DNA with three base pairs: details

A new genetic code and the first semi-synthetic bacterium

Andrey Vasilkov, Computerra

Researchers from the Scripps Research Institute (TSRI) in California modified the E. coli bacterium by introducing two new complementary compounds not found in nature into its plasmid DNA code. So the scientific group received the world's first semi-synthetic living organism and forever changed genetics. One of the authors of the work is our compatriot – researcher Denis Malyshev. He studied at the Moscow Chemical Lyceum, after which he graduated from the D.I. Mendeleev Russian University of Chemical Technology and emigrated to the United States.

Modern biologists and biochemists can be considered programmers. After all, they have mastered the lowest–level language imaginable - the genetic code. Direct intervention in it is similar to reverse engineering. It became possible only recently and has made a real revolution in biotechnology.

Until about the eighties of the XX century, breeders acted blindly, relying on external signs and patterns of their inheritance. Even in such an imperfect way, sometimes amazing achievements were made on their own scale. For example, Nobel Prize winner Norman Ernest Borlaug is called the "father of Green" for the fact that he was able to breed wheat and rice varieties with exceptional yields. According to the UN, this has already saved about a billion people from starvation and helped to preserve the very existence of Mexico, India and Pakistan.

Sometimes the trial and error method led to annoying miscalculations. For example, in addition to increasing the yield of potatoes and tomatoes of new varieties, they increased the level of toxins typical of the entire Solanaceae family. Such varieties were rejected, but no one could return the years of time spent. The problem of deterring genetics lies precisely in the fear of complex technologies, and not in the danger of the altered DNA itself. After all, absolutely any organism (except its own) is genetically alien to us.

New biotechnological methods make it possible to avoid such mistakes by immediately making controlled changes to the genotype. In addition to plants, this method is widely used in bacteria, since in addition to the main DNA, they also contain a plasmid that is convenient for work. Modified strains turn into a plant for the production of complex proteins, which are most in demand in medicine. Among them are insulin, erythropoietin, interferon and others. According to WHO, genetically engineered insulin alone saves hundreds of millions of people worldwide from severe complications and death.

The scheme of obtaining insulin by genetic engineering methods (based on the materials: discoveryandinnovation.com ).

Today, the quality of our life directly depends on how quickly we can figure out the details of protein synthesis and learn how to manage this process. Simple methods of changing the genome are no longer enough – it is necessary to expand the genetic programming language itself by introducing new operators into it. This is exactly what was done at the Scripps Institute, combining the results of scientific work on this topic for more than twenty years.

In nature, the nucleic acids of all living beings contain only four nitrogenous bases: guanine (G), adenine (A), thymine (T) and cytosine (C) in DNA, plus an unmethylated form of thymine (uracil – U) in RNA. Each section of three consecutive bases forms a codon, in which the command to synthesize a certain amino acid, or "start/stop" signals, is encrypted.

The coding scheme of amino acids in DNA (image: mpnforum.com ).

With a large chemical diversity of amino acids as a group of substances, the proteins of any living organism consist of only twenty L-alpha amino acids. Their position determines the structure of proteins and their biological properties.

This code is characterized by redundancy: some amino acids can be encoded in different ways. For example, the entry CG*, where * is any third base, will lead to the synthesis of arginine inside the cell. Therefore, despite the three-letter system, in the process of protein biosynthesis, not 64 = 4 ³, but only twenty different variants of amino acids are formed. Rare selenocysteine, pyrrolysine and other "non-standard" alpha-amino acids do not violate this rule. They fall out of the general list, as they are formed differently – by modifying one of the main amino acids after its synthesis.

In laboratory conditions in addition to AT(U)GC can also use other coding molecules, such as d5SICS and DNAm. Adding just a couple of synthetic compounds to the standard set of nitrogenous bases actually creates a new genetic alphabet. With its help, it is possible to encode the biosynthesis of not twenty, but one hundred and seventy-two amino acids. The number of new protein variants that can be synthesized from them becomes simply astronomical.

Just two new compounds expand the number of possible amino acids from 20 to 172 (image: cen.acs.org ).

"In principle, we could encode completely new proteins made from naturally occurring amino acids," explains Floyd E. Romesberg, head of the group. "It would give us more power than ever. We could adapt the technology to create protein therapeutic and diagnostic tools, laboratory reagents and much more. Such aspects of application as nanomaterials are also possible."

Synthetic nucleotides d5SICS and DNAm bind via hydrophobic interactions, while natural ones form hydrogen bonds. This does not prevent them from being used to expand the genetic alphabet, but creates a number of surmountable difficulties.

Comparison of the bonds of synthetic (d5SICS-DNAm) and natural (C-G) nucleotides (image: nature.com ).

An experimental strain of bacteria with an altered genotype contains these two new nucleotides and retains viability, but does not yet produce offspring on its own. The reproduction of modified bacteria requires a number of manual manipulations with the solution, such as the addition of phosphate compounds obtained from algae.

"It is important to note that this also provides control over the system," says Denis Malyshev. – Our new nucleotides can enter the cell only with the help of carrier proteins. Without them, the cell will return to the standard ATGC set, and the d5SICS and DNAm compounds will disappear from its genome."

The authors of the study expect that in the future there will be a way to create a fully synthetic and reproducible strain of bacteria. To do this, you need to expand the "alphabet" of RNA in a similar way and, possibly, change the ribosomes themselves.

Portal "Eternal youth" http://vechnayamolodost.ru 15.005.2014