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Low-frequency vibrations of water molecules in DNA minor groove

  • Regular Article - Living Systems
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Abstract

Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm\(^{-1}\) depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra

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Acknowledgements

The present work was partially supported by the Project of the National Academy of Sciences of Ukraine (0120U100855).

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Authors and Affiliations

  1. Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine

    T. L. Bubon & S. M. Perepelytsya

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  1. T. L. Bubon
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  2. S. M. Perepelytsya
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TLB performed the analytical analysis and computations. SMP supervised the research. All authors discussed the results and contributed to the final manuscript.

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Correspondence to T. L. Bubon.

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Bubon, T.L., Perepelytsya, S.M. Low-frequency vibrations of water molecules in DNA minor groove. Eur. Phys. J. E 44, 84 (2021). https://doi.org/10.1140/epje/s10189-021-00080-3

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