Abstract

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Symmetry: Culture and Science
Volume 33, Number 3, pages 221-232 (2022)
https://doi.org/10.26830/symmetry_2022_3_221

APPROACHES TO SONIFICATION OF MECHANICAL PROPERTIES OF NUCLEOTIDE SEQUENCES

I. V. Stepanyan^1*, M. O. Savkin², Yu. D. Nechipurenko³

¹ Mechanical Engineering Research Institute of the Russian Academy of Sciences (IMASH RAN) M. Kharitonyevskiy Pereulok, 101990 Moscow, the Russian Federation.
Email: neurocomp.pro@gmail.com
ORCID: 0000-0003-3176-5279

² Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow, 117198, Russian Federation.
Email: zeronerorgb@gmail.com
ORCID: 0000-0003-2430-1118

³ Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991 Russia.

^* corresponding author

Abstract: Various approaches to DNA sonification are given: based on the mathematical analysis of DNA parameters and the effect of ultrasound DNA cleavage in solution. Parametric manifestations of DNA with the presence of a fractal structure are also given. The effect of fractality and the sonification of genetic information is discussed. The prospects of the bionic approach for man-machine-environment systems and interfaces of the future are discussed. The main message is bionic ergonomics, the principle of nature-like technologies. An example of the principle of simplifying the perception of complex genetic information in interfaces is given in the algorithms for visualization and sonification of nucleotide sequences. The study was conducted at the intersection of biomechanics, bionics and bioinformatics.

Keywords: multifractality, finite geometry, sonification, parametrization, golden ratio, DNA, ultrasonic DNA cleavage, conformational-dynamic characteristics of DNA.

References:
Anitas, E. M. (2022) Fractal Analysis of DNA Sequences Using Frequency Chaos Game Representation and Small-Angle Scattering, International Journal of Molecular Sciences, 23, 3, 1847. https://doi.org/10.3390/ijms23031847

Aristov, V. V., Buchelnikov, A. S., & Nechipurenko, Y. D. (2022) The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems, Entropy, 24, 2, 172. https://doi.org/10.3390/e24020172

Ball, T., Chaiser, R., Dustin, D., Edgar, T., & Lagarde, P. (2019) Some combinatorics from Zeckendorf representations, Involve, a Journal of Mathematics, 12, 7, 1241-1260. https://doi.org/10.2140/involve.2019.12.1241

Deininger, P. L. (1983) Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis, Analytical Biochemistry, 129, 1, 216-223. https://doi.org/10.1016/0003-2697(83)90072-6

Gena, P., & Strom, C. (2001) A physiological approach to DNA music, in 4th Computers in Art and Design Education Conference, Glasgow.

Grokhovsky, S. L. (2006) The specific cleavage of DNA with ultrasound, Molecular biology, 40, 2, 317-325. https://doi.org/10.1134/S0026893306020142

Grokhovsky, S. L., Il’icheva, I. A., Nechipurenko, D. Y., Panchenko, L. A., Polozov, R. V., & Nechipurenko, Y. D. (2008) Ultrasonic cleavage of DNA: Quantitative analysis of sequence specificity, Biophysics, 53, 3, 250-251. https://doi.org/10.1134/S0006350908030159

Grokhovsky, S. L., Il'Icheva, I. A., Nechipurenko, D. Y., Golovkin, M. V., Panchenko, L. A., Polozov, R. V., & Nechipurenko, Y. D. (2011) Sequence-specific ultrasonic cleavage of DNA, Biophysical Journal, 100, 1, 117-125. https://doi.org/10.1016/j.bpj.2010.10.052

Grond, F., & Hermann, T. (2012) Aesthetic strategies in sonification, AI & Society, 27, 2, 213-222. https://doi.org/10.1007/s00146-011-0341-7

He, M. X., Petoukhov, S. V., & Ricci, P. E. (2004) Genetic code, Hamming distance and stochastic matrices, Bulletin of Mathematical Biology, 66, 5, 1405-1421. https://doi.org/10.1016/j.bulm.2004.01.002

Il’icheva, I. A., Khodikov, M. V., Poptsova, M. S., Nechipurenko, D. Y., Nechipurenko, Y. D., & Grokhovsky, S. L. (2016) Structural features of DNA that determine RNA polymerase II core promoter, BMC Genomics, 17, 1, 1-21. https://doi.org/10.1186/s12864-016-3292-z

Il’icheva, I. A., Khodikov, M. V., Panchenko, L. A., Polozov, R. V., & Nechipurenko, Y. D. (2020) Ultrasonic DNA cleavage: An analysis of the conformational-dynamic features of regulatory genome regions and sequencing errors, Biophysics, 65, 3, 426-432. https://doi.org/10.1134/S0006350920030082

Nechipurenko, D. Y., Il’icheva, I. A., Khodikov, M. V., Poptsova, M. S., Nechipurenko, Y. D., & Grokhovsky, S. L. (2014) Modeling of mechanochemical DNA cleavage by the action of ultrasound, Biophysics, 59, 6, 861-868. https://doi.org/10.1134/S000635091406013X

Petoukhov, S. V. (2020) Letter to the editor: Genomes, symmetries and algebraic harmony in living bodies, Symmetry: Culture and Science, 31, 2, 222-223. https://doi.org/10.26830/symmetry_2020_2_222

Petoukhov, S. V. (2021) Algebraic harmony and probabilities in genomes; Long-range coherence in quantum code biology, Biosystems, 209, 104503. https://doi.org/10.1016/j.biosystems.2021.104503

Poptsova, M. S., Il'Icheva, I. A., Nechipurenko, D. Y., Panchenko, L. A., Khodikov, M. V., Oparina, N. Y., Polozov R. V., Nechipurenko, Y. D. & Grokhovsky, S. L. (2014) Non-random DNA fragmentation in next-generation sequencing, Scientific Reports, 4, 1, 1-6. https://doi.org/10.1038/srep04532

Quehenberger, R. C. Z., Stepanyan, I., & Skepper, B. (2020) [CGAT] Epita Matrix Genetics: Toward a visualization of genetic codes via “Genetic Music”, Leonardo, 53, 1, 88-89. https://doi.org/10.1162/leon_a_01840

Schmitt, A. O., & Herzel, H. (1997) Estimating the entropy of DNA sequences, Journal of Theoretical Biology, 188, 3, 369-377. https://doi.org/10.1006/jtbi.1997.0493

Semyonov, D. A., Eltsov, I. V., & Nechipurenko, Y. D. (2020) A new bias site for epigenetic modifications: How non‐canonical GC base pairs favour mechanochemical cleavage of DNA, BioEssays, 42, 1, 2000051. https://doi.org/10.1002/bies.202000051

Shayeghi, A., Rieser, P., Richter, G. et al. (2020) Matter-wave interference of a native polypeptide, Nat Commun 11, 1447. https://doi.org/10.1038/s41467-020-15280-2

Svidlov, A., Drobotenko, M., Basov, A., Gerasimenko, E., Elkina, A., Baryshev, M., ... & Dzhimak, S. (2021) Influence of environmental parameters on the stability of the DNA molecule, Entropy, 23, 11, 1446. https://doi.org/10.3390/e23111446

Stepanyan, I. V. (2020) A multiscale model of nucleic acid imaging, Sci. Visualization, 12, 3, 61-78. https://doi.org/10.26583/sv.12.3.06

Stepanyan, I., & Lednev, M. (2022) Spectral decomposition of mappings of molecular genetic information in the system basis of single nucleotide functions, Symmetry, 14, 5, 844. https://doi.org/10.3390/sym14050844

Stepanyan, I. V., & Petoukhov, S. V. (2017) The matrix method of representation, analysis and classification of long genetic sequences, Information, 8, 1, 12. https://doi.org/10.3390/info8010012

Tchurikov, N. A., Chernov, B. K., Golova, Y. B., & Nechipurenko, Y. D. (1988) Parallel DNA-possibility of existence, Proc. Acad. Sci. USSR, 303, 1254-1258.

Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., ... & Grokhovsky, S. L. (2020) A method for identification of the methylation level of CpG islands from NGS data, Scientific Reports, 10, 1, 1-5. https://doi.org/10.1038/s41598-020-65406-1