Phenomenological model and experimental study of DNA absorption spectra in THz range

  • V. L. Vaks
  • A. V. Semenova
  • Yu. S. Guseva
  • A. N. Panin
Part of the following topical collections:
  1. TERA-MIR Radiation: Materials, Generation, Detection and Applications (SMMO 2016)


The dielectric permittivity tensor is analyzed qualitatively for the DNA nematic liquid crystal in the THz frequency range. The analysis is performed within the self-consistent phonon approximation based on the PBD model. It is found that DNA depolarization and absorption spectra depend on such parameters as molecular length and helix period. Specifically it is shown that a localization of the absorption lines in the frequency range is determined by the DNA helix structure whereas the DNA length is responsible for a separation between the absorption lines. It is also shown that the gyrotropic properties of the considered liquid crystal depend on a relation between the molecular length and its helix period. The molecules with even number of half helix periods demonstrate the strongest gyrotrophy whereas the molecules with odd number of half helix periods have the weakest gyrotrophy. The model is used to suggest the experimental methodology for determining the DNA length and helix structure based on measurements of the depolarization and absorption spectra in aqueous solutions of biopolimers. Methods of applied THz spectroscopy for determination of the conformational state of molecules in solution is announced. Some preliminary experimental results are presented, including details of measuring the absorption spectra of dry DNA sample and aqueous solutions of biopolimers.


Terahertz high-resolution spectroscopy Modeling of DNA`s dynamics Conformers Biomolecules 



The study was supported in part by Ministry of Education and Science of the Russian Federation (Grants N 2014/134, 1822 and N 074-U01) and Government of the Russian Federation (the Grant N 11.G34.31.0066 (MedLab)).Besides authors acknowledges support from MPNS COST ACTION MP1204—TERA-MIR Radiation: Materials, Generation, Detection and Applications; and Center “Physics and technology of micro- and nanostructures” at IPM RAS. We also thank A.V. Antonov, B.A. Andreev and V.I. Gavrilenko from IPM RAS for their help in preparing experiments with the FTIR spectrometer.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Alexandrov, B.S., Gelev, V., Bishop, A.R., Ushevaet, A., et al.: DNA Breathing Dynamics in the Presence of a Terahertz Field. Phys. Lett. A 374(10), 1214–1217 (2010)ADSCrossRefMATHGoogle Scholar
  2. Alexandrov, B.S., Phipps, M.L., Alexandrov, L.B., Booshehri, L.G., et. al.: Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells. Scientific reports 3, p. 1–8, (2013)Google Scholar
  3. Blumberg, S., Gajraj, A., Pennington, M., Tkachenko, A., et. al.: The role of thermal fluctuations and mechanical constraints in protein-mediated DNA looping. In: Proceedings SPIE 5841, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems. III, 92, p. 92–102, (2005)Google Scholar
  4. Braakman, R., Blake, G.A.: Principles and promise of Fabry–Perot resonators at terahertz frequencies. J. Appl. Phys. 109(6), 1–11 (2011)CrossRefGoogle Scholar
  5. Chang, X.-C.: Terahertz wave imaging: horizons and hurdles. Phys. Med. Biol. 47, 3667–3677 (2002)CrossRefGoogle Scholar
  6. Chomet, S.: D.N.A. Genesis of a discovery. Newtman-Hemisphere, London (1995)Google Scholar
  7. Dauxois, T., Peyrard, M., Bishop, A.R.: Entropy-driven DNA denaturation. Phys. Rev. E 47(1), R44–47 (1993)ADSCrossRefMATHGoogle Scholar
  8. Ermilov, V.V., Tjurenkov, I.N., Nesterova A.A., Zagrebin V.L.: Bolezn’ Al’tsgeimera I gerontooftalmologicheskie zabolevania v aspect amiloidogeneza. Archiv patologii 2 (2013)Google Scholar
  9. Fil'kenshtejn, A.V., Pticyn, O.B.: Fizika belka. Kurs lekcij. RFFI, biblioteka, knigi, izdannye pri podderzhke RFFI (2002)
  10. Globus, T., Khromova, T., Gelmont, B., Woolard, D., et al.: Terahertz characterization of dilute solutions of DNA. Proc. SPIE. 6093, 1–12 (2006)Google Scholar
  11. Globus, T., Moyer, A.M., Gelmont, B., Khromova, T., et al.: Highly resolved sub-Terahertz vibrational spectroscopy of biological macromolecules and cells. Sens. J. IEEE 13(1), 72–79 (2013a)CrossRefGoogle Scholar
  12. Globus, T., Sizov, I., Gelmont, B.: Teraherz vibrational spectroscopy of E. coli and molecular constituents: computational modeling and experiment. Adv. Biosci. Biotechnol. 4, 493–503 (2013b)CrossRefGoogle Scholar
  13. Globus, T., Gelmont, B., Sizov, I.: Overview of terahertz spectral characterization for biological identification. In: Biological Identification: DNA Amplification and Sequencing, Optical Sensing, Lab-On-Chip and Portable Systems, pp.281–312. Elsevier (2014)Google Scholar
  14. Havenith, M.: THz spectroscopy as a new tool to probe hydration dynamics. Proc. SPIE 7600, 1–5 (2010)Google Scholar
  15. Kassi, S., Campargue, A.: Cavity ring down spectroscopy with 5 × 10−13 cm−1 sensitivity. J. Chem. Phys. 137(23), 1–6 (2012)CrossRefGoogle Scholar
  16. Kryzhanovskij, G.N.: Dizreguljacionnaja patologija i patologicheskie integracii v nervnoj sisteme. Zhurnal nevrologii i psihiatrii. 1 (2009)Google Scholar
  17. Lee, F., Yanofsky, Ch.: Transcriptional termination at the trp operon attenuators of Escherichia coli and Salmonella typhimirium: RNA secondary structure and reaulation of termination. Proc. Natl. Acad. Sci. USA 74, 4365–4368 (1977)ADSCrossRefGoogle Scholar
  18. Magonov, S.N., Reneker, D.H.: Characterization of polymer surfaces with atomic force microscopy. Annu. Rev. Matter. Sci. 27, 175–222 (1997)ADSCrossRefGoogle Scholar
  19. Matvejev, V., De Tandt, C., Ranson, W., Stiens, J., et al.: Integrated waveguide structure for highly sensitive THz spectroscopy of nano-liter liquids in capillary tubes. Prog. Electromagn. Res. 121, 89–101 (2011)CrossRefGoogle Scholar
  20. Milstein, J.N., Chen, Y.-F., Meiners, J.-C.: Protein-mediated DNA looping in a fluctuating micromechanical environment. Proc. SPIE. 7762, 77620B-1 (2010)Google Scholar
  21. Nazarov, M.M., Shkurinov, A.P., Tuchin, V.V., Zhernovaya, O.S.: Modification of terahertz pulsed spectrometer to study biological samples. International Society for Optics and Photonics, Saratov Fall Meeting 2006: Optical Technologies in Biophysics and Medicine VIII. vol. 6535 p. 65351J (2007)Google Scholar
  22. Piksa, P., Cerny, P., Zvanovec, S.: Specific millimeter-wave features of Fabry-Perot resonator for spectroscopic measurements. In: Microwave and Millimeter Wave Technologies: from Photonic Bandgap Devices to Antenna and Applications, pp. 451–468 INTECH Open Access Publisher (2010)Google Scholar
  23. Pleskova, S.N.: Atomno-silovaja mikroskopija v biologicheskih i medicinskih issledovanijah. Intellekt, Dolgoprudnyj (2011)Google Scholar
  24. Podlubnaja, Z.A., Marsagashvili, L.G.: Rol’ myshechnyh citoskeletnyh belkov v patogeneze amiloidozov, v ih diagnostike i retapii. Vestnik novyh medicinskih tehnologij. XIV, 4 (2007)Google Scholar
  25. Rahman, A., Stanley, B., Rahman, A.K.: Ultrasensitive label-free detection and quantitation of DNA hybridization via terahertz spectrometry.In: Proceedings of the SPIE. 7568 (2010). doi: 10.1117/12.839542
  26. Shkudina, I.S., Ter-Avanesjan, M.D.: Priony. Uspehi Biologicheskoj Himii. 46 (2006)Google Scholar
  27. Silva, M.T., Sousa, J.C.F., Polónia, J.J., Macedo, M.A.E., et al.: Bacterial mesosome: real structures or artifacts? Biochim. Biophys. Acta 443(1), 92–105 (1976)CrossRefGoogle Scholar
  28. Soldatenkov, A.T., Koljadina, N.M., Shendrik, I.V.: Osnovy organicheskoj himii lekarstvennyh veshhestv. Himija, Moscow (2001)Google Scholar
  29. Tsurkan, M.V., Balbekin, N.S., Sobakinskaya, E.A., Panin, A.N., Vaks, V.L.: Issledovanie spektra DNK metodami THz spektroskopii. Opt. Spectrosc. 114(6), 981–986 (2013)CrossRefGoogle Scholar
  30. Vaks, V.: High-precise spectrometry of the terahertz frequency range: the methods, approaches and applications. J. Infrared Milli Terahertz waves 33, 43–53 (2012)CrossRefGoogle Scholar
  31. Vaks, V.L., Domracheva, E.G., Sobakinskaya, E.A., Chernyaeva, M.B.: Exhaled breath analysis: physical methods, instruments, and medical diagnostics. Uspekhi Fizicheskikh Nauk Russian Academy of Sciences 57(7), 684–701, (2014)CrossRefGoogle Scholar
  32. Vol’kshtejn, M.V.: Biofizika. Nauka, Moscow (1988)Google Scholar
  33. Vondracek, H., Dielmann-Gessner, J., Lubitz, W., Knipp, M., Havenith, M.: THz absorption spectroscopy of solvated β-lactoglobulin. J. Chem. Phys. 141(22), 1–6 (2014)CrossRefGoogle Scholar
  34. Watson, J., Crick, F.: Molecular structure of nucleic acids: A structure for deoxiribose nucleic acid. Nature 171, 737–8 (1953)ADSCrossRefGoogle Scholar
  35. Xu, S., Sha, G., Xie, J.: Cavity ring-down spectroscopy in the liquid phase. Rev. Sci. Instrum. 73(2), 255–258 (2002)ADSCrossRefGoogle Scholar
  36. Yakushevich, L.V., Savin, A.V., Manevitch, L.I.: Nonlinear dynamics of topological solitons in DNA. Phys. Rev. E 66, 1–16 (2002)MathSciNetCrossRefGoogle Scholar
  37. Yoneyama, H., Yamashita, M., Kasai, S., Kawase, K., et al.: Membrane device for holding biomolecule samples for terahertz spectroscopy. Opt. Commun. 281(7), 1909–1913 (2008)ADSCrossRefGoogle Scholar
  38. Zuev, V.A.: Priony – osobyj klass vozbuditelej medlennyh infekcij cheloveka i zhivotnyh. RMZh №30, 1559 (2013)Google Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.IPM RASNizhny NovgorodRussia
  2. 2.Lobachevsky State UniversityNizhny NovgorodRussia
  3. 3.ITMO UniversitySaint PetersburgRussia

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