ARL-CR-0788 ● NOV 2015

US Army Research Laboratory

Terahertz Characterization of DNA: Enabling a 

Novel Approach

prepared by Sarah Stranieri

University of Illinois at Urbana-Champaign

Champaign, IL

Molleshree Karna

Columbia University

New York, NY

Daniel Shreiber

Oak Ridge Institute for Science and Education

Belcamp, MD

under contract W911NF-10-2-0074

Approved for public release; distribution is unlimited.
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ARL-CR-0788 ● NOV 2015

US Army Research Laboratory

Terahertz Characterization of DNA: Enabling a 

Novel Approach

prepared by Sarah Stranieri 

University of Illinois at Urbana-Champaign

Champaign, IL

Molleshree Karna

Columbia University

New York, NY

Daniel Shreiber

Oak Ridge Institute for Science and Education

Belcamp, MD

under contract W911NF-10-2-0074

Approved for public release; distribution is unlimited.
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4. TITLE AND SUBTITLE

Terahertz Characterization of DNA: Enabling a Novel Approach

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W911NF-10-2-0074

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6. AUTHOR(S)

Sarah Stranieri, Molleshree Karna, and Daniel Shreiber

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R.0014684.1.82

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University of Illinois at Urbana-Champaign, Champaign, IL

Columbia University, New York, NY

Oak Ridge Institute for Science and Education, Belcamp, MD

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13. SUPPLEMENTARY NOTES

14. ABSTRACT

The terahertz spectrum of radiation has been determined to be a promising candidate for the characterization of biological 

molecules, such as DNA. Several alternative methods, including fluorescent chromophore labeling and techniques that use 

terahertz radiation, have been proposed and are currently in use. Though established, they have disadvantages, such as 

alteration to the nucleic acid sequence, requirement of a thick DNA testing layer, and conductor structure complexity. This 

project enables a novel method to identify DNA in a more reliable and less procedurally complicated manner. The method 

involves the use of terahertz surface plasmon generated on the surface of a gold-coated stainless steel perforated foil. This 

approach is less expensive and requires smaller quantities of genetic testing material. Such advantages are due to overlapping 

resonance when the plasmon frequency generated by a foil coincides with that of the biological material. The interference of 

the impinging terahertz wave and surface plasmon produces spectral graphs, which can be analyzed to identify and 

characterize a DNA sample. This work sets the foundations of a systematic approach to successfully make the plasmon-based 

terahertz approach a promising candidate. The location and orientation of the samples were kept constant to obtain conclusive 

and comparative results. This work offers clear evidence that the DNA molecules under investigation interact with the 

terahertz wave.

15. SUBJECT TERMS

terahertz spectroscopy, DNA analysis, surface plasmon, DNA resonant peak, overlapping resonance

16. SECURITY CLASSIFICATION OF:

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Daniel Shreiber

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Standard Form 298 (Rev. 8/98)

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iii

Contents

List of Figures iv

List of Tables iv

Acknowledgments v

1. Introduction and Background 1

2. Experiment 2

3. Results 5

4. Discussion 8

5. Conclusions and Future Research 9

6. References 10

Distribution List 11
iv

List of Figures

Fig. 1 Gold-sputtered metal mesh ....................................................................2

Fig. 2 TERA K15 terahertz spectrometer. One lens in front of each antenna 

was used for focused beam testing. The iris was placed equidistant 

from the antenna. ...................................................................................3

Fig. 3 Focused beam setup (top view)..............................................................3

Fig. 4 Rapid scan after aligning the antenna and lenses in free space .............4

Fig. 5 Rapid scan with sample placed in the Iris. The signal height is 

significantly lower. ................................................................................4

Fig. 6 Bare gold mesh compared to mesh coated in sample 2. A distinct DNA 

resonance is present at 1.4 THz. ............................................................5

Fig. 7 Bare gold mesh compared to mesh coated in sample 3. The effect of 

TRIS resonance is present at 1.5 THz....................................................6

Fig. 8 Samples 2 and 3 on gold mesh. DNA has a distinct resonance effect 

from the TRIS buffer alone....................................................................6

Fig. 9 Interface of DNA layer and plain mesh in the corner of sample 2 ........7

Fig. 10 Side profile of sample 2 from a laser microscope. The DNA layer was 

determined to be about 27 μm thick. .....................................................8

List of Tables

Table. DNA sample properties .........................................................................2
v

Acknowledgments

The lead author of this report, Sarah Stranieri, would like to thank the US Army 

Research Laboratory and the College Qualified Leaders Program for allowing her 

to conduct research at the Rodman Materials Research Center throughout the 

summer of 2015. She would like to specifically thank Dr Mathew Ivill for providing 

texts on surface plasmon polaritons.
vi

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1

1. Introduction and Background

Proper and detailed identification of short DNA oligonucleotides has been a longsought goal of molecular biologists and medical researchers. These nucleic acid 

fragments are used to locate and analyze identical base pair sequences in full 

strands. Compilation of their nucleic acid sequences within a genetic library would 

pave the way for improved forensic analysis, genetic testing, and DNA production 

processes.

1 Other medical applications include earlier disease detection to initiate 

gene therapy, as well as a thorough analysis of metabolic behaviors dictated by 

mRNA.2

Within the submillimeter-wave frequency range of 0.01–10 THz, DNA molecules 

exhibit several types of internal vibrations. The nature of these movements dictates 

biological processes, such as transcription and replication of genetic material.3

Some occur between base pairs because of their weak hydrogen bonding 

interactions; others stretch, twist, and bend the entire double helix structure.3 These 

features, when measured via terahertz technology, reveal specific features of a 

DNA code.4 This terahertz spectral range has proved difficult to use with organic 

material. The high absorption of water in aqueous solution masks the weaker 

magnitude of absorption in biological materials. 

An emitted terahertz electromagnetic wave released from a semiconductor antenna

interacts with the array of metal holes along the metal mesh located on the path of 

the emitted terahertz wave. This interference generates surface plasmons—electron 

density waves that propagate laterally across the metal surface. The interference of 

this surface plasmon with the impinging terahertz wave is registered as a plasmon

peak on a spectrum. The surface plasmon always propagates across the interface 

between the metal mesh and the dielectric (which is the DNA sample in our case). 

Its properties are a function of dielectric properties of both the metal and the 

dielectric. The electrical properties of the dielectric can be studied if those of the 

metal are known. This project seeks to detect the interaction of DNA with surface 

plasmons.

The Drude model approximation calculates the expected wavelength, λλ, of the 

propagating surface plasmon wave,

λλ = LL

√mm2+nn2 √εε , (1)

where ɛ represents the dielectric constant of the DNA material, and m and n are the 

quantum orders of the propagating wave. Our DNA samples’ resonant frequencies 

were obtained on a metal mesh with a pitch (L) of 500 μm. 
2

2. Experiment

Two 16 cm2 stainless steel metal meshes, with a pitch of 500 μm and a hole 

diameter of 200 μm, were sputtered with a 452-nm gold layer. The base pressure 

of 2 mTorr was achieved in the sputtering system. Upon reaching this minimum 

pressure, the chamber was filled with argon gas, and 3 min of presputtering was 

performed to clean the target. The gold thin film deposition time was 4 min and 43 

s at a rate of 84.8 nm/min. A profilometer confirmed the 425-nm thickness of this 

gold layer at multiple surface spots, showing the uniformity of the deposition. The 

resulting perforated foil is depicted in Fig. 1. 

Fig. 1 Gold-sputtered metal mesh

After a day of air drying, the 4- × 4-cm squares were cut down to 2 × 2 cm. Solution 

containing 200 μL of DNA was spin coated onto the meshes at 203 rpm and dried 

at this rotational speed for 10 min. The DNA oligomer sequence used was 

5’-CATTAACGAGTTACTCAATGAGT5CTTTCTG-3’. The following table

details the solution parameters and concentrations of DNA in each sample that 

contains a tris(hydroxymethyl) (TRIS) buffer solution.

Table. DNA sample properties

Sample no. DNA quantity 

(mg) Solvent volume Mass concentration

1 0.23 1.0-mL TRIS buffer 0.230 gg

LL

2 0.23 0.33-mL TRIS buffer 0.696 gg

LL

3 0.00 0.33-mL TRIS buffer ...

A Menlo Systems TERA K15 terahertz time domain spectrometer (Figs. 2–5) was 

used to test each sample in transmission mode. A laser, with a wavelength of 1,560

nm and 120-fs pulse duration, was connected to 2 antennas via fiber optic cables.

Each mesh was secured to an iris in between the 2 antennas. The DNA-coated side 

of each sample faced the same direction. Nitrogen gas was pumped into the testing 

chamber for 2 h to purge the water vapor. All samples were tested with a 3-mmdiameter focused beam. Plasmon peaks were detected and analyzed with respect to 

DNA resonance behavior.
3

Fig. 2 TERA K15 terahertz spectrometer. One lens in front of each antenna was used for 

focused beam testing. The iris was placed equidistant from the antenna.

Fig. 3 Focused beam setup (top view)
4

Fig. 4 Rapid scan after aligning the antenna and lenses in free space

Fig. 5 Rapid scan with sample placed in the Iris. The signal height is significantly lower.
5

3. Results

Samples 2 and 3 were tested under focused beam in terahertz time domain 

spectroscope. The focused beam plots are shown in Figs. 6–8. A plain gold mesh 

without buffers or coatings was compared to each sample in the first 2 graphs. In 

Fig. 8, the samples were directly compared. All plots were normalized by division 

by free space.

Fig. 6 Bare gold mesh compared to mesh coated in sample 2. A distinct DNA resonance is 

present at 1.4 THz.

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5

0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2

Mesh vs DNA

mesh mesh+DNA
6

Fig. 7 Bare gold mesh compared to mesh coated in sample 3. The effect of TRIS resonance 

is present at 1.5 THz.

Fig. 8 Samples 2 and 3 on gold mesh. DNA has a distinct resonance effect from the TRIS 

buffer alone.
7

The Drude model approximation (Eq. 1) was used to first correlate with the pitch 

of the metal mesh. Using our first peak value of 0.58 THz, present on all 3 graphs, 

we calculated L to be 516 μm.

LL = λλ√mm2+nn2

√εε = 

(

νν

ff)√02+12

√1

= 

299792458 m

s

0.58∗1012Hz = 5.16 x 10−4 m = 516 μm . (2)

Using L in the second-order peak calculation,

λλ = LL√εε

√mm2+nn2 = 

516 μm

√12+12 = 364 x 10−4m x

1

299792458m

s

= 0.823 THz . (3)

This approximation is close to the 500-μm pitch of the material’s circular holes, 

even though the approximation assumed square holes. The 516-μm value was used 

in subsequent calculations. 

Under the focused beam, the TRIS buffer exhibits resonant behavior at 1.5 THz, 

whereas the resonance frequency is closer to 1.4 THz for the sample that contains 

DNA. 

The presence of DNA on the spin-coated samples was confirmed using a laser 

microscope image, magnified by a 5× lens (Figs. 9 and 10).

Fig. 9 Interface of DNA layer and plain mesh in the corner of sample 2
8

Fig. 10 Side profile of sample 2 from a laser microscope. The DNA layer was determined 

to be about 27 μm thick.

4. Discussion

Surface plasmons were successfully generated on both the DNA-coated and plain 

metal mesh samples, indicated by the spectral peaks. A nonlinear interaction,

generated by application of a focused terahertz beam, to a sample that contains both 

DNA strands and TRIS, caused the resonance peak to shift from 1.5 to 1.4 THz. 

This result indicates that the low terahertz spectrum is a good candidate for DNA 

testing in this experimental configuration. The result can be significantly enhanced 

if the idea of overlapping resonances is applied to investigate the DNA samples 

where the plasmon frequency of the terahertz surface plasmon is matched with the 

resonant frequency of the DNA sample. This was not the case in the current 

configuration, where the first-order surface plasmon peak has been demonstrated 

at 0.58 THz.

The proposed approach uses a set of standard sample preparation techniques, such 

as gold thin film sputtering and a standard spin coating technique for DNA 

deposition. The sputtering and spin-coating process could be scaled up to larger 

batches to test for consistency among identically prepared samples. 

In this proof-of-principle experiment, only the resonant frequency of a specific 

DNA sample in the terahertz spectrum was identified. By tuning the surface 

plasmon frequency of the sample by adjusting the specific pitch between the holes, 

we could achieve greater details and more specific terahertz readings to identify 

molecular movements and nucleic acid sequences. Comparison of DNA samples 
9

with minute differences in base pairs or molecular motions with this surface 

plasmon technique could identify resonant frequencies of specific DNA features. 

A surface plasmon library of genetic spectral data could be compiled to study 

oligomers in greater detail. 

5. Conclusions and Future Research

Spin coating of DNA and gold sputtering is a successful preparation method to 

fabricate DNA samples for terahertz investigation. The proposed terahertz

technique is a promising method to identify DNA molecules due to prevalent DNA 

resonant behavior in these frequencies. This work lays the foundations to a 

relatively inexpensive and precise technique to classify nucleic acid. 

The next objective is to prepare samples embedded with resonant gold 

nanoparticles in order to investigate the resonant behavior changes in the DNA 

sample as a function of the gold nanoparticles’ shape or plasmonic activity.

The random orientation of DNA with spin coating does not allow for specific 

alignment of the sample with the polarized electromagnetic field produced by the 

terahertz spectrometer. Using nanopores, carbon nanotubes, and other electrically 

conducting porous structures, DNA strands can be guided through these holes with 

an electric field.

5 The entire structure can be oriented parallel or perpendicular to 

the electromagnetic field of a terahertz system.6 Aligning the structures parallel or 

perpendicular to the terahertz field polarization will significantly enhance the 

response of the DNA structure under investigation and analysis capabilities of the 

proposed setup. 
10

6. References

1. Brucherseifer M, Nagel M, Haring Bolivar P. 2000. Label-free probing of the 

binding state of DNA by time-domain terahertz sensing. Applied Physics 

Letters. 2000;77:4049 [accessed 2015 Oct 30].

http://scitation.aip.org/content/aip/journal/apl/77/24/10.1063/1.1332415

2. Chernev AL, Bagraev NT, Klyachkin LE, Emelyanov AK, Dubina MV. DNA 

detection by THz pumping. Semiconductors. 2015;49(7):977–948 [accessed

2015 Oct 30]. 

http://arxiv.org/abs/1407.6520

3. Globus T, Khromova T, Woolard D. Terahertz Fourier transform 

characterization of biological materials in solid and liquid phases. Proc. SPIE

5268, Chemical and Biological Standoff Detection; 2004 Feb 27; p. 10.

doi:10.1117/12.519172; http://dx.doi.org/10.1117/12.519172 

4. Woodlard et al. Submillimeter-wave phonon modes in DNA macromolecules. 

Physical Review E. 2002;65:051903 [accessed 2015 Oct 30].

http://journals.aps.org/pre/pdf/10.1103/PhysRevE.65.051903

5. Muthukumar M, Plesa C, Dekker C. Single-molecule sensing with nanopores. 

Physics Today. 2015;68(8):40 [accessed 2015 Aug 06].

http://dx.doi.org/10.1063/PT.3.2881

6. Globus TR, Woolard DL, Khromova T. THz-spectroscopy of biological 

molecules. Journal of Biological Physics. 2003;29(2–3):89–100 [accessed 

2015 Oct 30]. 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3456403/pdf/10867_2004

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