Русская версия







Personal page number 1

Karasev Vladimir Aleksandrovich





Key words: genetic code, the spatial structure of the doublet and triplet genetic code, proteins, amino acids as physical operators, protein pentafragments, the nature of the triplet-amino acid assignment, the topological bases of the genetic code





Book V. Karasev “Genetic Code: New Horizons"  



Book V. Karasev and V. Luchinin "Introduction to the design of bionical nanosystems"



Book V. Karasev «Principles of topological coding of chain polymers and protein structure»New



Book V. Karasev , V. Luchinin,  A. Sokolov  «Bio- and quantum-information technologies in nanoelectronics»New



Sites V. Karasev:


Spatial structure of the canonical set of amino acids


Molecular vector machine of proteins


Aid to the atheist: A new theory explaining essence and origin of life


«Protein 3D - visualizer of supramolecular biostructures»New



Thank you for visiting my homepage. I hope it will be interesting.


I invite you to scientific voyage to the world of the Genetic code. I must warn you that it will be hard job and will require from you some intellectual efforts. However, like climbers, who have the reached top, receive incomparable pleasure, you too, having looked through the homepage, will see the world of beauty and original aesthetics, which is connected with the Genetic code.


This page is an updated version. Previous version was created about ten years ago and some out of date. Three groups of researchers, as far as we know, have come almost simultaneously and independently to the idea of ​​the spatial structure of the genetic code: H.H. Clamp from South Africa [1], M.A. Jimenez - Montaño and his colleagues from Mexico [2,3] and we, V.A. Karasev and S.S. Sorokin from Russia [4]. A little later the Russian researcher S.V. Petoukhov [5] has come to this idea too. Each of them offered his own version of this structure, and each has come to this idea  ​​his own way. Visitors can get acquainted with these matters in [6-8].

Over years past from the appearance time of this works many questions have made significant progress in development. There was a special literature on the spatial structure of the genetic code, which was the subject of an analytical review [9].


Our page describes the version of the structure of the genetic code and its interpretation of nature, to which we have come. There is a site, M.A. Jimenez - Montaño, which gives a 'live' presentation of his version of the spatial structure of the genetic code by using special software ( There are probably other sites devoted to this issue. We are not inclined to discuss here, whose path is more promising and correct. Time will tell and put everything to its place.


Most contemporary literature on the genetic code [9] suggests that not all problems of the genetic code have been fully resolved. You will get acquainted with what has become known.


So in a way.



Address for connection:


1.  Modern table of the genetic code





Modern genetic code table sets the assignment of triplets to certain amino acids, but does not reflect its real structure.


2.  The spatial structure of the genetic code


2.1. Rhombic variant of the genetic dictionary

2.2. Doublet genetic code

2.3. The triplet genetic code





1.    Based on the principle of complementarity a two-dimensional structure of the doublet code, having the symmetry, was built.

2.    Using the principle of single transitions between the bases in doublet and triplet genetic code, spatial structures of doublet and triplet genetic code, isomorphic, respectively, to the Boolean hypercubes B4 and B6 were built.


3.  Topological basis of the genetic code


3.1. Definition of basic concepts

3.2. Supermatrix and its spatial representation

3.3. Supermatrix transformation into triplet topological code


Protein pentafragment


4-arc chain






Matrix for the description of bonds




1.    The notion of an elementary fragment of the protein, consisting of four links (a fragment of five amino acids - pentafragments) and its analogue - 4-arc graph described by triangular matrices of six variables taking values ​​0 and 1, was introduced.

2.    On the basis of 64 triangular matrices the Supermatrix consisting of 4 blocks, describing all the conformations of 4-arc graph and pentafragments of protein was constructed.

3.    By assignment  to the three pairs of variables first letters of names of the nitrogenous bases (00 <---> C, 01 <---> U, 10 <---> G, 11 <---> A) triangular matrices are transformed to triplets, and the Supermatrix itself  is transformed into a triplet genetic code.


Thereby it is shown, that in the basis of a genetic code the encoded by means of triplets conformations description of protein and its analogue - 4-arc chain graph lays.


Spatial structure for the Supermatrix is hypercube B6. Hence the answer to the question why the spatial structure of the triplet genetic code, obtained by other means, proved to be isomorphic to the Boolean hypercube В6.


4. Amino acids as physical operators. The problem of  triplets – amino acids assignment in the genetic code


4.1. Concept of «physical operator»

4.2. Amino acids as physical operators








Non polar amino acids – operators of anti-connectivity

Polar amino acids – operators of connectivity

Physical operators

4.3.   Assignment of amino acids side chains to blocks of a genetic code triplets

4.4.   Recreation of symmetric conformation of the protein


Operators of anti-connectivity

















Operators of connectivity









1.    Concepts of physical operators of connectivity and anti-connectivity of the side chains recreating, respectively, cyclic and acyclic conformation of the protein are introduced.

2.      It is shown that non-polar amino acid side chains can be regarded as anti-connectivity operators, and polar amino acids - the operators of the connectivity.

3.    To the blocks of triplets coding the acyclic conformations of the protein (C, U), correspond nonpolar and weakly polar amino acids (anti-connectivity operators), and to the blocks of triplets coding the cyclic conformations (G, U) – the polar amino acids capable of forming hydrogen bonds.


Thus found a fundamental solution to the problem of triplet - amino acid assignment in the genetic code: amino acids correspond to the triplets, which encode the protein conformation, reconstituted by these amino acids as the physical operators.


4.     It is shown that the reconstruction of symmetric conformation of the protein requires different physical operators.



In the course of the analysis it has been revealed, that various side chains (e.g., identical in properties, but different in length amino acids) can have different directions of the applied force (in other words, different vectors of action). This was the starting point to a special analysis of the physical operators in the area of the main chain bond цепипNiH...Oi-4=C and resulted in the development of model of molecular vector machine of proteins. On the basis of these representations the highly effective method for predicting of secondary structure of proteins, which has become a patent basis, is developed. More in detail it is possible to familiarise with these questions on our site «Molecular vector machine of proteins»: 



We wish you the further successful scientific travel!








Address for connection:


RThe Work was carried out at the Centre of Microtechnologies and Diagnostics (CMID) of the St.-Petersburg State Electrotechnical University "LETI", at financial support of University


I express my sincere gratitude to A.I. Belyaev for help in editing the English version of this page.