Periodic Triplet system
LETI scientists have created a "Periodic Table" to systematize the elements of the genetic code
Many objects in the world are amenable to systematization. The most famous example is the periodic system of chemical elements, the regularities for which were established by the Russian scientist Dmitry Ivanovich Mendeleev. Such cases of systematization are extremely important. For example, the periodic Table can be used to study the origin of chemical elements or to predict the properties of previously unknown substances that may have beneficial properties for humans.
One of the scientific directions that needs systematization of elements today is genetics. In the 1960s, a generally accepted table of elements of the genetic code (nucleotides and amino acids) was formulated. However, the rapid development of big data processing technologies has made it possible to significantly refine our ideas about genes. It became clear that the systematization of that time was significantly outdated and did not explain many properties of the genetic code. In addition, the principles of constructing a generally accepted table have developed historically and do not have a strict mathematical justification. Therefore, there is a need to search for natural principles to systematize the genetic code.
"We have developed and theoretically justified the location of triplets (a unit of the genetic code consisting of three nucleotides) and the amino acids encoded by them in the form of a Canonical table of the genetic code. The name "canonical" table was given in connection with the location of triplet blocks in it in the sequence of four nucleotides of the gene: cytosine, guanine, uracil, adenine, which is called canonical. We compared the Canonical Table of the Genetic Code with the Periodic Table of Chemical Elements and noted their similarity: the presence of an initial element, the sequential filling of bond vacancies within triplet blocks. But there are also differences, for example, the number of triplets, unlike chemical elements, is limited," says Vladimir Aleksandrovich Karasev, a leading researcher at the Engineering Center for Microtechnology and Diagnostics (IC CMID) of SPBSET "LETI".
In the past, to compile the periodic table, it was necessary to find some fundamental regularity between the elements. This is how the periodic law was formulated – the properties of chemical elements are in periodic dependence on the weight of atoms. Therefore, to build a table of the genetic code, LETI scientists needed to find a similar natural fundamental principle for systematization.
The study used an extensive database of biopolymers. During the search for patterns, experts found that each triplet has connections only with certain protein fragments consisting of five amino acids (they are called pentafragments). Thanks to the construction of a mathematical model, it turned out that there are 64 possible combinations of triplets and related pentafragments, and 16 variants of various spatial structures. Based on these two parameters, four rows of a table of 16 columns were formed, where each element was assigned a correspondence between a triplet and a pentafragment.
The resulting table made it possible to visualize in the genetic code the elements of symmetry and antisymmetry and their transformations into each other, the cyclic periodicity of triplets both within the rows and the entire table as a whole. The results of the work are published in the scientific journal Biosystems (Karasev, The Canonical Table of the Genetic Code as a periodic system of triplets).
"Our Canonical table of the genetic code can be used to predict spatial structures consisting of known proteins or to construct new proteins with predetermined useful biological properties. For example, it can be potential enzymes, medicines and even technical electronic devices of molecular size," says Vladimir Aleksandrovich Karasev.
The development of the table was carried out as part of the development of the scientific section of the CMID IC "Principles of topological coding of chain polymers", which is part of the bionic direction. The research is conducted under the direction of the Director of the CI CMID Viktor Viktorovich Luchinin. The key goal of the direction is to use biological patterns to create robots and other technical devices.
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