Abstract

We use terahertz time-domain spectroscopy (THz-TDS) to measure the far-infrared dielectric function of two artificial RNA single strands, composed of polyadenylic acid (poly-A) and polycytidylic acid (poly-C). We find a significant difference in the absorption between the two types of RNA strands, and we show that we can use this difference to record images of spot arrays of the RNA strands. Under controlled conditions it is possible to use the THz image to distinguish between the two RNA strands. We discuss the requirements to sample preparation imposed by the lack of sharp spectral features in the absorption spectra.

© 2005 Optical Society of America

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  1. A. Doria, G. P. Gallerano, E. Giovenale, G. Messina, A. Lai, A. Ramundo-Orlando, V. Spotsato, M. D�??Arienzo, A. Perrotta, M. Romano, M. Sarti, M. R. Scarfi, I. Spassovsky, and O. Zeni, �??THz radiation studies on biological systems at the ENEA FEL facility,�?? Infrared Phys. Technol. 45, 339 (2004)
    [CrossRef]
  2. E. Pickwell, B. E. Cole, A. J. Fitzgerald, V. P.Wallace, and M. Pepper, �??Simulation of terahertz pulse propagation in biological systems,�?? Appl. Phys. Lett. 84, 2190 (2004)
    [CrossRef]
  3. S. W. Smye, J. M. Chamberlain, A. J. Fitzgerald, and E. Berry, �??The interaction between terahertz radiation and biological tissue,�?? Phys. Med. Biol. 46, R101 (2001)
    [CrossRef] [PubMed]
  4. E. R. Brown, J. E. Bjarnason, T. L. J. Chan, A. W. M. Lee, and M. A. Celis, �??Optical attenuation signatures of Bacillus subtillis in the THz region,�?? Appl. Phys. Lett. 84, 3438 (2004)
    [CrossRef]
  5. T. Globus, M. Bykhovskaia, D. Woolard, and B. Gelmont, �??Sub-millimetre wave absorption spectra of artificial RNA molecules,�?? J. Phys. D 36, 1314 (2003)
    [CrossRef]
  6. D. L. Woolard, T. R. Globus, B. L. Gelmont, M. Bykhovskaia, A. C. Samuels, D. Cookmeyer, J. L. Hesler, T. W. Crowe, J. O. Jensen, J. L. Jensen, and W. R. Loerop, �??Submillimeter-wave phonon modes in DNA macromolecules,�?? Phys. Rev. E 65, 051903 (2002)
    [CrossRef]
  7. R. M. Woodward, V. P. Wallace, D. D. Arnone, E. H. Linfield, and M. Pepper, �??Terahertz pulsed imaging of skin cancer in the time and frequency domain,�?? J. Biol. Phys. 29, 257 (2003)
    [CrossRef]
  8. J. Xu, G. J. Ramian, Jhenny F. Galan, Pavlos G. Savvidis, A. M. Scopatz, R. R. Birge, S. James Allen, and K. W. Plaxco, �??Terahertz circular dichroism spectroscopy: A potential approach to the in situ detection of life�??s metabolic and genetic machinery,�?? Astrobiol. 3, 489 (2003)
    [CrossRef]
  9. A. Markelz, S. Whitmire, J. Hillebrecht, and R. Birge, �??THz time domain spectroscopy of biomolecular conformational modes,�?? Phys. Med. Biol. 47, 3797 (2002)
    [CrossRef] [PubMed]
  10. S. E. Whitmire, D. Wolpert, A. G. Markelz, J. R. Hillebrecht, J. Galan, and R. R. Birge, �??Protein flexibility and conformational state: A comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin,�?? Biophys. J. 85, 1269 (2003)
    [CrossRef] [PubMed]
  11. M. Walther, B. M. Fischer, and P. Uhd Jepsen, �??Noncovalent intermolecular forces in polycrystalline and amorphous saccharides in the far infrared,�?? Chem. Phys. 288, 261 (2003)
    [CrossRef]
  12. F. Rutz, R. Wilk, T. Kleine-Ostmann, and M. Koch, �??Experimental and theoretical study of the THz absorption spectra of selected tripeptides,�?? Proc. SPIE 5727, (2005)
    [CrossRef]
  13. M. Brucherseifer, M. Nagel, P. Haring Bolivar, H. Kurz, A. Bosserhoff, and R. Büttner, �??Label-free probing of the binding state of DNA by time-domain terahertz sensing,�?? Appl. Phys. Lett. 77, 4049 (2000)
    [CrossRef]
  14. M. Nagel, P. Haring Bolivar, M. Brucherseifer, H. Kurz, A. Bosserhoff, and R. Büttner, �??Integrated THz technology for label-free genetics diagnostics,�?? Appl. Phys. Lett. 80, 154 (2002)
    [CrossRef]
  15. M. Walther, B. Fischer, M. Schall, H. Helm, and P. Uhd Jepsen, �??Far-infrared vibrational spectra of all-trans, 9-cis, and 13-cis retinal measured by THz time-domain spectroscopy,�?? Chem. Phys. Lett. 332, 389 (2000)
    [CrossRef]
  16. M. Schall, M.Walther, and P. Uhd Jepsen, �??Fundamental and second-order phonon processes in CdTe and ZnTe,�?? Phys. Rev. B 64, 094301 (2001)
    [CrossRef]
  17. P. Knobloch, C. Schildknecht, T. Kleine-Ostmann, M. Koch, S. Hoffmann, M. Hofmann, E. Rehberg, M. Sperling, K. Donhuijsen, G. Hein, and K. Pierz, �??Medical THz imaging: an investigation of histopathological samples,�?? Phys. Med. Biol. 47, 3875 (2002)
    [CrossRef] [PubMed]
  18. P. Uhd Jepsen and B. M. Fischer, �??Dynamic range in terahertz time-domain transmission and reflection spectroscopy,�?? Opt. Lett. 30, 29 (2005)
    [CrossRef]
  19. M. L. T. Asaki, A. Redondo, T. A. Zawodzinski, and A. J. Taylor, �??Dielectric relaxation of electrolyte solutions using terahertz transmission spectroscopy,�?? J. Chem. Phys. 116, 8469 (2002)
    [CrossRef]

Appl. Phys. Lett. (4)

E. Pickwell, B. E. Cole, A. J. Fitzgerald, V. P.Wallace, and M. Pepper, �??Simulation of terahertz pulse propagation in biological systems,�?? Appl. Phys. Lett. 84, 2190 (2004)
[CrossRef]

E. R. Brown, J. E. Bjarnason, T. L. J. Chan, A. W. M. Lee, and M. A. Celis, �??Optical attenuation signatures of Bacillus subtillis in the THz region,�?? Appl. Phys. Lett. 84, 3438 (2004)
[CrossRef]

M. Brucherseifer, M. Nagel, P. Haring Bolivar, H. Kurz, A. Bosserhoff, and R. Büttner, �??Label-free probing of the binding state of DNA by time-domain terahertz sensing,�?? Appl. Phys. Lett. 77, 4049 (2000)
[CrossRef]

M. Nagel, P. Haring Bolivar, M. Brucherseifer, H. Kurz, A. Bosserhoff, and R. Büttner, �??Integrated THz technology for label-free genetics diagnostics,�?? Appl. Phys. Lett. 80, 154 (2002)
[CrossRef]

Astrobiol. (1)

J. Xu, G. J. Ramian, Jhenny F. Galan, Pavlos G. Savvidis, A. M. Scopatz, R. R. Birge, S. James Allen, and K. W. Plaxco, �??Terahertz circular dichroism spectroscopy: A potential approach to the in situ detection of life�??s metabolic and genetic machinery,�?? Astrobiol. 3, 489 (2003)
[CrossRef]

Biophys. J. (1)

S. E. Whitmire, D. Wolpert, A. G. Markelz, J. R. Hillebrecht, J. Galan, and R. R. Birge, �??Protein flexibility and conformational state: A comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin,�?? Biophys. J. 85, 1269 (2003)
[CrossRef] [PubMed]

Chem. Phys. (1)

M. Walther, B. M. Fischer, and P. Uhd Jepsen, �??Noncovalent intermolecular forces in polycrystalline and amorphous saccharides in the far infrared,�?? Chem. Phys. 288, 261 (2003)
[CrossRef]

Chem. Phys. Lett. (1)

M. Walther, B. Fischer, M. Schall, H. Helm, and P. Uhd Jepsen, �??Far-infrared vibrational spectra of all-trans, 9-cis, and 13-cis retinal measured by THz time-domain spectroscopy,�?? Chem. Phys. Lett. 332, 389 (2000)
[CrossRef]

Infrared Phys. Technol. (1)

A. Doria, G. P. Gallerano, E. Giovenale, G. Messina, A. Lai, A. Ramundo-Orlando, V. Spotsato, M. D�??Arienzo, A. Perrotta, M. Romano, M. Sarti, M. R. Scarfi, I. Spassovsky, and O. Zeni, �??THz radiation studies on biological systems at the ENEA FEL facility,�?? Infrared Phys. Technol. 45, 339 (2004)
[CrossRef]

J. Biol. Phys. (1)

R. M. Woodward, V. P. Wallace, D. D. Arnone, E. H. Linfield, and M. Pepper, �??Terahertz pulsed imaging of skin cancer in the time and frequency domain,�?? J. Biol. Phys. 29, 257 (2003)
[CrossRef]

J. Chem. Phys. (1)

M. L. T. Asaki, A. Redondo, T. A. Zawodzinski, and A. J. Taylor, �??Dielectric relaxation of electrolyte solutions using terahertz transmission spectroscopy,�?? J. Chem. Phys. 116, 8469 (2002)
[CrossRef]

J. Phys. D (1)

T. Globus, M. Bykhovskaia, D. Woolard, and B. Gelmont, �??Sub-millimetre wave absorption spectra of artificial RNA molecules,�?? J. Phys. D 36, 1314 (2003)
[CrossRef]

Opt. Lett. (1)

Phys. Med. Biol. (3)

S. W. Smye, J. M. Chamberlain, A. J. Fitzgerald, and E. Berry, �??The interaction between terahertz radiation and biological tissue,�?? Phys. Med. Biol. 46, R101 (2001)
[CrossRef] [PubMed]

A. Markelz, S. Whitmire, J. Hillebrecht, and R. Birge, �??THz time domain spectroscopy of biomolecular conformational modes,�?? Phys. Med. Biol. 47, 3797 (2002)
[CrossRef] [PubMed]

P. Knobloch, C. Schildknecht, T. Kleine-Ostmann, M. Koch, S. Hoffmann, M. Hofmann, E. Rehberg, M. Sperling, K. Donhuijsen, G. Hein, and K. Pierz, �??Medical THz imaging: an investigation of histopathological samples,�?? Phys. Med. Biol. 47, 3875 (2002)
[CrossRef] [PubMed]

Phys. Rev. B (1)

M. Schall, M.Walther, and P. Uhd Jepsen, �??Fundamental and second-order phonon processes in CdTe and ZnTe,�?? Phys. Rev. B 64, 094301 (2001)
[CrossRef]

Phys. Rev. E (1)

D. L. Woolard, T. R. Globus, B. L. Gelmont, M. Bykhovskaia, A. C. Samuels, D. Cookmeyer, J. L. Hesler, T. W. Crowe, J. O. Jensen, J. L. Jensen, and W. R. Loerop, �??Submillimeter-wave phonon modes in DNA macromolecules,�?? Phys. Rev. E 65, 051903 (2002)
[CrossRef]

Proc. SPIE (1)

F. Rutz, R. Wilk, T. Kleine-Ostmann, and M. Koch, �??Experimental and theoretical study of the THz absorption spectra of selected tripeptides,�?? Proc. SPIE 5727, (2005)
[CrossRef]

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Figures (10)

Fig. 1.
Fig. 1.

Chemical structure of (a) polyadenylic acid (poly-A) and (b) polycytidylic acid (poly-C). The negative charge of the backbone is neutralized by potassium ions.

Fig. 2.
Fig. 2.

Schematic illustration of the experimental setup for THz time-domain spectroscopy (THz-TDS). The inset shows details about the photoconductive antennas.

Fig. 3.
Fig. 3.

(a) Absorption coefficient and (b) index of refraction of pressed pellets (samples BR-1 and BR-2) of poly-A and poly-C at room temperature in the frequency range 0.15–2.0 THz. Traces represented by symbols correspond to individual measurements whereas traces represented by full lines show the average value.

Fig. 4.
Fig. 4.

(a) Absorption coefficient and (b) index of refraction of pressed pellets (samples FR-1 and FR-2) poly-A and poly-C at room temperature in the frequency range 0.1–2.45 THz. The vertical error bars indicate the standard deviation of the mean values in each experiment.

Fig. 5.
Fig. 5.

(a) Absorption coefficient and (b) index of refraction of free-standing, dry films of poly-A and poly-C (samples FR-3 and FR-4) at room temperature in the frequency range 0.1–3.0 THz. The vertical error bars indicate the standard deviation of the mean values in each experiment.

Fig. 6.
Fig. 6.

Absorption coefficient of spots of poly-A and poly-C on the substrate surface of sample BR-3 at room temperature in the frequency range 0.1–1.5 THz. Traces represented by symbols correspond to individual measurements whereas traces represented by full lines show the average value.

Fig. 7.
Fig. 7.

(a) THz transmission image of the polyethylene pellet containing 6 mg of poly-A and 6 mg of poly-C at different regions (sample BR-4). (b) Photograph of the sample for comparison, indicating the location of the sample material.

Fig. 8.
Fig. 8.

THz transmission image of the sample FR-5, again showing stronger absorption in poly-C compared to poly-A. Each spot contained 200 µg of either poly-A or poly-C in alternating order, as indicated in the diagram to the right. The dashed line indicates the scan path of the surface profiler.

Fig. 9.
Fig. 9.

Surface height profile of the sample FR-5 along the path indicated by the dashed line in Fig. 8.

Fig. 10.
Fig. 10.

THz transmission image of sample FR-6 prepared with poly-A and poly-C spots of varying mass, ranging from 20 µg to 200 µg.

Tables (1)

Tables Icon

Table 1. Overview of the samples used in the study. The preparation methods are described in the text. Samples denoted FR-1 - FR-6 were prepared and characterized in Freiburg, and samples denoted BR-1 - BR-4 were prepared and characterized in Braunschweig.

Equations (2)

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n ( ν ) = 1 + c 2 π ν d Δ ϕ ( ν ) ,
α ( ν ) = 2 d ln [ A ( ν ) ( n ( ν ) + 1 ) 2 4 n ( ν ) ] ,

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