (E and F), which is read using fluorescence.Thus, the work of three nanorobots led to the realization of two outcomes – to release the molecular cargo or not to release it.

To solve more complex problems, the authors used additional effector robots F (similar to E, but not interfering with it) and Eo (unlike E, it is initially open). This solution made it possible to build much more complex logic circuits. The researchers claim that with the addition of additional effector robots and special regulators, nothing prevents this technology from exceeding the power of the old 8-bit Commodore 64 and Atari 800 computers on which they played as children. The only difficulty is to assemble as many logic gates that interact with each other correctly as possible.

Almost any molecule can act as a molecular load of an effector robot. It can be an activator or an inhibitor of certain molecular reactions, or an antibody that binds a virus or other harmful compound. In the described experiment, the robot was bound to cockroach blood cells, which were then examined using flow cytometry. When examining the blood of the experimental subjects, part of the blood cells fluoresced in the required wavelength range, which indicates the binding of the antibody to the hemocyte and, consequently, the successful activation of effector nanorobots (Fig. 3A).

Figure 3. The use of DNA robots. A. From above: an image of three complexes of nanorobots simulating the behavior of logic gates AND, OR and XOR (atomic force microscopy). From below: a fluorescence signal recorded by flow cytometry obtained from these valves when registering PDGF and VEGF molecules in the blood of a cockroach. B. One of the options for constructing a complex logic circuit for registering four molecules and making a diagnosis. Based on their presence, a decision is made to release three types of therapeutic molecules (one for each logic gate).

For the first stage of research, the choice fell on the cockroaches Blaberus discoidalis, and it was not by chance that this was done. Firstly, they have a small volume of blood (insects actually do not have blood, but hemolymph – VM), and, as a result, fewer nanorobots are required in order to show the consistency of the technique. Secondly, the concentration of nucleases destroying foreign DNA in the blood of cockroaches is low, which ensures the long-term stable operation of DNA structures. So far, all experiments have been conducted only on cockroaches, but scientists believe that with the addition of some modifications to the design of nanorobots, the same principle of operation will be implemented in other organisms. For example, an obstacle that represents the work of nucleases can be overcome by using closed nucleic acids (LNA) as a building material instead of DNA.

The results obtained can find their application in information technology, biotechnology and medicine. The technique described above simulates the behavior of an arithmetic logic unit (ALU) of a computer, which can be used in the development of molecular computers of the future. With the help of the basic elements proposed by the authors, it is possible to build quite complex logic circuits implementing intricate algorithms (Fig. 3B). Since almost any molecule can play the role of cargo in an effector robot, such systems can be used as sensors, similar to the microchips currently existing. They will allow identifying even the most insignificant changes in the molecular environment (registration of single molecules). Only the way of reading information will change – each set of target molecules will have its own binary code.

Also an interesting prospect of using the described nanorobots is the creation of "smart" medicines. A team of nanorobots launched into the bloodstream, depending on the program and the substances present in the blood (molecules, viruses, bacteria, etc.), will diagnose themselves and release the necessary medications. For a healthy person, such a medicine will be completely harmless, because, without detecting pathogens, nanorobots will leave the molecular cargo with them. A scenario of targeted drug delivery to a specific organ and the subsequent removal of excess DNA robots from the body is possible. The undoubted advantages of such drugs include the possibility of early detection, for example, of single viruses, and their immediate destruction, as well as the low toxicity of such therapy.

Portal "Eternal youth" http://vechnayamolodost.ru26.06.2014

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