Izvestiya of Saratov University.

Physics

ISSN 1817-3020 (Print)
ISSN 2542-193X (Online)


For citation:

Zimnyakov D. A., Alonova M. V., Skripal A. V., Dobdin S. Y., Feodorova V. A. Small-angle polarimetry as a technique for identification of nucleotide sequences in bioinformatics. Izvestiya of Saratov University. Physics , 2023, vol. 23, iss. 1, pp. 46-55. DOI: 10.18500/1817-3020-2023-23-1-46-55, EDN: IQKRQK

This is an open access article distributed under the terms of Creative Commons Attribution 4.0 International License (CC-BY 4.0).
Published online: 
01.03.2023
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(downloads: 197)
Language: 
Russian
Article type: 
Article
UDC: 
535.512
EDN: 
IQKRQK

Small-angle polarimetry as a technique for identification of nucleotide sequences in bioinformatics

Autors: 
Zimnyakov Dmitry Aleksandrovich, Yuri Gagarin State Technical University of Saratov
Alonova Marina Vasil'evna, Yuri Gagarin State Technical University of Saratov
Skripal Anatoly Vladimirovich, Saratov State University
Dobdin Sergey Yur'evich, Saratov State University
Feodorova Valentina Anatol'evna, Saratov State University
Abstract: 

Background and Objectives: The method of identification of symbolic sequences associated with the genetic structure of biological objects using the principles of small-angle polarimetry is considered. This method of analyzing and visualizing symbolic sequences obtained by sequencing DNA fragments can be defined as small-angle polarimetry of phase-modulating structures associated with genetic information. Materials and Methods: The analyzed symbolic sequence is represented by a two-dimensional phase-modulating matrix, each element of which corresponds to one of the four basic nucleotides (adenine, cytosine, thymine, guanine), and the depth of modulation of the phase of the reading coherent linearly polarized beam is determined by the content of this nucleotide in the corresponding triplet in the nucleotide sequence. As a result of the diffraction of a reading coherent beam with a polarization plane oriented at an angle of 45° to the sides of the phase-modulating matrix, a spatial distribution of local polarization states of the reading field diffracted on the matrix is formed in the paraxial region of the far diffraction zone. Discrimination of local polarization states in accordance with the proposed algorithm makes it possible to synthesize a binary spatial distribution, which is a unique identifier of the analyzed symbol sequence. Results: Modeling of the processes of phase coding and subsequent analysis of local polarization states in the near-axial region using sequencing results for the strains “Wuhan”, “Delta” and “Omicron” of the SARS-CoV-2 virus has shown a high sensitivity of the method to local changes in the structure of nucleotide sequences. Conclusion: The results of the simulation allow us to conclude that binary distributions of local polarization states of light fields diffracted on DNA-associated phase-modulating structures recorded in the axial region are characterized by high sensitivity to local mutational changes in the structure of nucleotide sequences. The results obtained can be used as a basis for creating effective hybrid methods for analyzing genetic information using the principles of polarization coding and small-angle polarimetry.

Acknowledgments: 
This work was supported by the Russian Science Foundation (project no. 22-21-00194).
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Received: 
30.10.2022
Accepted: 
14.12.2022
Published: 
01.03.2023