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

• Published in: Journal of biological physics Vol. 44; no. 1; pp. 101 - 116
• Main Authors: Boiko, V. V., Romanyuk, V. R., Gnatyuk, O. P., Ilchenko, O. O., Karakhim, S. O., Korovin, A. V., Dovbeshko, G. I.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-03-2018; Springer Nature B.V
• Subjects: Biochemistry; Biological and Medical Physics; Biophysics; Cavities; Complex Fluids and Microfluidics; Complex Systems; Conformation; Crystals; Deoxyribonucleic acid; DNA; DNA - chemistry; Electricity; Electromagnetic fields; Localization; Neurosciences; Original Paper; Photons; Physics; Physics and Astronomy; Soft and Granular Matter; Spectrum Analysis, Raman; Vibration; Raman spectra; Photonic crystal; DNA; 87.15.-v; DNA conformation; Vibrational modes; 87.64.mk; 78.67.Pt; Confined volume; FDTD simulations; 87.64.kp
• ISSN: 0092-0606; 1573-0689
• DOI: 10.1007/s10867-018-9480-0

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.