Aptamers on nucleic acid-based

Chemist Dr. Doping tells aboutcomplementary molecule, the chemical synthesis of DNA by SELEX and aptamers medical perspectives. What are the benefits of DNA drug use compared with antibodies? What are the methods of chemical synthesis of DNA? How to create a drug that acts for 15 minutes?

Let us imagine how modern medicine - are small molecules that are produced by chemical synthesis. The features of these molecules is that they possess a certain complementarity surface protein or DNA in which they interact, and this determines the specificity and complementarity of the recognition molecule of the desired object. But we know that in a cage similar role is played not only small, small organic molecules, but also large biopolymers such as proteins and DNA, and this formed part of these molecules in the course of evolution. Important, that Cyanocobalamin injection - is essential for DNA synthesis.

The question is: if we can somehow, using modern approaches of molecular biology, chemistry, to ensure that the evolution is much faster, and we can observe the evolution in a test tube? This approach exists, this method is called SELEX. Its essence is that initially via chemical synthesis method is obtained a great variety of different DNA molecules of about the same length. It is necessary to mention that it can be not only DNA, but also RNA. After that, by successive enrichment and amplification it is a natural selection of those molecules that are capable of binding to a predetermined target.

And then comes the most interesting. At the moment you can find articles, which reported that the target can be a small molecule, such as ATP, the molecule can be more - a protein may be a cell as a whole, may be even chto-nibud that really has a certain surface, which can qualify the structure of DNA with a complementary surface. It should be well understood that there is a difference between the complementary DNA, when one letter corresponds to the other, and the complementary surface. Naturally, the surface complementarity involves a complex three-dimensional structure.

The result of using SELEX procedures with respect to any molecule or target leads to the fact that we find a sequence capable of forming a complex three-dimensional spatial structure, which is complementary to the pre-selected target. And if we know this sequence, we can then synthesize any DNA again, and it will still form the very structure. That is quite a time by SELEX to find a sequence that is able to interact with a particular target, and then we already know that there is a sequence that forms a complex three-dimensional structure, and will recognize the target. Then we can turn out the sequence of chemical process to create conditions in order to form a three-dimensional structure, and use it for their own purposes. What could be the purpose? A goal can be quite varied. This may be an analogue antibody, then there is an aptamer molecule is DNA, it will bind to some proteins and affect its function.

What is the general idea of using DNA as an antibody analogues? The fact is that we must understand that in the present moment you can buy in a drugstore antibodies as drugs. Cost, I can tell you quite significant - it's tens of thousands of rubles. And all because the antibodies are produced, as though it may sound ridiculous, for example, a special line of hamster cells. Do not worry, hamsters do not kill for the sake of these antibodies in large quantities - just building up this culture. And the selection of the culture - it is quite a complicated process, which may be large losses and a bunch of other problems. Naturally, the selection of live substances leads to the fact that these substances may be present any toxins additional allergenic components and so on. This is a very complex process that leads to the high cost of such products.

If we turn to the chemical synthesis - and the DNA can be synthesized chemically, - that then everything becomes much easier. We do not need so much to clean, because most of today's well-known drugs are chemically synthesized. Thus, it appears that we can achieve the same effect as the antibody synthesizing DNA aptamer to some protein, which is necessary to affect its function. On the other hand, we synthesize it chemically - it worked well to date processes that allow us to obtain pure chemicals.

What is another fun feature of such substances, drugs?

Such DNA is synthesized by block, ie nucleotide adding each nucleotide - is as a designer.

In this constructor modified base can be added, additional additives to the ends of the molecules in order to affect its properties: lifetime in the blood, kidney excretion rate, and so on. And most interesting is that these modifications are done very simply - in the course of chemical synthesis. And we can choose for these drugs - will be called aptamers candidates for drugs - a structure that will meet the requirements set by your doctor. For example, if we need an aptamer, which operates 15 minutes - in fact quite difficult to think of themselves the organic matter, which in 15 minutes completely eliminated from the body - there is no problem. You simply take a naked DNA, and it really circulates in the bloodstream where some 15-20 minutes and then simply excreted by the kidneys.

Thus, by introducing the drug - it is valid for 15 minutes, - the doctor can do something, it can accurately control the time and after the expiry of a cure absolutely disappears, because the DNA - is a component of our cells, like everything else, the it has a totally biodegradable and there will be no accumulation of byproducts. And as a result, we can say that in principle aptamers are potentially very promising class of compounds for use not only in therapeutics, but also in diagnostics.

But there is one drawback. The fact that the SELEX procedure involves selection from a library of random sequences. In order to achieve full representation of the library, the chemical synthesis of advanced features are not enough, so it is often necessary after the SELEX method to bring some ways to the optimum state for this molecule. That is, we are actually after SELEX do not get ready to order - medication, and some preparation, and it is necessary to invest still a lot of work to create from it the molecule that must be satisfied by, for example, a doctor needs or some other requirements . But the main advantage of this approach is that the modular structure of DNA, block, any character can be replaced at any time during chemical synthesis, and it's really simple.

Of course, the main problem of this area is that not always the results that are obtained after the application of such a simple procedure as the SELEX, are acceptable for use, and often for the optimization of these things are already starting to use robotic systems. For example, when there is a selection of the right candidates is not just handed a researcher, and a robot that can do a lot of operations in different conditions. Thus, it is possible to find the best among a large pool of molecules that we had at the inlet. Here, perhaps, we can say that the number of options - it is about 1015-1020 of input molecules, that is their lots.

What might be the prospects in this area? The problems I have are more or less described and consist in the fact that it is not always possible to find the best option - it has to be further developed, and if found good option, ensure that it is used by the body's purpose, even more difficult, because DNA - it's not quite the molecule that successfully passes through the membrane, is not well diffused in the tissues due to its large size. Therefore, there is still a lot of work, which would ensure the delivery, although delivery is a known problem, not only for aptamers, but also for almost all therapeutic substances.

But the future is, of course, thanks to the success of the chemical synthesis of DNA is sufficiently bright. Why? Because, firstly, we have at the moment the cost of synthesis of one molecule is constantly decreasing, and most importantly, large corporations already become interested in synthesizing DNA is not in the microgram, not milligrams quantities and kilograms. Already there are reports on the synthesis of nucleic acids in a scale of 100 kg of DNA, this is done mainly in Japan and Korea. Therefore, it is hoped that this promising class of compounds, through the development of large-scale production of DNA or RNA in the future will play an important role in the treatment of diseases, and we hope that in this way we will ensure that the organic compounds, which can be deposited in human tissue They disappear from our pharmacies, and only natural ingredients remain.