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Vibrational spectra of DNA in the confined interglobular volume of photonic crystal

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Abstract

The impact of confinement of DNA molecules in a limited volume of the cavity of photonic crystals (PC) on the vibrational properties of the DNA molecule and its conformation is studied. According to our preliminary study, the aqueous shell is removed when the DNA molecules are infiltrated into the PC cavities. Raman scattering (RS) DNA marker lines showed a dramatic conformational change of DNA in the PC cavities and the appearance of new unknown conformational states. We observed the enhancement of vibrational modes of DNA in the PC in comparison with free DNA of about tenfold and the absence of vibrational modes in DNA bases in a region of 1450–1700 cm−1. The observed features in the RS spectra of DNA are explained by the impact of confined interglobular volume and strong localization of the electromagnetic field. Namely, FDTD simulations in linear regime demonstrate the localization of light in cavities of PC with an approximately ninefold enhancement of the electric field within the photonic stop-band, which is the main reason for RS amplification.

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Acknowledgements

This work was supported by the program of NAS of Ukraine № ВЦ-156 and scholarships of NASU for young scientists. We are grateful to Prof. Vladimir Gorelik from the P.N. Lebedev Physical Institute of Russian Academy of Sciences for the samples of synthetic opals, Prof. Dmitrij Lando from Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus for the ultra-pure calf thymus DNA fibers and Viktor Sobolev from the Technical Centre of NASU for the SEM imaging of synthetic opals.

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Authors and Affiliations

  1. Department of Physics of Biological Systems, Institute of Physics, NAS of Ukraine, Prospect Nauki, 46, Kyiv, 03680, Ukraine

    V. V. Boiko, O. P. Gnatyuk & G. I. Dovbeshko

  2. Department of Polaritonic Optoelectronics, Institute for Physics of Semiconductors, NAS of Ukraine, Prospect Nauki, 41, Kyiv, 03028, Ukraine

    V. R. Romanyuk & A. V. Korovin

  3. Department of Epigenetics, D.F. Chebotarev State Institute of Gerontology, NAMS of Ukraine, Vyshhorodska Str, 67, Kyiv, 04114, Ukraine

    O. O. Ilchenko

  4. Department of Muscle Biochemistry, Palladin Institute of Biochemistry, NAS of Ukraine, Leontovicha Str. 9, Kyiv, 01601, Ukraine

    S. O. Karakhim

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  1. V. V. Boiko
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Boiko, V.V., Romanyuk, V.R., Gnatyuk, O.P. et al. Vibrational spectra of DNA in the confined interglobular volume of photonic crystal. J Biol Phys 44, 101–116 (2018). https://doi.org/10.1007/s10867-018-9480-0

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