Abstract
The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearch has shown that such measurementsare both possible and fruitful. Spectra ofdifferent DNA samples reveal a large numberof modes and a reasonable level ofsequence-specific uniqueness. In an attemptto show that the long wavelength absorptionfeatures are intrinsic properties ofbiological materials determined by phononmodes, a normal mode analysis has been usedto predict the absorption spectra ofpolynucleotide RNA Poly[G]-Poly[C]. Directcomparison demonstrated a correlationbetween calculated and experimentallyobserved spectra of the RNA polymers, thusconfirming that the fundamental physicalnature of the observed resonance structureis caused by the internal vibration modesin the macromolecules.In this work we demonstrate results fromFourier-Transform Infrared (FTIR)spectroscopy of DNA macromolecules andrelated biological materials in theterahertz frequency range. Carefulattention was paid to the possibility ofinterference or etalon effects in thesamples, and phenomena were clearlydifferentiated from the actual phononmodes. In addition, we studied thedependence of transmission spectra ofaligned DNA and polynucleotide film sampleson molecule orientation relative to theelectromagnetic field, showing the expectedchange in mode strength as a function ofsample orientation. Further, the absorptioncharacteristics were extracted from thetransmission data using the interferencespectroscopy technique, and a stronganisotropy of terahertz characteristics wasdemonstrated.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Sarkar, M., Sigurdsson, S., Tomac, S., Sen, S., Rozners, E., Sjoberg, B.-M., Stromberg, R. and Graslund, A.: A Synthetic Model for Triple-Helical Domains in Self-Splicing Group I Introns Studied by Ultraviolet and Circular Dichroism Spectroscopy,Biochemistry 35 (1996), 4678-4688.
Van Zandt, L.L. and Saxena, V.K.: In: R.H. Sarma and M.H. Sarma (eds.),Structure & Functions Volume 1:Nucleic Acids, Adenine Press, 1992 and references therein.
Beetz, C.P. and Ascarelli, G.: Far Infrared Absorption of dNA and PolyI-PolyC RNA,Biopolymers 21 (1982), 1569.
Wittlin, A., Genzel, L., Kremer, F., Haseler, S., Poglitsch, A. and Rupprecht, A.: Far-Infrared Spectroscopy on Oriented Films of Dry and Hydrated DNA,Phys. Rev. A 34 (1986), 493.
Powell, J.W., Edwards, G.S., Genzel, L., Kremer, F., Wittlin, A., Kubasek, W. and Peticolas, W.: Investigation of Far-Infrared VibrationalModes in Polynucleotides,Phys. Rev. A 35 (1987), 3929-3939.
Weidlich, T., Powell, J.W., Genzel, L. and Rupprecht, A.: Counterion Effects on the far-IR Vibrational Spectra of Poly (rI):Poly(rC),Biopolymers 30 (1990), 477-480.
Powell, J.W., Peticolas, W. and Genzel, L.: Observation of the far-IR Spectra of Five Oligonucleotides,J. Mol. Struct. 247 (1991), 119.
Markeltz, A.G., Roitberg, A. and Heilweil, E.J.: Pulsed Terahertz Spectroscopy of DNA, Bovine Serum Albumin and Collagen between 0.1 and 2.0 THz,Chem. Phys. Lett. 320 (2000), 42.
Globus, T., Woolard, D.L., Bykhovskaia, M., Gelmont, B., Hesler, J.L., Crowe, T.W. and Samuels, A.C.:Proc of International Semiconductor Device Researsh Symposium (ISDRS), Charlottesville VA, 1999, p. 485.
Globus, T., Dolmatova-Werbos, L., Woolard, D., Samuels, A., Gelmont, B. and Bykhovskaia, M.: Application of Neural Network Analysis to Submillimeter-Wave Vibrational Spectroscopy of DNA Macromolecules,International Symposium on Spectral Sensing Research Proceedings (ISSSR), Canada, Quebec, June 2001, p. 439.
Globus, T., Woolard, D.L., Samuels, A.C., Gelmont, B.L., Hesler, J., Crowe, T.W. and Bykhovskaia, M.: Submillimeter-Wave FTIR Spectroscopy of DNA Macromolecules and Related Materials,J. Appl. Phys. 91 (May 2002), 6106-6113.
Woolard, D.L., Globus, T.R., Gelmont, B.L., Bykhovskaia, M., Samuels, A.C., Cookmeyer, D., Hesler, J.L., Crowe, T.W., Jensen, J.O., Jensen, J.L. and Loerop, W.R.: Submillimeter-Wave Phonon Modes in DNA Macromolecules,Phys. Rev E 65 (May 2002), 051903.
Van Zandt, L.L. and Saxena, V.K.: Vibrational Local Modes in DNA Polymer,J. Biomol. Struct. & Dyn. 11 (1994), 1149-1159.
Bykhovskaia, M., Gelmont, B., Globus, T., Woolard, D.L., Samuels, A.C., Ha-Duong, T. and Zakrzewska, K.: Prediction of DNA Far IR Absorption Spectra Basing on Normal Mode Analysis,Theor. Chem. Acc. 106 (2001), 22-27.
Globus, T., Bykhovskaia, M., Gelmont, B. and Woolard, D.L.: Far-infrared Phonon Modes of Selected RNA Molecules, In: J.O. Jensen and R.L. Spellicy (eds.),Instrumentation for Air Pollution and Global Atmospheric Monitoring, Proceedings of SPIE,45742002, pp. 119-128.
Mei, W.N., Kohli, M., Prohofsky, E.W. and Van Zandt, L.L.: Acoustic Modes and Nonbonded Interactions of the Double Helix,Biopolymers 20 (1981), 833-852.
Young, L., Prabhu, V.V. and Prohovsky, E.W.: Calculation of Far-Infrared Absorption in Polymer DNA,Phys. Rev. A 39 (1989), 3173.
Feng, Y. and Prohofski, E.M.: Vibrational Fluctuations of Hydrogen Bonds in a DNA Double Helix with Nonuniform Base Pairs,Biophys. J. 57 (1990), 547-553.
Lin, D., Matsumoto, A. and Go, N.: Normal Mode Analysis of a Double-Stranded DNA Dodecamer d(CGCGAATTCGCG),J. Chem. Phys. 107(9) (1997), 3684-3690.
Duong, T.H. and Zakrzewska, K.: Calculation and Analysis of Low Frequency Normal Modes for DNA,J. Comp. Chem. 18(6) (1997), 796-811.
Weidlich, T., Lindsay, S.M., Rui, Q., Rupprecht, A., Peticolas, W.L. and Thomas, G.A.: A Raman Study of Low Frequency Intrahelical Modes in A-, B-, and C-DNA,J. Biomol. Struct. Dyn. 8 (1990), 139.
Sinden, R.R.:DNA Structure and Function, Academic Press, San Diego, 1994.
Prohofsky, E.W.:Statistical Mechanics and Stability of Macromolecules, Cambridge University Press, 1995.
McCammon, J.A. and Harvey, S.C.:Dynamics of Proteins and Nucleic Acids, Cambridge University Press, 1986.
Lafontain, I. and Lavery, R.: Collective Variable Modeling of Nucleic Acids,Curr. Op. Struct. Biol. 9 (1999), 170-176.
Davidson, M.W., Rill, R.L. and Van Winkle, D.H.: http://micro.magnet.fsu.edu/dna/cholesteric.html
Moss, T.S., Burrell, G.J. and Ellis, B.:Semiconductor Opto-electronics, Butterworth & Co. (Publishers) Ltd., 1973.
Globus, T., Ganguly, G. and Roca i Cabarrocas, P.: Optical Characterization of Hydrogenated Silicon Films using Interference Technique,J. Appl. Phys. 88 (2000), 1907.
Woolard, D., Globus, T., Brown, E., Werbos, L., Gelmont, B. and Samuels, A.: Sensitivity Limits & Discrimination Capability of Thz Transmission Spectroscopy as a Technique for Biological Agent Detection,Proc. of 5 th Joint Conference on Standoff Detection for Chemical and Biological Defence (5JCSD), Williamsburg, VA, Sept. 2001.
Genzel, L., Poglitsh, A. and Haeseler, S.: Dispersive Polarizing mm-wave Interferometer,Int. J. Infrared Millimeter Waves 6 (1985), 741-750.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Globus, T., Woolard, D., Khromova, T. et al. THz-Spectroscopy of Biological Molecules. Journal of Biological Physics 29, 89–100 (2003). https://doi.org/10.1023/A:1024420104400
Issue Date:
DOI: https://doi.org/10.1023/A:1024420104400